August 2011 - moab-dev - mailman3.cels.anl.gov

Make check failure (5143)
by Xiabing Xu 01 Sep '11

01 Sep '11

Error messages: Making check in itaps make[2]: Entering directory `/fusion/gpfs/home/xbxu/parvis/moab-trunk-build/examples/itaps' make FindConnectF TagIterateC TagIterateF make[3]: Entering directory `/fusion/gpfs/home/xbxu/parvis/moab-trunk-build/examples/itaps' PPF77 FindConnectF.o In file included from ../../itaps/imesh/iMesh_f.h:5, from FindConnectF.F:11: ../../itaps/iBase_f.h:21: error: #error "Unknown compiler. Please define PTRSIZE." make[3]: *** [FindConnectF.o] Error 1 make[3]: Leaving directory `/fusion/gpfs/home/xbxu/parvis/moab-trunk-build/examples/itaps' make[2]: *** [check-am] Error 2 make[2]: Leaving directory `/fusion/gpfs/home/xbxu/parvis/moab-trunk-build/examples/itaps' make[1]: *** [check-recursive] Error 1 make[1]: Leaving directory `/fusion/gpfs/home/xbxu/parvis/moab-trunk-build/examples' make: *** [check-recursive] Error 1 My configuration: ./configure --prefix=/homes/xbxu/parvis/moab-trunk-build/install --with-mpi=/fusion/group/climate/software/mpi2/mpich2-1.4/install --with-pnetcdf=/fusion/group/climate/software/pnetcdf/parallel-netcdf-1.2.0/install --with-netcdf=/fusion/group/climate/software/netcdf/netcdf-4.1.2-parallel/install --with-hdf5=/fusion/group/climate/software/hdf5/hdf5-1.8.6-parallel/install --with-zlib=/fusion/group/climate/software/zlib/zlib-1.2.5/install --with-szip=/fusion/group/climate/software/szip/szip-2.1/install --enable-debug CC=/fusion/group/climate/software/mpi2/mpich2-1.4/install/bin/mpicc CXX=/fusion/group/climate/software/mpi2/mpich2-1.4/install/bin/mpicxx FC=/fusion/group/climate/software/mpi2/mpich2-1.4/install/bin/mpif90 F77=/fusion/group/climate/software/mpi2/mpich2-1.4/install/bin/mpif77 F77=gfortran Thanks, Xiabing

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r5145 - MOAB/trunk/src/parallel
by kraftche＠cae.wisc.edu 31 Aug '11

31 Aug '11

Author: kraftche Date: 2011-08-31 16:53:33 -0500 (Wed, 31 Aug 2011) New Revision: 5145 Modified: MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp Log: Fix bug in WriteHDF5Parallel: If no process is writing an element type that the root process is not, but the root process plans to write an element type that one or more other processes is not aware of then update the type list on other processes appropriately. Fixes problem where write fails if root proccess has mesh but one or more others do not. Modified: MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp =================================================================== --- MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp 2011-08-31 20:58:56 UTC (rev 5144) +++ MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp 2011-08-31 21:53:33 UTC (rev 5145) @@ -1179,7 +1179,7 @@ // Build local list of any types that root did not know about typelist non_root_types; viter = root_types.begin(); - for (typelist::iterator iter = my_types.begin(); iter != my_types.end(); ++iter) { + for (typelist::iterator iter = my_types.begin(); iter != my_types.end(); ++iter) { if (viter == root_types.end() || *viter != *iter) non_root_types.push_back( *iter ); else @@ -1191,61 +1191,66 @@ int not_done; result = MPI_Allreduce( &non_root_count, &not_done, 1, MPI_INT, MPI_LOR, comm ); CHECK_MPI(result); - if (!not_done) - return MB_SUCCESS; - - // Get number of types each processor has that root does not - std::vector<int> counts(myPcomm->proc_config().proc_size()); - int two_count = 2*non_root_count; - result = MPI_Gather( &two_count, 1, MPI_INT, &counts[0], 1, MPI_INT, 0, comm ); - CHECK_MPI(result); + if (not_done) { + // Get number of types each processor has that root does not + std::vector<int> counts(myPcomm->proc_config().proc_size()); + int two_count = 2*non_root_count; + result = MPI_Gather( &two_count, 1, MPI_INT, &counts[0], 1, MPI_INT, 0, comm ); + CHECK_MPI(result); - // Get list of types from each processor - std::vector<int> displs(myPcomm->proc_config().proc_size() + 1); - VALGRIND_MAKE_VEC_UNDEFINED( displs ); - displs[0] = 0; - for (unsigned long i = 1; i <= myPcomm->proc_config().proc_size(); ++i) - displs[i] = displs[i-1] + counts[i-1]; - int total = displs[myPcomm->proc_config().proc_size()]; - typelist alltypes(total/2); - VALGRIND_MAKE_VEC_UNDEFINED( alltypes ); - VALGRIND_CHECK_MEM_IS_DEFINED( &non_root_types[0], non_root_types.size()*sizeof(int) ); - result = MPI_Gatherv( &non_root_types[0], 2*non_root_count, MPI_INT, - &alltypes[0], &counts[0], &displs[0], MPI_INT, 0, comm ); - CHECK_MPI(result); - - // Merge type lists. - // Prefer O(n) insertions with O(ln n) search time because - // we expect data from a potentially large number of processes, - // but with a small total number of element types. - if (0 == myPcomm->proc_config().proc_rank()) {

