June 2012 - moab-dev - mailman3.cels.anl.gov

buildbot failure in moab-32bit-handles: failed compile
by moab-dev＠mcs.anl.gov 30 Jun '12

30 Jun '12

1 0

r5621 - in MOAB/trunk: . itaps/imesh src src/io src/moab test test/parallel
by tautges＠mcs.anl.gov 29 Jun '12

29 Jun '12

Author: tautges Date: 2012-06-29 19:54:55 -0500 (Fri, 29 Jun 2012) New Revision: 5621 Modified: MOAB/trunk/ MOAB/trunk/itaps/imesh/iMesh_MOAB.cpp MOAB/trunk/src/ScdElementData.cpp MOAB/trunk/src/ScdElementData.hpp MOAB/trunk/src/ScdInterface.cpp MOAB/trunk/src/SequenceManager.cpp MOAB/trunk/src/SequenceManager.hpp MOAB/trunk/src/StructuredElementSeq.cpp MOAB/trunk/src/StructuredElementSeq.hpp MOAB/trunk/src/io/ReadNC.cpp MOAB/trunk/src/io/ReadNC.hpp MOAB/trunk/src/moab/ScdInterface.hpp MOAB/trunk/test/parallel/Makefile.am MOAB/trunk/test/scdseq_test.cpp Log: Fixed the scdpart test and representation of structured meshes, in parallel, with periodic boundaries. Tests run in serial and parallel. Property changes on: MOAB/trunk ___________________________________________________________________ Modified: svn:mergeinfo - /MOAB/branches/Version4.0:4323-4497 /MOAB/branches/jk-direct-tag:4069-4327 + /MOAB/branches/NCparperiodic:5611-5620 /MOAB/branches/Version4.0:4323-4497 /MOAB/branches/jk-direct-tag:4069-4327 Modified: MOAB/trunk/itaps/imesh/iMesh_MOAB.cpp =================================================================== --- MOAB/trunk/itaps/imesh/iMesh_MOAB.cpp 2012-06-30 00:34:27 UTC (rev 5620) +++ MOAB/trunk/itaps/imesh/iMesh_MOAB.cpp 2012-06-30 00:54:55 UTC (rev 5621) @@ -3307,7 +3307,9 @@ CHKERR(rval, "Trouble creating scd vertex sequence."); // set the global box parameters - if (global_dims) scd_box->set_global_box_dims(global_dims); + if (global_dims) { + for (int i = 0; i < 6; i++) scd_box->par_data().gDims[i] = global_dims[i]; + } tmp_range.insert(scd_box->start_vertex(), scd_box->start_vertex()+scd_box->num_vertices()-1); tmp_range.insert(scd_box->start_element(), scd_box->start_element()+scd_box->num_elements()-1); Modified: MOAB/trunk/src/ScdElementData.cpp =================================================================== --- MOAB/trunk/src/ScdElementData.cpp 2012-06-30 00:34:27 UTC (rev 5620) +++ MOAB/trunk/src/ScdElementData.cpp 2012-06-30 00:54:55 UTC (rev 5621) @@ -25,14 +25,14 @@ EntityID ScdElementData::calc_num_entities(EntityHandle start_handle, int irange, int jrange, int krange, - bool is_periodic_i, bool is_periodic_j) + int *is_periodic) { size_t result = 1; switch (CN::Dimension(TYPE_FROM_HANDLE(start_handle))) { default: result = 0; assert( false ); case 3: result *= krange; - case 2: result *= (is_periodic_j ? (jrange+1) : jrange); - case 1: result *= (is_periodic_i ? (irange+1) : irange); + case 2: result *= (is_periodic && is_periodic[1] ? (jrange+1) : jrange); + case 1: result *= (is_periodic && is_periodic[0] ? (irange+1) : irange); } return result; } @@ -41,17 +41,17 @@ EntityHandle start_handle, const int imin, const int jmin, const int kmin,

1 0

r5620 - in MOAB/branches/NCparperiodic: src src/io src/moab test/parallel
by tautges＠mcs.anl.gov 29 Jun '12

