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April 2014

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commit/MOAB: danwu: Minor updates for unit test write_nc.
by commits-noreply＠bitbucket.org 30 Apr '14

30 Apr '14

1 new commit in MOAB: https://bitbucket.org/fathomteam/moab/commits/54bc99a5bafa/ Changeset: 54bc99a5bafa Branch: master User: danwu Date: 2014-05-01 00:47:53 Summary: Minor updates for unit test write_nc. Affected #: 1 file diff --git a/test/io/write_nc.cpp b/test/io/write_nc.cpp index 2dc8e9a..3332d4b 100644 --- a/test/io/write_nc.cpp +++ b/test/io/write_nc.cpp @@ -36,7 +36,6 @@ static const char example_mpas[] = "/io/mpasx1.642.t.2.nc"; // CAM-EUL void test_eul_read_write_T(); void test_eul_check_T(); -void test_eul_read_write_append(); // CAM-FV void test_fv_read_write_T(); @@ -50,6 +49,16 @@ void test_homme_check_T(); void test_mpas_read_write_vars(); void test_mpas_check_vars(); +// Test append option +void test_eul_read_write_append(); +void test_eul_check_append(); + +#ifdef USE_MPI +// Test mesh with ghosted entities +void test_eul_read_write_ghosting(); +void test_eul_check_ghosting(); +#endif + void get_eul_read_options(std::string& opts); void get_fv_read_options(std::string& opts); void get_homme_read_options(std::string& opts); @@ -69,14 +78,24 @@ int main(int argc, char* argv[]) result += RUN_TEST(test_eul_read_write_T); result += RUN_TEST(test_eul_check_T); - result += RUN_TEST(test_eul_read_write_append); + result += RUN_TEST(test_fv_read_write_T); result += RUN_TEST(test_fv_check_T); + result += RUN_TEST(test_homme_read_write_T); result += RUN_TEST(test_homme_check_T); + result += RUN_TEST(test_mpas_read_write_vars); result += RUN_TEST(test_mpas_check_vars); + result += RUN_TEST(test_eul_read_write_append); + result += RUN_TEST(test_eul_check_append); + +#ifdef USE_MPI + result += RUN_TEST(test_eul_read_write_ghosting); + result += RUN_TEST(test_eul_check_ghosting); +#endif + #ifdef USE_MPI fail = MPI_Finalize(); if (fail) @@ -111,19 +130,10 @@ void test_eul_read_write_T() ErrorCode rval = mb.create_meshset(MESHSET_SET, set); CHECK_ERR(rval); -#ifdef USE_MPI - read_opts = "PARALLEL=READ_PART;PARTITION;PARALLEL_RESOLVE_SHARED_ENTS;PARALLEL_GHOSTS=2.0.1;PARTITION_METHOD=SQIJ;VARIABLE="; - rval = mb.load_file(example_eul, &set, read_opts.c_str()); - CHECK_ERR(rval); - - read_opts = "PARALLEL=READ_PART;PARTITION;PARTITION_METHOD=SQIJ;VARIABLE=T,gw;NOMESH"; - rval = mb.load_file(example_eul, &set, read_opts.c_str()); - CHECK_ERR(rval); -#else + // Load non-set variable T, set variable gw, and the mesh read_opts += ";DEBUG_IO=0;VARIABLE=T,gw"; rval = mb.load_file(example_eul, &set, read_opts.c_str()); CHECK_ERR(rval); -#endif // Write variables T and gw std::string write_opts; @@ -246,75 +256,6 @@ void test_eul_check_T() } } -// We read and write variables T and U; U after we write T, so we append -// we will also write gw, just to test the file after writing -void test_eul_read_write_append() -{ - int procs = 1; -#ifdef USE_MPI - MPI_Comm_size(MPI_COMM_WORLD, &procs); -#endif - -// We will not test NC writer in parallel without pnetcdf support -#ifndef PNETCDF_FILE - if (procs > 1) - return; -#endif - - Core moab; - Interface& mb = moab; - - std::string read_opts; - get_eul_read_options(read_opts); - - EntityHandle set; - ErrorCode rval = mb.create_meshset(MESHSET_SET, set); - CHECK_ERR(rval); - - // Load non-set variable T, set variable gw, and the mesh - read_opts += ";DEBUG_IO=0;VARIABLE=T,U,V,gw"; - rval = mb.load_file(example_eul, &set, read_opts.c_str()); - CHECK_ERR(rval); - - // Write variables T and gw - std::string write_opts; - write_opts = std::string(";;VARIABLE=T,gw;DEBUG_IO=0"); -#ifdef USE_MPI - // Use parallel options - write_opts += std::string(";PARALLEL=WRITE_PART"); -#endif - if (procs > 1) - rval = mb.write_file("test_par_eul_TU.nc", 0, write_opts.c_str(), &set, 1); - else - rval = mb.write_file("test_eul_TU.nc", 0, write_opts.c_str(), &set, 1); - CHECK_ERR(rval); - // append to the file variable U - std::string write_opts2; - write_opts2 = std::string(";;VARIABLE=U;DEBUG_IO=0;APPEND"); -#ifdef USE_MPI - // Use parallel options - write_opts2 += std::string(";PARALLEL=WRITE_PART"); -#endif - if (procs > 1) - rval = mb.write_file("test_par_eul_TU.nc", 0, write_opts2.c_str(), &set, 1); - else - rval = mb.write_file("test_eul_TU.nc", 0, write_opts2.c_str(), &set, 1); - CHECK_ERR(rval); - - // append to the file variable V, renamed to VNEWNAME - std::string write_opts3; - write_opts3 = std::string(";;VARIABLE=V;RENAME=VNEWNAME;DEBUG_IO=0;APPEND"); -#ifdef USE_MPI - // Use parallel options - write_opts3 += std::string(";PARALLEL=WRITE_PART"); -#endif - if (procs > 1) - rval = mb.write_file("test_par_eul_TU.nc", 0, write_opts3.c_str(), &set, 1); - else - rval = mb.write_file("test_eul_TU.nc", 0, write_opts3.c_str(), &set, 1); - CHECK_ERR(rval); -} - // We also write coordinate variables slat and slon to the output file, so that // it can be recognized by NC reader later in test_fv_check_T() void test_fv_read_write_T() @@ -715,6 +656,125 @@ void test_mpas_check_vars() } } +// We read and write variables T and U; U after we write T, so we append +// we will also write gw, just to test the file after writing +void test_eul_read_write_append() +{ + int procs = 1; +#ifdef USE_MPI + MPI_Comm_size(MPI_COMM_WORLD, &procs); +#endif + +// We will not test NC writer in parallel without pnetcdf support +#ifndef PNETCDF_FILE + if (procs > 1) + return; +#endif + + Core moab; + Interface& mb = moab; + + std::string read_opts; + get_eul_read_options(read_opts); + + EntityHandle set; + ErrorCode rval = mb.create_meshset(MESHSET_SET, set); + CHECK_ERR(rval); + + // Load non-set variables T, U, V, and the mesh + read_opts += ";DEBUG_IO=0;VARIABLE=T,U,V"; + rval = mb.load_file(example_eul, &set, read_opts.c_str()); + CHECK_ERR(rval); + + // Write variable T + std::string write_opts; + write_opts = std::string(";;VARIABLE=T;DEBUG_IO=0"); +#ifdef USE_MPI + // Use parallel options + write_opts += std::string(";PARALLEL=WRITE_PART"); +#endif + if (procs > 1) + rval = mb.write_file("test_par_eul_append.nc", 0, write_opts.c_str(), &set, 1); + else + rval = mb.write_file("test_eul_append.nc", 0, write_opts.c_str(), &set, 1); + CHECK_ERR(rval); + + // Append to the file variable U + std::string write_opts2; + write_opts2 = std::string(";;VARIABLE=U;DEBUG_IO=0;APPEND"); +#ifdef USE_MPI + // Use parallel options + write_opts2 += std::string(";PARALLEL=WRITE_PART"); +#endif + if (procs > 1) + rval = mb.write_file("test_par_eul_append.nc", 0, write_opts2.c_str(), &set, 1); + else + rval = mb.write_file("test_eul_append.nc", 0, write_opts2.c_str(), &set, 1); + CHECK_ERR(rval); + + // Append to the file variable V, renamed to VNEWNAME + std::string write_opts3; + write_opts3 = std::string(";;VARIABLE=V;RENAME=VNEWNAME;DEBUG_IO=0;APPEND"); +#ifdef USE_MPI + // Use parallel options + write_opts3 += std::string(";PARALLEL=WRITE_PART"); +#endif + if (procs > 1) + rval = mb.write_file("test_par_eul_append.nc", 0, write_opts3.c_str(), &set, 1); + else + rval = mb.write_file("test_eul_append.nc", 0, write_opts3.c_str(), &set, 1); + CHECK_ERR(rval); +} + +void test_eul_check_append() +{ + // TBD +} + +#ifdef USE_MPI +// NC writer should filter entities that are not owned, e.g. ghosted elements +void test_eul_read_write_ghosting() +{ + int procs = 1; + MPI_Comm_size(MPI_COMM_WORLD, &procs); + +// We will not test NC writer in parallel without pnetcdf support +#ifndef PNETCDF_FILE + if (procs > 1) + return; +#endif + + Core moab; + Interface& mb = moab; + + EntityHandle set; + ErrorCode rval = mb.create_meshset(MESHSET_SET, set); + CHECK_ERR(rval); + + std::string read_opts = "PARALLEL=READ_PART;PARTITION;PARALLEL_RESOLVE_SHARED_ENTS;PARALLEL_GHOSTS=2.0.1;PARTITION_METHOD=SQIJ;VARIABLE="; + rval = mb.load_file(example_eul, &set, read_opts.c_str()); + CHECK_ERR(rval); + + read_opts = "PARALLEL=READ_PART;PARTITION;PARTITION_METHOD=SQIJ;VARIABLE=T;NOMESH"; + rval = mb.load_file(example_eul, &set, read_opts.c_str()); + CHECK_ERR(rval); + + // Write variable T + std::string write_opts; + write_opts = std::string(";;PARALLEL=WRITE_PART;VARIABLE=T;DEBUG_IO=0"); + if (procs > 1) + rval = mb.write_file("test_par_eul_ghosting.nc", 0, write_opts.c_str(), &set, 1); + else + rval = mb.write_file("test_eul_ghosting.nc", 0, write_opts.c_str(), &set, 1); + CHECK_ERR(rval); +} + +void test_eul_check_ghosting() +{ + // TBD +} +#endif + void get_eul_read_options(std::string& opts) { #ifdef USE_MPI Repository URL: https://bitbucket.org/fathomteam/moab/ -- This is a commit notification from bitbucket.org. 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commit/MOAB: iulian07: append error when build with netcdf only
by commits-noreply＠bitbucket.org 30 Apr '14

30 Apr '14

1 new commit in MOAB: https://bitbucket.org/fathomteam/moab/commits/fae72f00a208/ Changeset: fae72f00a208 Branch: master User: iulian07 Date: 2014-04-30 23:39:40 Summary: append error when build with netcdf only wrong open mode Affected #: 2 files diff --git a/src/io/NCWriteHelper.cpp b/src/io/NCWriteHelper.cpp index 995bf3f..58d95c2 100644 --- a/src/io/NCWriteHelper.cpp +++ b/src/io/NCWriteHelper.cpp @@ -224,7 +224,11 @@ ErrorCode NCWriteHelper::init_file(std::vector<std::string>& var_names, std::vec // if append mode, make sure we are in define mode; a simple open will not allow creation of new variables if (append) - NCFUNC(redef)(_fileId); + { + int errcode = NCFUNC(redef)(_fileId); + if (errcode != NC_NOERR) + ERRORR(MB_FAILURE, "Can't open file in redefine mode"); + } // First initialize all coordinates, then fill VarData for actual variables (and dimensions) // Check that for used coordinates we have found the tags for (std::set<std::string>::iterator setIt = usedCoordinates.begin(); diff --git a/src/io/WriteNC.cpp b/src/io/WriteNC.cpp index d4d79dd..0ec1aa8 100644 --- a/src/io/WriteNC.cpp +++ b/src/io/WriteNC.cpp @@ -95,15 +95,15 @@ ErrorCode WriteNC::write_file(const char* file_name, if (append) { -#ifdef PNETCDF_FILE int omode = NC_WRITE; +#ifdef PNETCDF_FILE if (isParallel) success = NCFUNC(open)(myPcomm->proc_config().proc_comm(), file_name, omode, MPI_INFO_NULL, &fileId); else success = NCFUNC(open)(MPI_COMM_SELF, file_name, omode, MPI_INFO_NULL, &fileId); #else - // This is a regular netcdf file - success = NCFUNC(open)(file_name, overwrite ? NC_CLOBBER : NC_NOCLOBBER, &fileId); + // This is a regular netcdf file, open in write mode + success = NCFUNC(open)(file_name, omode, &fileId); #endif ERRORS(success, "Failed to open file for appending."); } Repository URL: https://bitbucket.org/fathomteam/moab/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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Build failed in Jenkins: moab_serial #282
by jenkins-ci＠mcs.anl.gov 30 Apr '14

30 Apr '14

See <https://jenkins-ci.mcs.anl.gov/job/moab_serial/282/changes> Changes: [iulian] filter out not owned entities, for writing ------------------------------------------ [...truncated 568 lines...] mv -f .deps/testc_cbind.Tpo .deps/testc_cbind.Po /bin/sh ../../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o testc_cbind testc_cbind.o libiMesh.la ../../src/libMOAB.la -L/usr/lib/gcc/x86_64-linux-gnu/4.6 -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu 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/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -L/usr/lib/gcc/x86_64-linux-gnu/4.6 -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../.. -lstdc++ -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/moab -I../../src/parallel -I../../src -I/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/include -I/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/include -isystem /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/include -DTEMPLATE_SPECIALIZATION -DTEMPLATE_FUNC_SPECIALIZATION -DHAVE_VSNPRINTF -D_FILE_OFFSET_BITS=64 -DHDF5_FILE -DNETCDF_FILE -DSRCDIR=. -DMESHDIR=../../MeshFiles/unittest -I./.. -I../../src -I../../src -I../../itaps -I../../test -DUNORDERED_MAP_NS=std::tr1 -DHAVE_UNORDERED_MAP=tr1/unordered_map -DHAVE_UNORDERED_SET=tr1/unordered_set -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -MT MOAB_iMesh_unit_tests.o -MD -MP -MF .deps/MOAB_iMesh_unit_tests.Tpo -c -o MOAB_iMesh_unit_tests.o MOAB_iMesh_unit_tests.cpp mv -f .deps/MOAB_iMesh_unit_tests.Tpo .deps/MOAB_iMesh_unit_tests.Po /bin/sh ../../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o MOAB_iMesh_unit_tests MOAB_iMesh_unit_tests.o libiMesh.la ../../src/libMOAB.la -L/usr/lib/gcc/x86_64-linux-gnu/4.6 -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../.. -lstdc++ -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o MOAB_iMesh_unit_tests MOAB_iMesh_unit_tests.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ./.libs/libiMesh.a <https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/src/.libs/libMOAB.a> ../../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -L/usr/lib/gcc/x86_64-linux-gnu/4.6 -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../.. -lstdc++ -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/moab -I../../src/parallel -I../../src -I/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/include -I/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/include -isystem /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/include -DTEMPLATE_SPECIALIZATION -DTEMPLATE_FUNC_SPECIALIZATION -DHAVE_VSNPRINTF -D_FILE_OFFSET_BITS=64 -DHDF5_FILE -DNETCDF_FILE -DSRCDIR=. -DMESHDIR=../../MeshFiles/unittest -I./.. -I../../src -I../../src -I../../itaps -I../../test -DUNORDERED_MAP_NS=std::tr1 -DHAVE_UNORDERED_MAP=tr1/unordered_map -DHAVE_UNORDERED_SET=tr1/unordered_set -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -MT MOAB_iMesh_extensions_tests.o -MD -MP -MF .deps/MOAB_iMesh_extensions_tests.Tpo -c -o MOAB_iMesh_extensions_tests.o MOAB_iMesh_extensions_tests.cpp mv -f .deps/MOAB_iMesh_extensions_tests.Tpo .deps/MOAB_iMesh_extensions_tests.Po /bin/sh ../../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o MOAB_iMesh_extensions_tests MOAB_iMesh_extensions_tests.o libiMesh.la ../../src/libMOAB.la -L/usr/lib/gcc/x86_64-linux-gnu/4.6 -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../.. -lstdc++ -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o MOAB_iMesh_extensions_tests MOAB_iMesh_extensions_tests.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ./.libs/libiMesh.a <https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/src/.libs/libMOAB.a> ../../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -L/usr/lib/gcc/x86_64-linux-gnu/4.6 -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../.. -lstdc++ 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-Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../../libtool --tag=FC --mode=link gfortran -O2 -fcray-pointer -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o FindAdjacencyF90 FindAdjacencyF90.o libiMesh.la ../../src/libMOAB.la -L/usr/lib/gcc/x86_64-linux-gnu/4.6 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/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -L/usr/lib/gcc/x86_64-linux-gnu/4.6 -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../.. -lstdc++ -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib make[4]: Leaving directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/itaps/imesh'> make check-TESTS make[4]: Entering directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/itaps/imesh'> make[5]: Entering directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/itaps/imesh'> PASS: testc_cbind PASS: MOAB_iMesh_unit_tests PASS: MOAB_iMesh_extensions_tests PASS: ScdMeshF90 PASS: ScdMeshF77 PASS: FindAdjacencyF90 ================== All 6 tests passed ================== make[5]: Leaving directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/itaps/imesh'> make[4]: Leaving directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/itaps/imesh'> make[3]: Leaving directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/itaps/imesh'> make[2]: Leaving directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/itaps/imesh'> make[2]: Entering directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/itaps'> make[2]: Nothing to be done for `check-am'. make[2]: Leaving directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/itaps'> make[1]: Leaving directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/itaps'> Making check in tools make[1]: Entering directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/tools'> Making check in . make[2]: Entering directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/tools'> make[2]: Nothing to be done for `check-am'. make[2]: Leaving directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/tools'> Making check in dagmc make[2]: Entering directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/tools/dagmc'> make test_geom pt_vol_test ray_fire_test make[3]: Entering directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/tools/dagmc'> /bin/sh ../../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 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./.libs/libdagmc.a ../../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o ray_fire_test ray_fire_test.o libdagmc.la ../../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o ray_fire_test ray_fire_test.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ./.libs/libdagmc.a ../../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib make[3]: Leaving directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/tools/dagmc'> make check-TESTS make[3]: Entering directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/tools/dagmc'> make[4]: Entering directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/tools/dagmc'> PASS: test_geom ============= 1 test passed ============= make[4]: Leaving directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/tools/dagmc'> make[3]: Leaving directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/tools/dagmc'> make[2]: Leaving directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/tools/dagmc'> make[1]: Leaving directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/tools'> Making check in test make[1]: Entering directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/test'> Making check in . make[2]: Entering directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/test'> make range_test moab_test homxform_test scdseq_test scd_test_partn test_adj seq_man_test geom_util_test xform_test obb_test adaptive_kd_tree_tests bsp_tree_test file_options_test kd_tree_test var_len_test var_len_test_no_template tag_test mesh_set_test mbcn_test bsp_tree_poly_test reorder_test test_prog_opt coords_connect_iterate elem_eval_test spatial_locator_test test_boundbox mbfacet_test gttool_test cropvol_test mergemesh_test mbground_test lloyd_smoother_test kd_tree_tool kd_tree_time make[3]: Entering directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/test'> /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o range_test range_test.o ../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra 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-Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o moab_test moab_test-MBTest.o ../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith 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-Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o homxform_test homxform_test-HomXform.o ../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith 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-Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o scdseq_test scdseq_test.o ../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o scdseq_test scdseq_test.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o scd_test_partn scd_test_partn.o ../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o scd_test_partn scd_test_partn.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o test_adj test_adj.o ../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o test_adj test_adj.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o seq_man_test TestTypeSequenceManager.o ../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o seq_man_test TestTypeSequenceManager.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o geom_util_test GeomUtilTests.o ../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o geom_util_test GeomUtilTests.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o xform_test xform_test-AffineXform.o ../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o xform_test xform_test-AffineXform.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o obb_test OBBTest.o ../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o obb_test OBBTest.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o adaptive_kd_tree_tests adaptive_kd_tree_tests.o ../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o adaptive_kd_tree_tests adaptive_kd_tree_tests.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o bsp_tree_test bsp_tree_test.o ../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o bsp_tree_test bsp_tree_test.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib make[3]: `file_options_test' is up to date. /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o kd_tree_test kd_tree_test-kd_tree_test.o ../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o kd_tree_test kd_tree_test-kd_tree_test.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o var_len_test VarLenTagTest.o ../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o var_len_test VarLenTagTest.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o var_len_test_no_template var_len_test_no_template-VarLenTagTest.o ../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o var_len_test_no_template var_len_test_no_template-VarLenTagTest.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o tag_test TagTest.o ../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o tag_test TagTest.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o mesh_set_test Test_MBMeshSet.o ../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o mesh_set_test Test_MBMeshSet.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib g++ -DHAVE_CONFIG_H -I. -I.. -I../src/moab -I../src/parallel -I../src -I/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/include -I/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/include -isystem /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/include -DTEMPLATE_SPECIALIZATION -DTEMPLATE_FUNC_SPECIALIZATION -DHAVE_VSNPRINTF -D_FILE_OFFSET_BITS=64 -DHDF5_FILE -DNETCDF_FILE -DIS_BUILDING_MB -DSRCDIR=. -DMESHDIR=../MeshFiles/unittest -I../src -I../src -I../src/LocalDiscretization -DUNORDERED_MAP_NS=std::tr1 -DHAVE_UNORDERED_MAP=tr1/unordered_map -DHAVE_UNORDERED_SET=tr1/unordered_set -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -MT CN.o -MD -MP -MF .deps/CN.Tpo -c -o CN.o `test -f '../src/CN.cpp' || echo './'`../src/CN.cpp mv -f .deps/CN.Tpo .deps/CN.Po /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o mbcn_test CN.o mbcn_test.o ../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o mbcn_test CN.o mbcn_test.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o bsp_tree_poly_test bsp_tree_poly_test.o ../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o bsp_tree_poly_test bsp_tree_poly_test.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o reorder_test reorder_test.o ../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o reorder_test reorder_test.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o test_prog_opt test_prog_opt-test_prog_opt.o ../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o test_prog_opt test_prog_opt-test_prog_opt.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o coords_connect_iterate coords_connect_iterate-coords_connect_iterate.o ../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o coords_connect_iterate coords_connect_iterate-coords_connect_iterate.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o elem_eval_test elem_eval_test.o ../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o elem_eval_test elem_eval_test.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o spatial_locator_test spatial_locator_test.o ../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o spatial_locator_test spatial_locator_test.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o test_boundbox test_boundbox.o ../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o test_boundbox test_boundbox.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o mbfacet_test mbfacet_test.o ../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o mbfacet_test mbfacet_test.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o gttool_test gttool_test.o ../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o gttool_test gttool_test.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o cropvol_test crop_vol_test.o ../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o cropvol_test crop_vol_test.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o mergemesh_test mergemesh_test.o ../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o mergemesh_test mergemesh_test.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o mbground_test mbground_test.o ../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o mbground_test mbground_test.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o lloyd_smoother_test lloyd_smoother_test.o ../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o lloyd_smoother_test lloyd_smoother_test.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so 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-L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o kd_tree_tool kd_tree_tool.o ../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o kd_tree_tool kd_tree_tool.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o kd_tree_time kd_tree_time.o ../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o kd_tree_time kd_tree_time.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib make[3]: Leaving directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/test'> make check-TESTS make[3]: Entering directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/test'> make[4]: Entering directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/test'> PASS: range_test PASS: moab_test PASS: homxform_test PASS: scdseq_test PASS: scd_test_partn PASS: test_adj PASS: seq_man_test PASS: geom_util_test PASS: xform_test PASS: obb_test PASS: adaptive_kd_tree_tests PASS: bsp_tree_test PASS: file_options_test PASS: kd_tree_test PASS: var_len_test PASS: var_len_test_no_template PASS: tag_test PASS: mesh_set_test PASS: mbcn_test PASS: bsp_tree_poly_test PASS: reorder_test PASS: test_prog_opt PASS: coords_connect_iterate PASS: elem_eval_test PASS: spatial_locator_test PASS: test_boundbox PASS: mbfacet_test PASS: gttool_test PASS: cropvol_test PASS: mergemesh_test PASS: mbground_test PASS: lloyd_smoother_test =================== All 32 tests passed =================== make[4]: Leaving directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/test'> make[3]: Leaving directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/test'> make[2]: Leaving directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/test'> Making check in io make[2]: Entering directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/test/io'> make readutil_test tqdcfr vtk_test cub_file_test exodus_test gmsh_test nastran_test read_nc read_ucd_nc read_mpas_nc write_nc ideas_test stl_test smf_test make[3]: Entering directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/test/io'> /bin/sh ../../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o readutil_test readutil_test.o ../../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic 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-L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o vtk_test VtkTest.o ../../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o vtk_test VtkTest.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o cub_file_test cub_file_test.o ../../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o cub_file_test cub_file_test.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../../src/.libs/libMOAB.a 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-L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o exodus_test exodus_test.o ../../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o exodus_test exodus_test.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../../src/.libs/libMOAB.a 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-L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o nastran_test nastran_test.o ../../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o nastran_test nastran_test.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../../src/.libs/libMOAB.a 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-L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o read_nc read_nc.o ../../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o read_nc read_nc.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o read_ucd_nc read_ucd_nc.o ../../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o read_ucd_nc read_ucd_nc.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../../src/.libs/libMOAB.a 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-L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o read_mpas_nc read_mpas_nc.o ../../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o read_mpas_nc read_mpas_nc.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/moab -I../../src/parallel -I../../src -I/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/include -I/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/include -isystem /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/include -DTEMPLATE_SPECIALIZATION -DTEMPLATE_FUNC_SPECIALIZATION -DHAVE_VSNPRINTF -D_FILE_OFFSET_BITS=64 -DHDF5_FILE -DNETCDF_FILE -DSRCDIR=. -DMESHDIR=../../MeshFiles/unittest -I. -I.. -I./.. -I../../src -I../../src -I../../src/io -I../../src/parallel -DUNORDERED_MAP_NS=std::tr1 -DHAVE_UNORDERED_MAP=tr1/unordered_map -DHAVE_UNORDERED_SET=tr1/unordered_set -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -MT write_nc.o -MD -MP -MF .deps/write_nc.Tpo -c -o write_nc.o write_nc.cpp mv -f .deps/write_nc.Tpo .deps/write_nc.Po /bin/sh ../../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o write_nc write_nc.o ../../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o write_nc write_nc.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o ideas_test ideas_test.o ../../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o ideas_test ideas_test.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o stl_test stl_test.o ../../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o stl_test stl_test.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib /bin/sh ../../libtool --tag=CXX --mode=link g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -lnetcdf -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -lhdf5_hl -lhdf5 -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -lz -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -o smf_test smf_test.o ../../src/libMOAB.la -lm libtool: link: g++ -Wall -pipe -pedantic -Wno-long-long -Wextra -Wcast-align -Wpointer-arith -Wformat -Wformat-security -Wshadow -Wunused-parameter -O2 -DNDEBUG -o smf_test smf_test.o -L/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc/lib -L/home/fathom/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/hdf5/hdf5-1.8.3/serial/gcc -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -L/home/fathom/3rdparty/zlib/zlib-1.2.4/gcc -L/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib ../../src/.libs/libMOAB.a /home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib/libnetcdf.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5_hl.so /homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib/libhdf5.so /homes/sharp/3rdparty/szip/szip-2.1/gcc/lib/libsz.so -lz -lm -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib -Wl,-rpath -Wl,/home/fathom/3rdparty/netcdf/netcdf-4.0.1/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/serial/gcc/lib -Wl,-rpath -Wl,/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib make[3]: Leaving directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/test/io'> make check-TESTS make[3]: Entering directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/test/io'> make[4]: Entering directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/test/io'> PASS: readutil_test PASS: tqdcfr PASS: vtk_test PASS: cub_file_test PASS: exodus_test PASS: gmsh_test PASS: nastran_test PASS: read_nc PASS: read_ucd_nc PASS: read_mpas_nc FAIL: write_nc PASS: ideas_test PASS: stl_test PASS: smf_test ========================== 1 of 14 tests failed See test/io/test-suite.log ========================== make[4]: *** [test-suite.log] Error 1 make[4]: Leaving directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/test/io'> make[3]: *** [check-TESTS] Error 2 make[3]: Leaving directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/test/io'> make[2]: *** [check-am] Error 2 make[2]: Leaving directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/test/io'> make[1]: *** [check-recursive] Error 1 make[1]: Leaving directory `<https://jenkins-ci.mcs.anl.gov/job/moab_serial/ws/test'> make: *** [check-recursive] Error 1 Build step 'Execute shell' marked build as failure