1 0

r5144 - MOAB/trunk/src/parallel
by kraftche＠cae.wisc.edu 31 Aug '11

31 Aug '11

Author: kraftche Date: 2011-08-31 15:58:56 -0500 (Wed, 31 Aug 2011) New Revision: 5144 Modified: MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp MOAB/trunk/src/parallel/WriteHDF5Parallel.hpp Log: add more debug output to paralell hdf5 writer Modified: MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp =================================================================== --- MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp 2011-08-30 23:07:30 UTC (rev 5143) +++ MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp 2011-08-31 20:58:56 UTC (rev 5144) @@ -1362,6 +1362,66 @@ return MB_SUCCESS; } +const unsigned SSVB = 3; + +void WriteHDF5Parallel::print_set_sharing_data( const Range& range, const char* label, Tag idt ) +{ + dbgOut.printf(SSVB,"set\tid\towner\t%-*s\tfid\tshared\n",(int)(sizeof(EntityHandle)*2),"handle"); + for (Range::iterator it = range.begin(); it != range.end(); ++it) { + int id; + iFace->tag_get_data( idt, &*it, 1, &id ); + EntityHandle handle = 0; + unsigned owner = 0; + id_t file_id = 0; + myPcomm->get_entityset_owner( *it, owner, &handle ); + if (!idMap.find( *it, file_id )) + file_id = 0; + dbgOut.printf(SSVB,"%s\t%d\t%u\t%lx\t%lu\t", label, id, owner, (unsigned long)handle, (unsigned long)file_id); + std::vector<unsigned> procs; + myPcomm->get_entityset_procs( *it, procs ); + if (procs.empty()) + dbgOut.print(SSVB,"<none>\n"); + else { + for (unsigned i = 0; i < procs.size()-1; ++i) + dbgOut.printf(SSVB,"%u,", procs[i]); + dbgOut.printf(SSVB,"%u\n",procs.back()); + } + } +} + + +void WriteHDF5Parallel::print_shared_sets() +{ + const char* tag_names[][2] = { { MATERIAL_SET_TAG_NAME, "block" }, + { DIRICHLET_SET_TAG_NAME, "nodeset" }, + { NEUMANN_SET_TAG_NAME, "sideset" }, + { 0, 0 } }; + + for (int i = 0; tag_names[i][0]; ++i) { + Tag tag; + if (MB_SUCCESS != iFace->tag_get_handle( tag_names[i][0], 1, MB_TYPE_INTEGER, tag )) + continue; + + Range tagged; + iFace->get_entities_by_type_and_tag( 0, MBENTITYSET, &tag, 0, 1, tagged ); + print_set_sharing_data( tagged, tag_names[i][1], tag );

