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

r4115 - in MOAB/trunk/test: . io
by kraftche＠cae.wisc.edu 31 Aug '10

31 Aug '10

Author: kraftche Date: 2010-08-31 17:51:57 -0500 (Tue, 31 Aug 2010) New Revision: 4115 Modified: MOAB/trunk/test/MBTest.cpp MOAB/trunk/test/io/exodus_test.cc Log: Work towards removing dependency on NetCDF for MBTest: o Change test function signature to accept no arguments o Add new create_some_mesh() utility function o Change some tests that loaded mbtest1.g to use create_some_mesh instead o Move some tests that were highly dependent on exodus to exodus_test.cc (e.g. check that the 5th hex read from file has connectivity {1,3,4,...}) The following tests still need to be updated to work w/out reading an ExodusII file: - mb_adjacencies_test - mb_delete_mesh_test - mb_meshset_tracking_test - mb_tags_test - mb_entity_conversion_test - mb_merge_test - mb_stress_test Modified: MOAB/trunk/test/MBTest.cpp =================================================================== --- MOAB/trunk/test/MBTest.cpp 2010-08-31 16:26:54 UTC (rev 4114) +++ MOAB/trunk/test/MBTest.cpp 2010-08-31 22:51:57 UTC (rev 4115) @@ -79,6 +79,23 @@ std::cerr << "Test failed at " __FILE__ ":" << __LINE__ << std::endl; \ return MB_FAILURE; } } while(false) + +ErrorCode load_file_one( Interface* iface ) +{ + std::string file_name = TestDir + "/mbtest1.g"; + ErrorCode error = iface->load_mesh( file_name.c_str() ); + if (MB_SUCCESS != error) { + std::cout << "Failed to load input file: " << file_name << std::endl; + std::string error_reason; + iface->get_last_error(error_reason); + cout << error_reason << std::endl; + } + return error; +} + +/* Create a regular 2x2x2 hex mesh */ +ErrorCode create_some_mesh( Interface* iface ); + /*! @test Vertex Coordinates @@ -86,107 +103,55 @@ @li Get coordinates of vertex 8 correctly @li Get coordinates of vertex 6 correctly */ - -ErrorCode mb_vertex_coordinate_test(Interface *MB) +ErrorCode mb_vertex_coordinate_test() { - double coords[3]; - EntityHandle handle; - ErrorCode error; - int err; + Core moab; + Interface* MB = &moab; + ErrorCode error = create_some_mesh( MB ); + CHKERR(error); - // coordinate 2 should be {1.5, -1.5, 3.5} - - handle = CREATE_HANDLE(MBVERTEX, 2, err); - error = MB->get_coords(&handle, 1, coords ); - if (error != MB_SUCCESS) - return error;

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r4114 - MOAB/trunk/itaps/imesh
by kraftche＠cae.wisc.edu 31 Aug '10

31 Aug '10

Author: kraftche Date: 2010-08-31 11:26:54 -0500 (Tue, 31 Aug 2010) New Revision: 4114 Modified: MOAB/trunk/itaps/imesh/iMesh.h Log: merge changes from ITAPS repo: documentation changes and some version macros Modified: MOAB/trunk/itaps/imesh/iMesh.h =================================================================== --- MOAB/trunk/itaps/imesh/iMesh.h 2010-08-31 16:14:06 UTC (rev 4113) +++ MOAB/trunk/itaps/imesh/iMesh.h 2010-08-31 16:26:54 UTC (rev 4114) @@ -1,9 +1,26 @@ #ifndef _ITAPS_iMesh #define _ITAPS_iMesh -#define IMESH_MAJOR_VERSION 0 -#define IMESH_MINOR_VERSION 8 + /**\brief iMesh Interface Specification Major Release Number + */ +#define IMESH_MAJOR_VERSION 1 + /**\brief iMesh Interface Specification Minor Release Number + */ +#define IMESH_MINOR_VERSION 0 + + /**\brief iMesh Interface Specification Patch Release Number + * + * Technically speaking, there is not much practical value in + * a 'patch' digit for an interface specification. A 'patch' + * release is typically only used for bug fix releases. That + * is unlikely to apply to an interface specification such as + * iMesh. Nonetheless, there is non-technical value in having + * a bit finer grained control over version numbers that a patch + * digit affords. So, we define one for iMesh. + */ +#define IMESH_PATCH_VERSION 0 + /** \mainpage The ITAPS Mesh Interface iMesh * * The ITAPS Mesh Interface iMesh provides a common interface for @@ -13,7 +30,7 @@ * to this interface, for example mesh smoothing, adaptive mesh refinement, * and parallel mesh support. * - * \section DataModel Data Model + * \section ITAPS Data Model * * The ITAPS interfaces use a data model composed of four basic data types: \n * \em Entity: basic topological entities in a mesh, e.g. vertices, @@ -28,7 +45,7 @@ * \em Tag: application data associated with objects of any of the other * data types. Each tag has a designated name, size, and data type. * - * \section JTAPS Entity Type, Topology + * \section ITAPS Entity Type, Topology * Each entity has a specific Entity Type and Entity Topology. The Entity * Type is one of VERTEX, EDGE, FACE, and REGION, and is synonymous with * the topological dimension of the entity. The Entity Topology denotes