1 1

commit/MOAB: danwu: Updated unit test write_nc for serial MOAB, which failed with "PARALLEL option not valid, this instance compiled for serial execution".
by commits-noreply＠bitbucket.org 30 Apr '14

30 Apr '14

1 new commit in MOAB: https://bitbucket.org/fathomteam/moab/commits/967a5ee16b1b/ Changeset: 967a5ee16b1b Branch: master User: danwu Date: 2014-04-30 22:40:13 Summary: Updated unit test write_nc for serial MOAB, which failed with "PARALLEL option not valid, this instance compiled for serial execution". Affected #: 1 file diff --git a/test/io/write_nc.cpp b/test/io/write_nc.cpp index 54d16d5..2dc8e9a 100644 --- a/test/io/write_nc.cpp +++ b/test/io/write_nc.cpp @@ -111,13 +111,20 @@ void test_eul_read_write_T() ErrorCode rval = mb.create_meshset(MESHSET_SET, set); CHECK_ERR(rval); +#ifdef USE_MPI read_opts = "PARALLEL=READ_PART;PARTITION;PARALLEL_RESOLVE_SHARED_ENTS;PARALLEL_GHOSTS=2.0.1;PARTITION_METHOD=SQIJ;VARIABLE="; rval = mb.load_file(example_eul, &set, read_opts.c_str()); CHECK_ERR(rval); - read_opts = "PARALLEL=READ_PART;PARTITION;PARTITION_METHOD=SQIJ;VARIABLE=T,gw;NOMESH;"; + read_opts = "PARALLEL=READ_PART;PARTITION;PARTITION_METHOD=SQIJ;VARIABLE=T,gw;NOMESH"; + rval = mb.load_file(example_eul, &set, read_opts.c_str()); + CHECK_ERR(rval); +#else + read_opts += ";DEBUG_IO=0;VARIABLE=T,gw"; rval = mb.load_file(example_eul, &set, read_opts.c_str()); CHECK_ERR(rval); +#endif + // Write variables T and gw std::string write_opts; write_opts = std::string(";;VARIABLE=T,gw;DEBUG_IO=0"); Repository URL: https://bitbucket.org/fathomteam/moab/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/MOAB: iulian07: filter out not owned entities, for writing
by commits-noreply＠bitbucket.org 30 Apr '14

30 Apr '14

1 new commit in MOAB: https://bitbucket.org/fathomteam/moab/commits/912e5d377ff3/ Changeset: 912e5d377ff3 Branch: master User: iulian07 Date: 2014-04-30 21:17:09 Summary: filter out not owned entities, for writing modify the test also, as Jayesh needs cleanup Affected #: 2 files diff --git a/src/io/NCWriteHelper.cpp b/src/io/NCWriteHelper.cpp index 9072e38..995bf3f 100644 --- a/src/io/NCWriteHelper.cpp +++ b/src/io/NCWriteHelper.cpp @@ -12,6 +12,7 @@ #include "NCWriteMPAS.hpp" #include "moab/WriteUtilIface.hpp" +#include "MBTagConventions.hpp" #include <sstream> @@ -540,8 +541,18 @@ ErrorCode ScdNCWriteHelper::write_values(std::vector<std::string>& var_names) switch (variableData.entLoc) { case WriteNC::ENTLOCFACE: // Faces + { rval = mbImpl->get_entities_by_dimension(_fileSet, 2, ents); ERRORR(rval, "Can't get entities for faces."); +#ifdef USE_MPI + bool &isParallel = _writeNC->isParallel; + if (isParallel) { + ParallelComm*& myPcomm = _writeNC->myPcomm; + rval = myPcomm->filter_pstatus(ents, PSTATUS_NOT_OWNED, PSTATUS_NOT); + ERRORR(rval, "Can't get filter for owned entities"); + } +#endif + } break; default: ERRORR(MB_FAILURE, "Not implemented yet."); diff --git a/test/io/write_nc.cpp b/test/io/write_nc.cpp index 7f9df60..54d16d5 100644 --- a/test/io/write_nc.cpp +++ b/test/io/write_nc.cpp @@ -111,11 +111,13 @@ void test_eul_read_write_T() ErrorCode rval = mb.create_meshset(MESHSET_SET, set); CHECK_ERR(rval); - // Load non-set variable T, set variable gw, and the mesh - read_opts += ";DEBUG_IO=0;VARIABLE=T,gw"; + read_opts = "PARALLEL=READ_PART;PARTITION;PARALLEL_RESOLVE_SHARED_ENTS;PARALLEL_GHOSTS=2.0.1;PARTITION_METHOD=SQIJ;VARIABLE="; rval = mb.load_file(example_eul, &set, read_opts.c_str()); CHECK_ERR(rval); + read_opts = "PARALLEL=READ_PART;PARTITION;PARTITION_METHOD=SQIJ;VARIABLE=T,gw;NOMESH;"; + rval = mb.load_file(example_eul, &set, read_opts.c_str()); + CHECK_ERR(rval); // Write variables T and gw std::string write_opts; write_opts = std::string(";;VARIABLE=T,gw;DEBUG_IO=0"); Repository URL: https://bitbucket.org/fathomteam/moab/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/MOAB: 2 new changesets
by commits-noreply＠bitbucket.org 29 Apr '14

29 Apr '14

2 new commits in MOAB: https://bitbucket.org/fathomteam/moab/commits/091ff53b306d/ Changeset: 091ff53b306d Branch: None User: iulian07 Date: 2014-04-30 00:33:12 Summary: introduce RENAME option option to rename a variable, requested by Jayesh Some users might want to save a variable with a different name only the initialization is modified; keep a list of desired names, which is parallel to the variable names; the test exercises the append option at the same time Affected #: 5 files diff --git a/src/io/NCWriteHelper.cpp b/src/io/NCWriteHelper.cpp index 923fe02..9072e38 100644 --- a/src/io/NCWriteHelper.cpp +++ b/src/io/NCWriteHelper.cpp @@ -209,7 +209,7 @@ ErrorCode NCWriteHelper::collect_variable_data(std::vector<std::string>& var_nam return MB_SUCCESS; } -ErrorCode NCWriteHelper::init_file(std::vector<std::string>& var_names, bool append) +ErrorCode NCWriteHelper::init_file(std::vector<std::string>& var_names, std::vector<std::string>& desired_names, bool append) { std::vector<std::string>& dimNames = _writeNC->dimNames; std::set<std::string>& usedCoordinates = _writeNC->usedCoordinates; @@ -334,13 +334,14 @@ ErrorCode NCWriteHelper::init_file(std::vector<std::string>& var_names, bool app } // Define the variable now: - int errCode = NCFUNC(def_var)(_fileId, var_names[i].c_str(), variableData.varDataType, + int errCode = NCFUNC(def_var)(_fileId, desired_names[i].c_str(), variableData.varDataType, (int)variableData.varDims.size(), &(variableData.varDims[0]), &variableData.varId); if ( errCode != NC_NOERR) ERRORR(MB_FAILURE, "Failed to create coordinate variable."); - dbgOut.tprintf(2, " for variable %s variable id is %d \n", var_names[i].c_str(), variableData.varId); + dbgOut.tprintf(2, " for variable %s with desired name %s variable id is %d \n", var_names[i].c_str(), + desired_names[i].c_str(), variableData.varId); // Now define the variable, with all dimensions } diff --git a/src/io/NCWriteHelper.hpp b/src/io/NCWriteHelper.hpp index ed2443a..25a3120 100644 --- a/src/io/NCWriteHelper.hpp +++ b/src/io/NCWriteHelper.hpp @@ -34,7 +34,7 @@ public: //! Initialize file: this is where all defines are done //! The VarData dimension ids are filled up after define - ErrorCode init_file(std::vector<std::string>& var_names, bool _append); + ErrorCode init_file(std::vector<std::string>& var_names, std::vector<std::string>& desired_names, bool _append); protected: template <typename T> void jik_to_kji(size_t ni, size_t nj, size_t nk, T* dest, T* source) diff --git a/src/io/WriteNC.cpp b/src/io/WriteNC.cpp index 98f4e3b..d4d79dd 100644 --- a/src/io/WriteNC.cpp +++ b/src/io/WriteNC.cpp @@ -62,6 +62,7 @@ ErrorCode WriteNC::write_file(const char* file_name, ErrorCode rval; // See if opts has variable(s) specified std::vector<std::string> var_names; + std::vector<std::string> desired_names; std::vector<int> tstep_nums; std::vector<double> tstep_vals; @@ -75,7 +76,7 @@ ErrorCode WriteNC::write_file(const char* file_name, if (num_set != 1) ERRORR(MB_FAILURE, "We should write only one set, the file set used to read data into."); - rval = parse_options(options, var_names, tstep_nums, tstep_vals); + rval = parse_options(options, var_names, desired_names, tstep_nums, tstep_vals); ERRORR(rval, "Trouble parsing option string."); // Important to create some data that will be used to write the file; dimensions, variables, etc @@ -135,7 +136,7 @@ ErrorCode WriteNC::write_file(const char* file_name, rval = myHelper->collect_variable_data(var_names); ERRORR(rval, "Trouble collecting variable data."); - rval = myHelper->init_file(var_names, append); + rval = myHelper->init_file(var_names, desired_names, append); ERRORR(rval, "Failed to initialize file."); rval = myHelper->write_values(var_names); @@ -147,7 +148,8 @@ ErrorCode WriteNC::write_file(const char* file_name, return MB_SUCCESS; } -ErrorCode WriteNC::parse_options(const FileOptions& opts, std::vector<std::string>& var_names, std::vector<int>& tstep_nums, +ErrorCode WriteNC::parse_options(const FileOptions& opts, std::vector<std::string>& var_names, + std::vector<std::string>& desired_names, std::vector<int>& tstep_nums, std::vector<double>& tstep_vals) { int tmpval; @@ -161,6 +163,20 @@ ErrorCode WriteNC::parse_options(const FileOptions& opts, std::vector<std::strin noVars = true; else noVars = false; + + + rval = opts.get_strs_option("RENAME", desired_names); + if (MB_ENTITY_NOT_FOUND == rval) + { + if(!noVars) + { + desired_names.resize(var_names.size()); + std::copy(var_names.begin(), var_names.end(), desired_names.begin()); + } + } + // either way + assert(desired_names.size() == var_names.size()); + opts.get_ints_option("TIMESTEP", tstep_nums); opts.get_reals_option("TIMEVAL", tstep_vals); rval = opts.get_null_option("NOMESH"); diff --git a/src/io/WriteNC.hpp b/src/io/WriteNC.hpp index 5827680..60c295e 100644 --- a/src/io/WriteNC.hpp +++ b/src/io/WriteNC.hpp @@ -153,6 +153,7 @@ private: ErrorCode parse_options(const FileOptions& opts, std::vector<std::string>& var_names, + std::vector<std::string>& desired_names, std::vector<int>& tstep_nums, std::vector<double>& tstep_vals); /* diff --git a/test/io/write_nc.cpp b/test/io/write_nc.cpp index f48e4c6..7fe2e82 100644 --- a/test/io/write_nc.cpp +++ b/test/io/write_nc.cpp @@ -261,7 +261,7 @@ void test_eul_read_write_append() CHECK_ERR(rval); // Load non-set variable T, set variable gw, and the mesh - read_opts += ";DEBUG_IO=0;VARIABLE=T,U,gw"; + read_opts += ";DEBUG_IO=0;VARIABLE=T,U,V,gw"; rval = mb.load_file(example_eul, &set, read_opts.c_str()); CHECK_ERR(rval); @@ -289,6 +289,19 @@ void test_eul_read_write_append() else rval = mb.write_file("test_eul_TU.nc", 0, write_opts2.c_str(), &set, 1); CHECK_ERR(rval); + + // append to the file variable V, renamed to VNEWNAME + std::string write_opts3; + write_opts3 = std::string(";;VARIABLE=V;RENAME=VNEWNAME;DEBUG_IO=0;APPEND"); +#ifdef USE_MPI + // Use parallel options + write_opts3 += std::string(";PARALLEL=WRITE_PART"); +#endif + if (procs > 1) + rval = mb.write_file("test_par_eul_TU.nc", 0, write_opts3.c_str(), &set, 1); + else + rval = mb.write_file("test_eul_TU.nc", 0, write_opts3.c_str(), &set, 1); + CHECK_ERR(rval); } // We also write coordinate variables slat and slon to the output file, so that https://bitbucket.org/fathomteam/moab/commits/3bac343d8274/ Changeset: 3bac343d8274 Branch: master User: iulian07 Date: 2014-04-30 00:40:14 Summary: Merge branch 'master' of https://bitbucket.org/fathomteam/moab Affected #: 3 files diff --git a/src/io/NCWriteMPAS.cpp b/src/io/NCWriteMPAS.cpp index 72dc35f..8058726 100644 --- a/src/io/NCWriteMPAS.cpp +++ b/src/io/NCWriteMPAS.cpp @@ -6,6 +6,7 @@ #include "NCWriteMPAS.hpp" #include "moab/WriteUtilIface.hpp" +#include "MBTagConventions.hpp" #define ERRORR(rval, str) \ if (MB_SUCCESS != rval) { _writeNC->mWriteIface->report_error("%s", str); return rval; } @@ -22,12 +23,401 @@ NCWriteMPAS::~NCWriteMPAS() ErrorCode NCWriteMPAS::collect_mesh_info() { - return MB_NOT_IMPLEMENTED; + Interface*& mbImpl = _writeNC->mbImpl; + std::vector<std::string>& dimNames = _writeNC->dimNames; + std::vector<int>& dimLens = _writeNC->dimLens; + Tag& mGlobalIdTag = _writeNC->mGlobalIdTag; + + ErrorCode rval; + + // Look for time dimension + std::vector<std::string>::iterator vecIt; + if ((vecIt = std::find(dimNames.begin(), dimNames.end(), "Time")) != dimNames.end()) + tDim = vecIt - dimNames.begin(); + else if ((vecIt = std::find(dimNames.begin(), dimNames.end(), "time")) != dimNames.end()) + tDim = vecIt - dimNames.begin(); + else { + ERRORR(MB_FAILURE, "Couldn't find 'Time' or 'time' dimension."); + } + nTimeSteps = dimLens[tDim]; + + // Get number of levels + if ((vecIt = std::find(dimNames.begin(), dimNames.end(), "nVertLevels")) != dimNames.end()) + levDim = vecIt - dimNames.begin(); + else { + ERRORR(MB_FAILURE, "Couldn't find 'nVertLevels' dimension."); + } + nLevels = dimLens[levDim]; + + Range local_verts; + rval = mbImpl->get_entities_by_dimension(_fileSet, 0, local_verts); + ERRORR(rval, "Trouble getting local vertices in current file set."); + assert(!local_verts.empty()); + + // Depends on whether NO_EDGES read option is set or not + Range local_edges; + rval = mbImpl->get_entities_by_dimension(_fileSet, 1, local_edges); + ERRORR(rval, "Trouble getting local edges in current file set."); + noEdges = local_edges.empty(); + + Range local_cells; + rval = mbImpl->get_entities_by_dimension(_fileSet, 2, local_cells); + ERRORR(rval, "Trouble getting local cells in current file set."); + assert(!local_cells.empty()); + +#ifdef USE_MPI + bool& isParallel = _writeNC->isParallel; + if (isParallel) { + ParallelComm*& myPcomm = _writeNC->myPcomm; + int rank = myPcomm->proc_config().proc_rank(); + int procs = myPcomm->proc_config().proc_size(); + if (procs > 1) { + rval = myPcomm->filter_pstatus(local_verts, PSTATUS_NOT_OWNED, PSTATUS_NOT, -1, &localVertsOwned); + ERRORR(rval, "Trouble getting owned vertices in set."); + // Assume that PARALLEL_RESOLVE_SHARED_ENTS option is set + // We should avoid writing in parallel with overlapped data + if (procs - 1 == rank) + assert("PARALLEL_RESOLVE_SHARED_ENTS option is set" && localVertsOwned.size() < local_verts.size()); + + if (!noEdges) { + rval = myPcomm->filter_pstatus(local_edges, PSTATUS_NOT_OWNED, PSTATUS_NOT, -1, &localEdgesOwned); + ERRORR(rval, "Trouble getting owned edges in set."); + } + + rval = myPcomm->filter_pstatus(local_cells, PSTATUS_NOT_OWNED, PSTATUS_NOT, -1, &localCellsOwned); + ERRORR(rval, "Trouble getting owned cells in set."); + } + else { + localVertsOwned = local_verts; + localEdgesOwned = local_edges; + localCellsOwned = local_cells; + } + } + else { + // Not running in parallel, but still with MPI + localVertsOwned = local_verts; + localEdgesOwned = local_edges; + localCellsOwned = local_cells; + } +#else + localVertsOwned = local_verts; + localEdgesOwned = local_edges; + localCellsOwned = local_cells; +#endif + + std::vector<int> gids(localVertsOwned.size()); + rval = mbImpl->tag_get_data(mGlobalIdTag, localVertsOwned, &gids[0]); + ERRORR(rval, "Trouble getting global IDs on local vertices."); + + // Restore localGidVerts + std::copy(gids.rbegin(), gids.rend(), range_inserter(localGidVertsOwned)); + nLocalVerticesOwned = localGidVertsOwned.size(); + + gids.resize(localEdgesOwned.size()); + rval = mbImpl->tag_get_data(mGlobalIdTag, localEdgesOwned, &gids[0]); + ERRORR(rval, "Trouble getting global IDs on local edges."); + + // Restore localGidEdges + std::copy(gids.rbegin(), gids.rend(), range_inserter(localGidEdgesOwned)); + nLocalEdgesOwned = localGidEdgesOwned.size(); + + gids.resize(localCellsOwned.size()); + rval = mbImpl->tag_get_data(mGlobalIdTag, localCellsOwned, &gids[0]); + ERRORR(rval, "Trouble getting global IDs on local cells."); + + // Restore localGidCells + std::copy(gids.rbegin(), gids.rend(), range_inserter(localGidCellsOwned)); + nLocalCellsOwned = localGidCellsOwned.size(); + + return MB_SUCCESS; } -ErrorCode NCWriteMPAS::write_values(std::vector<std::string>& /* var_names */) +ErrorCode NCWriteMPAS::collect_variable_data(std::vector<std::string>& var_names) { - return MB_NOT_IMPLEMENTED; + NCWriteHelper::collect_variable_data(var_names); + + std::vector<std::string>& dimNames = _writeNC->dimNames; + std::vector<int>& dimLens = _writeNC->dimLens; + + // Dimension numbers for other optional levels + std::vector<unsigned int> opt_lev_dims; + + unsigned int lev_idx; + std::vector<std::string>::iterator vecIt; + + // Get number of vertex levels P1 + if ((vecIt = std::find(dimNames.begin(), dimNames.end(), "nVertLevelsP1")) != dimNames.end()) { + lev_idx = vecIt - dimNames.begin(); + opt_lev_dims.push_back(lev_idx); + } + + // Get number of vertex levels P2 + if ((vecIt = std::find(dimNames.begin(), dimNames.end(), "nVertLevelsP2")) != dimNames.end()) { + lev_idx = vecIt - dimNames.begin(); + opt_lev_dims.push_back(lev_idx); + } + + // Get number of soil levels + if ((vecIt = std::find(dimNames.begin(), dimNames.end(), "nSoilLevels")) != dimNames.end()) { + lev_idx = vecIt - dimNames.begin(); + opt_lev_dims.push_back(lev_idx); + } + + std::map<std::string, WriteNC::VarData>& varInfo = _writeNC->varInfo; + + for (size_t i = 0; i < var_names.size(); i++) { + std::string varname = var_names[i]; + std::map<std::string, WriteNC::VarData>::iterator vit = varInfo.find(varname); + if (vit == varInfo.end()) + ERRORR(MB_FAILURE, "Can't find one variable."); + + WriteNC::VarData& currentVarData = vit->second; + std::vector<int>& varDims = currentVarData.varDims; + + // If nVertLevels dimension is not found, try other optional levels such as nVertLevelsP1 + if (std::find(varDims.begin(), varDims.end(), levDim) == varDims.end()) { + for (unsigned int j = 0; j < opt_lev_dims.size(); j++) { + if (std::find(varDims.begin(), varDims.end(), opt_lev_dims[j]) != varDims.end()) { + currentVarData.numLev = dimLens[opt_lev_dims[j]]; + break; + } + } + } + + if (currentVarData.has_tsteps) { + // Support non-set variables with 3 dimensions like (Time, nCells, nVertLevels), or + // 2 dimensions like (Time, nCells) + assert(3 == currentVarData.varDims.size() || 2 == currentVarData.varDims.size()); + + // Time should be the first dimension + assert(tDim == currentVarData.varDims[0]); + + // Set up writeStarts and writeCounts + currentVarData.writeStarts.resize(3); + currentVarData.writeCounts.resize(3); + + // First: Time + currentVarData.writeStarts[0] = 0; // This value is timestep dependent, will be set later + currentVarData.writeCounts[0] = 1; + + // Next: nVertices / nCells / nEdges + switch (currentVarData.entLoc) { + case WriteNC::ENTLOCVERT: + // Vertices + // Start from the first localGidVerts + // Actually, this will be reset later for writing + currentVarData.writeStarts[1] = localGidVertsOwned[0] - 1; + currentVarData.writeCounts[1] = nLocalVerticesOwned; + break; + case WriteNC::ENTLOCFACE: + // Faces + // Start from the first localGidCells + // Actually, this will be reset later for writing + currentVarData.writeStarts[1] = localGidCellsOwned[0] - 1; + currentVarData.writeCounts[1] = nLocalCellsOwned; + break; + case WriteNC::ENTLOCEDGE: + // Edges + // Start from the first localGidEdges + // Actually, this will be reset later for writing + currentVarData.writeStarts[1] = localGidEdgesOwned[0] - 1; + currentVarData.writeCounts[1] = nLocalEdgesOwned; + break; + default: + ERRORR(MB_FAILURE, "Unexpected entity location type for MPAS non-set variable."); + } + + // Finally: nVertLevels or other optional levels, it is possible that there + // is no level dimension for this non-set variable + currentVarData.writeStarts[2] = 0; + currentVarData.writeCounts[2] = currentVarData.numLev; + } + + // Get variable size + currentVarData.sz = 1; + for (std::size_t idx = 0; idx != currentVarData.writeCounts.size(); idx++) + currentVarData.sz *= currentVarData.writeCounts[idx]; + } + + return MB_SUCCESS; +} + +ErrorCode NCWriteMPAS::write_values(std::vector<std::string>& var_names) +{ + Interface*& mbImpl = _writeNC->mbImpl; + std::set<std::string>& usedCoordinates = _writeNC->usedCoordinates; + std::set<std::string>& dummyVarNames = _writeNC->dummyVarNames; + std::map<std::string, WriteNC::VarData>& varInfo = _writeNC->varInfo; + + int success; + Range* pLocalEntsOwned = NULL; + Range* pLocalGidEntsOwned = NULL; + + // Now look at requested var_names; if they have time, we will have a list, and write one at a time + // For each variable tag in the indexed lists, write a time step data + // Assume the first dimension is time (need to check); if not, just write regularly + for (size_t i = 0; i < var_names.size(); i++) { + std::map<std::string, WriteNC::VarData>::iterator vit = varInfo.find(var_names[i]); + if (vit == varInfo.end()) + ERRORR(MB_FAILURE, "Can't find variable requested."); + + WriteNC::VarData& variableData = vit->second; + int numTimeSteps = (int)variableData.varTags.size(); + if (variableData.has_tsteps) { + // Time should be the first dimension + assert(tDim == variableData.varDims[0]); + + // Assume this variable is on vertices for the time being + switch (variableData.entLoc) { + case WriteNC::ENTLOCVERT: + // Vertices + pLocalEntsOwned = &localVertsOwned; + pLocalGidEntsOwned = &localGidVertsOwned; + break; + case WriteNC::ENTLOCEDGE: + // Edges + pLocalEntsOwned = &localEdgesOwned; + pLocalGidEntsOwned = &localGidEdgesOwned; + break; + case WriteNC::ENTLOCFACE: + // Cells + pLocalEntsOwned = &localCellsOwned; + pLocalGidEntsOwned = &localGidCellsOwned; + break; + default: + ERRORR(MB_FAILURE, "Unexpected entity location type for MPAS non-set variable."); + } + + // A typical variable has 3 dimensions as (Time, nCells, nVertLevels) + // FIXME: Should use tstep_nums (from writing options) later + for (int j = 0; j < numTimeSteps; j++) { + // We will write one time step, and count will be one; start will be different + // Use tag_get_data instead of tag_iterate to get values, as localEntsOwned + // might not be contiguous. + variableData.writeStarts[0] = j; // This is time, again + std::vector<double> tag_data(pLocalEntsOwned->size() * variableData.numLev); + ErrorCode rval = mbImpl->tag_get_data(variableData.varTags[j], *pLocalEntsOwned, &tag_data[0]); + ERRORR(rval, "Trouble getting tag data on owned vertices."); + +#ifdef PNETCDF_FILE + size_t nb_writes = pLocalGidEntsOwned->psize(); + std::vector<int> requests(nb_writes), statuss(nb_writes); + size_t idxReq = 0; +#endif + + // Now write from memory directly + switch (variableData.varDataType) { + case NC_DOUBLE: { + size_t indexInDoubleArray = 0; + size_t ic = 0; + for (Range::pair_iterator pair_iter = pLocalGidEntsOwned->pair_begin(); + pair_iter != pLocalGidEntsOwned->pair_end(); ++pair_iter, ic++) { + EntityHandle starth = pair_iter->first; + EntityHandle endh = pair_iter->second; + variableData.writeStarts[1] = (NCDF_SIZE)(starth - 1); + variableData.writeCounts[1] = (NCDF_SIZE)(endh - starth + 1); + + // Do a partial write, in each subrange +#ifdef PNETCDF_FILE + // Wait outside this loop + success = NCFUNCREQP(_vara_double)(_fileId, variableData.varId, + &(variableData.writeStarts[0]), &(variableData.writeCounts[0]), + &(tag_data[indexInDoubleArray]), &requests[idxReq++]); +#else + success = NCFUNCAP(_vara_double)(_fileId, variableData.varId, + &(variableData.writeStarts[0]), &(variableData.writeCounts[0]), + &(tag_data[indexInDoubleArray])); +#endif + ERRORS(success, "Failed to read double data in loop"); + // We need to increment the index in double array for the + // next subrange + indexInDoubleArray += (endh - starth + 1) * variableData.numLev; + } + assert(ic == pLocalGidEntsOwned->psize()); +#ifdef PNETCDF_FILE + success = ncmpi_wait_all(_fileId, requests.size(), &requests[0], &statuss[0]); + ERRORS(success, "Failed on wait_all."); +#endif + break; + } + default: + ERRORR(MB_FAILURE, "Not implemented yet."); + } + } + } // if (variableData.has_tsteps) + else { + switch (variableData.varDataType) { + case NC_DOUBLE: + success = NCFUNCAP(_vara_double)(_fileId, variableData.varId, &variableData.writeStarts[0], + &variableData.writeCounts[0], (double*)(variableData.memoryHogs[0])); + ERRORS(success, "Failed to write double data."); + break; + default: + ERRORR(MB_FAILURE, "Not implemented yet."); + } + } + } + + // Write coordinates used by requested var_names + // Use independent I/O mode put, since this write is only for the root processor + // CAUTION: if the NetCDF ID is from a previous call to ncmpi_create rather than ncmpi_open, + // all processors need to call ncmpi_begin_indep_data(). If only the root processor does so, + // ncmpi_begin_indep_data() call will be blocked forever :( +#ifdef PNETCDF_FILE + // Enter independent I/O mode + success = NCFUNC(begin_indep_data)(_fileId); + ERRORS(success, "Failed to begin independent I/O mode."); +#endif + + int rank = 0; +#ifdef USE_MPI + bool& isParallel = _writeNC->isParallel; + if (isParallel) { + ParallelComm*& myPcomm = _writeNC->myPcomm; + rank = myPcomm->proc_config().proc_rank(); + } +#endif + if (0 == rank) { + for (std::set<std::string>::iterator setIt = usedCoordinates.begin(); + setIt != usedCoordinates.end(); ++setIt) { + const std::string& coordName = *setIt; + + // Skip dummy coordinate variables (e.g. ncol) + if (dummyVarNames.find(coordName) != dummyVarNames.end()) + continue; + + std::map<std::string, WriteNC::VarData>::iterator vit = varInfo.find(coordName); + if (vit == varInfo.end()) + ERRORR(MB_FAILURE, "Can't find one coordinate variable."); + + WriteNC::VarData& varCoordData = vit->second; + + switch (varCoordData.varDataType) { + case NC_DOUBLE: + // Independent I/O mode put + success = NCFUNCP(_vara_double)(_fileId, varCoordData.varId, &varCoordData.writeStarts[0], + &varCoordData.writeCounts[0], (double*)(varCoordData.memoryHogs[0])); + ERRORS(success, "Failed to write double data."); + break; + case NC_INT: + // Independent I/O mode put + success = NCFUNCP(_vara_int)(_fileId, varCoordData.varId, &varCoordData.writeStarts[0], + &varCoordData.writeCounts[0], (int*)(varCoordData.memoryHogs[0])); + ERRORS(success, "Failed to write int data."); + break; + default: + ERRORR(MB_FAILURE, "Not implemented yet."); + } + } + } + +#ifdef PNETCDF_FILE + // End independent I/O mode + success = NCFUNC(end_indep_data)(_fileId); + ERRORS(success, "Failed to end independent I/O mode."); +#endif + + return MB_SUCCESS; } } /* namespace moab */ diff --git a/src/io/NCWriteMPAS.hpp b/src/io/NCWriteMPAS.hpp index 702984f..89842f3 100644 --- a/src/io/NCWriteMPAS.hpp +++ b/src/io/NCWriteMPAS.hpp @@ -17,7 +17,7 @@ class NCWriteMPAS: public UcdNCWriteHelper { public: NCWriteMPAS(WriteNC* writeNC, int fileId, const FileOptions& opts, EntityHandle fileSet) -: UcdNCWriteHelper(writeNC, fileId, opts, fileSet) {} +: UcdNCWriteHelper(writeNC, fileId, opts, fileSet), noEdges(false) {} virtual ~NCWriteMPAS(); @@ -26,7 +26,13 @@ private: virtual ErrorCode collect_mesh_info(); //! Collect data for specified variables + virtual ErrorCode collect_variable_data(std::vector<std::string>& var_names); + + //! Implementation of NCWriteHelper::write_values() virtual ErrorCode write_values(std::vector<std::string>& var_names); + +private: + bool noEdges; }; } // namespace moab diff --git a/test/io/write_nc.cpp b/test/io/write_nc.cpp index 7fe2e82..7f9df60 100644 --- a/test/io/write_nc.cpp +++ b/test/io/write_nc.cpp @@ -71,10 +71,11 @@ int main(int argc, char* argv[]) result += RUN_TEST(test_eul_check_T); result += RUN_TEST(test_eul_read_write_append); result += RUN_TEST(test_fv_read_write_T); + result += RUN_TEST(test_fv_check_T); result += RUN_TEST(test_homme_read_write_T); result += RUN_TEST(test_homme_check_T); - // result += RUN_TEST(test_mpas_read_write_vars); - // result += RUN_TEST(test_mpas_check_vars); + result += RUN_TEST(test_mpas_read_write_vars); + result += RUN_TEST(test_mpas_check_vars); #ifdef USE_MPI fail = MPI_Finalize(); @@ -235,6 +236,7 @@ void test_eul_check_T() } } } + // We read and write variables T and U; U after we write T, so we append // we will also write gw, just to test the file after writing void test_eul_read_write_append() @@ -466,7 +468,7 @@ void test_homme_read_write_T() CHECK_ERR(rval); // Write variables T, lat and lon - std::string write_opts = ";;VARIABLE=T,lat,lon;DEBUG_IO=0;"; + std::string write_opts = ";;VARIABLE=T,lat,lon;DEBUG_IO=0"; #ifdef USE_MPI // Use parallel options write_opts += std::string(";PARALLEL=WRITE_PART"); @@ -626,7 +628,7 @@ void test_mpas_read_write_vars() CHECK_ERR(rval); // Write variables u, ke and vorticity (no mesh information) - std::string write_opts = ";;VARIABLE=u,ke,vorticity;DEBUG_IO=0;"; + std::string write_opts = ";;VARIABLE=u,ke,vorticity;DEBUG_IO=0"; #ifdef USE_MPI // Use parallel options write_opts += std::string(";PARALLEL=WRITE_PART"); @@ -662,9 +664,9 @@ void test_mpas_check_vars() std::string filename; if (procs > 1) - filename = "test_mpas_vars.nc"; - else filename = "test_par_mpas_vars.nc"; + else + filename = "test_mpas_vars.nc"; #ifdef PNETCDF_FILE success = NCFUNC(open)(MPI_COMM_SELF, filename.c_str(), NC_NOWRITE, MPI_INFO_NULL, &ncid); Repository URL: https://bitbucket.org/fathomteam/moab/ -- This is a commit notification from bitbucket.org. 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commit/MOAB: danwu: Updated NC writer and its unit test. Serial and parallel write should work now for MPAS.
by commits-noreply＠bitbucket.org 29 Apr '14

