December 2010 - moab-dev - mailman3.cels.anl.gov

r4412 - MOAB/trunk
by kraftche＠cae.wisc.edu 22 Dec '10

22 Dec '10

Author: kraftche Date: 2010-12-22 17:06:49 -0600 (Wed, 22 Dec 2010) New Revision: 4412 Modified: MOAB/trunk/configure.ac Log: Clean up VTK configuration: o Remove duplicate VTK detection logic (qvdual & vtkMOABReader) o Make --enable-vtkMOABReader imply --with-vtk o Make --enable-qvdual imply --with-vtk o Make --with-vtk imply --enable-vtkMOABReader o Do not check for VTK unless --with-vtk is specified (or implied) o Check for VTK headers in additional default directories o Fail early if --with-vtk is specified (or implied) and not found o Remove bogus warnings about build failing if VTK is not found when neither vtkMOABReader nor qvdual is going to be built Modified: MOAB/trunk/configure.ac =================================================================== --- MOAB/trunk/configure.ac 2010-12-22 21:52:09 UTC (rev 4411) +++ MOAB/trunk/configure.ac 2010-12-22 23:06:49 UTC (rev 4412) @@ -505,6 +505,26 @@ esac] ) + +################################################################################ +# Optional Libraries +################################################################################ + +AC_ARG_WITH([vtk], + [AC_HELP_STRING([--with-vtk@<:@=DIR@:>@], [Enable VTK support, and specify VTK location])], + [WITH_VTK=$withval + DISTCHECK_CONFIGURE_FLAGS="$DISTCHECK_CONFIGURE_FLAGS --with-vtk=\"${withval}\"" + ],[WITH_VTK=]) + +VTKMOAB_DEFAULT=no +if test "x$WITH_VTK" != "xno" -a "x$WITH_VTK" != "x"; then + VTKMOAB_DEFAULT=yes +fi + +echo "WITH_VTK=$WITH_VTK" +echo "VTKMOAB_DEFAULT=$VTKMOAB_DEFAULT" + + ############################################################################### # Optional Tools ############################################################################### @@ -539,7 +559,7 @@ MB_OPTIONAL_TOOL([mbconvert], [yes]) MB_OPTIONAL_TOOL([hexmodops], [yes]) MB_OPTIONAL_TOOL([qvdual], [no] ) -MB_OPTIONAL_TOOL([vtkMOABReader],[no] ) +MB_OPTIONAL_TOOL([vtkMOABReader],[${VTKMOAB_DEFAULT}] ) MB_OPTIONAL_TOOL([mbsize], [yes]) MB_OPTIONAL_TOOL([mbskin], [yes]) MB_OPTIONAL_TOOL([mbtagprop], [yes]) @@ -560,7 +580,26 @@ fi fi +if test "xyes" = "x$ENABLE_vtkMOABReader"; then + if test "xno" == "x$WITH_VTK"; then + AC_MSG_ERROR([vtkMOABReader requires VTK]) + elif test "x" == "x$WITH_VTK"; then + WITH_VTK=yes + fi +fi

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getEverything?
by Rajeev Jain 22 Dec '10

22 Dec '10

Very often we repeat the "get" functions for various types of operations, do you think it would be useful to have a function 'getEverything' in MOAB/iMesh (iMesh_getEverything) ? Basically, getting *only* the building blocks of the mesh model: Input: root_set Output: 1. Nodes (Node number and co-ordinates) 2. Elements (Element number and connectivity) --- would need rules for connectivity definition. 3. Sets (Set number, tag, tag value and contents associated with this set) There is a function iMesh_getStructure - defined in MeshKit: http://trac.mcs.anl.gov/projects/fathom/browser/MeshKit/trunk/algs/CopyUtil… This gets "the entities and unique adjacent vertices of a set", should this be changed to get the complete building block/structure of the mesh file. Rajeev

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r4411 - MOAB/trunk/src
by kraftche＠cae.wisc.edu 22 Dec '10