1 0

r5143 - MOAB/trunk/doc
by kraftche＠cae.wisc.edu 31 Aug '11

31 Aug '11

Author: kraftche Date: 2011-08-30 18:07:30 -0500 (Tue, 30 Aug 2011) New Revision: 5143 Added: MOAB/trunk/doc/MeshSet.dia Modified: MOAB/trunk/doc/Makefile.am MOAB/trunk/doc/seq.pdf MOAB/trunk/doc/seq.tex Log: fix out of date documentation on MeshSetSequence and document MeshSet class Modified: MOAB/trunk/doc/Makefile.am =================================================================== --- MOAB/trunk/doc/Makefile.am 2011-08-30 21:44:50 UTC (rev 5142) +++ MOAB/trunk/doc/Makefile.am 2011-08-30 23:07:30 UTC (rev 5143) @@ -4,7 +4,8 @@ seq.pdf seq_dia = seq-uml-class.dia \ - seq-data.dia + seq-data.dia \ + MeshSet.dia EXTRA_DIST = $(doc_DATA) \ seq.tex $(seq_dia) Added: MOAB/trunk/doc/MeshSet.dia =================================================================== (Binary files differ) Property changes on: MOAB/trunk/doc/MeshSet.dia ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Modified: MOAB/trunk/doc/seq.pdf =================================================================== (Binary files differ) Modified: MOAB/trunk/doc/seq.tex =================================================================== --- MOAB/trunk/doc/seq.tex 2011-08-30 21:44:50 UTC (rev 5142) +++ MOAB/trunk/doc/seq.tex 2011-08-30 23:07:30 UTC (rev 5143) @@ -5,7 +5,7 @@ \title{MOAB Entity Storage} \author{Jason Kraftcheck} -\date{November 12, 2007} +\date{August, 2011} \begin{document} \section{\texttt{EntitySequence} \& \texttt{SequenceData}} @@ -46,7 +46,7 @@ \end{center} \end{figure*} -The \texttt{TypeSequenceManager} class maintains an organized set of \texttt{EntitySequence} instances and corresponding \texttt{SequenceData} instances. It is used to manage all such instances for entities of a single \texttt{MBEntityType}. \texttt{TypeSequenceManager} enforces the following four rules on its contained data: +The \texttt{TypeSequenceManager} class maintains an organized set of \texttt{EntitySequence} instances and corresponding \texttt{SequenceData} instances. It is used to manage all such instances for entities of a single \texttt{EntityType}. \texttt{TypeSequenceManager} enforces the following four rules on its contained data: \begin{enumerate} \item No two \texttt{SequenceData} instances may overlap. \item No two \texttt{EntitySequence} instances may overlap.

3 2

r5142 - MOAB/trunk/test/h5file
by tautges＠mcs.anl.gov 30 Aug '11

30 Aug '11

Author: tautges Date: 2011-08-30 16:44:50 -0500 (Tue, 30 Aug 2011) New Revision: 5142 Modified: MOAB/trunk/test/h5file/h5portable.cpp Log: Fixing another test. Modified: MOAB/trunk/test/h5file/h5portable.cpp =================================================================== --- MOAB/trunk/test/h5file/h5portable.cpp 2011-08-30 21:30:00 UTC (rev 5141) +++ MOAB/trunk/test/h5file/h5portable.cpp 2011-08-30 21:44:50 UTC (rev 5142) @@ -630,9 +630,18 @@ int main( int argc, char* argv[] ) { +#ifdef USE_MPI + int fail = MPI_Init(&argc, &argv); + if (fail) return fail; +#endif REGISTER_TEST( test_native_read ); REGISTER_TEST_SET( x86_64 ); REGISTER_TEST_SET( x86_32 ); REGISTER_TEST_SET( power_32 ); - return RUN_TESTS( argc, argv ); + int result = RUN_TESTS( argc, argv ); +#ifdef USE_MPI + fail = MPI_Finalize(); + if (fail) return fail; +#endif + return result; }