29 Apr '14

1 new commit in MOAB: https://bitbucket.org/fathomteam/moab/commits/735eb40d80f7/ Changeset: 735eb40d80f7 Branch: master User: danwu Date: 2014-04-30 00:05:41 Summary: Updated NC writer and its unit test. Serial and parallel write should work now for MPAS. Affected #: 3 files diff --git a/src/io/NCWriteMPAS.cpp b/src/io/NCWriteMPAS.cpp index 72dc35f..8058726 100644 --- a/src/io/NCWriteMPAS.cpp +++ b/src/io/NCWriteMPAS.cpp @@ -6,6 +6,7 @@ #include "NCWriteMPAS.hpp" #include "moab/WriteUtilIface.hpp" +#include "MBTagConventions.hpp" #define ERRORR(rval, str) \ if (MB_SUCCESS != rval) { _writeNC->mWriteIface->report_error("%s", str); return rval; } @@ -22,12 +23,401 @@ NCWriteMPAS::~NCWriteMPAS() ErrorCode NCWriteMPAS::collect_mesh_info() { - return MB_NOT_IMPLEMENTED; + Interface*& mbImpl = _writeNC->mbImpl; + std::vector<std::string>& dimNames = _writeNC->dimNames; + std::vector<int>& dimLens = _writeNC->dimLens; + Tag& mGlobalIdTag = _writeNC->mGlobalIdTag; + + ErrorCode rval; + + // Look for time dimension + std::vector<std::string>::iterator vecIt; + if ((vecIt = std::find(dimNames.begin(), dimNames.end(), "Time")) != dimNames.end()) + tDim = vecIt - dimNames.begin(); + else if ((vecIt = std::find(dimNames.begin(), dimNames.end(), "time")) != dimNames.end()) + tDim = vecIt - dimNames.begin(); + else { + ERRORR(MB_FAILURE, "Couldn't find 'Time' or 'time' dimension."); + } + nTimeSteps = dimLens[tDim]; + + // Get number of levels + if ((vecIt = std::find(dimNames.begin(), dimNames.end(), "nVertLevels")) != dimNames.end()) + levDim = vecIt - dimNames.begin(); + else { + ERRORR(MB_FAILURE, "Couldn't find 'nVertLevels' dimension."); + } + nLevels = dimLens[levDim]; + + Range local_verts; + rval = mbImpl->get_entities_by_dimension(_fileSet, 0, local_verts); + ERRORR(rval, "Trouble getting local vertices in current file set."); + assert(!local_verts.empty()); + + // Depends on whether NO_EDGES read option is set or not + Range local_edges; + rval = mbImpl->get_entities_by_dimension(_fileSet, 1, local_edges); + ERRORR(rval, "Trouble getting local edges in current file set."); + noEdges = local_edges.empty(); + + Range local_cells; + rval = mbImpl->get_entities_by_dimension(_fileSet, 2, local_cells); + ERRORR(rval, "Trouble getting local cells in current file set."); + assert(!local_cells.empty()); + +#ifdef USE_MPI + bool& isParallel = _writeNC->isParallel; + if (isParallel) { + ParallelComm*& myPcomm = _writeNC->myPcomm; + int rank = myPcomm->proc_config().proc_rank(); + int procs = myPcomm->proc_config().proc_size(); + if (procs > 1) { + rval = myPcomm->filter_pstatus(local_verts, PSTATUS_NOT_OWNED, PSTATUS_NOT, -1, &localVertsOwned); + ERRORR(rval, "Trouble getting owned vertices in set."); + // Assume that PARALLEL_RESOLVE_SHARED_ENTS option is set + // We should avoid writing in parallel with overlapped data + if (procs - 1 == rank) + assert("PARALLEL_RESOLVE_SHARED_ENTS option is set" && localVertsOwned.size() < local_verts.size()); + + if (!noEdges) { + rval = myPcomm->filter_pstatus(local_edges, PSTATUS_NOT_OWNED, PSTATUS_NOT, -1, &localEdgesOwned); + ERRORR(rval, "Trouble getting owned edges in set."); + } + + rval = myPcomm->filter_pstatus(local_cells, PSTATUS_NOT_OWNED, PSTATUS_NOT, -1, &localCellsOwned); + ERRORR(rval, "Trouble getting owned cells in set."); + } + else { + localVertsOwned = local_verts; + localEdgesOwned = local_edges; + localCellsOwned = local_cells; + } + } + else { + // Not running in parallel, but still with MPI + localVertsOwned = local_verts; + localEdgesOwned = local_edges; + localCellsOwned = local_cells; + } +#else + localVertsOwned = local_verts; + localEdgesOwned = local_edges; + localCellsOwned = local_cells; +#endif + + std::vector<int> gids(localVertsOwned.size()); + rval = mbImpl->tag_get_data(mGlobalIdTag, localVertsOwned, &gids[0]); + ERRORR(rval, "Trouble getting global IDs on local vertices."); + + // Restore localGidVerts + std::copy(gids.rbegin(), gids.rend(), range_inserter(localGidVertsOwned)); + nLocalVerticesOwned = localGidVertsOwned.size(); + + gids.resize(localEdgesOwned.size()); + rval = mbImpl->tag_get_data(mGlobalIdTag, localEdgesOwned, &gids[0]); + ERRORR(rval, "Trouble getting global IDs on local edges."); + + // Restore localGidEdges + std::copy(gids.rbegin(), gids.rend(), range_inserter(localGidEdgesOwned)); + nLocalEdgesOwned = localGidEdgesOwned.size(); + + gids.resize(localCellsOwned.size()); + rval = mbImpl->tag_get_data(mGlobalIdTag, localCellsOwned, &gids[0]); + ERRORR(rval, "Trouble getting global IDs on local cells."); + + // Restore localGidCells + std::copy(gids.rbegin(), gids.rend(), range_inserter(localGidCellsOwned)); + nLocalCellsOwned = localGidCellsOwned.size(); + + return MB_SUCCESS; } -ErrorCode NCWriteMPAS::write_values(std::vector<std::string>& /* var_names */) +ErrorCode NCWriteMPAS::collect_variable_data(std::vector<std::string>& var_names) { - return MB_NOT_IMPLEMENTED; + NCWriteHelper::collect_variable_data(var_names); + + std::vector<std::string>& dimNames = _writeNC->dimNames; + std::vector<int>& dimLens = _writeNC->dimLens; + + // Dimension numbers for other optional levels + std::vector<unsigned int> opt_lev_dims; + + unsigned int lev_idx; + std::vector<std::string>::iterator vecIt; + + // Get number of vertex levels P1 + if ((vecIt = std::find(dimNames.begin(), dimNames.end(), "nVertLevelsP1")) != dimNames.end()) { + lev_idx = vecIt - dimNames.begin(); + opt_lev_dims.push_back(lev_idx); + } + + // Get number of vertex levels P2 + if ((vecIt = std::find(dimNames.begin(), dimNames.end(), "nVertLevelsP2")) != dimNames.end()) { + lev_idx = vecIt - dimNames.begin(); + opt_lev_dims.push_back(lev_idx); + } + + // Get number of soil levels + if ((vecIt = std::find(dimNames.begin(), dimNames.end(), "nSoilLevels")) != dimNames.end()) { + lev_idx = vecIt - dimNames.begin(); + opt_lev_dims.push_back(lev_idx); + } + + std::map<std::string, WriteNC::VarData>& varInfo = _writeNC->varInfo; + + for (size_t i = 0; i < var_names.size(); i++) { + std::string varname = var_names[i]; + std::map<std::string, WriteNC::VarData>::iterator vit = varInfo.find(varname); + if (vit == varInfo.end()) + ERRORR(MB_FAILURE, "Can't find one variable."); + + WriteNC::VarData& currentVarData = vit->second; + std::vector<int>& varDims = currentVarData.varDims; + + // If nVertLevels dimension is not found, try other optional levels such as nVertLevelsP1 + if (std::find(varDims.begin(), varDims.end(), levDim) == varDims.end()) { + for (unsigned int j = 0; j < opt_lev_dims.size(); j++) { + if (std::find(varDims.begin(), varDims.end(), opt_lev_dims[j]) != varDims.end()) { + currentVarData.numLev = dimLens[opt_lev_dims[j]]; + break; + } + } + } + + if (currentVarData.has_tsteps) { + // Support non-set variables with 3 dimensions like (Time, nCells, nVertLevels), or + // 2 dimensions like (Time, nCells) + assert(3 == currentVarData.varDims.size() || 2 == currentVarData.varDims.size()); + + // Time should be the first dimension + assert(tDim == currentVarData.varDims[0]); + + // Set up writeStarts and writeCounts + currentVarData.writeStarts.resize(3); + currentVarData.writeCounts.resize(3); + + // First: Time + currentVarData.writeStarts[0] = 0; // This value is timestep dependent, will be set later + currentVarData.writeCounts[0] = 1; + + // Next: nVertices / nCells / nEdges + switch (currentVarData.entLoc) { + case WriteNC::ENTLOCVERT: + // Vertices + // Start from the first localGidVerts + // Actually, this will be reset later for writing + currentVarData.writeStarts[1] = localGidVertsOwned[0] - 1; + currentVarData.writeCounts[1] = nLocalVerticesOwned; + break; + case WriteNC::ENTLOCFACE: + // Faces + // Start from the first localGidCells + // Actually, this will be reset later for writing + currentVarData.writeStarts[1] = localGidCellsOwned[0] - 1; + currentVarData.writeCounts[1] = nLocalCellsOwned; + break; + case WriteNC::ENTLOCEDGE: + // Edges + // Start from the first localGidEdges + // Actually, this will be reset later for writing + currentVarData.writeStarts[1] = localGidEdgesOwned[0] - 1; + currentVarData.writeCounts[1] = nLocalEdgesOwned; + break; + default: + ERRORR(MB_FAILURE, "Unexpected entity location type for MPAS non-set variable."); + } + + // Finally: nVertLevels or other optional levels, it is possible that there + // is no level dimension for this non-set variable + currentVarData.writeStarts[2] = 0; + currentVarData.writeCounts[2] = currentVarData.numLev; + } + + // Get variable size + currentVarData.sz = 1; + for (std::size_t idx = 0; idx != currentVarData.writeCounts.size(); idx++) + currentVarData.sz *= currentVarData.writeCounts[idx]; + } + + return MB_SUCCESS; +} + +ErrorCode NCWriteMPAS::write_values(std::vector<std::string>& var_names) +{ + Interface*& mbImpl = _writeNC->mbImpl; + std::set<std::string>& usedCoordinates = _writeNC->usedCoordinates; + std::set<std::string>& dummyVarNames = _writeNC->dummyVarNames; + std::map<std::string, WriteNC::VarData>& varInfo = _writeNC->varInfo; + + int success; + Range* pLocalEntsOwned = NULL; + Range* pLocalGidEntsOwned = NULL; + + // Now look at requested var_names; if they have time, we will have a list, and write one at a time + // For each variable tag in the indexed lists, write a time step data + // Assume the first dimension is time (need to check); if not, just write regularly + for (size_t i = 0; i < var_names.size(); i++) { + std::map<std::string, WriteNC::VarData>::iterator vit = varInfo.find(var_names[i]); + if (vit == varInfo.end()) + ERRORR(MB_FAILURE, "Can't find variable requested."); + + WriteNC::VarData& variableData = vit->second; + int numTimeSteps = (int)variableData.varTags.size(); + if (variableData.has_tsteps) { + // Time should be the first dimension + assert(tDim == variableData.varDims[0]); + + // Assume this variable is on vertices for the time being + switch (variableData.entLoc) { + case WriteNC::ENTLOCVERT: + // Vertices + pLocalEntsOwned = &localVertsOwned; + pLocalGidEntsOwned = &localGidVertsOwned; + break; + case WriteNC::ENTLOCEDGE: + // Edges + pLocalEntsOwned = &localEdgesOwned; + pLocalGidEntsOwned = &localGidEdgesOwned; + break; + case WriteNC::ENTLOCFACE: + // Cells + pLocalEntsOwned = &localCellsOwned; + pLocalGidEntsOwned = &localGidCellsOwned; + break; + default: + ERRORR(MB_FAILURE, "Unexpected entity location type for MPAS non-set variable."); + } + + // A typical variable has 3 dimensions as (Time, nCells, nVertLevels) + // FIXME: Should use tstep_nums (from writing options) later + for (int j = 0; j < numTimeSteps; j++) { + // We will write one time step, and count will be one; start will be different + // Use tag_get_data instead of tag_iterate to get values, as localEntsOwned + // might not be contiguous. + variableData.writeStarts[0] = j; // This is time, again + std::vector<double> tag_data(pLocalEntsOwned->size() * variableData.numLev); + ErrorCode rval = mbImpl->tag_get_data(variableData.varTags[j], *pLocalEntsOwned, &tag_data[0]); + ERRORR(rval, "Trouble getting tag data on owned vertices."); + +#ifdef PNETCDF_FILE + size_t nb_writes = pLocalGidEntsOwned->psize(); + std::vector<int> requests(nb_writes), statuss(nb_writes); + size_t idxReq = 0; +#endif + + // Now write from memory directly + switch (variableData.varDataType) { + case NC_DOUBLE: { + size_t indexInDoubleArray = 0; + size_t ic = 0; + for (Range::pair_iterator pair_iter = pLocalGidEntsOwned->pair_begin(); + pair_iter != pLocalGidEntsOwned->pair_end(); ++pair_iter, ic++) { + EntityHandle starth = pair_iter->first; + EntityHandle endh = pair_iter->second; + variableData.writeStarts[1] = (NCDF_SIZE)(starth - 1); + variableData.writeCounts[1] = (NCDF_SIZE)(endh - starth + 1); + + // Do a partial write, in each subrange +#ifdef PNETCDF_FILE + // Wait outside this loop + success = NCFUNCREQP(_vara_double)(_fileId, variableData.varId, + &(variableData.writeStarts[0]), &(variableData.writeCounts[0]), + &(tag_data[indexInDoubleArray]), &requests[idxReq++]); +#else + success = NCFUNCAP(_vara_double)(_fileId, variableData.varId, + &(variableData.writeStarts[0]), &(variableData.writeCounts[0]), + &(tag_data[indexInDoubleArray])); +#endif + ERRORS(success, "Failed to read double data in loop"); + // We need to increment the index in double array for the + // next subrange + indexInDoubleArray += (endh - starth + 1) * variableData.numLev; + } + assert(ic == pLocalGidEntsOwned->psize()); +#ifdef PNETCDF_FILE + success = ncmpi_wait_all(_fileId, requests.size(), &requests[0], &statuss[0]); + ERRORS(success, "Failed on wait_all."); +#endif + break; + } + default: + ERRORR(MB_FAILURE, "Not implemented yet."); + } + } + } // if (variableData.has_tsteps) + else { + switch (variableData.varDataType) { + case NC_DOUBLE: + success = NCFUNCAP(_vara_double)(_fileId, variableData.varId, &variableData.writeStarts[0], + &variableData.writeCounts[0], (double*)(variableData.memoryHogs[0])); + ERRORS(success, "Failed to write double data."); + break; + default: + ERRORR(MB_FAILURE, "Not implemented yet."); + } + } + } + + // Write coordinates used by requested var_names + // Use independent I/O mode put, since this write is only for the root processor + // CAUTION: if the NetCDF ID is from a previous call to ncmpi_create rather than ncmpi_open, + // all processors need to call ncmpi_begin_indep_data(). If only the root processor does so, + // ncmpi_begin_indep_data() call will be blocked forever :( +#ifdef PNETCDF_FILE + // Enter independent I/O mode + success = NCFUNC(begin_indep_data)(_fileId); + ERRORS(success, "Failed to begin independent I/O mode."); +#endif + + int rank = 0; +#ifdef USE_MPI + bool& isParallel = _writeNC->isParallel; + if (isParallel) { + ParallelComm*& myPcomm = _writeNC->myPcomm; + rank = myPcomm->proc_config().proc_rank(); + } +#endif + if (0 == rank) { + for (std::set<std::string>::iterator setIt = usedCoordinates.begin(); + setIt != usedCoordinates.end(); ++setIt) { + const std::string& coordName = *setIt; + + // Skip dummy coordinate variables (e.g. ncol) + if (dummyVarNames.find(coordName) != dummyVarNames.end()) + continue; + + std::map<std::string, WriteNC::VarData>::iterator vit = varInfo.find(coordName); + if (vit == varInfo.end()) + ERRORR(MB_FAILURE, "Can't find one coordinate variable."); + + WriteNC::VarData& varCoordData = vit->second; + + switch (varCoordData.varDataType) { + case NC_DOUBLE: + // Independent I/O mode put + success = NCFUNCP(_vara_double)(_fileId, varCoordData.varId, &varCoordData.writeStarts[0], + &varCoordData.writeCounts[0], (double*)(varCoordData.memoryHogs[0])); + ERRORS(success, "Failed to write double data."); + break; + case NC_INT: + // Independent I/O mode put + success = NCFUNCP(_vara_int)(_fileId, varCoordData.varId, &varCoordData.writeStarts[0], + &varCoordData.writeCounts[0], (int*)(varCoordData.memoryHogs[0])); + ERRORS(success, "Failed to write int data."); + break; + default: + ERRORR(MB_FAILURE, "Not implemented yet."); + } + } + } + +#ifdef PNETCDF_FILE + // End independent I/O mode + success = NCFUNC(end_indep_data)(_fileId); + ERRORS(success, "Failed to end independent I/O mode."); +#endif + + return MB_SUCCESS; } } /* namespace moab */ diff --git a/src/io/NCWriteMPAS.hpp b/src/io/NCWriteMPAS.hpp index 702984f..89842f3 100644 --- a/src/io/NCWriteMPAS.hpp +++ b/src/io/NCWriteMPAS.hpp @@ -17,7 +17,7 @@ class NCWriteMPAS: public UcdNCWriteHelper { public: NCWriteMPAS(WriteNC* writeNC, int fileId, const FileOptions& opts, EntityHandle fileSet) -: UcdNCWriteHelper(writeNC, fileId, opts, fileSet) {} +: UcdNCWriteHelper(writeNC, fileId, opts, fileSet), noEdges(false) {} virtual ~NCWriteMPAS(); @@ -26,7 +26,13 @@ private: virtual ErrorCode collect_mesh_info(); //! Collect data for specified variables + virtual ErrorCode collect_variable_data(std::vector<std::string>& var_names); + + //! Implementation of NCWriteHelper::write_values() virtual ErrorCode write_values(std::vector<std::string>& var_names); + +private: + bool noEdges; }; } // namespace moab diff --git a/test/io/write_nc.cpp b/test/io/write_nc.cpp index f48e4c6..740ec5f 100644 --- a/test/io/write_nc.cpp +++ b/test/io/write_nc.cpp @@ -71,10 +71,11 @@ int main(int argc, char* argv[]) result += RUN_TEST(test_eul_check_T); result += RUN_TEST(test_eul_read_write_append); result += RUN_TEST(test_fv_read_write_T); + result += RUN_TEST(test_fv_check_T); result += RUN_TEST(test_homme_read_write_T); result += RUN_TEST(test_homme_check_T); - // result += RUN_TEST(test_mpas_read_write_vars); - // result += RUN_TEST(test_mpas_check_vars); + result += RUN_TEST(test_mpas_read_write_vars); + result += RUN_TEST(test_mpas_check_vars); #ifdef USE_MPI fail = MPI_Finalize(); @@ -235,6 +236,7 @@ void test_eul_check_T() } } } + // We read and write variables T and U; U after we write T, so we append // we will also write gw, just to test the file after writing void test_eul_read_write_append() @@ -453,7 +455,7 @@ void test_homme_read_write_T() CHECK_ERR(rval); // Write variables T, lat and lon - std::string write_opts = ";;VARIABLE=T,lat,lon;DEBUG_IO=0;"; + std::string write_opts = ";;VARIABLE=T,lat,lon;DEBUG_IO=0"; #ifdef USE_MPI // Use parallel options write_opts += std::string(";PARALLEL=WRITE_PART"); @@ -613,7 +615,7 @@ void test_mpas_read_write_vars() CHECK_ERR(rval); // Write variables u, ke and vorticity (no mesh information) - std::string write_opts = ";;VARIABLE=u,ke,vorticity;DEBUG_IO=0;"; + std::string write_opts = ";;VARIABLE=u,ke,vorticity;DEBUG_IO=0"; #ifdef USE_MPI // Use parallel options write_opts += std::string(";PARALLEL=WRITE_PART"); @@ -649,9 +651,9 @@ void test_mpas_check_vars() std::string filename; if (procs > 1) - filename = "test_mpas_vars.nc"; - else filename = "test_par_mpas_vars.nc"; + else + filename = "test_mpas_vars.nc"; #ifdef PNETCDF_FILE success = NCFUNC(open)(MPI_COMM_SELF, filename.c_str(), NC_NOWRITE, MPI_INFO_NULL, &ncid); Repository URL: https://bitbucket.org/fathomteam/moab/ -- This is a commit notification from bitbucket.org. 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commit/MOAB: iulian07: first pass at append option
by commits-noreply＠bitbucket.org 29 Apr '14