22 Dec '10

Author: kraftche Date: 2010-12-22 15:52:09 -0600 (Wed, 22 Dec 2010) New Revision: 4411 Modified: MOAB/trunk/src/DenseTag.cpp MOAB/trunk/src/VarLenDenseTag.cpp Log: fix build error when configured with 32-bit handles on 64-bit platform Modified: MOAB/trunk/src/DenseTag.cpp =================================================================== --- MOAB/trunk/src/DenseTag.cpp 2010-12-22 21:39:56 UTC (rev 4410) +++ MOAB/trunk/src/DenseTag.cpp 2010-12-22 21:52:09 UTC (rev 4411) @@ -361,7 +361,7 @@ if (MB_SUCCESS != rval) return rval; - const EntityHandle end = std::min(p->second + 1, start + avail ); + const EntityHandle end = std::min<EntityHandle>(p->second + 1, start + avail ); while (start != end) { memcpy( array, *pointers, get_size() ); ++start; Modified: MOAB/trunk/src/VarLenDenseTag.cpp =================================================================== --- MOAB/trunk/src/VarLenDenseTag.cpp 2010-12-22 21:39:56 UTC (rev 4410) +++ MOAB/trunk/src/VarLenDenseTag.cpp 2010-12-22 21:52:09 UTC (rev 4411) @@ -310,7 +310,7 @@ if (MB_SUCCESS != rval) return rval; - const EntityHandle end = std::min(p->second + 1, start + avail ); + const EntityHandle end = std::min<EntityHandle>(p->second + 1, start + avail ); while (start != end) { array->set( *pointers, *lengths ); ++start; @@ -402,7 +402,7 @@ if (MB_SUCCESS != rval) return rval; - const EntityHandle end = std::min(p->second + 1, start + avail ); + const EntityHandle end = std::min<EntityHandle>(p->second + 1, start + avail ); if (array) { while (start != end) { array->clear();

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r4410 - in MOAB/trunk/src/parallel: . moab
by kraftche＠cae.wisc.edu 22 Dec '10

22 Dec '10

Author: kraftche Date: 2010-12-22 15:39:56 -0600 (Wed, 22 Dec 2010) New Revision: 4410 Modified: MOAB/trunk/src/parallel/ParallelComm.cpp MOAB/trunk/src/parallel/moab/ParallelComm.hpp Log: update ParallelComm for recent tag reorganizaiton: fixes parallel build issues Modified: MOAB/trunk/src/parallel/ParallelComm.cpp =================================================================== --- MOAB/trunk/src/parallel/ParallelComm.cpp 2010-12-22 21:39:31 UTC (rev 4409) +++ MOAB/trunk/src/parallel/ParallelComm.cpp 2010-12-22 21:39:56 UTC (rev 4410) @@ -4,7 +4,6 @@ #include "moab/ReadUtilIface.hpp" #include "SequenceManager.hpp" #include "EntitySequence.hpp" -#include "TagServer.hpp" #include "MBTagConventions.hpp" #include "moab/Skinner.hpp" #include "MBParallelConventions.h" @@ -14,6 +13,7 @@ #include "moab/CN.hpp" #include "moab/RangeMap.hpp" #include "moab/MeshTopoUtil.hpp" +#include "TagInfo.hpp" #include <iostream> #include <sstream> @@ -351,7 +351,6 @@ void ParallelComm::initialize() { - tagServer = dynamic_cast<Core*>(mbImpl)->tag_server(); sequenceManager = dynamic_cast<Core*>(mbImpl)->sequence_manager(); // initialize MPI, if necessary @@ -2684,30 +2683,29 @@ std::vector<int> var_len_sizes; std::vector<const void*> var_len_values; - const TagInfo *tinfo = tagServer->get_tag_info(tag); // default value count += sizeof(int); - if (NULL != tinfo->default_value()) - count += tinfo->default_value_size(); + if (NULL != tag->get_default_value()) + count += tag->get_default_value_size(); // size, type, data type count += 3*sizeof(int); // name count += sizeof(int); - count += tinfo->get_name().size(); + count += tag->get_name().size(); // range of tag count += sizeof(int) + tagged_entities.size() * sizeof(EntityHandle);

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r4409 - MOAB/trunk/src/parallel
by kraftche＠cae.wisc.edu 22 Dec '10

