November 2013 - moab-dev - mailman3.cels.anl.gov

buildbot failure in moab-cub-ser-trunk: failed shell test install
by moab-dev＠mcs.anl.gov 06 Nov '13

06 Nov '13

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buildbot failure in moab-occ-sertru: failed shell test install
by moab-dev＠mcs.anl.gov 06 Nov '13

06 Nov '13

1 0

buildbot failure in moab-cub-serstatrunk: failed shell test install
by moab-dev＠mcs.anl.gov 06 Nov '13

06 Nov '13

1 0

buildbot failure in moab-cub-par-tru-dbg: failed shell test install
by moab-dev＠mcs.anl.gov 06 Nov '13

06 Nov '13

1 0

buildbot failure in moab-cub-par-tru: failed shell test install
by moab-dev＠mcs.anl.gov 06 Nov '13

06 Nov '13

1 0

buildbot failure in moab-occ-sersta-trunk: failed shell test install
by moab-dev＠mcs.anl.gov 06 Nov '13

06 Nov '13

1 0

buildbot failure in moab-cub-par-nopnet: failed shell test install
by moab-dev＠mcs.anl.gov 06 Nov '13

06 Nov '13

1 0

memory leak
by Lukasz Kaczmarczyk 05 Nov '13

05 Nov '13

Hello All, I add entity (meshset) to another meshset. This generate memory leak according to valgrind. Pleas see attached log. Should I manage meshsets using childs and parents, or adding meshset to another meshest using add_entities is accepted by moab. Kind regards, Lukasz ==35039== 8 bytes in 1 blocks are indirectly lost in loss record 796 of 2,690 ==35039== at 0x4C2B1C7: operator new(unsigned long) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so) ==35039== by 0xAB14A1: __gnu_cxx::new_allocator<unsigned long>::allocate(unsigned long, void const*) (new_allocator.h:92) ==35039== by 0xCA82A8: std::_Vector_base<unsigned long, std::allocator<unsigned long> >::_M_allocate(unsigned long) (in /home/lukasz/tmp/mofem/build/atom_tests/arc_length_nonlinear_elasticity_atom) ==35039== by 0xD7080C: std::vector<unsigned long, std::allocator<unsigned long> >::_M_insert_aux(__gnu_cxx::__normal_iterator<unsigned long*, std::vector<unsigned long, std::allocator<unsigned long> > >, unsigned long const&) (vector.tcc:327) ==35039== by 0xD6ED55: std::vector<unsigned long, std::allocator<unsigned long> >::push_back(unsigned long const&) (stl_vector.h:834) ==35039== by 0xF6D458: moab::AEntityFactory::add_adjacency(unsigned long, unsigned long, bool) (AEntityFactory.cpp:395) ==35039== by 0xD8B69F: moab::range_tool<std::pair<unsigned long, unsigned long> const*>::ranged_insert_entities(moab::MeshSet::Count&, moab::MeshSet::CompactList&, std::pair<unsigned long, unsigned long> const*, std::pair<unsigned long, unsigned long> const*, unsigned long, moab::AEntityFactory*) (MeshSet.cpp:610) ==35039== by 0xD8A6A3: moab::MeshSet::insert_entity_vector(unsigned long const*, unsigned long, unsigned long, moab::AEntityFactory*) (MeshSet.cpp:1111) ==35039== by 0xD6D215: moab::MeshSet::add_entities(unsigned long const*, int, unsigned long, moab::AEntityFactory*) (MeshSet.hpp:762) ==35039== by 0xD66249: moab::Core::add_entities(unsigned long, unsigned long const*, int) (Core.cpp:3224) ==35039== by 0xC0A148: MoFEM::FieldCore::add_ents_to_finite_element_by_MESHSET(unsigned long, std::string const&) (FieldCore.cpp:1404) ==35039== by 0xA75B7F: main (arc_length_nonlinear_elasticity_atom.cpp:177) ==35039== ==35039== 32 (24 direct, 8 indirect) bytes in 1 blocks are definitely lost in loss record 1,518 of 2,690 ==35039== at 0x4C2B1C7: operator new(unsigned long) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so) ==35039== by 0xF6DCCE: moab::AEntityFactory::get_adjacencies(unsigned long, std::vector<unsigned long, std::allocator<unsigned long> >*&, bool) (AEntityFactory.cpp:567) ==35039== by 0xF6D37B: moab::AEntityFactory::add_adjacency(unsigned long, unsigned long, bool) (AEntityFactory.cpp:378) ==35039== by 0xD8B69F: moab::range_tool<std::pair<unsigned long, unsigned long> const*>::ranged_insert_entities(moab::MeshSet::Count&, moab::MeshSet::CompactList&, std::pair<unsigned long, unsigned long> const*, std::pair<unsigned long, unsigned long> const*, unsigned long, moab::AEntityFactory*) (MeshSet.cpp:610) ==35039== by 0xD8A6A3: moab::MeshSet::insert_entity_vector(unsigned long const*, unsigned long, unsigned long, moab::AEntityFactory*) (MeshSet.cpp:1111) ==35039== by 0xD6D215: moab::MeshSet::add_entities(unsigned long const*, int, unsigned long, moab::AEntityFactory*) (MeshSet.hpp:762) ==35039== by 0xD66249: moab::Core::add_entities(unsigned long, unsigned long const*, int) (Core.cpp:3224) ==35039== by 0xC0A148: MoFEM::FieldCore::add_ents_to_finite_element_by_MESHSET(unsigned long, std::string const&) (FieldCore.cpp:1404) ==35039== by 0xA75B7F: main (arc_length_nonlinear_elasticity_atom.cpp:177) Full listing is here, http://cdash.eng.gla.ac.uk/cdash/viewDynamicAnalysisFile.php?id=181