29 Jun '12

Author: tautges Date: 2012-06-29 19:34:27 -0500 (Fri, 29 Jun 2012) New Revision: 5620 Modified: MOAB/branches/NCparperiodic/src/ScdInterface.cpp MOAB/branches/NCparperiodic/src/io/ReadNC.cpp MOAB/branches/NCparperiodic/src/moab/ScdInterface.hpp MOAB/branches/NCparperiodic/test/parallel/Makefile.am Log: Lots of bug fixes, scdpart now works (on 2 procs at least). Modified: MOAB/branches/NCparperiodic/src/ScdInterface.cpp =================================================================== --- MOAB/branches/NCparperiodic/src/ScdInterface.cpp 2012-06-29 21:39:36 UTC (rev 5619) +++ MOAB/branches/NCparperiodic/src/ScdInterface.cpp 2012-06-30 00:34:27 UTC (rev 5620) @@ -676,12 +676,14 @@ pto = -1; across_bdy[0] = across_bdy[1] = 0; - int ldims[6], pijk[3], lperiodic[3]; + int ldims[6], pijk[3], lperiodic[2]; ErrorCode rval = compute_partition_alljkbal(np, pfrom, gdims, gperiodic, ldims, lperiodic, pijk); if (MB_SUCCESS != rval) return rval; assert(pijk[1] * pijk[2] == np); pto = -1; + bool bot_j = pfrom < pijk[2], + top_j = pfrom > np - pijk[2]; if ((1 == pijk[2] && dijk[2]) || // 1d in j means no neighbors with dk != 0 (!(pfrom%pijk[2]) && -1 == dijk[2]) || // at -k bdy (pfrom%pijk[2] == pijk[2]-1 && 1 == dijk[2]) || // at +k bdy @@ -699,7 +701,7 @@ int dj = (gdims[4] - gdims[1]) / pijk[1], extra = (gdims[4] - gdims[1]) % pijk[1]; if (-1 == dijk[1]) { facedims[4] = facedims[1]; - if (pfrom < pijk[2]) { + if (bot_j) { // going across periodic lower bdy in j rdims[4] = gdims[4]; across_bdy[1] = -1; @@ -713,7 +715,7 @@ else { if (pfrom > np-pijk[2]) facedims[4] = gdims[1]; facedims[1] = facedims[4]; - if (pfrom > np - pijk[2]) { + if (top_j) { // going across periodic upper bdy in j rdims[1] = gdims[1]; across_bdy[1] = 1; @@ -742,22 +744,21 @@ } } - assert(-1 == pto || - (rdims[0] >= gdims[0] && rdims[3] <= gdims[3] && - rdims[1] >= gdims[1] && rdims[4] <= gdims[4] && - rdims[2] >= gdims[2] && rdims[5] <= gdims[5] && - (facedims[0] >= rdims[0] || (gperiodic[0] && rdims[3] == gdims[3] && facedims[0] == gdims[0])) && - facedims[3] <= rdims[3] && - (facedims[1] >= rdims[1] || (gperiodic[1] && rdims[4] == gdims[4] && facedims[1] == gdims[1])) && - facedims[4] <= rdims[4] && - facedims[2] >= rdims[2] &&