29 Apr '14

1 new commit in MOAB: https://bitbucket.org/fathomteam/moab/commits/f48ec38dbf3e/ Changeset: f48ec38dbf3e Branch: master User: iulian07 Date: 2014-04-29 23:32:58 Summary: first pass at append option small test now for euler only maybe it should be tested for more formats assumes that if a dimension is already defined, there should be a variable with the same name (coordinate) Affected #: 5 files diff --git a/src/io/NCWriteHelper.cpp b/src/io/NCWriteHelper.cpp index 4f95ef8..923fe02 100644 --- a/src/io/NCWriteHelper.cpp +++ b/src/io/NCWriteHelper.cpp @@ -209,7 +209,7 @@ ErrorCode NCWriteHelper::collect_variable_data(std::vector<std::string>& var_nam return MB_SUCCESS; } -ErrorCode NCWriteHelper::init_file(std::vector<std::string>& var_names) +ErrorCode NCWriteHelper::init_file(std::vector<std::string>& var_names, bool append) { std::vector<std::string>& dimNames = _writeNC->dimNames; std::set<std::string>& usedCoordinates = _writeNC->usedCoordinates; @@ -221,6 +221,9 @@ ErrorCode NCWriteHelper::init_file(std::vector<std::string>& var_names) int tDim_in_dimNames = tDim; int levDim_in_dimNames = levDim; + // if append mode, make sure we are in define mode; a simple open will not allow creation of new variables + if (append) + NCFUNC(redef)(_fileId); // First initialize all coordinates, then fill VarData for actual variables (and dimensions) // Check that for used coordinates we have found the tags for (std::set<std::string>::iterator setIt = usedCoordinates.begin(); @@ -234,6 +237,40 @@ ErrorCode NCWriteHelper::init_file(std::vector<std::string>& var_names) WriteNC::VarData& varCoordData = vit->second; varCoordData.varDims.resize(1); + // if not append, create it for sure + // if append, we might already have it, including the tag / variable with the same name + /* + * int ncmpi_inq_dimid(int ncid, const char *name, int *idp); + */ + if (append) + { + int dimId; + if (NCFUNC(inq_dimid)(_fileId, coordName.c_str(), &dimId) == NC_NOERR) + // if not found, create it later + { + varCoordData.varDims[0] = dimId; + // check that the coordinate is a variable too + // Skip dummy coordinate variables (e.g. ncol) + dbgOut.tprintf(2, " file already has coordName %s dim id is %d \n", coordName.c_str(), (int)varCoordData.varDims[0]); + if (dummyVarNames.find(coordName) != dummyVarNames.end()) + continue; + // inquire for a variable with the same name + + int varId; + if (NCFUNC(inq_varid)(_fileId, coordName.c_str(), &varId) != NC_NOERR) + ERRORR(MB_FAILURE, "we do not have a variable with the same name."); + // we should also check that this variable has one dimension, and it is dimId + varCoordData.varId = varId; + dbgOut.tprintf(2, " file already has coordinate %s and varId is %d \n", coordName.c_str(), varId); + // Update tDim and levDim to actual dimension id + if (coordName == dimNames[tDim_in_dimNames]) + tDim = varCoordData.varDims[0]; + else if (coordName == dimNames[levDim_in_dimNames]) + levDim = varCoordData.varDims[0]; + continue; // maybe more checks are needed here + } + + } /* int nc_def_dim (int ncid, const char *name, size_t len, int *dimidp); * example: status = nc_def_dim(fileId, "lat", 18L, &latid); */ @@ -297,9 +334,10 @@ ErrorCode NCWriteHelper::init_file(std::vector<std::string>& var_names) } // Define the variable now: - if (NCFUNC(def_var)(_fileId, var_names[i].c_str(), variableData.varDataType, + int errCode = NCFUNC(def_var)(_fileId, var_names[i].c_str(), variableData.varDataType, (int)variableData.varDims.size(), &(variableData.varDims[0]), - &variableData.varId) != NC_NOERR) + &variableData.varId); + if ( errCode != NC_NOERR) ERRORR(MB_FAILURE, "Failed to create coordinate variable."); dbgOut.tprintf(2, " for variable %s variable id is %d \n", var_names[i].c_str(), variableData.varId); diff --git a/src/io/NCWriteHelper.hpp b/src/io/NCWriteHelper.hpp index b05fe12..ed2443a 100644 --- a/src/io/NCWriteHelper.hpp +++ b/src/io/NCWriteHelper.hpp @@ -34,7 +34,7 @@ public: //! Initialize file: this is where all defines are done //! The VarData dimension ids are filled up after define - ErrorCode init_file(std::vector<std::string>& var_names); + ErrorCode init_file(std::vector<std::string>& var_names, bool _append); protected: template <typename T> void jik_to_kji(size_t ni, size_t nj, size_t nk, T* dest, T* source) @@ -50,7 +50,7 @@ protected: //! Allow NCWriteHelper to directly access members of WriteNC WriteNC* _writeNC; - //! Cache some information from ReadNC + //! Cache some information from WriteNC int _fileId; const FileOptions& _opts; EntityHandle _fileSet; diff --git a/src/io/WriteNC.cpp b/src/io/WriteNC.cpp index e665e26..98f4e3b 100644 --- a/src/io/WriteNC.cpp +++ b/src/io/WriteNC.cpp @@ -33,7 +33,7 @@ WriteNC::WriteNC(Interface* impl) : #ifdef USE_MPI myPcomm(NULL), #endif - noMesh(false), noVars(false), + noMesh(false), noVars(false), append(false), mGlobalIdTag(0), isParallel(false), myHelper(NULL) { @@ -84,23 +84,42 @@ ErrorCode WriteNC::write_file(const char* file_name, rval = process_conventional_tags(*file_set); ERRORR(rval, "Trouble processing conventional tags."); - // Create the file ; assume we will overwrite always, for the time being - dbgOut.tprintf(1, "creating file %s\n", file_name); + // Create or append the file + if (append) + dbgOut.tprintf(1, "opening file %s for appending \n", file_name); + else + dbgOut.tprintf(1, "creating file %s\n", file_name); fileName = file_name; int success; + if (append) + { #ifdef PNETCDF_FILE - int cmode = overwrite ? NC_CLOBBER : NC_NOCLOBBER; - if (isParallel) - success = NCFUNC(create)(myPcomm->proc_config().proc_comm(), file_name, cmode, MPI_INFO_NULL, &fileId); - else - success = NCFUNC(create)(MPI_COMM_SELF, file_name, cmode, MPI_INFO_NULL, &fileId); + int omode = NC_WRITE; + if (isParallel) + success = NCFUNC(open)(myPcomm->proc_config().proc_comm(), file_name, omode, MPI_INFO_NULL, &fileId); + else + success = NCFUNC(open)(MPI_COMM_SELF, file_name, omode, MPI_INFO_NULL, &fileId); #else - // This is a regular netcdf file - success = NCFUNC(create)(file_name, overwrite ? NC_CLOBBER : NC_NOCLOBBER, &fileId); + // This is a regular netcdf file + success = NCFUNC(open)(file_name, overwrite ? NC_CLOBBER : NC_NOCLOBBER, &fileId); #endif - ERRORS(success, "Failed to create file."); - + ERRORS(success, "Failed to open file for appending."); + } + else // case when the file is new, will be overwritten, most likely + { +#ifdef PNETCDF_FILE + int cmode = overwrite ? NC_CLOBBER : NC_NOCLOBBER; + if (isParallel) + success = NCFUNC(create)(myPcomm->proc_config().proc_comm(), file_name, cmode, MPI_INFO_NULL, &fileId); + else + success = NCFUNC(create)(MPI_COMM_SELF, file_name, cmode, MPI_INFO_NULL, &fileId); +#else + // This is a regular netcdf file + success = NCFUNC(create)(file_name, overwrite ? NC_CLOBBER : NC_NOCLOBBER, &fileId); +#endif + ERRORS(success, "Failed to create file."); + } if (NULL != myHelper) delete myHelper; @@ -116,7 +135,7 @@ ErrorCode WriteNC::write_file(const char* file_name, rval = myHelper->collect_variable_data(var_names); ERRORR(rval, "Trouble collecting variable data."); - rval = myHelper->init_file(var_names); + rval = myHelper->init_file(var_names, append); ERRORR(rval, "Failed to initialize file."); rval = myHelper->write_values(var_names); @@ -148,6 +167,10 @@ ErrorCode WriteNC::parse_options(const FileOptions& opts, std::vector<std::strin if (MB_SUCCESS == rval) noMesh = true; + rval = opts.get_null_option("APPEND"); + if (MB_SUCCESS == rval) + append = true; + if (2 <= dbgOut.get_verbosity()) { if (!var_names.empty()) { std::cerr << "Variables requested: "; diff --git a/src/io/WriteNC.hpp b/src/io/WriteNC.hpp index 1c5d78e..5827680 100644 --- a/src/io/WriteNC.hpp +++ b/src/io/WriteNC.hpp @@ -185,6 +185,7 @@ private: //! Write options bool noMesh; bool noVars; + bool append; //! Cached tags for writing. This will be important for ordering the data, in parallel Tag mGlobalIdTag; diff --git a/test/io/write_nc.cpp b/test/io/write_nc.cpp index 2d9bdae..f48e4c6 100644 --- a/test/io/write_nc.cpp +++ b/test/io/write_nc.cpp @@ -36,6 +36,7 @@ static const char example_mpas[] = "/io/mpasx1.642.t.2.nc"; // CAM-EUL void test_eul_read_write_T(); void test_eul_check_T(); +void test_eul_read_write_append(); // CAM-FV void test_fv_read_write_T(); @@ -68,12 +69,12 @@ int main(int argc, char* argv[]) result += RUN_TEST(test_eul_read_write_T); result += RUN_TEST(test_eul_check_T); + result += RUN_TEST(test_eul_read_write_append); result += RUN_TEST(test_fv_read_write_T); - result += RUN_TEST(test_fv_check_T); result += RUN_TEST(test_homme_read_write_T); result += RUN_TEST(test_homme_check_T); - //result += RUN_TEST(test_mpas_read_write_vars); - //result += RUN_TEST(test_mpas_check_vars); + // result += RUN_TEST(test_mpas_read_write_vars); + // result += RUN_TEST(test_mpas_check_vars); #ifdef USE_MPI fail = MPI_Finalize(); @@ -234,6 +235,61 @@ void test_eul_check_T() } } } +// We read and write variables T and U; U after we write T, so we append +// we will also write gw, just to test the file after writing +void test_eul_read_write_append() +{ + int procs = 1; +#ifdef USE_MPI + MPI_Comm_size(MPI_COMM_WORLD, &procs); +#endif + +// We will not test NC writer in parallel without pnetcdf support +#ifndef PNETCDF_FILE + if (procs > 1) + return; +#endif + + Core moab; + Interface& mb = moab; + + std::string read_opts; + get_eul_read_options(read_opts); + + EntityHandle set; + ErrorCode rval = mb.create_meshset(MESHSET_SET, set); + CHECK_ERR(rval); + + // Load non-set variable T, set variable gw, and the mesh + read_opts += ";DEBUG_IO=0;VARIABLE=T,U,gw"; + rval = mb.load_file(example_eul, &set, read_opts.c_str()); + CHECK_ERR(rval); + + // Write variables T and gw + std::string write_opts; + write_opts = std::string(";;VARIABLE=T,gw;DEBUG_IO=0"); +#ifdef USE_MPI + // Use parallel options + write_opts += std::string(";PARALLEL=WRITE_PART"); +#endif + if (procs > 1) + rval = mb.write_file("test_par_eul_TU.nc", 0, write_opts.c_str(), &set, 1); + else + rval = mb.write_file("test_eul_TU.nc", 0, write_opts.c_str(), &set, 1); + CHECK_ERR(rval); + // append to the file variable U + std::string write_opts2; + write_opts2 = std::string(";;VARIABLE=U;DEBUG_IO=0;APPEND"); +#ifdef USE_MPI + // Use parallel options + write_opts2 += std::string(";PARALLEL=WRITE_PART"); +#endif + if (procs > 1) + rval = mb.write_file("test_par_eul_TU.nc", 0, write_opts2.c_str(), &set, 1); + else + rval = mb.write_file("test_eul_TU.nc", 0, write_opts2.c_str(), &set, 1); + CHECK_ERR(rval); +} // We also write coordinate variables slat and slon to the output file, so that // it can be recognized by NC reader later in test_fv_check_T() Repository URL: https://bitbucket.org/fathomteam/moab/ -- This is a commit notification from bitbucket.org. 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commit/MOAB: danwu: Merged ncwriter into master
by commits-noreply＠bitbucket.org 28 Apr '14