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commit/MOAB: danwu: In unit test read_mpas_nc, added test_read_no_edges() and test_gather_onevar(). Also removed gather set testing code from test_read_onevar().
by commits-noreply＠bitbucket.org 05 Nov '13

05 Nov '13

1 new commit in MOAB: https://bitbucket.org/fathomteam/moab/commits/9ad0c3d6dde9/ Changeset: 9ad0c3d6dde9 Branch: master User: danwu Date: 2013-11-05 18:45:25 Summary: In unit test read_mpas_nc, added test_read_no_edges() and test_gather_onevar(). Also removed gather set testing code from test_read_onevar(). Affected #: 1 file diff --git a/test/io/read_mpas_nc.cpp b/test/io/read_mpas_nc.cpp index 5ceb994..d6e886f 100644 --- a/test/io/read_mpas_nc.cpp +++ b/test/io/read_mpas_nc.cpp @@ -1,6 +1,7 @@ #include "TestUtil.hpp" #include "moab/Core.hpp" #include "moab/ReadUtilIface.hpp" +#include "MBTagConventions.hpp" using namespace moab; @@ -20,7 +21,9 @@ void test_read_onevar(); void test_read_onetimestep(); void test_read_nomesh(); void test_read_novars(); -void test_read_no_mixed_elements(); +void test_read_no_mixed_elements(); // Test read option NO_MIXED_ELEMENTS +void test_read_no_edges(); // Test read option NO_EDGES +void test_gather_onevar(); // Test gather set with one variable ErrorCode get_options(std::string& opts); @@ -41,8 +44,9 @@ int main(int argc, char* argv[]) result += RUN_TEST(test_read_onetimestep); result += RUN_TEST(test_read_nomesh); result += RUN_TEST(test_read_novars); - // Test read option NO_MIXED_ELEMENTS result += RUN_TEST(test_read_no_mixed_elements); + result += RUN_TEST(test_read_no_edges); + result += RUN_TEST(test_gather_onevar); #ifdef USE_MPI fail = MPI_Finalize(); @@ -163,8 +167,6 @@ void test_read_onevar() CHECK_ERR(rval); opts += std::string(";VARIABLE=ke"); - // Create gather set - opts += std::string(";GATHER_SET="); rval = mb.load_file(example, NULL, opts.c_str()); CHECK_ERR(rval); @@ -187,38 +189,15 @@ void test_read_onevar() Range cells; rval = mb.get_entities_by_type(0, MBPOLYGON, cells); assert(rval == MB_SUCCESS); - CHECK_EQUAL((size_t)1284, cells.size()); // Gather set cells included -#ifdef USE_MPI - // If MOAB is compiled parallel, sequence size requested are increased - // by a factor of 1.5, to allow for ghosts. This will introduce a gap - // between the two face sequences. - CHECK_EQUAL((size_t)4, cells.psize()); // Gather set cells included -#else - CHECK_EQUAL((size_t)1, cells.psize()); // Gather set cells included -#endif - - // Get gather set - EntityHandle gather_set; - ReadUtilIface* readUtilIface; - mb.query_interface(readUtilIface); - rval = readUtilIface->get_gather_set(gather_set); - CHECK_ERR(rval); - - // Get gather set entities - Range gather_ents; - rval = mb.get_entities_by_handle(gather_set, gather_ents); - CHECK_ERR(rval); + CHECK_EQUAL((size_t)642, cells.size()); - // Remove gather set cells - cells = subtract(cells, gather_ents); - CHECK_EQUAL((size_t)642, cells.size()); // Gather set cells excluded #ifdef USE_MPI // If MOAB is compiled parallel, sequence size requested are increased // by a factor of 1.5, to allow for ghosts. This will introduce a gap // between the two face sequences. - CHECK_EQUAL((size_t)2, cells.psize()); // Gather set cells excluded + CHECK_EQUAL((size_t)2, cells.psize()); #else - CHECK_EQUAL((size_t)1, cells.psize()); // Gather set cells excluded + CHECK_EQUAL((size_t)1, cells.psize()); #endif // Check ke tag values on first pentagon and first hexagon @@ -368,7 +347,8 @@ void test_read_no_mixed_elements() rval = mb.get_entities_by_type(0, MBPOLYGON, cells); assert(rval == MB_SUCCESS); CHECK_EQUAL((size_t)642, cells.size()); - // Only one group of cells (each cell is actually represented by a 10-vertex polygon) + // Only one group of cells (pentagons are padded to hexagons, + // e.g. connectivity [1 2 3 4 5] => [1 2 3 4 5 5]) CHECK_EQUAL((size_t)1, cells.psize()); const double eps = 1e-20; @@ -385,7 +365,104 @@ void test_read_no_mixed_elements() } } -ErrorCode get_options(std::string &opts) +void test_read_no_edges() +{ + Core moab; + Interface& mb = moab; + std::string opts; + ErrorCode rval = get_options(opts); + CHECK_ERR(rval); + + opts += std::string(";NO_EDGES;VARIABLE="); + rval = mb.load_file(example, NULL, opts.c_str()); + CHECK_ERR(rval); + + int procs = 1; +#ifdef USE_MPI + ParallelComm* pcomm = ParallelComm::get_pcomm(&mb, 0); + procs = pcomm->proc_config().proc_size(); +#endif + + // Make check runs this test in one processor + if (1 == procs) { + // Get edges + Range edges; + rval = mb.get_entities_by_type(0, MBEDGE, edges); + assert(rval == MB_SUCCESS); + CHECK_EQUAL((size_t)0, edges.size()); + } +} + +void test_gather_onevar() +{ + Core moab; + Interface& mb = moab; + std::string opts; + ErrorCode rval = get_options(opts); + CHECK_ERR(rval); + + EntityHandle file_set; + rval = mb.create_meshset(MESHSET_SET, file_set); + CHECK_ERR(rval); + + // Get cell variable ke + opts += std::string(";VARIABLE=ke;"); + // Create gather set + opts += std::string(";GATHER_SET=0;"); + rval = mb.load_file(example, &file_set, opts.c_str()); + CHECK_ERR(rval); + +#ifdef USE_MPI + ParallelComm* pcomm = ParallelComm::get_pcomm(&mb, 0); + int procs = pcomm->proc_config().proc_size(); + + // Make check runs this test in one processor + if (1 == procs) { + Range cells, cells_owned; + rval = mb.get_entities_by_type(file_set, MBPOLYGON, cells); + CHECK_ERR(rval); + + // Get locally owned cells + rval = pcomm->filter_pstatus(cells, PSTATUS_NOT_OWNED, PSTATUS_NOT, -1, &cells_owned); + CHECK_ERR(rval); + CHECK_EQUAL((size_t)642, cells_owned.size()); + CHECK_EQUAL((size_t)2, cells_owned.psize()); + + // Get gather set + EntityHandle gather_set; + ReadUtilIface* readUtilIface; + mb.query_interface(readUtilIface); + rval = readUtilIface->get_gather_set(gather_set); + CHECK_ERR(rval); + + Tag ke_tag0, gid_tag; + rval = mb.tag_get_handle("ke0", 1, MB_TYPE_DOUBLE, ke_tag0, MB_TAG_DENSE); + CHECK_ERR(rval); + + rval = mb.tag_get_handle(GLOBAL_ID_TAG_NAME, 1, MB_TYPE_INTEGER, gid_tag, MB_TAG_DENSE); + CHECK_ERR(rval); + + pcomm->gather_data(cells_owned, ke_tag0, gid_tag, gather_set); + + // Get gather set cells + Range gather_set_cells; + rval = mb.get_entities_by_type(gather_set, MBPOLYGON, gather_set_cells); + CHECK_EQUAL((size_t)642, gather_set_cells.size()); + CHECK_EQUAL((size_t)2, gather_set_cells.psize()); + + const double eps = 1e-20; + double val[2]; + + // Check ke0 tag values on first pentagon and first hexagon of the gather set cells + EntityHandle cell_ents[] = {gather_set_cells[0], gather_set_cells[12]}; + rval = mb.tag_get_data(ke_tag0, &cell_ents[0], 2, val); + CHECK_REAL_EQUAL(15.001, val[0], eps); + CHECK_REAL_EQUAL(16.013, val[1], eps); + } +#endif +} + +ErrorCode get_options(std::string& opts) { #ifdef USE_MPI // Use parallel options Repository URL: https://bitbucket.org/fathomteam/moab/ -- This is a commit notification from bitbucket.org. 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commit/MOAB: danwu: In ParallelComm::gather_data(), current code that copies tag data to each sequence of gents is incorrect (bytes per tag should be taken into account).
by commits-noreply＠bitbucket.org 05 Nov '13