1 0

r5618 - MOAB/trunk/tools/dagmc
by sjackson＠mcs.anl.gov 29 Jun '12

29 Jun '12

Author: sjackson Date: 2012-06-29 15:04:24 -0500 (Fri, 29 Jun 2012) New Revision: 5618 Modified: MOAB/trunk/tools/dagmc/DagMC.cpp MOAB/trunk/tools/dagmc/DagMC.hpp Log: Add two more helper functions for DagMC properties Valid property values may be looked up by property name, and property-bearing entities can be looked up by property and, optionally, by property value. Modified: MOAB/trunk/tools/dagmc/DagMC.cpp =================================================================== --- MOAB/trunk/tools/dagmc/DagMC.cpp 2012-06-29 19:01:12 UTC (rev 5617) +++ MOAB/trunk/tools/dagmc/DagMC.cpp 2012-06-29 20:04:24 UTC (rev 5618) @@ -1859,6 +1859,70 @@ } + +ErrorCode DagMC::get_all_prop_values( const std::string& prop, std::vector<std::string>& return_list ) +{ + ErrorCode rval; + std::map<std::string, Tag>::iterator it = property_tagmap.find(prop); + if( it == property_tagmap.end() ){ + return MB_TAG_NOT_FOUND; + } + Tag proptag = (*it).second; + Range all_ents; + + rval = MBI->get_entities_by_type_and_tag( 0, MBENTITYSET, &proptag, NULL, 1, all_ents ); + if( MB_SUCCESS != rval ) return rval; + + std::set<std::string> unique_values; + for( Range::iterator i = all_ents.begin(); i!= all_ents.end(); ++i){ + std::vector<std::string> values; + rval = prop_values( *i, prop, values ); + if( MB_SUCCESS != rval ) return rval; + unique_values.insert( values.begin(), values.end() ); + } + + return_list.assign( unique_values.begin(), unique_values.end() ); + return MB_SUCCESS; +} + +ErrorCode DagMC::entities_by_property( const std::string& prop, std::vector<EntityHandle>& return_list, + int dimension, const std::string* value ) +{ + ErrorCode rval; + std::map<std::string, Tag>::iterator it = property_tagmap.find(prop); + if( it == property_tagmap.end() ){ + return MB_TAG_NOT_FOUND; + } + Tag proptag = (*it).second; + Range all_ents; + + // Note that we cannot specify values for proptag here-- the passed value, + // if it exists, may be only a subset of the packed string representation + // of this tag. + Tag tags[2] = {proptag, geomTag }; + void* vals[2] = {NULL, (dimension!=0) ? &dimension : NULL }; + rval = MBI->get_entities_by_type_and_tag( 0, MBENTITYSET, tags, vals, 2, all_ents );

1 0

r5617 - in MOAB/trunk/src: . io
by tautges＠mcs.anl.gov 29 Jun '12

29 Jun '12

Author: tautges Date: 2012-06-29 14:01:12 -0500 (Fri, 29 Jun 2012) New Revision: 5617 Added: MOAB/trunk/src/io/ReadTxt.cpp MOAB/trunk/src/io/ReadTxt.hpp Modified: MOAB/trunk/src/ReaderWriterSet.cpp MOAB/trunk/src/io/Makefile.am Log: Adding a skeleton txt reader for Farah. Modified: MOAB/trunk/src/ReaderWriterSet.cpp =================================================================== --- MOAB/trunk/src/ReaderWriterSet.cpp 2012-06-29 18:16:04 UTC (rev 5616) +++ MOAB/trunk/src/ReaderWriterSet.cpp 2012-06-29 19:01:12 UTC (rev 5617) @@ -41,6 +41,7 @@ #include "WriteSTL.hpp" #include "WriteGmsh.hpp" #include "WriteSmf.hpp" +#include "ReadTxt.hpp" #ifdef NETCDF_FILE # include "ReadNCDF.hpp" @@ -150,6 +151,9 @@ const char* tetgen_sufxs[] = { "node", "ele", "face", "edge", NULL }; register_factory( ReadTetGen::factory, 0, "TetGen output files", tetgen_sufxs, "TETGEN" ); + + const char* txt_sufxs[] = { "txt", NULL }; + register_factory( ReadTxt::factory, 0, "Txt input files", txt_sufxs, "TXT" ); } Modified: MOAB/trunk/src/io/Makefile.am =================================================================== --- MOAB/trunk/src/io/Makefile.am 2012-06-29 18:16:04 UTC (rev 5616) +++ MOAB/trunk/src/io/Makefile.am 2012-06-29 19:01:12 UTC (rev 5617) @@ -95,6 +95,8 @@ ReadSTL.hpp \ ReadTetGen.cpp \ ReadTetGen.hpp \ + ReadTxt.cpp \ + ReadTxt.hpp \ ReadVtk.cpp \ ReadVtk.hpp \ SMF_State.cpp \ Added: MOAB/trunk/src/io/ReadTxt.cpp =================================================================== --- MOAB/trunk/src/io/ReadTxt.cpp (rev 0) +++ MOAB/trunk/src/io/ReadTxt.cpp 2012-06-29 19:01:12 UTC (rev 5617) @@ -0,0 +1,78 @@ +/** + * MOAB, a Mesh-Oriented datABase, is a software component for creating, + * storing and accessing finite element mesh data. + * + * Copyright 2004 Sandia Corporation. Under the terms of Contract + * DE-AC04-94AL85000 with Sandia Coroporation, the U.S. Government + * retains certain rights in this software. + * + * This library is free software; you can redistribute it and/or