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r4113 - MOAB/trunk/src/io
by kraftche＠cae.wisc.edu 31 Aug '10

31 Aug '10

Author: kraftche Date: 2010-08-31 11:14:06 -0500 (Tue, 31 Aug 2010) New Revision: 4113 Modified: MOAB/trunk/src/io/ReadHDF5Dataset.cpp Log: fix resource leak in currently unused code path Modified: MOAB/trunk/src/io/ReadHDF5Dataset.cpp =================================================================== --- MOAB/trunk/src/io/ReadHDF5Dataset.cpp 2010-08-31 14:09:02 UTC (rev 4112) +++ MOAB/trunk/src/io/ReadHDF5Dataset.cpp 2010-08-31 16:14:06 UTC (rev 4113) @@ -473,6 +473,8 @@ err = H5Dread( dataSet, dataType, mem_id, dataSpace, ioProp, 0 ); if (err < 0) throw Exception(__LINE__); + + H5Sclose( mem_id ); } } // namespace moab

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r4109 - MOAB/trunk/itaps/imesh
by kraftche＠cae.wisc.edu 27 Aug '10

27 Aug '10

Author: kraftche Date: 2010-08-27 10:16:44 -0500 (Fri, 27 Aug 2010) New Revision: 4109 Modified: MOAB/trunk/itaps/imesh/partest.cpp Log: change partest to go through iMeshP rather than iMesh when loading a file Modified: MOAB/trunk/itaps/imesh/partest.cpp =================================================================== --- MOAB/trunk/itaps/imesh/partest.cpp 2010-08-25 19:11:34 UTC (rev 4108) +++ MOAB/trunk/itaps/imesh/partest.cpp 2010-08-27 15:16:44 UTC (rev 4109) @@ -2,7 +2,7 @@ #include <stdio.h> #include <string.h> #include "moab_mpi.h" -#include "iMesh.h" +#include "iMeshP.h" #define IMESH_ASSERT(ierr) if (ierr!=0) printf("imesh assert\n"); @@ -13,24 +13,28 @@ printf("Hello\n"); iMesh_Instance imesh; + iMeshP_PartitionHandle partn; int ierr, num_sets; - + iBase_EntitySetHandle root; imesh = IMESH_NULL; - iMesh_newMesh("PARALLEL", &imesh, &ierr, 8); + iMesh_newMesh(0, &imesh, &ierr, 0); IMESH_ASSERT(ierr); + iMesh_getRootSet( imesh, &root, &ierr ); + IMESH_ASSERT(ierr); - const char options[] = "PARALLEL=BCAST_DELETE;PARTITION=MATERIAL_SET;PARTITION_DISTRIBUTE;"; + const char options[] = ";PARTITION=MATERIAL_SET"; const char filename[] = "64bricks_1mhex.h5m"; - iMesh_load(imesh, - IMESH_NULL, - filename, - options, - &ierr, - strlen(filename), - strlen(options)); + iMeshP_loadAll(imesh, + partn, + root, + filename, + options, + &ierr, + strlen(filename), + strlen(options)); IMESH_ASSERT(ierr);

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r4108 - MOAB/trunk/tools/dagmc
by bmsmith6＠wisc.edu 25 Aug '10