28 Apr '14

1 new commit in MOAB: https://bitbucket.org/fathomteam/moab/commits/7e36def04100/ Changeset: 7e36def04100 Branch: master User: danwu Date: 2014-04-29 00:02:09 Summary: Merged ncwriter into master Affected #: 20 files diff --git a/.gitignore b/.gitignore index ba9fe1e..d686ffa 100644 --- a/.gitignore +++ b/.gitignore @@ -155,6 +155,7 @@ test/io/*.g test/io/gmsh_test test/io/ideas_test test/io/nastran_test +test/io/*.nc test/io/read_cgm_basic_test test/io/read_cgm_connectivity_test test/io/read_cgm_group_test @@ -168,6 +169,7 @@ test/io/smf_test test/io/stl_test test/io/tqdcfr test/io/vtk_test +test/io/write_nc test/kd_tree_test test/kd_tree_time test/kd_tree_tool @@ -187,6 +189,7 @@ test/parallel/*.h5m test/parallel/mbparallelcomm_test test/parallel/mhdf_parallel test/parallel/mpastrvpart +test/parallel/*.nc test/parallel/par_coupler_test test/parallel/par_intx_sph test/parallel/parallel_hdf5_test @@ -206,6 +209,7 @@ test/parallel/structured3 test/parallel/uber_parallel_test test/parallel/ucdtrvpart test/parallel/*.vtk +test/parallel/write_nc_par test/perf/adj_time test/perf/perf test/perf/perftool diff --git a/src/ReaderWriterSet.cpp b/src/ReaderWriterSet.cpp index 5015a7f..1f254b0 100644 --- a/src/ReaderWriterSet.cpp +++ b/src/ReaderWriterSet.cpp @@ -48,6 +48,7 @@ #ifdef NETCDF_FILE # include "ReadNCDF.hpp" # include "WriteNCDF.hpp" +# include "WriteNC.hpp" # include "WriteSLAC.hpp" # include "ReadNC.hpp" # include "ReadGCRM.hpp" @@ -105,7 +106,7 @@ ReaderWriterSet::ReaderWriterSet( Core* mdb, Error* handler ) const char* exo_sufxs[] = { "exo", "exoII", "exo2", "g", "gen", NULL }; register_factory( ReadNCDF::factory, WriteNCDF::factory, "Exodus II", exo_sufxs, "EXODUS" ); register_factory( ReadGCRM::factory, NULL, "GCRM NC", "nc", "GCRM" ); - register_factory( ReadNC::factory, NULL, "Climate NC", "nc", "NC" ); + register_factory( ReadNC::factory, WriteNC::factory, "Climate NC", "nc", "NC" ); #endif #ifdef CGNS_FILE diff --git a/src/io/Makefile.am b/src/io/Makefile.am index 09fe3d3..1269523 100644 --- a/src/io/Makefile.am +++ b/src/io/Makefile.am @@ -17,11 +17,17 @@ if NETCDF_FILE WriteNCDF.cpp WriteNCDF.hpp \ WriteSLAC.cpp WriteSLAC.hpp \ ReadNC.cpp ReadNC.hpp \ + WriteNC.cpp WriteNC.hpp \ NCHelper.cpp NCHelper.hpp \ NCHelperEuler.cpp NCHelperEuler.hpp \ NCHelperFV.cpp NCHelperFV.hpp \ NCHelperHOMME.cpp NCHelperHOMME.hpp \ NCHelperMPAS.cpp NCHelperMPAS.hpp \ + NCWriteHelper.cpp NCWriteHelper.hpp \ + NCWriteEuler.cpp NCWriteEuler.hpp \ + NCWriteFV.cpp NCWriteFV.hpp \ + NCWriteHOMME.cpp NCWriteHOMME.hpp \ + NCWriteMPAS.cpp NCWriteMPAS.hpp \ ReadGCRM.cpp ReadGCRM.hpp else MOAB_NETCDF_SRCS = @@ -30,11 +36,17 @@ endif if PNETCDF_FILE if !NETCDF_FILE MOAB_NETCDF_SRCS += ReadNC.cpp ReadNC.hpp \ + WriteNC.cpp WriteNC.hpp \ NCHelper.cpp NCHelper.hpp \ NCHelperEuler.cpp NCHelperEuler.hpp \ NCHelperFV.cpp NCHelperFV.hpp \ NCHelperHOMME.cpp NCHelperHOMME.hpp \ NCHelperMPAS.cpp NCHelperMPAS.hpp \ + NCWriteHelper.cpp NCWriteHelper.hpp \ + NCWriteEuler.cpp NCWriteEuler.hpp \ + NCWriteFV.cpp NCWriteFV.hpp \ + NCWriteHOMME.cpp NCWriteHOMME.hpp \ + NCWriteMPAS.cpp NCWriteMPAS.hpp \ ReadGCRM.cpp ReadGCRM.hpp endif endif diff --git a/src/io/NCHelper.cpp b/src/io/NCHelper.cpp index 9ef1332..0e970d9 100644 --- a/src/io/NCHelper.cpp +++ b/src/io/NCHelper.cpp @@ -192,16 +192,16 @@ ErrorCode NCHelper::create_conventional_tags(const std::vector<int>& tstep_nums) unsigned int varDimSz = varInfo[mapIter->first].varDims.size(); if (varDimSz == 0) continue; - varInfo[mapIter->first].varTags.resize(varDimSz, 0); + std::vector<Tag> varDimTags(varDimSz); for (unsigned int i = 0; i != varDimSz; i++) { Tag tmptag = 0; std::string tmptagname = dimNames[varInfo[mapIter->first].varDims[i]]; mbImpl->tag_get_handle(tmptagname.c_str(), 0, MB_TYPE_OPAQUE, tmptag, MB_TAG_ANY); - varInfo[mapIter->first].varTags[i] = tmptag; + varDimTags[i] = tmptag; } rval = mbImpl->tag_get_handle(tag_name.c_str(), varDimSz, MB_TYPE_HANDLE, varNamesDimsTag, MB_TAG_SPARSE | MB_TAG_CREAT); ERRORR(rval, "Trouble creating __<var_name>_DIMS tag."); - rval = mbImpl->tag_set_data(varNamesDimsTag, &_fileSet, 1, &(varInfo[mapIter->first].varTags[0])); + rval = mbImpl->tag_set_data(varNamesDimsTag, &_fileSet, 1, &(varDimTags[0])); ERRORR(rval, "Trouble setting data for __<var_name>_DIMS tag."); if (MB_SUCCESS == rval) dbgOut.tprintf(2, "Tag created for variable %s\n", tag_name.c_str()); @@ -252,21 +252,37 @@ ErrorCode NCHelper::create_conventional_tags(const std::vector<int>& tstep_nums) Tag varAttTag = 0; rval = mbImpl->tag_get_handle(tag_name.c_str(), 0, MB_TYPE_OPAQUE, varAttTag, MB_TAG_CREAT | MB_TAG_SPARSE | MB_TAG_VARLEN); ERRORR(rval, "Trouble creating __<var_name>_ATTRIBS tag."); + std::string varAttVal; std::vector<int> varAttLen; - rval = create_attrib_string(mapIter->second.varAtts, varAttVal, varAttLen); - ERRORR(rval, "Trouble creating attribute strings."); + if (mapIter->second.numAtts < 1) { + if (dummyVarNames.find(mapIter->first) != dummyVarNames.end()) { + // This variable is a dummy dimension variable + varAttVal = "DUMMY_VAR"; + } + else { + // This variable has no attributes + varAttVal = "NO_ATTRIBS"; + } + } + else { + rval = create_attrib_string(mapIter->second.varAtts, varAttVal, varAttLen); + ERRORR(rval, "Trouble creating attribute string."); + } const void* varAttPtr = varAttVal.c_str(); int varAttSz = varAttVal.size(); + if (0 == varAttSz) + varAttSz = 1; rval = mbImpl->tag_set_by_ptr(varAttTag, &_fileSet, 1, &varAttPtr, &varAttSz); ERRORR(rval, "Trouble setting data for __<var_name>_ATTRIBS tag."); if (MB_SUCCESS == rval) dbgOut.tprintf(2, "Tag created for variable %s\n", tag_name.c_str()); - if (varAttLen.size() == 0) - varAttLen.push_back(0); + ssTagName << "_LEN"; tag_name = ssTagName.str(); Tag varAttLenTag = 0; + if (0 == varAttLen.size()) + varAttLen.push_back(0); rval = mbImpl->tag_get_handle(tag_name.c_str(), varAttLen.size(), MB_TYPE_INTEGER, varAttLenTag, MB_TAG_SPARSE | MB_TAG_CREAT); ERRORR(rval, "Trouble creating __<var_name>_ATTRIBS_LEN tag."); rval = mbImpl->tag_set_data(varAttLenTag, &_fileSet, 1, &varAttLen[0]); @@ -324,6 +340,11 @@ ErrorCode NCHelper::read_variable_setup(std::vector<std::string>& var_names, std dummyVarNames.find(vd.varName) != dummyVarNames.end()) continue; + // Dimension variables were read before creating conventional tags + std::vector<std::string>& dimNames = _readNC->dimNames; + if (std::find(dimNames.begin(), dimNames.end(), vd.varName) != dimNames.end()) + continue; + if (vd.entLoc == ReadNC::ENTLOCSET) vsetdatas.push_back(vd); else diff --git a/src/io/NCWriteEuler.cpp b/src/io/NCWriteEuler.cpp new file mode 100644 index 0000000..4b3f1ff --- /dev/null +++ b/src/io/NCWriteEuler.cpp @@ -0,0 +1,23 @@ +/* + * NCWriteEuler.cpp + * + * Created on: Mar 28, 2014 + */ + +#include "NCWriteEuler.hpp" +#include "moab/WriteUtilIface.hpp" + +#define ERRORR(rval, str) \ + if (MB_SUCCESS != rval) { _writeNC->mWriteIface->report_error("%s", str); return rval; } + +#define ERRORS(err, str) \ + if (err) { _writeNC->mWriteIface->report_error("%s", str); return MB_FAILURE; } + +namespace moab { + +NCWriteEuler::~NCWriteEuler() +{ + // TODO Auto-generated destructor stub +} + +} /* namespace moab */ diff --git a/src/io/NCWriteEuler.hpp b/src/io/NCWriteEuler.hpp new file mode 100644 index 0000000..2cb6486 --- /dev/null +++ b/src/io/NCWriteEuler.hpp @@ -0,0 +1,27 @@ +/* + * NCWriteEuler.hpp + * + * nc write helper for euler type data (CAM) + * Created on: Mar 28, 2014 + * + */ + +#ifndef NCWRITEEULER_HPP_ +#define NCWRITEEULER_HPP_ + +#include "NCWriteHelper.hpp" + +namespace moab { + +class NCWriteEuler: public ScdNCWriteHelper +{ +public: + NCWriteEuler(WriteNC* writeNC, int fileId, const FileOptions& opts, EntityHandle fileSet) +: ScdNCWriteHelper(writeNC, fileId, opts, fileSet) {} + + virtual ~NCWriteEuler(); +}; + +} // namespace moab + +#endif diff --git a/src/io/NCWriteFV.cpp b/src/io/NCWriteFV.cpp new file mode 100644 index 0000000..8de489f --- /dev/null +++ b/src/io/NCWriteFV.cpp @@ -0,0 +1,23 @@ +/* + * NCWriteFV.cpp + * + * Created on: April 9, 2014 + */ + +#include "NCWriteFV.hpp" +#include "moab/WriteUtilIface.hpp" + +#define ERRORR(rval, str) \ + if (MB_SUCCESS != rval) { _writeNC->mWriteIface->report_error("%s", str); return rval; } + +#define ERRORS(err, str) \ + if (err) { _writeNC->mWriteIface->report_error("%s", str); return MB_FAILURE; } + +namespace moab { + +NCWriteFV::~NCWriteFV() +{ + // TODO Auto-generated destructor stub +} + +} /* namespace moab */ diff --git a/src/io/NCWriteFV.hpp b/src/io/NCWriteFV.hpp new file mode 100644 index 0000000..d3286fc --- /dev/null +++ b/src/io/NCWriteFV.hpp @@ -0,0 +1,27 @@ +/* + * NCWriteFV.hpp + * + * nc write helper for FV type data (CAM) + * Created on: April 9, 2014 + * + */ + +#ifndef NCWRITEFV_HPP_ +#define NCWRITEFV_HPP_ + +#include "NCWriteHelper.hpp" + +namespace moab { + +class NCWriteFV: public ScdNCWriteHelper +{ +public: + NCWriteFV(WriteNC* writeNC, int fileId, const FileOptions& opts, EntityHandle fileSet) +: ScdNCWriteHelper(writeNC, fileId, opts, fileSet) {} + + virtual ~NCWriteFV(); +}; + +} // namespace moab + +#endif // NCWRITEFV_HPP_ diff --git a/src/io/NCWriteHOMME.cpp b/src/io/NCWriteHOMME.cpp new file mode 100644 index 0000000..9320f62 --- /dev/null +++ b/src/io/NCWriteHOMME.cpp @@ -0,0 +1,316 @@ +/* + * NCWriteHOMME.cpp + * + * Created on: April 9, 2014 + */ + +#include "NCWriteHOMME.hpp" +#include "moab/WriteUtilIface.hpp" +#include "MBTagConventions.hpp" + +#define ERRORR(rval, str) \ + if (MB_SUCCESS != rval) { _writeNC->mWriteIface->report_error("%s", str); return rval; } + +#define ERRORS(err, str) \ + if (err) { _writeNC->mWriteIface->report_error("%s", str); return MB_FAILURE; } + +namespace moab { + +NCWriteHOMME::~NCWriteHOMME() +{ + // TODO Auto-generated destructor stub +} + +ErrorCode NCWriteHOMME::collect_mesh_info() +{ + Interface*& mbImpl = _writeNC->mbImpl; + std::vector<std::string>& dimNames = _writeNC->dimNames; + std::vector<int>& dimLens = _writeNC->dimLens; + Tag& mGlobalIdTag = _writeNC->mGlobalIdTag; + + ErrorCode rval; + + // Look for time dimension + std::vector<std::string>::iterator vecIt; + if ((vecIt = std::find(dimNames.begin(), dimNames.end(), "time")) != dimNames.end()) + tDim = vecIt - dimNames.begin(); + else { + ERRORR(MB_FAILURE, "Couldn't find 'time' dimension."); + } + nTimeSteps = dimLens[tDim]; + + // Get number of levels + if ((vecIt = std::find(dimNames.begin(), dimNames.end(), "lev")) != dimNames.end()) + levDim = vecIt - dimNames.begin(); + else { + ERRORR(MB_FAILURE, "Couldn't find 'lev' dimension."); + } + nLevels = dimLens[levDim]; + + Range local_verts; + rval = mbImpl->get_entities_by_dimension(_fileSet, 0, local_verts); + ERRORR(rval, "Trouble getting local vertices in current file set."); + assert(!local_verts.empty()); + +#ifdef USE_MPI + bool& isParallel = _writeNC->isParallel; + if (isParallel) { + ParallelComm*& myPcomm = _writeNC->myPcomm; + int rank = myPcomm->proc_config().proc_rank(); + int procs = myPcomm->proc_config().proc_size(); + if (procs > 1) { + rval = myPcomm->filter_pstatus(local_verts, PSTATUS_NOT_OWNED, PSTATUS_NOT, -1, &localVertsOwned); + ERRORR(rval, "Trouble getting owned vertices in set."); + // Assume that PARALLEL_RESOLVE_SHARED_ENTS option is set + // We should avoid writing in parallel with overlapped data + if (rank > 0) + assert("PARALLEL_RESOLVE_SHARED_ENTS option is set" && localVertsOwned.size() < local_verts.size()); + } + else + localVertsOwned = local_verts; + } + else + localVertsOwned = local_verts; // Not running in parallel, but still with MPI +#else + localVertsOwned = local_verts; +#endif + + std::vector<int> gids(localVertsOwned.size()); + rval = mbImpl->tag_get_data(mGlobalIdTag, localVertsOwned, &gids[0]); + ERRORR(rval, "Trouble getting global IDs on local vertices."); + + // Restore localGidVerts + std::copy(gids.rbegin(), gids.rend(), range_inserter(localGidVertsOwned)); + nLocalVerticesOwned = localGidVertsOwned.size(); + + return MB_SUCCESS; +} + +ErrorCode NCWriteHOMME::collect_variable_data(std::vector<std::string>& var_names) +{ + NCWriteHelper::collect_variable_data(var_names); + + std::map<std::string, WriteNC::VarData>& varInfo = _writeNC->varInfo; + + for (size_t i = 0; i < var_names.size(); i++) { + std::string varname = var_names[i]; + std::map<std::string, WriteNC::VarData>::iterator vit = varInfo.find(varname); + if (vit == varInfo.end()) + ERRORR(MB_FAILURE, "Can't find one variable."); + + WriteNC::VarData& currentVarData = vit->second; + if (currentVarData.has_tsteps) { + // Support non-set variables with 3 dimensions like (time, lev, ncol) + assert(3 == currentVarData.varDims.size()); + + // Time should be the first dimension + assert(tDim == currentVarData.varDims[0]); + + // Set up writeStarts and writeCounts + currentVarData.writeStarts.resize(3); + currentVarData.writeCounts.resize(3); + + // First: time + currentVarData.writeStarts[0] = 0; // This value is timestep dependent, will be set later + currentVarData.writeCounts[0] = 1; + + // Next: lev + currentVarData.writeStarts[1] = 0; + currentVarData.writeCounts[1] = currentVarData.numLev; + + // Finally: ncol + switch (currentVarData.entLoc) { + case WriteNC::ENTLOCVERT: + // Vertices + // Start from the first localGidVerts + // Actually, this will be reset later for writing + currentVarData.writeStarts[2] = localGidVertsOwned[0] - 1; + currentVarData.writeCounts[2] = nLocalVerticesOwned; + break; + default: + ERRORR(MB_FAILURE, "Unexpected entity location type for HOMME non-set variable."); + } + } + + // Get variable size + currentVarData.sz = 1; + for (std::size_t idx = 0; idx != currentVarData.writeCounts.size(); idx++) + currentVarData.sz *= currentVarData.writeCounts[idx]; + } + + return MB_SUCCESS; +} + +ErrorCode NCWriteHOMME::write_values(std::vector<std::string>& var_names) +{ + Interface*& mbImpl = _writeNC->mbImpl; + std::set<std::string>& usedCoordinates = _writeNC->usedCoordinates; + std::set<std::string>& dummyVarNames = _writeNC->dummyVarNames; + std::map<std::string, WriteNC::VarData>& varInfo = _writeNC->varInfo; + + int success; + + // Now look at requested var_names; if they have time, we will have a list, and write one at a time + // Need to transpose from lev dimension + // For each variable tag in the indexed lists, write a time step data + // Assume the first dimension is time (need to check); if not, just write regularly + for (size_t i = 0; i < var_names.size(); i++) { + std::map<std::string, WriteNC::VarData>::iterator vit = varInfo.find(var_names[i]); + if (vit == varInfo.end()) + ERRORR(MB_FAILURE, "Can't find variable requested."); + + WriteNC::VarData& variableData = vit->second; + int numTimeSteps = (int)variableData.varTags.size(); + if (variableData.has_tsteps) { + // Time should be the first dimension + assert(tDim == variableData.varDims[0]); + + // Assume this variable is on vertices for the time being + switch (variableData.entLoc) { + case WriteNC::ENTLOCVERT: + // Vertices + break; + default: + ERRORR(MB_FAILURE, "Unexpected entity location type for HOMME non-set variable."); + } + + // A typical variable has 3 dimensions as (time, lev, ncol) + // At each timestep, we need to transpose tag format (ncol, lev) back + // to NC format (lev, ncol) for writing + // FIXME: Should use tstep_nums (from writing options) later + for (int j = 0; j < numTimeSteps; j++) { + // We will write one time step, and count will be one; start will be different + // Use tag_get_data instead of tag_iterate to get values, as localVertsOwned + // might not be contiguous. We should also transpose for level so that means + // deep copy for transpose + variableData.writeStarts[0] = j; // This is time, again + std::vector<double> tag_data(nLocalVerticesOwned * variableData.numLev); + ErrorCode rval = mbImpl->tag_get_data(variableData.varTags[j], localVertsOwned, &tag_data[0]); + ERRORR(rval, "Trouble getting tag data on owned vertices."); + +#ifdef PNETCDF_FILE + size_t nb_writes = localGidVertsOwned.psize(); + std::vector<int> requests(nb_writes), statuss(nb_writes); + size_t idxReq = 0; +#endif + + // Now write from memory directly + switch (variableData.varDataType) { + case NC_DOUBLE: { + std::vector<double> tmpdoubledata(nLocalVerticesOwned * variableData.numLev); + // Transpose (ncol, lev) back to (lev, ncol) + jik_to_kji(nLocalVerticesOwned, 1, variableData.numLev, &tmpdoubledata[0], &tag_data[0]); + + size_t indexInDoubleArray = 0; + size_t ic = 0; + for (Range::pair_iterator pair_iter = localGidVertsOwned.pair_begin(); + pair_iter != localGidVertsOwned.pair_end(); ++pair_iter, ic++) { + EntityHandle starth = pair_iter->first; + EntityHandle endh = pair_iter->second; + variableData.writeStarts[2] = (NCDF_SIZE)(starth - 1); + variableData.writeCounts[2] = (NCDF_SIZE)(endh - starth + 1); + + // Do a partial write, in each subrange +#ifdef PNETCDF_FILE + // Wait outside this loop + success = NCFUNCREQP(_vara_double)(_fileId, variableData.varId, + &(variableData.writeStarts[0]), &(variableData.writeCounts[0]), + &(tmpdoubledata[indexInDoubleArray]), &requests[idxReq++]); +#else + success = NCFUNCAP(_vara_double)(_fileId, variableData.varId, + &(variableData.writeStarts[0]), &(variableData.writeCounts[0]), + &(tmpdoubledata[indexInDoubleArray])); +#endif + ERRORS(success, "Failed to read double data in loop"); + // We need to increment the index in double array for the + // next subrange + indexInDoubleArray += (endh - starth + 1) * variableData.numLev; + } + assert(ic == localGidVertsOwned.psize()); +#ifdef PNETCDF_FILE + success = ncmpi_wait_all(_fileId, requests.size(), &requests[0], &statuss[0]); + ERRORS(success, "Failed on wait_all."); +#endif + break; + } + default: + ERRORR(MB_FAILURE, "Not implemented yet."); + } + } + } // if (variableData.has_tsteps) + else { + switch (variableData.varDataType) { + case NC_DOUBLE: + success = NCFUNCAP(_vara_double)(_fileId, variableData.varId, &variableData.writeStarts[0], + &variableData.writeCounts[0], (double*)(variableData.memoryHogs[0])); + ERRORS(success, "Failed to write double data."); + break; + default: + ERRORR(MB_FAILURE, "Not implemented yet."); + } + } + } + + // Write coordinates used by requested var_names + // Use independent I/O mode put, since this write is only for the root processor + // CAUTION: if the NetCDF ID is from a previous call to ncmpi_create rather than ncmpi_open, + // all processors need to call ncmpi_begin_indep_data(). If only the root processor does so, + // ncmpi_begin_indep_data() call will be blocked forever :( +#ifdef PNETCDF_FILE + // Enter independent I/O mode + success = NCFUNC(begin_indep_data)(_fileId); + ERRORS(success, "Failed to begin independent I/O mode."); +#endif + + int rank = 0; +#ifdef USE_MPI + bool& isParallel = _writeNC->isParallel; + if (isParallel) { + ParallelComm*& myPcomm = _writeNC->myPcomm; + rank = myPcomm->proc_config().proc_rank(); + } +#endif + if (0 == rank) { + for (std::set<std::string>::iterator setIt = usedCoordinates.begin(); + setIt != usedCoordinates.end(); ++setIt) { + const std::string& coordName = *setIt; + + // Skip dummy coordinate variables (e.g. ncol) + if (dummyVarNames.find(coordName) != dummyVarNames.end()) + continue; + + std::map<std::string, WriteNC::VarData>::iterator vit = varInfo.find(coordName); + if (vit == varInfo.end()) + ERRORR(MB_FAILURE, "Can't find one coordinate variable."); + + WriteNC::VarData& varCoordData = vit->second; + + switch (varCoordData.varDataType) { + case NC_DOUBLE: + // Independent I/O mode put + success = NCFUNCP(_vara_double)(_fileId, varCoordData.varId, &varCoordData.writeStarts[0], + &varCoordData.writeCounts[0], (double*)(varCoordData.memoryHogs[0])); + ERRORS(success, "Failed to write double data."); + break; + case NC_INT: + // Independent I/O mode put + success = NCFUNCP(_vara_int)(_fileId, varCoordData.varId, &varCoordData.writeStarts[0], + &varCoordData.writeCounts[0], (int*)(varCoordData.memoryHogs[0])); + ERRORS(success, "Failed to write int data."); + break; + default: + ERRORR(MB_FAILURE, "Not implemented yet."); + } + } + } + +#ifdef PNETCDF_FILE + // End independent I/O mode + success = NCFUNC(end_indep_data)(_fileId); + ERRORS(success, "Failed to end independent I/O mode."); +#endif + + return MB_SUCCESS; +} + +} /* namespace moab */ diff --git a/src/io/NCWriteHOMME.hpp b/src/io/NCWriteHOMME.hpp new file mode 100644 index 0000000..7bb99d9 --- /dev/null +++ b/src/io/NCWriteHOMME.hpp @@ -0,0 +1,37 @@ +/* + * NCWriteHOMME.hpp + * + * nc write helper for HOMME type data (CAM) + * Created on: April 9, 2014 + * + */ + +#ifndef NCWRITEHOMME_HPP_ +#define NCWRITEHOMME_HPP_ + +#include "NCWriteHelper.hpp" + +namespace moab { + +class NCWriteHOMME: public UcdNCWriteHelper +{ +public: + NCWriteHOMME(WriteNC* writeNC, int fileId, const FileOptions& opts, EntityHandle fileSet) +: UcdNCWriteHelper(writeNC, fileId, opts, fileSet) {} + + virtual ~NCWriteHOMME(); + +private: + //! Implementation of NCWriteHelper::collect_mesh_info() + virtual ErrorCode collect_mesh_info(); + + //! Collect data for specified variables + virtual ErrorCode collect_variable_data(std::vector<std::string>& var_names); + + //! Implementation of NCWriteHelper::write_values() + virtual ErrorCode write_values(std::vector<std::string>& var_names); +}; + +} // namespace moab + +#endif diff --git a/src/io/NCWriteHelper.cpp b/src/io/NCWriteHelper.cpp new file mode 100644 index 0000000..4f95ef8 --- /dev/null +++ b/src/io/NCWriteHelper.cpp @@ -0,0 +1,622 @@ +/* + * NCWriteHelper.cpp + * + * Created on: Mar 28, 2014 + * Author: iulian + */ + +#include "NCWriteHelper.hpp" +#include "NCWriteEuler.hpp" +#include "NCWriteFV.hpp" +#include "NCWriteHOMME.hpp" +#include "NCWriteMPAS.hpp" + +#include "moab/WriteUtilIface.hpp" + +#include <sstream> + +#define ERRORR(rval, str) \ + if (MB_SUCCESS != rval) { _writeNC->mWriteIface->report_error("%s", str); return rval; } + +#define ERRORS(err, str) \ + if (err) { _writeNC->mWriteIface->report_error("%s", str); return MB_FAILURE; } + +namespace moab { + +//! Get appropriate helper instance for WriteNC class; based on some info in the file set +NCWriteHelper* NCWriteHelper::get_nc_helper(WriteNC* writeNC, int fileId, const FileOptions& opts, EntityHandle fileSet) +{ + std::string& grid_type = writeNC->grid_type; + if (grid_type == "CAM_EUL") + return new (std::nothrow) NCWriteEuler(writeNC, fileId, opts, fileSet); + else if (grid_type == "CAM_FV") + return new (std::nothrow) NCWriteFV(writeNC, fileId, opts, fileSet); + else if (grid_type == "CAM_SE") + return new (std::nothrow) NCWriteHOMME(writeNC, fileId, opts, fileSet); + else if (grid_type == "MPAS") + return new (std::nothrow) NCWriteMPAS(writeNC, fileId, opts, fileSet); + + // Unknown NetCDF grid + return NULL; +} + +ErrorCode NCWriteHelper::collect_variable_data(std::vector<std::string>& var_names) +{ + Interface*& mbImpl = _writeNC->mbImpl; + std::vector<std::string>& dimNames = _writeNC->dimNames; + std::vector<int>& dimLens = _writeNC->dimLens; + std::set<std::string>& usedCoordinates = _writeNC->usedCoordinates; + std::set<std::string>& dummyVarNames = _writeNC->dummyVarNames; + std::map<std::string, WriteNC::VarData>& varInfo = _writeNC->varInfo; + DebugOutput& dbgOut = _writeNC->dbgOut; + + ErrorCode rval; + + usedCoordinates.clear(); + + for (size_t i = 0; i < var_names.size(); i++) { + std::string varname = var_names[i]; + std::map<std::string, WriteNC::VarData>::iterator vit = varInfo.find(varname); + if (vit == varInfo.end()) + ERRORR(MB_FAILURE, "Can't find one variable."); + + WriteNC::VarData& currentVarData = vit->second; + + currentVarData.has_tsteps = false; + if ((std::find(currentVarData.varDims.begin(), currentVarData.varDims.end(), tDim) != currentVarData.varDims.end()) + && (currentVarData.varDims.size() > 1)) // So it is not time itself + currentVarData.has_tsteps = true; + + currentVarData.numLev = 1; + if ((std::find(currentVarData.varDims.begin(), currentVarData.varDims.end(), levDim) != currentVarData.varDims.end())) + currentVarData.numLev = nLevels; + + dbgOut.tprintf(2, " for variable %s varDims.size %d \n", varname.c_str(), (int)currentVarData.varDims.size()); + for (size_t j = 0; j < currentVarData.varDims.size(); j++) { + std::string dimName = dimNames[currentVarData.varDims[j]]; + vit = varInfo.find(dimName); + if (vit == varInfo.end()) + ERRORR(MB_FAILURE, "Can't find one coordinate variable."); + + usedCoordinates.insert(dimName); // Collect those used, we will need to write them to the file + dbgOut.tprintf(2, " for variable %s need dimension %s with length %d\n", varname.c_str(), dimName.c_str(), dimLens[currentVarData.varDims[j]]); + } + + // Process coordinate variables later + if (usedCoordinates.find(varname) != usedCoordinates.end()) + continue; + + // Process non-set variables with time steps + if (currentVarData.has_tsteps) { + int index = 0; + // FIXME: Should use tstep_nums (from writing options) later + while (true) { + Tag indexedTag = 0; + std::stringstream ssTagNameWithIndex; + ssTagNameWithIndex << varname << index; + rval = mbImpl->tag_get_handle(ssTagNameWithIndex.str().c_str(), indexedTag); + if (MB_SUCCESS != rval) + break; + dbgOut.tprintf(2, " found indexed tag %d with name %s\n", index, ssTagNameWithIndex.str().c_str()); + currentVarData.varTags.push_back(indexedTag); + index++; // We should get out of the loop at some point + + // The type of the tag is fixed though + DataType type; + rval = mbImpl->tag_get_data_type(indexedTag, type); + ERRORR(rval, "Can't get tag type."); + + currentVarData.varDataType = NC_DOUBLE; + if (MB_TYPE_INTEGER == type) + currentVarData.varDataType = NC_INT; + } + } + // Process set variables that are not coordinate variables + else { + // Get the tag with varname + Tag tag = 0; + rval = mbImpl->tag_get_handle(varname.c_str(), tag); + ERRORR(rval, "Can't find one tag."); + currentVarData.varTags.push_back(tag); // Really, only one for these + const void* data; + int size; + rval = mbImpl->tag_get_by_ptr(tag, &_fileSet, 1, &data, &size); + ERRORR(rval, "Can't get tag values."); + + // Find the type of tag, and use it + DataType type; + rval = mbImpl->tag_get_data_type(tag, type); + ERRORR(rval, "Can't get tag type."); + + currentVarData.varDataType = NC_DOUBLE; + if (MB_TYPE_INTEGER == type) + currentVarData.varDataType = NC_INT; + + assert(0 == currentVarData.memoryHogs.size()); // Nothing so far + currentVarData.memoryHogs.push_back((void*)data); + + if (currentVarData.varDims.empty()) { + // Scalar variable + currentVarData.writeStarts.push_back(0); + currentVarData.writeCounts.push_back(1); + } + else { + assert(1 == currentVarData.varDims.size()); + currentVarData.writeStarts.push_back(0); + currentVarData.writeCounts.push_back(dimLens[currentVarData.varDims[0]]); + } + } + } + + // Process coordinate variables + // Check that for used coordinates we have found the tags + for (std::set<std::string>::iterator setIt = usedCoordinates.begin(); + setIt != usedCoordinates.end(); ++setIt) { + const std::string& coordName = *setIt; + + std::map<std::string, WriteNC::VarData>::iterator vit = varInfo.find(coordName); + if (vit == varInfo.end()) + ERRORR(MB_FAILURE, "Can't find one coordinate variable."); + + WriteNC::VarData& varCoordData = vit->second; + Tag coordTag = 0; + rval = mbImpl->tag_get_handle(coordName.c_str(), coordTag); + ERRORR(rval, "Can't find one tag."); + varCoordData.varTags.push_back(coordTag); // Really, only one for these + + const void* data; + int sizeCoordinate; + rval = mbImpl->tag_get_by_ptr(coordTag, &_fileSet, 1, &data, &sizeCoordinate); + ERRORR(rval, "Can't get coordinate values."); + dbgOut.tprintf(2, " found coordinate tag with name %s and length %d\n", coordName.c_str(), + sizeCoordinate); + + // Get dimension length (the only dimension of this coordinate variable, with the same name) + assert(1 == varCoordData.varDims.size()); + int coordDimLen = dimLens[varCoordData.varDims[0]]; + + if (dummyVarNames.find(coordName) != dummyVarNames.end()) { + // For a dummy coordinate variable, the tag size is always 1 + // The number of coordinates should be set to dimension length, instead of 1 + assert(1 == sizeCoordinate); + sizeCoordinate = coordDimLen; + } + else { + // The number of coordinates should be exactly the same as dimension length + assert(sizeCoordinate == coordDimLen); + } + + // This is the length + varCoordData.sz = sizeCoordinate; + varCoordData.writeStarts.resize(1); + varCoordData.writeStarts[0] = 0; + varCoordData.writeCounts.resize(1); + varCoordData.writeCounts[0] = sizeCoordinate; + + // Find the type of tag, and use it + DataType type; + rval = mbImpl->tag_get_data_type(coordTag, type); + ERRORR(rval, "Can't get tag type."); + + varCoordData.varDataType = NC_DOUBLE; + if (MB_TYPE_INTEGER == type) + varCoordData.varDataType = NC_INT; + + assert(0 == varCoordData.memoryHogs.size()); // Nothing so far + varCoordData.memoryHogs.push_back((void*)data); + } + + return MB_SUCCESS; +} + +ErrorCode NCWriteHelper::init_file(std::vector<std::string>& var_names) +{ + std::vector<std::string>& dimNames = _writeNC->dimNames; + std::set<std::string>& usedCoordinates = _writeNC->usedCoordinates; + std::set<std::string>& dummyVarNames = _writeNC->dummyVarNames; + std::map<std::string, WriteNC::VarData>& varInfo = _writeNC->varInfo; + std::map<std::string, WriteNC::AttData>& globalAtts = _writeNC->globalAtts; + DebugOutput& dbgOut = _writeNC->dbgOut; + + int tDim_in_dimNames = tDim; + int levDim_in_dimNames = levDim; + + // First initialize all coordinates, then fill VarData for actual variables (and dimensions) + // Check that for used coordinates we have found the tags + for (std::set<std::string>::iterator setIt = usedCoordinates.begin(); + setIt != usedCoordinates.end(); ++setIt) { + const std::string& coordName = *setIt; + + std::map<std::string, WriteNC::VarData>::iterator vit = varInfo.find(coordName); + if (vit == varInfo.end()) + ERRORR(MB_FAILURE, "Can't find one coordinate variable."); + + WriteNC::VarData& varCoordData = vit->second; + varCoordData.varDims.resize(1); + + /* int nc_def_dim (int ncid, const char *name, size_t len, int *dimidp); + * example: status = nc_def_dim(fileId, "lat", 18L, &latid); + */ + + // Actually define a dimension + if (NCFUNC(def_dim)(_fileId, coordName.c_str(), (size_t)varCoordData.sz, + &varCoordData.varDims[0]) != NC_NOERR) + ERRORR(MB_FAILURE, "Failed to generate dimension."); + + dbgOut.tprintf(2, " for coordName %s dim id is %d \n", coordName.c_str(), (int)varCoordData.varDims[0]); + + // Update tDim and levDim to actual dimension id + if (coordName == dimNames[tDim_in_dimNames]) + tDim = varCoordData.varDims[0]; + else if (coordName == dimNames[levDim_in_dimNames]) + levDim = varCoordData.varDims[0]; + + // Create a variable with the same name, and its only dimension the one we just defined + /* + * int nc_def_var (int ncid, const char *name, nc_type xtype, + int ndims, const int dimids[], int *varidp); + example: http://www.unidata.ucar.edu/software/netcdf/docs/netcdf-c/nc_005fdef_005fva… + */ + + // Skip dummy coordinate variables (e.g. ncol) + if (dummyVarNames.find(coordName) != dummyVarNames.end()) + continue; + + // Define a coordinate variable + if (NCFUNC(def_var)(_fileId, coordName.c_str(), varCoordData.varDataType, + 1, &(varCoordData.varDims[0]), &varCoordData.varId) != NC_NOERR) + ERRORR(MB_FAILURE, "Failed to create coordinate variable."); + + dbgOut.tprintf(2, " for coordName %s variable id is %d \n", coordName.c_str(), varCoordData.varId); + } + + // Now look at requested variables, and update from the index in dimNames to the actual dimension id + for (size_t i = 0; i < var_names.size(); i++) { + std::map<std::string, WriteNC::VarData>::iterator vit = varInfo.find(var_names[i]); + if (vit == varInfo.end()) + ERRORR(MB_FAILURE, "Can't find variable requested."); + + // Skip coordinate variables + if (usedCoordinates.find(var_names[i]) != usedCoordinates.end()) + continue; + + WriteNC::VarData& variableData = vit->second; + int numDims = (int)variableData.varDims.size(); + // The index is for dimNames; we need to find out the actual dimension id (from above) + for (int j = 0; j < numDims; j++) { + std::string dimName = dimNames[variableData.varDims[j]]; + std::map<std::string, WriteNC::VarData>::iterator vit2 = varInfo.find(dimName); + if (vit2 == varInfo.end()) + ERRORR(MB_FAILURE, "Can't find coordinate variable requested."); + + WriteNC::VarData& coordData = vit2->second; + // Index in dimNames to actual dimension id + variableData.varDims[j] = coordData.varDims[0]; // This one, being a coordinate, is the only one + dbgOut.tprintf(2, " dimension with index %d name %s has ID %d \n", + j, dimName.c_str(), variableData.varDims[j]); + } + + // Define the variable now: + if (NCFUNC(def_var)(_fileId, var_names[i].c_str(), variableData.varDataType, + (int)variableData.varDims.size(), &(variableData.varDims[0]), + &variableData.varId) != NC_NOERR) + ERRORR(MB_FAILURE, "Failed to create coordinate variable."); + + dbgOut.tprintf(2, " for variable %s variable id is %d \n", var_names[i].c_str(), variableData.varId); + // Now define the variable, with all dimensions + } + + // Define global attributes (exactly copied from the original file for the time being) + // Should we modify some of them (e.g. revision_Id) later? + std::map<std::string, WriteNC::AttData>::iterator attIt; + for (attIt = globalAtts.begin(); attIt != globalAtts.end(); ++attIt) { + const std::string& attName = attIt->first; + WriteNC::AttData& attData = attIt->second; + NCDF_SIZE& attLen = attData.attLen; + nc_type& attDataType = attData.attDataType; + const std::string& attValue = attData.attValue; + + switch (attDataType) { + case NC_BYTE: + case NC_CHAR: + if (NC_NOERR != NCFUNC(put_att_text)(_fileId, NC_GLOBAL, attName.c_str(), attLen, attValue.c_str())) + ERRORR(MB_FAILURE, "Failed to define text type attribute."); + break; + case NC_DOUBLE: + if (NC_NOERR != NCFUNC(put_att_double)(_fileId, NC_GLOBAL, attName.c_str(), NC_DOUBLE, 1, (double*)attValue.c_str())) + ERRORR(MB_FAILURE, "Failed to define double type attribute."); + break; + case NC_FLOAT: + if (NC_NOERR != NCFUNC(put_att_float)(_fileId, NC_GLOBAL, attName.c_str(), NC_FLOAT, 1, (float*)attValue.c_str())) + ERRORR(MB_FAILURE, "Failed to define float type attribute."); + break; + case NC_INT: + if (NC_NOERR != NCFUNC(put_att_int)(_fileId, NC_GLOBAL, attName.c_str(), NC_INT, 1, (int*)attValue.c_str())) + ERRORR(MB_FAILURE, "Failed to define int type attribute."); + break; + case NC_SHORT: + if (NC_NOERR != NCFUNC(put_att_short)(_fileId, NC_GLOBAL, attName.c_str(), NC_SHORT, 1, (short*)attValue.c_str())) + ERRORR(MB_FAILURE, "Failed to define short type attribute."); + break; + default: + ERRORR(MB_FAILURE, "Unknown attribute data type."); + } + } + + // Take it out of define mode + if (NC_NOERR != NCFUNC(enddef)(_fileId)) + ERRORR(MB_FAILURE, "Failed to close define mode."); + + return MB_SUCCESS; +} + +ErrorCode ScdNCWriteHelper::collect_mesh_info() +{ + Interface*& mbImpl = _writeNC->mbImpl; + std::vector<std::string>& dimNames = _writeNC->dimNames; + std::vector<int>& dimLens = _writeNC->dimLens; + + ErrorCode rval; + + // Look for time dimension + std::vector<std::string>::iterator vecIt; + if ((vecIt = std::find(dimNames.begin(), dimNames.end(), "time")) != dimNames.end()) + tDim = vecIt - dimNames.begin(); + else if ((vecIt = std::find(dimNames.begin(), dimNames.end(), "t")) != dimNames.end()) + tDim = vecIt - dimNames.begin(); + else { + ERRORR(MB_FAILURE, "Couldn't find 'time' or 't' dimension."); + } + nTimeSteps = dimLens[tDim]; + + // Get number of levels + if ((vecIt = std::find(dimNames.begin(), dimNames.end(), "lev")) != dimNames.end()) + levDim = vecIt - dimNames.begin(); + else if ((vecIt = std::find(dimNames.begin(), dimNames.end(), "ilev")) != dimNames.end()) + levDim = vecIt - dimNames.begin(); + else { + ERRORR(MB_FAILURE, "Couldn't find 'lev' or 'ilev' dimension."); + } + nLevels = dimLens[levDim]; + + // __<dim_name>_LOC_MINMAX (for slon, slat, lon and lat) + Tag convTag = 0; + rval = mbImpl->tag_get_handle("__slon_LOC_MINMAX", 0, MB_TYPE_INTEGER, convTag, MB_TAG_ANY); + ERRORR(rval, "Trouble getting conventional tag __slon_LOC_MINMAX."); + int val[2]; + rval = mbImpl->tag_get_data(convTag, &_fileSet, 1, val); + ERRORR(rval, "Trouble getting values for conventional tag __slon_LOC_MINMAX."); + lDims[0] = val[0]; + lDims[3] = val[1]; + + rval = mbImpl->tag_get_handle("__slat_LOC_MINMAX", 0, MB_TYPE_INTEGER, convTag, MB_TAG_ANY); + ERRORR(rval, "Trouble getting conventional tag __slat_LOC_MINMAX."); + rval = mbImpl->tag_get_data(convTag, &_fileSet, 1, val); + ERRORR(rval, "Trouble getting values for conventional tag __slat_LOC_MINMAX."); + lDims[1] = val[0]; + lDims[4] = val[1]; + + rval = mbImpl->tag_get_handle("__lon_LOC_MINMAX", 0, MB_TYPE_INTEGER, convTag, MB_TAG_ANY); + ERRORR(rval, "Trouble getting conventional tag __lon_LOC_MINMAX."); + rval = mbImpl->tag_get_data(convTag, &_fileSet, 1, val); + ERRORR(rval, "Trouble getting values for conventional tag __lon_LOC_MINMAX."); + lCDims[0] = val[0]; + lCDims[3] = val[1]; + + rval = mbImpl->tag_get_handle("__lat_LOC_MINMAX", 0, MB_TYPE_INTEGER, convTag, MB_TAG_ANY); + ERRORR(rval, "Trouble getting conventional tag __lat_LOC_MINMAX."); + rval = mbImpl->tag_get_data(convTag, &_fileSet, 1, val); + ERRORR(rval, "Trouble getting values for conventional tag __lat_LOC_MINMAX."); + lCDims[1] = val[0]; + lCDims[4] = val[1]; + + return MB_SUCCESS; +} + +ErrorCode ScdNCWriteHelper::collect_variable_data(std::vector<std::string>& var_names) +{ + NCWriteHelper::collect_variable_data(var_names); + + std::map<std::string, WriteNC::VarData>& varInfo = _writeNC->varInfo; + + for (size_t i = 0; i < var_names.size(); i++) { + std::string varname = var_names[i]; + std::map<std::string, WriteNC::VarData>::iterator vit = varInfo.find(varname); + if (vit == varInfo.end()) + ERRORR(MB_FAILURE, "Can't find one variable."); + + WriteNC::VarData& currentVarData = vit->second; + if (currentVarData.has_tsteps) { + // Support non-set variables with 4 dimensions like (time, lev, lat, lon) + assert(4 == currentVarData.varDims.size()); + + // Time should be the first dimension + assert(tDim == currentVarData.varDims[0]); + + // Set up writeStarts and writeCounts + currentVarData.writeStarts.resize(4); + currentVarData.writeCounts.resize(4); + + // First: time + currentVarData.writeStarts[0] = 0; // This value is timestep dependent, will be set later + currentVarData.writeCounts[0] = 1; + + // Next: lev + currentVarData.writeStarts[1] = 0; + currentVarData.writeCounts[1] = currentVarData.numLev; + + // Finally: lat (or slat) and lon (or slon) + switch (currentVarData.entLoc) { + case WriteNC::ENTLOCFACE: + // Faces + currentVarData.writeStarts[2] = lCDims[1]; + currentVarData.writeCounts[2] = lCDims[4] - lCDims[1] + 1; + currentVarData.writeStarts[3] = lCDims[0]; + currentVarData.writeCounts[3] = lCDims[3] - lCDims[0] + 1; + break; + default: + ERRORR(MB_FAILURE, "Not implemented yet."); + } + } + + // Get variable size + currentVarData.sz = 1; + for (std::size_t idx = 0; idx != currentVarData.writeCounts.size(); idx++) + currentVarData.sz *= currentVarData.writeCounts[idx]; + } + + return MB_SUCCESS; +} + +ErrorCode ScdNCWriteHelper::write_values(std::vector<std::string>& var_names) +{ + Interface*& mbImpl = _writeNC->mbImpl; + std::set<std::string>& usedCoordinates = _writeNC->usedCoordinates; + std::set<std::string>& dummyVarNames = _writeNC->dummyVarNames; + std::map<std::string, WriteNC::VarData>& varInfo = _writeNC->varInfo; + + ErrorCode rval; + int success; + + // Now look at requested var_names; if they have time, we will have a list, and write one at a time + // If not, just write regularly + // For parallel write, we assume that the data ranges do not overlap across processors (this is true + // for Euler and FV variables on quads) + // While overlapped writing might still work, we should better not take that risk + // Use collective I/O mode put (synchronous write) for the time being, we can try nonblocking put + // (request aggregation) later + for (size_t i = 0; i < var_names.size(); i++) { + std::map<std::string, WriteNC::VarData>::iterator vit = varInfo.find(var_names[i]); + if (vit == varInfo.end()) + ERRORR(MB_FAILURE, "Can't find variable requested."); + + WriteNC::VarData& variableData = vit->second; + int numTimeSteps = (int)variableData.varTags.size(); + if (variableData.has_tsteps) { + // Time should be the first dimension + assert(tDim == variableData.varDims[0]); + + // Get entities of this variable + Range ents; + switch (variableData.entLoc) { + case WriteNC::ENTLOCFACE: + // Faces + rval = mbImpl->get_entities_by_dimension(_fileSet, 2, ents); + ERRORR(rval, "Can't get entities for faces."); + break; + default: + ERRORR(MB_FAILURE, "Not implemented yet."); + } + + // A typical variable has 4 dimensions as (time, lev, lat, lon) + // At each timestep, we need to transpose tag format (lat, lon, lev) back + // to NC format (lev, lat, lon) for writing + size_t ni = variableData.writeCounts[3]; // lon + size_t nj = variableData.writeCounts[2]; // lat + size_t nk = variableData.writeCounts[1]; // lev + + variableData.writeCounts[0] = 1; // We will write one time step + // FIXME: Should use tstep_nums (from writing options) later + for (int j = 0; j < numTimeSteps; j++) { + // We will write one time step, and count will be one; start will be different + // We will write values directly from tag_iterate, but we should also transpose for level + // so that means deep copy for transpose + variableData.writeStarts[0] = j; // This is time, again + int count; + void* dataptr; + rval = mbImpl->tag_iterate(variableData.varTags[j], ents.begin(), ents.end(), count, dataptr); + assert(count == (int)ents.size()); + + // Now write from memory directly + switch (variableData.varDataType) { + case NC_DOUBLE: { + std::vector<double> tmpdoubledata(ni*nj*nk); + // Transpose (lat, lon, lev) back to (lev, lat, lon) + jik_to_kji(ni, nj, nk, &tmpdoubledata[0], (double*)(dataptr)); + success = NCFUNCAP(_vara_double)(_fileId, variableData.varId, + &variableData.writeStarts[0], &variableData.writeCounts[0], + &tmpdoubledata[0]); + ERRORS(success, "Failed to write double data."); + break; + } + default: + ERRORR(MB_FAILURE, "Not implemented yet."); + } + } + } + else { + switch (variableData.varDataType) { + case NC_DOUBLE: + success = NCFUNCAP(_vara_double)(_fileId, variableData.varId, &variableData.writeStarts[0], + &variableData.writeCounts[0], (double*)(variableData.memoryHogs[0])); + ERRORS(success, "Failed to write double data."); + break; + default: + ERRORR(MB_FAILURE, "Not implemented yet."); + } + } + } + + // Write coordinates used by requested var_names + // Use independent I/O mode put, since this write is only for the root processor + // CAUTION: if the NetCDF ID is from a previous call to ncmpi_create rather than ncmpi_open, + // all processors need to call ncmpi_begin_indep_data(). If only the root processor does so, + // ncmpi_begin_indep_data() call will be blocked forever :( +#ifdef PNETCDF_FILE + // Enter independent I/O mode + success = NCFUNC(begin_indep_data)(_fileId); + ERRORS(success, "Failed to begin independent I/O mode."); +#endif + + int rank = 0; +#ifdef USE_MPI + bool& isParallel = _writeNC->isParallel; + if (isParallel) { + ParallelComm*& myPcomm = _writeNC->myPcomm; + rank = myPcomm->proc_config().proc_rank(); + } +#endif + if (0 == rank) { + for (std::set<std::string>::iterator setIt = usedCoordinates.begin(); + setIt != usedCoordinates.end(); ++setIt) { + const std::string& coordName = *setIt; + + // Skip dummy coordinate variables (if any) + if (dummyVarNames.find(coordName) != dummyVarNames.end()) + continue; + + std::map<std::string, WriteNC::VarData>::iterator vit = varInfo.find(coordName); + if (vit == varInfo.end()) + ERRORR(MB_FAILURE, "Can't find one coordinate variable."); + + WriteNC::VarData& varCoordData = vit->second; + + switch (varCoordData.varDataType) { + case NC_DOUBLE: + // Independent I/O mode put + success = NCFUNCP(_vara_double)(_fileId, varCoordData.varId, &varCoordData.writeStarts[0], + &varCoordData.writeCounts[0], (double*)(varCoordData.memoryHogs[0])); + ERRORS(success, "Failed to write double data."); + break; + case NC_INT: + // Independent I/O mode put + success = NCFUNCP(_vara_int)(_fileId, varCoordData.varId, &varCoordData.writeStarts[0], + &varCoordData.writeCounts[0], (int*)(varCoordData.memoryHogs[0])); + ERRORS(success, "Failed to write int data."); + break; + default: + ERRORR(MB_FAILURE, "Not implemented yet."); + } + } + } + +#ifdef PNETCDF_FILE + // End independent I/O mode + success = NCFUNC(end_indep_data)(_fileId); + ERRORS(success, "Failed to end independent I/O mode."); +#endif + + return MB_SUCCESS; +} + +} /* namespace moab */ diff --git a/src/io/NCWriteHelper.hpp b/src/io/NCWriteHelper.hpp new file mode 100644 index 0000000..b05fe12 --- /dev/null +++ b/src/io/NCWriteHelper.hpp @@ -0,0 +1,125 @@ +/* + * NCWriteHelper.hpp + * + * Purpose : Climate NC writer file helper; abstract, will be implemented for each type + * + * Created on: Mar 28, 2014 + */ + +#ifndef NCWRITEHELPER_HPP_ +#define NCWRITEHELPER_HPP_ +#include "WriteNC.hpp" + +namespace moab { + +class NCWriteHelper +{ +public: + NCWriteHelper(WriteNC* writeNC, int fileId, const FileOptions& opts, EntityHandle fileSet) +: _writeNC(writeNC), _fileId(fileId), _opts(opts), _fileSet(fileSet), + nTimeSteps(0), nLevels(1), tDim(-1), levDim(-1) {} + virtual ~NCWriteHelper() {}; + + //! Get appropriate helper instance for WriteNC class based on some info in the file set + static NCWriteHelper* get_nc_helper(WriteNC* writeNC, int fileId, const FileOptions& opts, EntityHandle fileSet); + + //! Collect necessary info about local mesh + virtual ErrorCode collect_mesh_info() = 0; + + //! Collect data for specified variables + virtual ErrorCode collect_variable_data(std::vector<std::string>& var_names); + + //! Take the info from VarData and write first the coordinates, then the actual variables + virtual ErrorCode write_values(std::vector<std::string>& var_names) = 0; + + //! Initialize file: this is where all defines are done + //! The VarData dimension ids are filled up after define + ErrorCode init_file(std::vector<std::string>& var_names); + +protected: + template <typename T> void jik_to_kji(size_t ni, size_t nj, size_t nk, T* dest, T* source) + { + size_t nik = ni * nk, nij = ni * nj; + for (std::size_t k = 0; k != nk; k++) + for (std::size_t j = 0; j != nj; j++) + for (std::size_t i = 0; i != ni; i++) + dest[k*nij + j*ni + i] = source[j*nik + i*nk + k]; + } + +protected: + //! Allow NCWriteHelper to directly access members of WriteNC + WriteNC* _writeNC; + + //! Cache some information from ReadNC + int _fileId; + const FileOptions& _opts; + EntityHandle _fileSet; + + //! Dimensions of time and level + int nTimeSteps, nLevels; + + //! Dimension numbers for time and level + int tDim, levDim; +}; + +//! Child helper class for scd mesh, e.g. CAM_EL or CAM_FV +class ScdNCWriteHelper : public NCWriteHelper +{ +public: + ScdNCWriteHelper(WriteNC* writeNC, int fileId, const FileOptions& opts, EntityHandle fileSet) +: NCWriteHelper(writeNC, fileId, opts, fileSet) + { + for (unsigned int i = 0; i < 6; i++) { + lDims[i] = -1; + lCDims[i] = -1; + } + } + virtual ~ScdNCWriteHelper() {} + +private: + //! Implementation of NCWriteHelper::collect_mesh_info() + virtual ErrorCode collect_mesh_info(); + + //! Collect data for specified variables + virtual ErrorCode collect_variable_data(std::vector<std::string>& var_names); + + //! Implementation of NCWriteHelper::write_values() + virtual ErrorCode write_values(std::vector<std::string>& var_names); + +protected: + //! Dimensions of my local part of grid + int lDims[6]; + + //! Center dimensions of my local part of grid + int lCDims[6]; +}; + +//! Child helper class for ucd mesh, e.g. CAM_SE (HOMME) or MPAS +class UcdNCWriteHelper : public NCWriteHelper +{ +public: + UcdNCWriteHelper(WriteNC* writeNC, int fileId, const FileOptions& opts, EntityHandle fileSet) +: NCWriteHelper(writeNC, fileId, opts, fileSet), + nLocalCellsOwned(0), nLocalEdgesOwned(0), nLocalVerticesOwned(0), + cDim(-1), eDim(-1), vDim(-1) {} + virtual ~UcdNCWriteHelper() {} + +protected: + //! Dimensions of my local owned part of grid + int nLocalCellsOwned; + int nLocalEdgesOwned; + int nLocalVerticesOwned; + + //! Dimension numbers for nCells, nEdges and nVertices + int cDim, eDim, vDim; + + //! Local owned cells, edges and vertices + Range localCellsOwned, localEdgesOwned, localVertsOwned; + + //! Local global ID for owned cells, edges and vertices + Range localGidCellsOwned, localGidEdgesOwned, localGidVertsOwned; +}; + +} // namespace moab + +#endif diff --git a/src/io/NCWriteMPAS.cpp b/src/io/NCWriteMPAS.cpp new file mode 100644 index 0000000..72dc35f --- /dev/null +++ b/src/io/NCWriteMPAS.cpp @@ -0,0 +1,33 @@ +/* + * NCWriteMPAS.cpp + * + * Created on: April 9, 2014 + */ + +#include "NCWriteMPAS.hpp" +#include "moab/WriteUtilIface.hpp" + +#define ERRORR(rval, str) \ + if (MB_SUCCESS != rval) { _writeNC->mWriteIface->report_error("%s", str); return rval; } + +#define ERRORS(err, str) \ + if (err) { _writeNC->mWriteIface->report_error("%s", str); return MB_FAILURE; } + +namespace moab { + +NCWriteMPAS::~NCWriteMPAS() +{ + // TODO Auto-generated destructor stub +} + +ErrorCode NCWriteMPAS::collect_mesh_info() +{ + return MB_NOT_IMPLEMENTED; +} + +ErrorCode NCWriteMPAS::write_values(std::vector<std::string>& /* var_names */) +{ + return MB_NOT_IMPLEMENTED; +} + +} /* namespace moab */ diff --git a/src/io/NCWriteMPAS.hpp b/src/io/NCWriteMPAS.hpp new file mode 100644 index 0000000..702984f --- /dev/null +++ b/src/io/NCWriteMPAS.hpp @@ -0,0 +1,34 @@ +/* + * NCWriteMPAS.hpp + * + * nc write helper for MPAS type data (CAM) + * Created on: April 9, 2014 + * + */ + +#ifndef NCWRITEMPAS_HPP_ +#define NCWRITEMPAS_HPP_ + +#include "NCWriteHelper.hpp" + +namespace moab { + +class NCWriteMPAS: public UcdNCWriteHelper +{ +public: + NCWriteMPAS(WriteNC* writeNC, int fileId, const FileOptions& opts, EntityHandle fileSet) +: UcdNCWriteHelper(writeNC, fileId, opts, fileSet) {} + + virtual ~NCWriteMPAS(); + +private: + //! Implementation of NCWriteHelper::collect_mesh_info() + virtual ErrorCode collect_mesh_info(); + + //! Collect data for specified variables + virtual ErrorCode write_values(std::vector<std::string>& var_names); +}; + +} // namespace moab + +#endif diff --git a/src/io/ReadNC.cpp b/src/io/ReadNC.cpp index a0e02b4..0a41cfa 100644 --- a/src/io/ReadNC.cpp +++ b/src/io/ReadNC.cpp @@ -118,6 +118,28 @@ ErrorCode ReadNC::load_file(const char* file_name, const EntityHandle* file_set, ERRORR(rval, "Trouble checking mesh from last read.\n"); } + // Create some conventional tags, e.g. __NUM_DIMS + // Keep a flag on the file set to prevent conventional tags from being created again on a second read + Tag convTagsCreated = 0; + int def_val = 0; + rval = mbImpl->tag_get_handle("__CONV_TAGS_CREATED", 1, MB_TYPE_INTEGER, convTagsCreated, + MB_TAG_SPARSE | MB_TAG_CREAT, &def_val); + ERRORR(rval, "Trouble getting _CONV_TAGS_CREATED tag."); + int create_conv_tags_flag = 0; + rval = mbImpl->tag_get_data(convTagsCreated, &tmp_set, 1, &create_conv_tags_flag); + if (0 == create_conv_tags_flag) { + // Read dimension variables to create tags like __<var_name>_DIMS + rval = myHelper->read_variables(dimNames, tstep_nums); + ERRORR(rval, "Trouble reading dimension variables."); + + rval = myHelper->create_conventional_tags(tstep_nums); + ERRORR(rval, "Trouble creating NC conventional tags."); + + create_conv_tags_flag = 1; + rval = mbImpl->tag_set_data(convTagsCreated, &tmp_set, 1, &create_conv_tags_flag); + ERRORR(rval, "Trouble setting data for _CONV_TAGS_CREATED tag."); + } + // Create mesh vertex/edge/face sequences Range faces; if (!noMesh) { @@ -125,26 +147,10 @@ ErrorCode ReadNC::load_file(const char* file_name, const EntityHandle* file_set, ERRORR(rval, "Trouble creating mesh."); } - // Read variables onto grid + // Read specified variables onto grid if (!noVars) { rval = myHelper->read_variables(var_names, tstep_nums); - if (MB_FAILURE == rval) - return rval; - } - else { - // Read dimension variables by default (the dimensions that are also variables) - std::vector<std::string> dim_var_names; - for (unsigned int i = 0; i < dimNames.size(); i++) { - std::map<std::string, VarData>::iterator mit = varInfo.find(dimNames[i]); - if (mit != varInfo.end()) - dim_var_names.push_back(dimNames[i]); - } - - if (!dim_var_names.empty()) { - rval = myHelper->read_variables(dim_var_names, tstep_nums); - if (MB_FAILURE == rval) - return rval; - } + ERRORR(rval, "Trouble reading specified variables."); } #ifdef USE_MPI @@ -175,12 +181,6 @@ ErrorCode ReadNC::load_file(const char* file_name, const EntityHandle* file_set, } #endif - // Create NC conventional tags when loading header info only - if (noMesh && noVars) { - rval = myHelper->create_conventional_tags(tstep_nums); - ERRORR(rval, "Trouble creating NC conventional tags."); - } - mbImpl->release_interface(scdi); scdi = NULL; This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/fathomteam/moab/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/MOAB: danwu: Merged master into ncwriter
by commits-noreply＠bitbucket.org 28 Apr '14