1 0

r5616 - MOAB/branches/NCparperiodic/src/io
by xbxu＠mcs.anl.gov 29 Jun '12

29 Jun '12

Author: xbxu Date: 2012-06-29 13:16:04 -0500 (Fri, 29 Jun 2012) New Revision: 5616 Modified: MOAB/branches/NCparperiodic/src/io/ReadNC.cpp Log: fix the read_nc test Modified: MOAB/branches/NCparperiodic/src/io/ReadNC.cpp =================================================================== --- MOAB/branches/NCparperiodic/src/io/ReadNC.cpp 2012-06-29 16:39:04 UTC (rev 5615) +++ MOAB/branches/NCparperiodic/src/io/ReadNC.cpp 2012-06-29 18:16:04 UTC (rev 5616) @@ -430,7 +430,11 @@ ERRORR(rval, "Couldn't get vertex coordinate arrays."); int i, j, k, il, jl, kl, itmp; - int dil = lDims[3] - lDims[0] + 1; + int dil; + if (!locallyPeriodic[0] && globallyPeriodic[0] && lDims[3] > gDims[3]) + dil = lDims[3] - lDims[0]; + else + dil = lDims[3] - lDims[0] + 1; int djl = lDims[4] - lDims[1] + 1; int di = gDims[3] - gDims[0] + 1; int dj = gDims[4] - gDims[1] + 1;

1 0

r5615 - MOAB/branches/NCparperiodic/src/io
by xbxu＠mcs.anl.gov 29 Jun '12

29 Jun '12

Author: xbxu Date: 2012-06-29 11:39:04 -0500 (Fri, 29 Jun 2012) New Revision: 5615 Modified: MOAB/branches/NCparperiodic/src/io/ReadNC.cpp Log: fix the local dimension for cell centers Modified: MOAB/branches/NCparperiodic/src/io/ReadNC.cpp =================================================================== --- MOAB/branches/NCparperiodic/src/io/ReadNC.cpp 2012-06-29 16:15:07 UTC (rev 5614) +++ MOAB/branches/NCparperiodic/src/io/ReadNC.cpp 2012-06-29 16:39:04 UTC (rev 5615) @@ -1794,11 +1794,19 @@ ilCVals.resize(lDims[3] - lDims[0] + 1); lCDims[3] = lDims[3]; } - else if (!locallyPeriodic[0] && globallyPeriodic[0] && lDims[3] > gDims[3]) { + else { + if (!locallyPeriodic[0] && globallyPeriodic[0] && lDims[3] > gDims[3]) { // globally periodic and I'm the last proc, get fewer vertex coords than vertices in i - ilVals.resize(lDims[3] - lDims[0]); - ilCVals.resize(lDims[3] - lDims[0]); - lCDims[3] = lDims[3]-1; + ilVals.resize(lDims[3] - lDims[0]); + ilCVals.resize(lDims[3] - lDims[0]); + lCDims[3] = lDims[3]-1; + } + else + { + ilVals.resize(lDims[3] - lDims[0] + 1); + ilCVals.resize(lDims[3] - lDims[0]); + lCDims[3] = lDims[3]-1; + } } lCDims[0] = lDims[0];