25 Aug '10

Author: bmsmith Date: 2010-08-25 14:11:34 -0500 (Wed, 25 Aug 2010) New Revision: 4108 Modified: MOAB/trunk/tools/dagmc/cub2h5m.cc Log: -Add facet_tolerance to ACIS file import. Increasing the facet_tolerance beyond the default (0.001 cm) will result in more accurate mass conservation. -Replace geometric test used to determine sense of quad faces wrt hex elements. It should be a logical operation, as exists in MOAB's CN.hpp. Modified: MOAB/trunk/tools/dagmc/cub2h5m.cc =================================================================== --- MOAB/trunk/tools/dagmc/cub2h5m.cc 2010-08-20 22:54:53 UTC (rev 4107) +++ MOAB/trunk/tools/dagmc/cub2h5m.cc 2010-08-25 19:11:34 UTC (rev 4108) @@ -1,6 +1,7 @@ #include "GeometryQueryTool.hpp" #include "InitCGMA.hpp" #include "CGMApp.hpp" +#include "moab/CN.hpp" #include "moab/Core.hpp" #include "moab/CartVect.hpp" #include "cubfile.h" @@ -332,51 +333,30 @@ if(MB_SUCCESS != result) return result; if(1 != adj_elem.size()) return MB_INVALID_SIZE; - // get center of element + // get connectivity for element and face const EntityHandle *elem_conn; - int n_nodes; - result = MBI->get_connectivity( adj_elem.front(), elem_conn, n_nodes ); + int elem_n_nodes; + result = MBI->get_connectivity( adj_elem.front(), elem_conn, elem_n_nodes ); if(MB_SUCCESS != result) return result; - CartVect elem_coords[n_nodes]; - result = MBI->get_coords( elem_conn, n_nodes, elem_coords[0].array() ); - if(MB_SUCCESS != result) return result; - CartVect elem_center(0.0); - for(int j=0; j<n_nodes; ++j) elem_center += elem_coords[j]; - elem_center /= n_nodes; - - // get the center of the face const EntityHandle *face_conn; - result = MBI->get_connectivity( *i, face_conn, n_nodes ); + int face_n_nodes; + result = MBI->get_connectivity( *i, face_conn, face_n_nodes ); if(MB_SUCCESS != result) return result; - CartVect face_coords[n_nodes]; - result = MBI->get_coords( face_conn, n_nodes, face_coords[0].array() ); - if(MB_SUCCESS != result) return result; - assert(4 == n_nodes); - CartVect face_center(0.0); - for(int j=0; j<n_nodes; ++j) face_center += face_coords[j]; - face_center /= n_nodes; - if(debug) std::cout << " center of mesh face exposed by dead element=" - << face_center << std::endl; - // get the normal of the face - CartVect face_normal, a, b; - a = face_coords[2] - face_coords[1]; - b = face_coords[0] - face_coords[1];

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r4107 - in MOAB/trunk: doc itaps/imesh src src/io src/moab
by tautges＠mcs.anl.gov 20 Aug '10