1 0

r5141 - MOAB/trunk/test/obb
by kraftche＠cae.wisc.edu 30 Aug '11

30 Aug '11

Author: kraftche Date: 2011-08-30 16:30:00 -0500 (Tue, 30 Aug 2011) New Revision: 5141 Modified: MOAB/trunk/test/obb/Makefile.am MOAB/trunk/test/obb/obb_test.cpp Log: yet another test that needs to call MPI_Init and MPI_Finalize even though it doesn't do anything parallel Modified: MOAB/trunk/test/obb/Makefile.am =================================================================== --- MOAB/trunk/test/obb/Makefile.am 2011-08-30 18:14:08 UTC (rev 5140) +++ MOAB/trunk/test/obb/Makefile.am 2011-08-30 21:30:00 UTC (rev 5141) @@ -5,7 +5,8 @@ AM_CPPFLAGS += -DSRCDIR=$(srcdir) \ -DMESHDIR=$(MESHDIR) \ - -I$(top_srcdir)/src -I$(top_builddir)/src -I.. + -I$(top_srcdir)/src -I$(top_builddir)/src -I.. \ + -I$(top_srcdir)/src/parallel -I$(top_builddir)/src/parallel LDADD = $(top_builddir)/src/libMOAB.la Modified: MOAB/trunk/test/obb/obb_test.cpp =================================================================== --- MOAB/trunk/test/obb/obb_test.cpp 2011-08-30 18:14:08 UTC (rev 5140) +++ MOAB/trunk/test/obb/obb_test.cpp 2011-08-30 21:30:00 UTC (rev 5141) @@ -6,6 +6,10 @@ #include "moab/GeomUtil.hpp" #include "moab/CN.hpp" +#ifdef USE_MPI +#include "moab_mpi.h" +#endif + #include <iostream> #include <sstream> #include <stdlib.h> @@ -119,6 +123,11 @@ int main( int argc, char* argv[] ) { +#ifdef USE_MPI + int fail = MPI_Init(&argc, &argv); + if (fail) return fail; +#endif + std::vector<const char*> file_names; bool flags = true; for (int i = 1; i < argc; ++i) { @@ -204,6 +213,11 @@ for (unsigned j = 0; j < file_names.size(); ++j) if (!do_file( file_names[j] )) ++exit_val; + +#ifdef USE_MPI + fail = MPI_Finalize(); + if (fail) return fail; +#endif

3 2

Make Check Failure
by Xiabing Xu 30 Aug '11

30 Aug '11

I was compiling trunk (5140) with --enable-debug option. Error messages: Making check in obb make[2]: Entering directory `/fusion/gpfs/home/xbxu/parvis/moab-trunk-build-check/test/obb' make obb_test obb_time obb_tree_tool make[3]: Entering directory `/fusion/gpfs/home/xbxu/parvis/moab-trunk-build-check/test/obb' CXX obb_test.o CXXLD obb_test CXX obb_time.o CXXLD obb_time CXX obb_tree_tool.o CXXLD obb_tree_tool make[3]: Leaving directory `/fusion/gpfs/home/xbxu/parvis/moab-trunk-build-check/test/obb' make check-TESTS make[3]: Entering directory `/fusion/gpfs/home/xbxu/parvis/moab-trunk-build-check/test/obb' make[4]: Entering directory `/fusion/gpfs/home/xbxu/parvis/moab-trunk-build-check/test/obb' FAIL: obb_test =========================== 1 of 1 test failed See test/obb/test-suite.log =========================== make[4]: *** [test-suite.log] Error 1 make[4]: Leaving directory `/fusion/gpfs/home/xbxu/parvis/moab-trunk-build-check/test/obb' make[3]: *** [check-TESTS] Error 2 make[3]: Leaving directory `/fusion/gpfs/home/xbxu/parvis/moab-trunk-build-check/test/obb' make[2]: *** [check-am] Error 2 make[2]: Leaving directory `/fusion/gpfs/home/xbxu/parvis/moab-trunk-build-check/test/obb' make[1]: *** [check-recursive] Error 1 make[1]: Leaving directory `/fusion/gpfs/home/xbxu/parvis/moab-trunk-build-check/test' make: *** [check-recursive] Error 1 Xiabing

4 3

r5140 - MOAB/trunk/test/parallel
by kraftche＠cae.wisc.edu 30 Aug '11

30 Aug '11

Author: kraftche Date: 2011-08-30 13:14:08 -0500 (Tue, 30 Aug 2011) New Revision: 5140 Modified: MOAB/trunk/test/parallel/parallel_hdf5_test.cc Log: add test to verify that parallel HDF5 write works when some procs have no data Modified: MOAB/trunk/test/parallel/parallel_hdf5_test.cc =================================================================== --- MOAB/trunk/test/parallel/parallel_hdf5_test.cc 2011-08-30 18:13:47 UTC (rev 5139) +++ MOAB/trunk/test/parallel/parallel_hdf5_test.cc 2011-08-30 18:14:08 UTC (rev 5140) @@ -56,6 +56,7 @@ void test_write_different_element_types(); void test_write_different_tags(); void test_write_polygons(); +void test_write_unbalanced(); const char PARTITION_TAG[] = "PARTITION"; @@ -193,6 +194,8 @@ MPI_Barrier(MPI_COMM_WORLD); result += RUN_TEST( test_write_polygons ); MPI_Barrier(MPI_COMM_WORLD); + result += RUN_TEST( test_write_unbalanced ); + MPI_Barrier(MPI_COMM_WORLD); } MPI_Finalize(); @@ -1332,4 +1335,91 @@ } +// Some processes have no mesh to write +void test_write_unbalanced() +{ + const char file_name[] = "test_write_unbalanced.h5m"; + int numproc, rank; + MPI_Comm_size( MPI_COMM_WORLD, &numproc ); + MPI_Comm_rank( MPI_COMM_WORLD, &rank ); + Core moab; + Interface &mb = moab; + ErrorCode rval; + Tag idtag; + + rval = mb.tag_get_handle( GLOBAL_ID_TAG_NAME, 1, MB_TYPE_INTEGER, idtag, MB_TAG_CREAT ); + CHECK_ERR(rval); + + // create a shared set + const int two = 2; + Range entities, sets; + EntityHandle set; + rval = mb.create_meshset( MESHSET_SET, set ); + CHECK_ERR(rval); + rval = mb.tag_set_data( idtag, &set, 1, &two ); + CHECK_ERR(rval); + sets.insert( set ); +