05 Nov '13

1 new commit in MOAB: https://bitbucket.org/fathomteam/moab/commits/b02855ba7891/ Changeset: b02855ba7891 Branch: master User: danwu Date: 2013-11-05 18:14:39 Summary: In ParallelComm::gather_data(), current code that copies tag data to each sequence of gents is incorrect (bytes per tag should be taken into account). Affected #: 1 file diff --git a/src/parallel/ParallelComm.cpp b/src/parallel/ParallelComm.cpp index ab29867..7c3f5c7 100644 --- a/src/parallel/ParallelComm.cpp +++ b/src/parallel/ParallelComm.cpp @@ -8738,7 +8738,7 @@ ErrorCode ParallelComm::post_irecv(std::vector<unsigned int>& shared_procs, int sz_buffer = sizeof(int) + gather_ents.size()*(sizeof(int) + bytes_per_tag); void* senddata = malloc(sz_buffer); ((int*)senddata)[0] = (int) gather_ents.size(); - int * ptr_int = (int*)senddata + 1; + int* ptr_int = (int*)senddata + 1; rval = mbImpl->tag_get_data(id_tag, gather_ents, (void*)ptr_int); ptr_int = (int*)(senddata) + 1 + gather_ents.size(); rval = mbImpl->tag_get_data(tag_handle, gather_ents, (void*)ptr_int); @@ -8792,7 +8792,7 @@ ErrorCode ParallelComm::post_irecv(std::vector<unsigned int>& shared_procs, } } - // If gents has multiple sequences, set tag data (stored in the temp buffer) on each sequence separately + // If gents has multiple sequences, copy tag data (stored in the temp buffer) to each sequence separately if (multiple_sequences) { Range::iterator iter = gents.begin(); size_t start_idx = 0; @@ -8800,8 +8800,9 @@ ErrorCode ParallelComm::post_irecv(std::vector<unsigned int>& shared_procs, int count; void* ptr; rval = mbImpl->tag_iterate(tag_handle, iter, gents.end(), count, ptr); - for (int i = 0; i < count; i++) - ((char*)ptr)[i] = ((char*)gvals)[start_idx + i]; + assert(NULL != ptr); + assert(count > 0); + memcpy((char*)ptr, (char*)gvals + start_idx * bytes_per_tag, bytes_per_tag * count); iter += count; start_idx += count; 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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