22 Dec '10

Author: kraftche Date: 2010-12-22 15:39:31 -0600 (Wed, 22 Dec 2010) New Revision: 4409 Modified: MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp Log: Comment out call to get_sharedset_tags in WriteHDF5Parallel This function is broken in that it causes all parallel HDF5 writes to fail given the limitations of the current implementation. It did not cause any failures prior to my recent reorganization of the tag code because, due to a bug, it didn't do anything at all. Modified: MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp =================================================================== --- MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp 2010-12-22 21:37:11 UTC (rev 4408) +++ MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp 2010-12-22 21:39:31 UTC (rev 4409) @@ -362,10 +362,10 @@ if (MB_SUCCESS != rval) return error(rval); /**************** get tag names for sets likely to be shared ***********/ - debug_barrier(); - dbgOut.tprint(1,"Getting shared entity sets\n"); - rval = get_sharedset_tags(); - if (MB_SUCCESS != rval) return error(rval); + //debug_barrier(); + //dbgOut.tprint(1,"Getting shared entity sets\n"); + //rval = get_sharedset_tags(); + //if (MB_SUCCESS != rval) return error(rval); /**************** Create actual file and write meta info ***************/

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r4408 - MOAB/trunk/src
by kraftche＠cae.wisc.edu 22 Dec '10

22 Dec '10

Author: kraftche Date: 2010-12-22 15:37:11 -0600 (Wed, 22 Dec 2010) New Revision: 4408 Modified: MOAB/trunk/src/Core.cpp Log: return MB_ALREADY_ALLOCATED from new tag_get_handle if default values don't match Modified: MOAB/trunk/src/Core.cpp =================================================================== --- MOAB/trunk/src/Core.cpp 2010-12-22 18:56:14 UTC (rev 4407) +++ MOAB/trunk/src/Core.cpp 2010-12-22 21:37:11 UTC (rev 4408) @@ -1986,6 +1986,12 @@ // check sizes if (!(flags & TAG_VARLEN) && tag_handle->get_size() != size) return MB_INVALID_SIZE; + + // If user passed a default value, check that it matches. + // If user did not pass a default value, assume they're OK + // with the existing one. + if (default_value && !tag_handle->equals_default_value(default_value,size)) + return MB_ALREADY_ALLOCATED; return MB_SUCCESS; }

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r4407 - MOAB/trunk/src/parallel
by kraftche＠cae.wisc.edu 22 Dec '10

22 Dec '10

Author: kraftche Date: 2010-12-22 12:56:14 -0600 (Wed, 22 Dec 2010) New Revision: 4407 Modified: MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp Log: fix typo in previous checkin of WriteHDF5Parallel.cpp Modified: MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp =================================================================== --- MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp 2010-12-22 18:51:57 UTC (rev 4406) +++ MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp 2010-12-22 18:56:14 UTC (rev 4407) @@ -1196,7 +1196,7 @@ all[j*numtypes+i] = prev; prev += tmp; } - all[myPcomm->proc_config().proc_size()+numtypes+i] = prev; + all[myPcomm->proc_config().proc_size()*numtypes+i] = prev; } // For each element type for which there is no adjacency data,

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r4406 - MOAB/trunk/src/parallel
by kraftche＠cae.wisc.edu 22 Dec '10

22 Dec '10

Author: kraftche Date: 2010-12-22 12:51:57 -0600 (Wed, 22 Dec 2010) New Revision: 4406 Modified: MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp Log: fix use of uninitialized value (step off end of array) in parallel HDF5 writer Modified: MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp =================================================================== --- MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp 2010-12-22 18:09:59 UTC (rev 4405) +++ MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp 2010-12-22 18:51:57 UTC (rev 4406) @@ -1070,7 +1070,7 @@ for (int i = 0; i < numtypes; i++) { long prev = 0; - for (unsigned int j = 0; j <= myPcomm->proc_config().proc_size(); j++) + for (unsigned int j = 0; j < myPcomm->proc_config().proc_size(); j++) { long tmp = counts[j*numtypes + i]; if (tmp > my_counts[i]) // put max count in my_counts @@ -1078,6 +1078,7 @@ counts[j*numtypes+i] = prev; prev += tmp; } + counts[myPcomm->proc_config().proc_size()*numtypes + i] = prev; } } @@ -1187,7 +1188,7 @@ for (i = 0; i < numtypes; i++) { long prev = 0; - for (j = 0; j <= myPcomm->proc_config().proc_size(); j++) + for (j = 0; j < myPcomm->proc_config().proc_size(); j++) { long tmp = all[j*numtypes + i]; if (tmp > local[i]) @@ -1195,6 +1196,7 @@ all[j*numtypes+i] = prev; prev += tmp; } + all[myPcomm->proc_config().proc_size()+numtypes+i] = prev; } // For each element type for which there is no adjacency data,