1 0

r5139 - MOAB/trunk/src/parallel
by kraftche＠cae.wisc.edu 30 Aug '11

30 Aug '11

Author: kraftche Date: 2011-08-30 13:13:47 -0500 (Tue, 30 Aug 2011) New Revision: 5139 Modified: MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp Log: WriteHDF5Parallel: fix bug where no set data is written during parallel write and fix bug communicating shared set data Modified: MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp =================================================================== --- MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp 2011-08-30 18:12:45 UTC (rev 5138) +++ MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp 2011-08-30 18:13:47 UTC (rev 5139) @@ -1524,7 +1524,7 @@ buffer[0] = flags; buffer[1] = tmp.size(); - if (buffer_size <= tmp.size()) + if (tmp.size() <= buffer_size) std::copy( tmp.begin(), tmp.end(), buffer + 4 ); rval = writeUtil->get_entity_list_pointers( it, nd, &ptr, WriteUtilIface::CHILDREN, &len ); @@ -1533,7 +1533,7 @@ rval = vector_to_id_list( ptr, len, &tmp[0], newlen, true ); tmp.resize( newlen ); buffer[2] = tmp.size(); - if (buffer_size - buffer[1] <= tmp.size()) + if (tmp.size() <= buffer_size - buffer[1]) std::copy( tmp.begin(), tmp.end(), buffer + 4 + buffer[1] ); rval = writeUtil->get_entity_list_pointers( it, nd, &ptr, WriteUtilIface::PARENTS, &len ); @@ -1542,7 +1542,7 @@ rval = vector_to_id_list( ptr, len, &tmp[0], newlen, true ); tmp.resize( newlen ); buffer[3] = tmp.size(); - if (buffer_size - buffer[1] - buffer[2] <= tmp.size()) + if (tmp.size() <= buffer_size - buffer[1] - buffer[2]) std::copy( tmp.begin(), tmp.end(), buffer + 4 + buffer[1] + buffer[2]); return MB_SUCCESS; @@ -1926,6 +1926,8 @@ SetDescCreator(), NULL, &setSet.first_id ); CHECK_MB(rval); + writeSets = setSet.max_num_ents > 0; + rval = assign_ids( setSet.range, setSet.first_id + setSet.offset ); CHECK_MB(rval); if (times) times[SET_OFFSET_TIME] = timer.elapsed();

1 0

r5138 - MOAB/trunk/src/io
by kraftche＠cae.wisc.edu 30 Aug '11

30 Aug '11

Author: kraftche Date: 2011-08-30 13:12:45 -0500 (Tue, 30 Aug 2011) New Revision: 5138 Modified: MOAB/trunk/src/io/WriteHDF5.cpp Log: WriteHDF5: fix bugs writing parallel shared sets Modified: MOAB/trunk/src/io/WriteHDF5.cpp =================================================================== --- MOAB/trunk/src/io/WriteHDF5.cpp 2011-08-30 18:12:06 UTC (rev 5137) +++ MOAB/trunk/src/io/WriteHDF5.cpp 2011-08-30 18:12:45 UTC (rev 5138) @@ -1278,6 +1278,7 @@ } memcpy( buffer+count, &list[0], append*sizeof(id_t) ); ++i; + ++si; count += append; continue; } @@ -1483,6 +1484,10 @@ ++r; ++n; } + else if (s != null_stripped_sets.end() && *i == *s) { + ++s; + ++n; + } } else { assert(si == specialSets.end() || si->setHandle > *i);

1 0