1 0

r5614 - MOAB/trunk/test/parallel
by iulian＠mcs.anl.gov 29 Jun '12

29 Jun '12

Author: iulian Date: 2012-06-29 11:15:07 -0500 (Fri, 29 Jun 2012) New Revision: 5614 Modified: MOAB/trunk/test/parallel/Makefile.am Log: recursive error Modified: MOAB/trunk/test/parallel/Makefile.am =================================================================== --- MOAB/trunk/test/parallel/Makefile.am 2012-06-29 16:10:58 UTC (rev 5613) +++ MOAB/trunk/test/parallel/Makefile.am 2012-06-29 16:15:07 UTC (rev 5614) @@ -14,7 +14,7 @@ # Run parallel tests in parallel if USE_MPIEXEC - OLD_ENVIRONMENT = ${TESTS_ENVIRONMENT} + OLD_ENVIRONMENT := ${TESTS_ENVIRONMENT} TESTS_ENVIRONMENT = ${MPIEXEC} ${MPIEXEC_NP} ${NP} ${OLD_ENVIRONMENT} endif

1 0

r5613 - MOAB/branches/NCparperiodic/test/parallel
by iulian＠mcs.anl.gov 29 Jun '12

29 Jun '12

Author: iulian Date: 2012-06-29 11:10:58 -0500 (Fri, 29 Jun 2012) New Revision: 5613 Modified: MOAB/branches/NCparperiodic/test/parallel/Makefile.am Log: revert a change from yesterday with respect to := assignments not portable I think it was committed on the trunk too, by Ryan It can't run tests without it Modified: MOAB/branches/NCparperiodic/test/parallel/Makefile.am =================================================================== --- MOAB/branches/NCparperiodic/test/parallel/Makefile.am 2012-06-29 15:57:34 UTC (rev 5612) +++ MOAB/branches/NCparperiodic/test/parallel/Makefile.am 2012-06-29 16:10:58 UTC (rev 5613) @@ -14,7 +14,7 @@ # Run parallel tests in parallel if USE_MPIEXEC - OLD_ENVIRONMENT = ${TESTS_ENVIRONMENT} + OLD_ENVIRONMENT := ${TESTS_ENVIRONMENT} TESTS_ENVIRONMENT = ${MPIEXEC} ${MPIEXEC_NP} ${NP} ${OLD_ENVIRONMENT} endif

1 0

r5612 - MOAB/branches/NCparperiodic/src/io
by xbxu＠mcs.anl.gov 29 Jun '12

29 Jun '12

Author: xbxu Date: 2012-06-29 10:57:34 -0500 (Fri, 29 Jun 2012) New Revision: 5612 Modified: MOAB/branches/NCparperiodic/src/io/ReadNC.cpp Log: set the local dimension for cell centers properly Modified: MOAB/branches/NCparperiodic/src/io/ReadNC.cpp =================================================================== --- MOAB/branches/NCparperiodic/src/io/ReadNC.cpp 2012-06-29 15:07:29 UTC (rev 5611) +++ MOAB/branches/NCparperiodic/src/io/ReadNC.cpp 2012-06-29 15:57:34 UTC (rev 5612) @@ -1792,14 +1792,19 @@ // if locally periodic, doesn't matter what global periodicity is, # vertex coords = # elem coords ilVals.resize(lDims[3] - lDims[0] + 1); ilCVals.resize(lDims[3] - lDims[0] + 1); + lCDims[3] = lDims[3]; } else if (!locallyPeriodic[0] && globallyPeriodic[0] && lDims[3] > gDims[3]) { // globally periodic and I'm the last proc, get fewer vertex coords than vertices in i ilVals.resize(lDims[3] - lDims[0]); ilCVals.resize(lDims[3] - lDims[0]); + lCDims[3] = lDims[3]-1; } - + lCDims[0] = lDims[0]; + lCDims[4] = lDims[4]-1; + lCDims[1] = lDims[1]; + if (-1 != lDims[1]) { jlVals.resize(lDims[4] - lDims[1] + 1); jlCVals.resize(lCDims[4] - lCDims[1] + 1);

1 0