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r4405 - MOAB/trunk/test/parallel
by kraftche＠cae.wisc.edu 22 Dec '10

22 Dec '10

Author: kraftche Date: 2010-12-22 12:09:59 -0600 (Wed, 22 Dec 2010) New Revision: 4405 Modified: MOAB/trunk/test/parallel/mhdf_parallel.c Log: fix non-standard C code in mhdf_parallel.c test Modified: MOAB/trunk/test/parallel/mhdf_parallel.c =================================================================== --- MOAB/trunk/test/parallel/mhdf_parallel.c 2010-12-22 18:09:40 UTC (rev 4404) +++ MOAB/trunk/test/parallel/mhdf_parallel.c 2010-12-22 18:09:59 UTC (rev 4405) @@ -57,13 +57,13 @@ hid_t data, tagdata[2]; long junk; + mhdf_Status status; + mhdf_FileHandle file; + time_t t; t = time(NULL); history[1] = ctime(&t); - mhdf_Status status; - mhdf_FileHandle file; - file = mhdf_createFile( filename, 1, elem_types, num_elem_types, &status ); CHECK(status); @@ -117,6 +117,7 @@ hid_t handle, handles[2]; mhdf_Status status; mhdf_FileHandle file; + int num_node, offset, dim; double coords[3*8] = { 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 1.0, @@ -127,7 +128,6 @@ 0.0, 0.0, 1.0 }; int i, list[10], tagdata[10]; for (i = 0; i < 10; i++) tagdata[i] = RANK; - int num_node, offset, dim; /* open file */

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r4404 - MOAB/trunk/test/parallel
by kraftche＠cae.wisc.edu 22 Dec '10

22 Dec '10

Author: kraftche Date: 2010-12-22 12:09:40 -0600 (Wed, 22 Dec 2010) New Revision: 4404 Modified: MOAB/trunk/test/parallel/parallel_unit_tests.cpp Log: fix bugs in parallel_unit_tests.cpp (incorrect size, incorrect assumption that global ids are zero-based, etc.) Modified: MOAB/trunk/test/parallel/parallel_unit_tests.cpp =================================================================== --- MOAB/trunk/test/parallel/parallel_unit_tests.cpp 2010-12-21 22:40:24 UTC (rev 4403) +++ MOAB/trunk/test/parallel/parallel_unit_tests.cpp 2010-12-22 18:09:40 UTC (rev 4404) @@ -7,6 +7,7 @@ #include "moab_mpi.h" #include <iostream> #include <algorithm> +#include <map> #include <sstream> #include <assert.h> #if !defined(_MSC_VER) && !defined(__MINGW32__) @@ -1125,12 +1126,12 @@ return MB_SUCCESS; } -bool check_consistent_ids( Interface& mb, - const EntityHandle* entities, - const int* orig_ids, - int num_ents, - const char* singular_name, - const char* plural_name ) +ErrorCode check_consistent_ids( Interface& mb, + const EntityHandle* entities, + const int* orig_ids, + int num_ents, + const char* singular_name, + const char* plural_name ) { ErrorCode rval; int rank, size, ierr; @@ -1141,16 +1142,20 @@ rval = mb.tag_get_handle( GLOBAL_ID_TAG_NAME, id_tag ); CHKERR(rval); std::vector<int> new_ids(num_ents); rval = mb.tag_get_data( id_tag, entities, num_ents, &new_ids[0] ); CHKERR(rval); - bool valid = true; - for (int i = 0; i < num_ents; ++i) - if (new_ids[i] < 0 || new_ids[i] >= num_ents*size) { - std::cerr << "ID out of bounds on proc " << rank - << " : " << new_ids[i] << " not in [0," << num_ents*size-1 - << "]" << std::endl; - valid = false; - } - if (!valid) - return false; + // This test is wrong. a) The caller can select a start ID so there's + // no guarantee that the IDs will be in any specific range and b) There + // is no reason to expect the global number of entities to be num_ents*size + // if there are any shared entities. J.Kraftcheck 2010-12-22 + //rval = MB_SUCCESS; + //for (int i = 0; i < num_ents; ++i)

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