28 Apr '14

1 new commit in MOAB: https://bitbucket.org/fathomteam/moab/commits/5ffa5b78d70f/ Changeset: 5ffa5b78d70f Branch: ncwriter User: danwu Date: 2014-04-28 19:45:45 Summary: Merged master into ncwriter Affected #: 10 files diff --git a/src/LocalDiscretization/SpectralQuad.cpp b/src/LocalDiscretization/SpectralQuad.cpp index d7355e6..7b581cb 100644 --- a/src/LocalDiscretization/SpectralQuad.cpp +++ b/src/LocalDiscretization/SpectralQuad.cpp @@ -109,7 +109,10 @@ bool SpectralQuad::reverseEvalFcn(const double *posn, const double *verts, const double dist = opt_findpt_2(&_data, (const double **)_xyz, x_star, r, &c); // if it did not converge, get out with throw... if (dist > 0.9e+30) - throw Map::EvaluationError(); + { + std::vector<CartVect> dummy; + throw Map::EvaluationError(CartVect(x_star), dummy); + } //c tells us if we landed inside the element or exactly on a face, edge, or node // also, dist shows the distance to the computed point. //copy parametric coords back diff --git a/src/io/mhdf/include/mhdf.h b/src/io/mhdf/include/mhdf.h index db36d63..b602bdf 100644 --- a/src/io/mhdf/include/mhdf.h +++ b/src/io/mhdf/include/mhdf.h @@ -67,7 +67,7 @@ extern "C" { * named \c max_id . This attribute, if present, should contain the * value of the largest entity ID used internally to the file. It can * be used to verify that the code reading the file is using an integer - * type of sufficient size to accomodate the entity IDs. + * type of sufficient size to accommodate the entity IDs. * * The \c tstt group contains four sub-groups, a datatype object, and a * dataset object. The four sub-groups are: \c nodes, \c elements, @@ -101,12 +101,12 @@ extern "C" { * * The \c coordinates * DataSet contains the coordinates of all vertices in the mesh. - * The DataSet should contain floating point values and have a dimenions + * The DataSet should contain floating point values and have a dimensions * \f$ n \times d \f$, where \c n is the number of vertices and \c d * is the number of coordinate values for each vertex. * - * The \c coodinates DataSet must have an integer attribute named \c start_id . - * The vertices are then defined to have IDs begining with this value + * The \c coordinates DataSet must have an integer attribute named \c start_id . + * The vertices are then defined to have IDs beginning with this value * and increasing sequentially in the order that they are defined in the * \c coordinates table. * @@ -128,7 +128,7 @@ extern "C" { * optional subgroup named \c tags. The \c tags subgroup is described in the * \ref Dense "section on dense tag storage". * - * The \c connectivty DataSet is an \f$ n \times m \f$ array of integer + * The \c connectivity DataSet is an \f$ n \times m \f$ array of integer * values. The DataSet contains one row for each of the \c n contained * elements, where the connectivity of each element contains \c m IDs. For * all element types supported by MOAB, with the exception of polyhedra, @@ -146,14 +146,14 @@ extern "C" { * The \c sets group contains the definitions of any entity sets stored * in the file. It contains 1 to 4 DataSets and the optional \c tags * subgroup. The \c contents, \c parents, and \c children data sets - * are one dimensional arrays containing the concatenation of of the + * are one dimensional arrays containing the concatenation of the * corresponding lists for all of the sets represented in the file. * * The \c lists DataSet is a \f$ n \times 4 \f$ table, having one * row of four integer values for each set. The first three values * for each set are the indices into the \c contents, \c children, * and \c parents DataSets, respectively, at which the \em last value - * for the set is stored. The contents, child, and parent lists for + * for set is stored. The contents, child, and parent lists for * sets are stored in the corresponding datasets in the same order as * the sets are listed in the \c lists DataSet, such that the index of * the first value in one of those tables is one greater than the @@ -168,7 +168,7 @@ extern "C" { * stored at position 0 of the \c parents DataSet and the second at position * 1. * - * The fourth colum of the \c lists DataSet is a series of bit flags + * The fourth column of the \c lists DataSet is a series of bit flags * defining some properties of the sets. The four bit values currently * defined are: * - 0x1 owner @@ -180,7 +180,7 @@ extern "C" { * data set, that the contents list for the corresponding set is stored * using a single range compression. Rather than storing the IDs of the * contained entities individually, each ID \c i is followed by a count - * \c n indicating that the set contains the cotiguous range of IDs + * \c n indicating that the set contains the contiguous range of IDs * \f$ [i, i+n-1] \f$. * * The three least significant bits specify intended properties of the @@ -208,16 +208,16 @@ extern "C" { * may also be stored in the "dense" format as described in the * \ref Dense "section on dense tag storage". * - * Each sub-group of the \c tags group contains the defintion for + * Each sub-group of the \c tags group contains the definition for * a single tag. The name of each sub-group is the name of the * corresponding tag. Non-printable characters, characters * prohibited in group names in the HDF5 file format, and the * backslash ('\') character are encoded * in the name string by a backslash ('\') character followed by - * the ASCII value of the character expressed as a pair of hexidecimal + * the ASCII value of the character expressed as a pair of hexadecimal * digits. Thus the backslash character would be represented as \c \5C . * Each tag group should also contain a comment which contains the - * unenconded tag name. + * unencoded tag name. * * The tag sub-group may have any or all of the following four attributes: * \c default, \c global, \c is_handle, and \c variable_length. diff --git a/src/moab/BoundBox.hpp b/src/moab/BoundBox.hpp index c74707a..3f1f07f 100644 --- a/src/moab/BoundBox.hpp +++ b/src/moab/BoundBox.hpp @@ -14,6 +14,15 @@ namespace moab { BoundBox(const CartVect &min, const CartVect &max) : bMin(min), bMax(max) {} BoundBox(const double *corners); + // constructor used in element maps + BoundBox(std::vector<CartVect> points): bMin(DBL_MAX), bMax(-DBL_MAX) + { + for (size_t i=0; i<points.size(); i++) + { + update_min( points[i].array() ); + update_max( points[i].array() ); + } + } ~BoundBox() {} bool contains_point(const double *point, const double tol = 0.0) const; diff --git a/test/dagmc/dagmc_pointinvol_test.cpp b/test/dagmc/dagmc_pointinvol_test.cpp index 47ee7c1..a859b65 100644 --- a/test/dagmc/dagmc_pointinvol_test.cpp +++ b/test/dagmc/dagmc_pointinvol_test.cpp @@ -26,7 +26,6 @@ static const char input_file[] = STRINGIFY(MESHDIR) "/dagmc/test_geom.h5m"; static const char input_file[] = STRINGIFY(MESHDIR) "/dagmc/test_geom.h5m"; #endif - void dagmc_setup_test() { ErrorCode rval = DAG->load_file(input_file); // open the Dag file @@ -34,250 +33,247 @@ void dagmc_setup_test() rval = DAG->init_OBBTree(); CHECK_ERR(rval); + /* int num_vols = DAG->num_entities(3); EntityHandle vol; - for ( int i = 0 ; i < num_vols ; i++ ) - { - vol = DAG->entity_by_index(3,i); - } + for (int i = 0; i < num_vols; i++) + vol = DAG->entity_by_index(3, i); + */ //EntityHandle volume = 12682136550675316765; - //CHECK_EQUAL(volume,vol); + //CHECK_EQUAL(volume, vol); } void dagmc_point_in() { int result = 0; - int expected_result=1; - double xyz[3]={0.0,0.0,0.0}; - int vol_idx=1; - EntityHandle vol_h = DAG->entity_by_index(3,vol_idx); - ErrorCode rval = DAG->point_in_volume(vol_h,xyz,result); + int expected_result = 1; + double xyz[3] = {0.0, 0.0, 0.0}; + int vol_idx = 1; + EntityHandle vol_h = DAG->entity_by_index(3, vol_idx); + ErrorCode rval = DAG->point_in_volume(vol_h, xyz, result); CHECK_ERR(rval); - CHECK_EQUAL(expected_result,result); + CHECK_EQUAL(expected_result, result); } -int dagmc_point_in_vol_dir(double origin[3],double dir[3],int vol_idx) +int dagmc_point_in_vol_dir(double origin[3], double dir[3], int vol_idx) { int result = 0; - EntityHandle vol_h = DAG->entity_by_index(3,vol_idx); + EntityHandle vol_h = DAG->entity_by_index(3, vol_idx); double xyz[3]; double next_surf_dist; EntityHandle next_surf; // normalise the vector - double dir_norm = (dir[0]*dir[0])+(dir[1]*dir[1])+(dir[2]*dir[2]); + double dir_norm = (dir[0]*dir[0]) + (dir[1]*dir[1]) + (dir[2]*dir[2]); - dir[0]=dir[0]/sqrt(dir_norm); - dir[1]=dir[1]/sqrt(dir_norm); - dir[2]=dir[2]/sqrt(dir_norm); + dir[0] = dir[0] / sqrt(dir_norm); + dir[1] = dir[1] / sqrt(dir_norm); + dir[2] = dir[2] / sqrt(dir_norm); - ErrorCode rval = DAG->ray_fire(vol_h,origin,dir,next_surf,next_surf_dist); - - xyz[0]=origin[0]+(next_surf_dist*dir[0]); - xyz[1]=origin[1]+(next_surf_dist*dir[1]); - xyz[2]=origin[2]+(next_surf_dist*dir[2]); + ErrorCode rval = DAG->ray_fire(vol_h, origin, dir, next_surf, next_surf_dist); + + xyz[0] = origin[0] + (next_surf_dist*dir[0]); + xyz[1] = origin[1] + (next_surf_dist*dir[1]); + xyz[2] = origin[2] + (next_surf_dist*dir[2]); std::cout << xyz[0] << " " << xyz[1] << " " << xyz[2] << std::endl; - rval = DAG->point_in_volume(vol_h,xyz,result,dir); + rval = DAG->point_in_volume(vol_h, xyz, result, dir); CHECK_ERR(rval); return result; } void dagmc_point_in_vol_1() { - double dir[3]={ -1.0,0.0,0.0}; - double origin[3]={0.0,0.0,0.0}; - int vol_idx=1; - int expected_result=1; - - int result = dagmc_point_in_vol_dir(origin,dir,vol_idx); - CHECK_EQUAL(expected_result,result); + double dir[3] = {-1.0, 0.0, 0.0}; + double origin[3] = {0.0, 0.0, 0.0}; + int vol_idx = 1; + int expected_result = 1; + int result = dagmc_point_in_vol_dir(origin, dir, vol_idx); + CHECK_EQUAL(expected_result, result); } void dagmc_point_in_vol_2() { - int expected_result=1; - int vol_idx=1; - double dir[3]={ 1.0,0.0,0.0}; - double origin[3]={0.0,0.0,0.0}; + int expected_result = 1; + int vol_idx = 1; + double dir[3] = {1.0, 0.0, 0.0}; + double origin[3] = {0.0, 0.0, 0.0}; - int result = dagmc_point_in_vol_dir(origin,dir,vol_idx); + int result = dagmc_point_in_vol_dir(origin, dir, vol_idx); - CHECK_EQUAL(expected_result,result); + CHECK_EQUAL(expected_result, result); } void dagmc_point_in_vol_3() { - int expected_result=1; - int vol_idx=1; - double dir[3]={ 0.0,-1.0,0.0}; - double origin[3]={0.0,0.0,0.0}; + int expected_result = 1; + int vol_idx = 1; + double dir[3] = {0.0, -1.0, 0.0}; + double origin[3] = {0.0, 0.0, 0.0}; - int result = dagmc_point_in_vol_dir(origin,dir,vol_idx); + int result = dagmc_point_in_vol_dir(origin, dir, vol_idx); - CHECK_EQUAL(expected_result,result); + CHECK_EQUAL(expected_result, result); } void dagmc_point_in_vol_4() { - int expected_result=1; - int vol_idx=1; - double dir[3]={ 0.0,1.0,0.0}; - double origin[3]={0.0,0.0,0.0}; - - int result = dagmc_point_in_vol_dir(origin,dir,vol_idx); + int expected_result = 1; + int vol_idx = 1; + double dir[3] = {0.0, 1.0, 0.0}; + double origin[3] = {0.0, 0.0, 0.0}; - CHECK_EQUAL(expected_result,result); + int result = dagmc_point_in_vol_dir(origin, dir, vol_idx); + CHECK_EQUAL(expected_result, result); } void dagmc_point_in_vol_5() { - int expected_result=1; - int vol_idx=1; - double dir[3]={ 0.0,0.0,-1.0}; - double origin[3]={0.0,0.0,0.0}; + int expected_result = 1; + int vol_idx = 1; + double dir[3] = {0.0, 0.0, -1.0}; + double origin[3] = {0.0, 0.0, 0.0}; - int result = dagmc_point_in_vol_dir(origin,dir,vol_idx); + int result = dagmc_point_in_vol_dir(origin, dir, vol_idx); - CHECK_EQUAL(expected_result,result); + CHECK_EQUAL(expected_result, result); } void dagmc_point_in_vol_6() { - int expected_result=1; - int vol_idx=1; - double dir[3]={ 0.0,0.0,1.0}; - double origin[3]={0.0,0.0,0.0}; - - int result = dagmc_point_in_vol_dir(origin,dir,vol_idx); + int expected_result = 1; + int vol_idx = 1; + double dir[3] = {0.0, 0.0, 1.0}; + double origin[3] = {0.0, 0.0, 0.0}; - CHECK_EQUAL(expected_result,result); + int result = dagmc_point_in_vol_dir(origin, dir, vol_idx); + CHECK_EQUAL(expected_result, result); } void dagmc_point_on_corner_1() { - int expected_result=1; - int vol_idx=1; - double dir[3]={ 1.0,1.0,1.0}; - double origin[3]={0.0,0.0,0.0}; + int expected_result = 1; + int vol_idx = 1; + double dir[3] = {1.0, 1.0, 1.0}; + double origin[3] = {0.0, 0.0, 0.0}; - int result = dagmc_point_in_vol_dir(origin,dir,vol_idx); + int result = dagmc_point_in_vol_dir(origin, dir, vol_idx); - CHECK_EQUAL(expected_result,result); + CHECK_EQUAL(expected_result, result); } void dagmc_point_on_corner_2() { - int expected_result=1; - int vol_idx=1; - double dir[3]={ -1.0,1.0,1.0}; - double origin[3]={0.0,0.0,0.0}; + int expected_result = 1; + int vol_idx = 1; + double dir[3] = {-1.0, 1.0, 1.0}; + double origin[3] = {0.0, 0.0, 0.0}; - int result = dagmc_point_in_vol_dir(origin,dir,vol_idx); + int result = dagmc_point_in_vol_dir(origin, dir, vol_idx); - CHECK_EQUAL(expected_result,result); + CHECK_EQUAL(expected_result, result); } void dagmc_point_on_corner_3() { int expected_result = 1; - int vol_idx=1; - double dir[3]={ 1.0,1.0,-1.0}; - double origin[3]={0.0,0.0,0.0}; + int vol_idx = 1; + double dir[3] = {1.0, 1.0, -1.0}; + double origin[3] = {0.0, 0.0, 0.0}; - int result = dagmc_point_in_vol_dir(origin,dir,vol_idx); + int result = dagmc_point_in_vol_dir(origin, dir, vol_idx); - CHECK_EQUAL(expected_result,result); + CHECK_EQUAL(expected_result, result); } void dagmc_point_on_corner_4() { int expected_result = 1; - int vol_idx=1; - double dir[3]={ -1.0,1.0,-1.0}; - double origin[3]={0.0,0.0,0.0}; + int vol_idx = 1; + double dir[3] = {-1.0, 1.0, -1.0}; + double origin[3] = {0.0, 0.0, 0.0}; - int result = dagmc_point_in_vol_dir(origin,dir,vol_idx); + int result = dagmc_point_in_vol_dir(origin, dir, vol_idx); - CHECK_EQUAL(expected_result,result); + CHECK_EQUAL(expected_result, result); } void dagmc_point_on_corner_5() { int expected_result = 1; - int vol_idx=1; - double dir[3]={ 1.0,-1.0,1.0}; - double origin[3]={0.0,0.0,0.0}; + int vol_idx = 1; + double dir[3] = {1.0, -1.0, 1.0}; + double origin[3] = {0.0, 0.0, 0.0}; - int result = dagmc_point_in_vol_dir(origin,dir,vol_idx); + int result = dagmc_point_in_vol_dir(origin, dir, vol_idx); - CHECK_EQUAL(expected_result,result); + CHECK_EQUAL(expected_result, result); } void dagmc_point_on_corner_6() { int expected_result = 1; - int vol_idx=1; - double dir[3]={ -1.0,-1.0,1.0}; - double origin[3]={0.0,0.0,0.0}; + int vol_idx = 1; + double dir[3] = {-1.0, -1.0, 1.0}; + double origin[3] = {0.0, 0.0, 0.0}; - int result = dagmc_point_in_vol_dir(origin,dir,vol_idx); + int result = dagmc_point_in_vol_dir(origin, dir, vol_idx); - CHECK_EQUAL(expected_result,result); + CHECK_EQUAL(expected_result, result); } void dagmc_point_on_corner_7() { int expected_result = 1; - int vol_idx=1; - double dir[3]={ 1.0,-1.0,-1.0}; - double origin[3]={0.0,0.0,0.0}; + int vol_idx = 1; + double dir[3] = {1.0, -1.0, -1.0}; + double origin[3] = {0.0, 0.0, 0.0}; - int result = dagmc_point_in_vol_dir(origin,dir,vol_idx); + int result = dagmc_point_in_vol_dir(origin, dir, vol_idx); - CHECK_EQUAL(expected_result,result); + CHECK_EQUAL(expected_result, result); } void dagmc_point_on_corner_8() { int expected_result = 1; - int vol_idx=1; - double dir[3]={ -1.0,-1.0,-1.0}; - double origin[3]={0.0,0.0,0.0}; + int vol_idx = 1; + double dir[3] = {-1.0, -1.0, -1.0}; + double origin[3] = {0.0, 0.0, 0.0}; - int result = dagmc_point_in_vol_dir(origin,dir,vol_idx); + int result = dagmc_point_in_vol_dir(origin, dir, vol_idx); - CHECK_EQUAL(expected_result,result); + CHECK_EQUAL(expected_result, result); } int main(int /* argc */, char** /* argv */) { int result = 0; - result += RUN_TEST( dagmc_setup_test ); // setup problem - result += RUN_TEST( dagmc_point_in ); // point in centre + result += RUN_TEST(dagmc_setup_test); // setup problem + result += RUN_TEST(dagmc_point_in); // point in centre // rays fired along cardinal directions - result += RUN_TEST( dagmc_point_in_vol_1); // point in centre - result += RUN_TEST( dagmc_point_in_vol_2); // point in centre - result += RUN_TEST( dagmc_point_in_vol_3); // point in centre - result += RUN_TEST( dagmc_point_in_vol_4); // point in centre - result += RUN_TEST( dagmc_point_in_vol_5); // point in centre - result += RUN_TEST( dagmc_point_in_vol_6); // point in centre + result += RUN_TEST(dagmc_point_in_vol_1); // point in centre + result += RUN_TEST(dagmc_point_in_vol_2); // point in centre + result += RUN_TEST(dagmc_point_in_vol_3); // point in centre + result += RUN_TEST(dagmc_point_in_vol_4); // point in centre + result += RUN_TEST(dagmc_point_in_vol_5); // point in centre + result += RUN_TEST(dagmc_point_in_vol_6); // point in centre // rays fired at nodes - result += RUN_TEST( dagmc_point_on_corner_1); - result += RUN_TEST( dagmc_point_on_corner_2); - result += RUN_TEST( dagmc_point_on_corner_3); - result += RUN_TEST( dagmc_point_on_corner_4); - - // result += RUN_TEST( dagmc_point_in({0.0,0.0,5.0}); // point in centre - // result += RUN_TEST( dagmc_point_in({0.0,0.0,-5.0}); // point in centre - // result += RUN_TEST( dagmc_point_in({0.0,5.0,0.0}); // point in centre - // result += RUN_TEST( dagmc_point_in({0.0,-5.0,0.0}); // point in centre - // result += RUN_TEST( dagmc_point_in({5.0,0.0,0.0}); // point in centre - // result += RUN_TEST( dagmc_point_in({-5.0,0.0,0.0}); // point in centre + result += RUN_TEST(dagmc_point_on_corner_1); + result += RUN_TEST(dagmc_point_on_corner_2); + result += RUN_TEST(dagmc_point_on_corner_3); + result += RUN_TEST(dagmc_point_on_corner_4); + + //result += RUN_TEST(dagmc_point_in({0.0, 0.0, 5.0}); // point in centre + //result += RUN_TEST(dagmc_point_in({0.0, 0.0, -5.0}); // point in centre + //result += RUN_TEST(dagmc_point_in({0.0, 5.0, 0.0}); // point in centre + //result += RUN_TEST(dagmc_point_in({0.0, -5.0, 0.0}); // point in centre + //result += RUN_TEST(dagmc_point_in({5.0, 0.0, 0.0}); // point in centre + //result += RUN_TEST(dagmc_point_in({-5.0, 0.0, 0.0}); // point in centre return result; } diff --git a/test/dagmc/dagmc_rayfire_test.cpp b/test/dagmc/dagmc_rayfire_test.cpp index 57aa625..ba5f309 100644 --- a/test/dagmc/dagmc_rayfire_test.cpp +++ b/test/dagmc/dagmc_rayfire_test.cpp @@ -35,80 +35,80 @@ void dagmc_setup_test() rval = DAG->init_OBBTree(); CHECK_ERR(rval); + /* int num_vols = DAG->num_entities(3); EntityHandle vol_h; - for ( int i = 0 ; i < num_vols ; i++ ) - { - vol_h = DAG->entity_by_index(3,i); - } + for (int i = 0; i < num_vols; i++) + vol_h = DAG->entity_by_index(3, i); + */ // EntityHandle volume = 12682136550675316765; - // CHECK_EQUAL(volume,vol); + // CHECK_EQUAL(volume, vol); } void dagmc_origin_face_rayfire() { int vol_idx = 1; - EntityHandle vol_h = DAG->entity_by_index(3,vol_idx); - double dir[3]={-1.0,0.0,0.0}; - double origin[3]={0.0,0.0,0.0}; + EntityHandle vol_h = DAG->entity_by_index(3, vol_idx); + double dir[3] = {-1.0, 0.0, 0.0}; + double origin[3] = {0.0, 0.0, 0.0}; double next_surf_dist; EntityHandle next_surf; - DAG->ray_fire(vol_h,origin,dir,next_surf,next_surf_dist); - double expected_next_surf_dist=5.0; - CHECK_REAL_EQUAL(expected_next_surf_dist,next_surf_dist,eps); + DAG->ray_fire(vol_h, origin, dir, next_surf, next_surf_dist); + double expected_next_surf_dist = 5.0; + CHECK_REAL_EQUAL(expected_next_surf_dist, next_surf_dist, eps); } void dagmc_outside_face_rayfire() { int vol_idx = 1; - EntityHandle vol_h = DAG->entity_by_index(3,vol_idx); - double dir[3]={1.0,0.0,0.0}; // ray along x direction - double origin[3]={-10.0,0.0,0.0}; // origin at -10 0 0 + EntityHandle vol_h = DAG->entity_by_index(3, vol_idx); + double dir[3] = {1.0, 0.0, 0.0}; // ray along x direction + double origin[3] = {-10.0, 0.0, 0.0}; // origin at -10 0 0 double next_surf_dist; EntityHandle next_surf; - DAG->ray_fire(vol_h,origin,dir,next_surf,next_surf_dist); + DAG->ray_fire(vol_h, origin, dir, next_surf, next_surf_dist); std::cout << next_surf_dist << std::endl; - double expected_next_surf_dist=15.0; - CHECK_REAL_EQUAL(expected_next_surf_dist,next_surf_dist,eps); + double expected_next_surf_dist = 15.0; + CHECK_REAL_EQUAL(expected_next_surf_dist, next_surf_dist, eps); } void dagmc_outside_face_rayfire_orient_exit() { DagMC::RayHistory history; int vol_idx = 1; - EntityHandle vol_h = DAG->entity_by_index(3,vol_idx); - double dir[3]={1.0,0.0,0.0}; // ray along x direction - double origin[3]={-10.0,0.0,0.0}; // origin at -10 0 0 + EntityHandle vol_h = DAG->entity_by_index(3, vol_idx); + double dir[3] = {1.0, 0.0, 0.0}; // ray along x direction + double origin[3] = {-10.0, 0.0, 0.0}; // origin at -10 0 0 double next_surf_dist; EntityHandle next_surf; - DAG->ray_fire(vol_h,origin,dir,next_surf,next_surf_dist,&history,0,1); + DAG->ray_fire(vol_h, origin, dir, next_surf, next_surf_dist, &history, 0, 1); std::cout << next_surf_dist << std::endl; - double expected_next_surf_dist=15.0; - CHECK_REAL_EQUAL(expected_next_surf_dist,next_surf_dist,eps); + double expected_next_surf_dist = 15.0; + CHECK_REAL_EQUAL(expected_next_surf_dist, next_surf_dist, eps); } void dagmc_outside_face_rayfire_orient_entrance() { DagMC::RayHistory history; int vol_idx = 1; - EntityHandle vol_h = DAG->entity_by_index(3,vol_idx); - double dir[3]={1.0,0.0,0.0}; // ray along x direction - double origin[3]={-10.0,0.0,0.0}; // origin at -10 0 0 + EntityHandle vol_h = DAG->entity_by_index(3, vol_idx); + double dir[3] = {1.0, 0.0, 0.0}; // ray along x direction + double origin[3] = {-10.0, 0.0, 0.0}; // origin at -10 0 0 double next_surf_dist; EntityHandle next_surf; - DAG->ray_fire(vol_h,origin,dir,next_surf,next_surf_dist,&history,0.0,-1); + DAG->ray_fire(vol_h, origin, dir, next_surf, next_surf_dist, &history, 0.0, -1); std::cout << next_surf_dist << std::endl; - double expected_next_surf_dist=5.0; - CHECK_REAL_EQUAL(expected_next_surf_dist,next_surf_dist,eps); + double expected_next_surf_dist = 5.0; + CHECK_REAL_EQUAL(expected_next_surf_dist, next_surf_dist, eps); } void dagmc_outside_face_rayfire_history_fail() { DagMC::RayHistory history; int vol_idx = 1; - EntityHandle vol_h = DAG->entity_by_index(3,vol_idx); - double dir[3]={1.0,0.0,0.0}; // ray along x direction - double origin[3]={-10.0,0.0,0.0}; // origin at -10 0 0 + EntityHandle vol_h = DAG->entity_by_index(3, vol_idx); + double dir[3] = {1.0, 0.0, 0.0}; // ray along x direction + double origin[3] = {-10.0, 0.0, 0.0}; // origin at -10 0 0 double xyz[3]; double next_surf_dist; EntityHandle next_surf; @@ -119,62 +119,60 @@ void dagmc_outside_face_rayfire_history_fail() // needs two ray_fires to cross, this is expected and ok // first ray fire with history - DAG->ray_fire(vol_h,origin,dir,next_surf,next_surf_dist,&history,0,1); + DAG->ray_fire(vol_h, origin, dir, next_surf, next_surf_dist, &history, 0, 1); // second ray fire with history - DAG->ray_fire(vol_h,xyz,dir,next_surf,next_surf_dist,&history,0,1); + DAG->ray_fire(vol_h, xyz, dir, next_surf, next_surf_dist, &history, 0, 1); // this fire should hit graveyard, i.e. next_surf = 0 - DAG->ray_fire(vol_h,xyz,dir,next_surf,next_surf_dist,&history,0,1); + DAG->ray_fire(vol_h, xyz, dir, next_surf, next_surf_dist, &history, 0, 1); // using history with this geom, there should be no next surface, i.e. 0 EntityHandle ZERO = 0; - CHECK_EQUAL(ZERO ,next_surf); + CHECK_EQUAL(ZERO, next_surf); } void dagmc_outside_face_rayfire_history() { DagMC::RayHistory history; int vol_idx = 1; - EntityHandle vol_h = DAG->entity_by_index(3,vol_idx); - double dir[3]={1.0,0.0,0.0}; // ray along x direction - double origin[3]={-10.0,0.0,0.0}; // origin at -10 0 0 + EntityHandle vol_h = DAG->entity_by_index(3, vol_idx); + double dir[3] = {1.0, 0.0, 0.0}; // ray along x direction + double origin[3] = {-10.0, 0.0, 0.0}; // origin at -10 0 0 double xyz[3]; double next_surf_dist; EntityHandle next_surf; history.reset(); // first ray fire with history - DAG->ray_fire(vol_h,origin,dir,next_surf,next_surf_dist,&history,0,1); + DAG->ray_fire(vol_h, origin, dir, next_surf, next_surf_dist, &history, 0, 1); std::cout << next_surf << " " << history.size() << std::endl; // second ray fire with history - xyz[0]=origin[0]+(next_surf_dist*dir[0]); - xyz[1]=origin[1]+(next_surf_dist*dir[1]); - xyz[2]=origin[2]+(next_surf_dist*dir[2]); + xyz[0] = origin[0] + (next_surf_dist*dir[0]); + xyz[1] = origin[1] + (next_surf_dist*dir[1]); + xyz[2] = origin[2] + (next_surf_dist*dir[2]); // ray fired execacyl - DAG->ray_fire(vol_h,xyz,dir,next_surf,next_surf_dist,&history,0,1); - - DAG->ray_fire(vol_h,xyz,dir,next_surf,next_surf_dist,&history,0,1); + DAG->ray_fire(vol_h, xyz, dir, next_surf, next_surf_dist, &history, 0, 1); + DAG->ray_fire(vol_h, xyz, dir, next_surf, next_surf_dist, &history, 0, 1); // using history with this geom, there should be no next surface, i.e. 0 EntityHandle ZERO = 0; - CHECK_EQUAL(ZERO ,next_surf); + CHECK_EQUAL(ZERO, next_surf); } - int main(int /* argc */, char** /* argv */) { int result = 0; - result += RUN_TEST( dagmc_setup_test ); // setup problem + result += RUN_TEST(dagmc_setup_test); // setup problem // rays fired along cardinal directions - result += RUN_TEST( dagmc_origin_face_rayfire ); // point in centre - result += RUN_TEST( dagmc_outside_face_rayfire ); - result += RUN_TEST( dagmc_outside_face_rayfire_orient_exit ); // fire ray from point outside volume looking for exit intersections - result += RUN_TEST( dagmc_outside_face_rayfire_orient_entrance ); // fire ray from point outside volume looking for entrance intersection - result += RUN_TEST( dagmc_outside_face_rayfire_history_fail ); // fire ray from point outside geometry using ray history - result += RUN_TEST( dagmc_outside_face_rayfire_history ); // fire ray from point outside geometry using ray history + result += RUN_TEST(dagmc_origin_face_rayfire); // point in centre + result += RUN_TEST(dagmc_outside_face_rayfire); + result += RUN_TEST(dagmc_outside_face_rayfire_orient_exit); // fire ray from point outside volume looking for exit intersections + result += RUN_TEST(dagmc_outside_face_rayfire_orient_entrance); // fire ray from point outside volume looking for entrance intersection + result += RUN_TEST(dagmc_outside_face_rayfire_history_fail); // fire ray from point outside geometry using ray history + result += RUN_TEST(dagmc_outside_face_rayfire_history); // fire ray from point outside geometry using ray history return result; } diff --git a/test/dagmc/dagmc_simple_test.cpp b/test/dagmc/dagmc_simple_test.cpp index bf253f6..b2a44eb 100644 --- a/test/dagmc/dagmc_simple_test.cpp +++ b/test/dagmc/dagmc_simple_test.cpp @@ -26,7 +26,6 @@ static const char input_file[] = STRINGIFY(MESHDIR) "/dagmc/test_geom.h5m"; static const char input_file[] = STRINGIFY(MESHDIR) "/dagmc/test_geom.h5m"; #endif - void dagmc_load_file() { ErrorCode rval = DAG->load_file(input_file); // open the Dag file @@ -41,97 +40,101 @@ void dagmc_build_obb() void dagmc_num_vols() { - int expect_num_vols=2; + int expect_num_vols = 2; int num_vols = DAG->num_entities(3); - CHECK_EQUAL(expect_num_vols,num_vols); + CHECK_EQUAL(expect_num_vols, num_vols); } void dagmc_entity_handle() { - int num_vols = DAG->num_entities(3); + /* + int num_vols = DAG->num_entities(3); EntityHandle vol_h; - for ( int i = 0 ; i < num_vols ; i++ ) - { - vol_h = DAG->entity_by_index(3,i); - } + for (int i = 0; i < num_vols; i++) + vol_h = DAG->entity_by_index(3, i); + */ //EntityHandle expect_vol_h = 12682136550675316765; - //CHECK_EQUAL(expect_vol_h,vol_h); + //CHECK_EQUAL(expect_vol_h, vol_h); } void dagmc_point_in() { int result = 0; - int expect_result=1; - int vol_idx=1; - double xyz[3]={0.0,0.0,0.0}; - EntityHandle vol_h = DAG->entity_by_index(3,vol_idx); - ErrorCode rval = DAG->point_in_volume(vol_h,xyz,result); - CHECK_EQUAL(expect_result,result); + int expect_result = 1; + int vol_idx = 1; + double xyz[3] = {0.0, 0.0, 0.0}; + EntityHandle vol_h = DAG->entity_by_index(3, vol_idx); + ErrorCode rval = DAG->point_in_volume(vol_h, xyz, result); + CHECK_ERR(rval); + CHECK_EQUAL(expect_result, result); } void dagmc_rayfire() { const double eps = 1e-6; // epsilon for test, faceting tol? - int vol_idx=1; + int vol_idx = 1; // note model is cube of side 10, centred at 0,0,0, so ray fire along // any unit direction should be exactly 5.0 - double xyz[3]={0.0,0.0,0.0}; - double dir[3]={0.0,0.0,1.0}; + double xyz[3] = {0.0, 0.0, 0.0}; + double dir[3] = {0.0, 0.0, 1.0}; EntityHandle next_surf; double next_surf_dist; - double expect_next_surf_dist=5.0; - EntityHandle vol_h = DAG->entity_by_index(3,vol_idx); + double expect_next_surf_dist = 5.0; + EntityHandle vol_h = DAG->entity_by_index(3, vol_idx); - ErrorCode rval = DAG->ray_fire(vol_h,xyz,dir,next_surf,next_surf_dist); - CHECK_REAL_EQUAL(expect_next_surf_dist,next_surf_dist,eps); + ErrorCode rval = DAG->ray_fire(vol_h, xyz, dir, next_surf, next_surf_dist); + CHECK_ERR(rval); + CHECK_REAL_EQUAL(expect_next_surf_dist, next_surf_dist, eps); } void dagmc_closest_to() { const double eps = 1e-6; // epsilon for test, faceting tol? - int vol_idx=1; + int vol_idx = 1; // note model is cube of side 10, centred at 0,0,0, so ray fire along // any unit direction should be exactly 5.0 - double xyz[3]={-6.0,0.0,0.0}; + double xyz[3] = {-6.0, 0.0, 0.0}; double distance; // distance from point to nearest surface - double expect_distance=1.0; - EntityHandle vol_h = DAG->entity_by_index(3,vol_idx); + double expect_distance = 1.0; + EntityHandle vol_h = DAG->entity_by_index(3, vol_idx); - ErrorCode rval = DAG->closest_to_location(vol_h,xyz,distance); + ErrorCode rval = DAG->closest_to_location(vol_h, xyz, distance); + CHECK_ERR(rval); // distance should be 1.0 cm - CHECK_REAL_EQUAL(expect_distance,distance,eps); + CHECK_REAL_EQUAL(expect_distance, distance, eps); } void dagmc_test_boundary() { - int vol_idx=1; - EntityHandle vol_h = DAG->entity_by_index(3,vol_idx); - int surf_idx=1; - EntityHandle surf_h = DAG->entity_by_index(2,surf_idx); + int vol_idx = 1; + EntityHandle vol_h = DAG->entity_by_index(3, vol_idx); + int surf_idx = 1; + EntityHandle surf_h = DAG->entity_by_index(2, surf_idx); - double xyz[3]={0.0,0.0,5.0}; - double dir[3]={0.0,0.0,1.0}; + double xyz[3] = {0.0, 0.0, 5.0}; + double dir[3] = {0.0, 0.0, 1.0}; int result; - int expect_result=0; + int expect_result = 0; - ErrorCode rval = DAG->test_volume_boundary(vol_h,surf_h,xyz,dir,result); + ErrorCode rval = DAG->test_volume_boundary(vol_h, surf_h, xyz, dir, result); + CHECK_ERR(rval); // check ray leaving volume - CHECK_EQUAL(expect_result,result); + CHECK_EQUAL(expect_result, result); } int main(int /* argc */, char** /* argv */) { int result = 0; - result += RUN_TEST( dagmc_load_file ); // test ray fire - result += RUN_TEST( dagmc_build_obb ); // build the obb - result += RUN_TEST( dagmc_num_vols ); // make sure the num of vols correct - // result += RUN_TEST( dagmc_entity_handle); // check the entity handle correct - result += RUN_TEST( dagmc_point_in); // check entity by point - result += RUN_TEST( dagmc_rayfire ) ; // ensure ray fire distance is correct - result += RUN_TEST( dagmc_closest_to ); // check the distance to surface nearest point - result += RUN_TEST( dagmc_test_boundary ); // check particle entering leaving + result += RUN_TEST(dagmc_load_file); // test ray fire + result += RUN_TEST(dagmc_build_obb); // build the obb + result += RUN_TEST(dagmc_num_vols); // make sure the num of vols correct + // result += RUN_TEST(dagmc_entity_handle); // check the entity handle correct + result += RUN_TEST(dagmc_point_in); // check entity by point + result += RUN_TEST(dagmc_rayfire); // ensure ray fire distance is correct + result += RUN_TEST(dagmc_closest_to); // check the distance to surface nearest point + result += RUN_TEST(dagmc_test_boundary); // check particle entering leaving return result; } diff --git a/tools/mbcoupler/Coupler.cpp b/tools/mbcoupler/Coupler.cpp index afee8af..fbfd8fb 100644 --- a/tools/mbcoupler/Coupler.cpp +++ b/tools/mbcoupler/Coupler.cpp @@ -446,7 +446,12 @@ ErrorCode Coupler::locate_points(double *xyz, int num_points, for (int i = 0; i < num_points; i++) { if (tl_tmp->vi_rd[3*i+1] == -1) + { missing_pts++; +#ifndef NDEBUG + printf(" %f %f %f\n", xyz[3*i], xyz[3*i+1], xyz[3*i+2] ); +#endif + } else if (tl_tmp->vi_rd[3*i]==(int)my_rank) local_pts++; @@ -668,7 +673,11 @@ ErrorCode Coupler::nat_param(double xyz[3], if (epsilon) { std::vector<double> dists; std::vector<EntityHandle> leaves; - result = myTree->distance_search(xyz, epsilon, leaves, 1.0e-10, 1.0e-6, &dists, NULL, &localRoot); + // two tolerances + result = myTree->distance_search(xyz, epsilon, leaves, + /*iter_tol*/ epsilon, + /*inside_tol*/ 10*epsilon, + &dists, NULL, &localRoot); if (leaves.empty()) // not found returns success here, with empty list, just like case with no epsilon return MB_SUCCESS; @@ -758,38 +767,53 @@ ErrorCode Coupler::nat_param(double xyz[3], std::cout << "Problems getting coordinates of vertices\n"; return result; } - + CartVect pos(xyz); if (etype == MBHEX) { if (8==num_connect) { Element::LinearHex hexmap(coords_vert); - tmp_nat_coords = hexmap.ievaluate(CartVect(xyz), epsilon); - bool inside = hexmap.inside_nat_space(tmp_nat_coords, epsilon); - if (!inside) + if (!hexmap.inside_box( pos, epsilon)) + continue; + try { + tmp_nat_coords = hexmap.ievaluate(pos, epsilon); + bool inside = hexmap.inside_nat_space(tmp_nat_coords, epsilon); + if (!inside) continue; + } + catch (Element::Map::EvaluationError) { continue; + } } else if (27==num_connect) { Element::QuadraticHex hexmap(coords_vert); - tmp_nat_coords = hexmap.ievaluate(CartVect(xyz), epsilon); - bool inside = hexmap.inside_nat_space(tmp_nat_coords, epsilon); - if (!inside) - continue; + if (!hexmap.inside_box( pos, epsilon)) + continue; + try { + tmp_nat_coords = hexmap.ievaluate(pos, epsilon); + bool inside = hexmap.inside_nat_space(tmp_nat_coords, epsilon); + if (!inside) continue; + } + catch (Element::Map::EvaluationError) { + continue; + } } else // TODO this case not treated yet, no interpolation continue; } else if (etype == MBTET){ Element::LinearTet tetmap(coords_vert); - tmp_nat_coords = tetmap.ievaluate(CartVect(xyz)); + // this is just a linear solve; unless degenerate, will not except + tmp_nat_coords = tetmap.ievaluate(pos); bool inside = tetmap.inside_nat_space(tmp_nat_coords, epsilon); if (!inside) continue; } else if (etype == MBQUAD){ Element::LinearQuad quadmap(coords_vert); + if (!quadmap.inside_box( pos, epsilon)) + continue; try { - tmp_nat_coords = quadmap.ievaluate(CartVect(xyz), epsilon); + tmp_nat_coords = quadmap.ievaluate(pos, epsilon); bool inside = quadmap.inside_nat_space(tmp_nat_coords, epsilon); if (!inside) continue; } diff --git a/tools/mbcoupler/ElemUtil.cpp b/tools/mbcoupler/ElemUtil.cpp index cfc36e0..ee338c0 100644 --- a/tools/mbcoupler/ElemUtil.cpp +++ b/tools/mbcoupler/ElemUtil.cpp @@ -3,6 +3,7 @@ #include <assert.h> #include "ElemUtil.hpp" +#include "moab/BoundBox.hpp" namespace moab { namespace ElemUtil { @@ -433,6 +434,15 @@ namespace Element { this->vertex = v; } + bool Map::inside_box(const CartVect & xi, double & tol) const + { + // bail out early, before doing an expensive NR iteration + // compute box + BoundBox box(this->vertex); + return box.contains_point(xi.array(), tol); + + } + // CartVect Map::ievaluate(const CartVect& x, double tol, const CartVect& x0) const { // TODO: should differentiate between epsilons used for @@ -448,12 +458,12 @@ namespace Element { int iters=0; while (delta % delta > error_tol_sqr) { if(++iters>10) - throw Map::EvaluationError(); + throw Map::EvaluationError(x, vertex); J = jacobian(xi); det = J.determinant(); if (det < std::numeric_limits<double>::epsilon()) - throw Map::EvaluationError(); + throw Map::EvaluationError(x, vertex); xi -= J.inverse(1.0/det) * delta; delta = evaluate( xi ) - x; } @@ -896,7 +906,10 @@ namespace Element { real dist = opt_findpt_3(&_data, (const real **)_xyz, x_star, r, &c); // if it did not converge, get out with throw... if (dist > 0.9e+30) - throw Map::EvaluationError(); + { + std::vector<CartVect> dummy; + throw Map::EvaluationError(xyz, dummy); + } //c tells us if we landed inside the element or exactly on a face, edge, or node // also, dist shows the distance to the computed point. //copy parametric coords back @@ -1184,7 +1197,11 @@ namespace Element { real dist = opt_findpt_2(&_data, (const real **)_xyz, x_star, r, &c); // if it did not converge, get out with throw... if (dist > 0.9e+30) - throw Map::EvaluationError(); + { + std::vector<CartVect> dummy; + throw Map::EvaluationError(xyz, dummy); + } + //c tells us if we landed inside the element or exactly on a face, edge, or node // also, dist shows the distance to the computed point. //copy parametric coords back diff --git a/tools/mbcoupler/ElemUtil.hpp b/tools/mbcoupler/ElemUtil.hpp index 219323b..b2a743a 100644 --- a/tools/mbcoupler/ElemUtil.hpp +++ b/tools/mbcoupler/ElemUtil.hpp @@ -103,10 +103,22 @@ namespace ElemUtil { /**\brief Set vertices. */ virtual void set_vertices(const std::vector<CartVect>& v); + // will look at the box formed by vertex coordinates, and before doing any NR, bail out if necessary + virtual bool inside_box(const CartVect & xi, double & tol) const; + /* Exception thrown when an evaluation fails (e.g., ievaluate fails to converge). */ class EvaluationError { public: - EvaluationError(){}; + EvaluationError(const CartVect & x, const std::vector<CartVect> & verts): p(x), vertices(verts){ +#ifndef NDEBUG + std::cout << "p:" << p << "\n vertices.size() " <<vertices.size() << "\n"; + for (size_t i=0; i<vertices.size(); i++) + std::cout << vertices[i] << "\n"; +#endif + }; + private: + CartVect p; + std::vector<CartVect> vertices; };// class EvaluationError /* Exception thrown when a bad argument is encountered. */ diff --git a/tools/mbcoupler/ElementTest.cpp b/tools/mbcoupler/ElementTest.cpp index 4f37602..ca6e9e2 100644 --- a/tools/mbcoupler/ElementTest.cpp +++ b/tools/mbcoupler/ElementTest.cpp @@ -24,7 +24,58 @@ void test_tet() { }// test_tet() void test_hex() { - moab::Element::LinearHex hex; + double positions[] = + { + 236.80706050970281, -139.55422526228017, 193.27999999999997, + 236.47511729348639, -141.33020962638582, 193.27999999999997, + 237.8457938295229, -142.57076074835663, 193.27999999999997, + 239.12702305519684, -139.96608933577852, 193.27999999999997, + 236.80841321361444, -139.55341321335499, 202.654, + 236.47655014713746, -141.32980272396816, 202.654, + 237.8477913707564, -142.57047282187165, 202.654, + 239.12865103844533, -139.96531051891105, 202.654 + }; + CartVect x(235.96518686964933, -142.43503000077749, 188.19999999999987); + std::vector<CartVect> vertices; + for (int i=0; i<8; i++) + vertices.push_back(CartVect(positions+3*i)); + + moab::Element::LinearHex hex(vertices); + double tol(0.0001); + if (hex.inside_box(x, tol)) + { + CartVect nat_par = hex.ievaluate(x, 0.0001); + std::cout <<nat_par <<"\n"; + } + + double positions2[] = + { 49.890500000000024, -20.376134375374882, 312.72000000000003, + 52.015875000000044, -19.149048546996006, 312.72000000000003, + 48.430375821458099, -18.548796774572125, 312.72000000000003, + 47.717616239031223, -21.191360829777231, 312.72000000000003, + 49.890500000000024, -20.376134375374882, 322.88, + 52.015875000000044, -19.149048546996006, 322.88, + 48.429930354643275, -18.52828610485021, 322.88, + 47.720552036968819, -21.167591146685712, 322.88}; + + CartVect x2(51.469000000000015, -20.145482942833631, 317.80000000000001); + + vertices.clear(); + for (int i=0; i<8; i++) + vertices.push_back(CartVect(positions2+3*i)); + moab::Element::LinearHex hex2(vertices); + if (hex2.inside_box(x2, tol)) + { + try { + CartVect nat_par = hex.ievaluate(x, 0.0001); + std::cout <<nat_par <<"\n"; + } + catch (Element::Map::EvaluationError) { + // nothing + } +} + + }// test_hex() #include "moab/Core.hpp" #include "moab/Range.hpp" Repository URL: https://bitbucket.org/fathomteam/moab/ -- This is a commit notification from bitbucket.org. 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