20 Aug '10

Author: tautges Date: 2010-08-20 17:54:53 -0500 (Fri, 20 Aug 2010) New Revision: 4107 Modified: MOAB/trunk/doc/metadata_info.doc MOAB/trunk/itaps/imesh/iMesh.h MOAB/trunk/src/Core.cpp MOAB/trunk/src/io/ReadNC.cpp MOAB/trunk/src/io/ReadNC.hpp MOAB/trunk/src/io/WriteCCMIO.cpp MOAB/trunk/src/moab/Interface.hpp Log: io/ReadNC.?pp: adding a bit more NC reader code io/WriteCCMIO.cpp: account for case where no material sets have been created doc/metadata_info.doc: small additions, for CCMIO file metadata and parallel status Core.cpp: changes to allow range-based deletion of entities, for efficiency Interface.hpp: adding \mainpage section to comments Passes make check in serial and parallel. Modified: MOAB/trunk/doc/metadata_info.doc =================================================================== (Binary files differ) Modified: MOAB/trunk/itaps/imesh/iMesh.h =================================================================== --- MOAB/trunk/itaps/imesh/iMesh.h 2010-08-18 21:07:01 UTC (rev 4106) +++ MOAB/trunk/itaps/imesh/iMesh.h 2010-08-20 22:54:53 UTC (rev 4107) @@ -13,7 +13,7 @@ * to this interface, for example mesh smoothing, adaptive mesh refinement, * and parallel mesh support. * - * \section ITAPS Data Model + * \section DataModel Data Model * * The ITAPS interfaces use a data model composed of four basic data types: \n * \em Entity: basic topological entities in a mesh, e.g. vertices, @@ -37,14 +37,14 @@ * types, Entity Type in the iBase_EntityType enumeration, and * Entity Topology in the iMesh_EntityTopology enumeration. * - * \section KTAPS Entity-, Array-, and Iterator-Based Access + * \section Access Entity-, Array-, and Iterator-Based Access * * The iMesh interface provides functions for accessing entities * individually, as arrays of entities, or using iterators. These access * methods have different memory versus execution time tradeoffs, * depending on the implementation. * - * \section LTAPS Lists Passed Through Interface + * \section Lists Lists Passed Through Interface * * Many of the functions in iMesh have arguments corresponding to lists of * objects. In-type arguments for lists consist of a pointer to an array and Modified: MOAB/trunk/src/Core.cpp =================================================================== --- MOAB/trunk/src/Core.cpp 2010-08-18 21:07:01 UTC (rev 4106) +++ MOAB/trunk/src/Core.cpp 2010-08-20 22:54:53 UTC (rev 4107) @@ -2183,6 +2183,7 @@ ErrorCode Core::delete_entities(const Range &range) { ErrorCode result = MB_SUCCESS, temp_result; + Range failed_ents; for (Range::const_reverse_iterator rit = range.rbegin(); rit != range.rend(); rit++) { @@ -2190,6 +2191,7 @@ temp_result = aEntityFactory->notify_delete_entity(*rit); if (MB_SUCCESS != temp_result) { result = temp_result;

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question on ddd
by iulian＠mcs.anl.gov 20 Aug '10

20 Aug '10

Hello, If you are on Ubuntu 10.04, and if you use ddd, you may have encountered this bug, for which the mouse is trapped, and x server is locked (when you use a right click in the data window) I do not understand what is the solution, (patch?). I know Rajeev experienced this problem back in May. https://bugs.launchpad.net/ubuntu/+source/ddd/+bug/574157 http://bugs.freedesktop.org/show_bug.cgi?id=25400 Do you have any solution? Thanks, Iulian

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cgm2moab as a script
by Steve Jackson 19 Aug '10

19 Aug '10

If MOAB is built with dagmc enabled and CGM support, one of the programs installed in bin/ is cgm2moab, a tool for converting CAD files to MOAB meshes. Over time, almost all the the functionality of this program has migrated into MOAB's native CGM reader, so it's now possible to do essentially everything that cgm2moab does using an appropriate call to mbconvert. (Not a terse or convenient call, though, because cgm2moab specifies a lot of lengthy arguments to ReadCGM.) This has led the dagmc users to consider changing cgm2moab into a wrapper script that calls mbconvert, instead of a C++ program. I'm wondering what our primary maintainers think about this idea. Can Tim and/or Jason comment on the following possibilities? * Convert cgm2moab to a python script. (Readability win, requires python, and possibly requires autoconf things to portably detect python.) * Convert cgm2moab to a plain bash script. (Messier code, but probably more portable.) * No thanks, leave it as C++. Thanks. ~S

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r4092 - MOAB/trunk/test/parallel
by kraftche＠cae.wisc.edu 16 Aug '10

16 Aug '10

Author: kraftche Date: 2010-08-16 16:25:25 -0500 (Mon, 16 Aug 2010) New Revision: 4092 Modified: MOAB/trunk/test/parallel/partcheck.cpp Log: print error message if no input file specified Modified: MOAB/trunk/test/parallel/partcheck.cpp =================================================================== --- MOAB/trunk/test/parallel/partcheck.cpp 2010-08-16 17:08:34 UTC (rev 4091) +++ MOAB/trunk/test/parallel/partcheck.cpp 2010-08-16 21:25:25 UTC (rev 4092) @@ -109,6 +109,12 @@ } } + if (!input_file) { + std::cerr << argv[0] << ": no input file specified" << std::endl; + usage(argv[0]); + } + + // build options string std::ostringstream opts;

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r4091 - MOAB/trunk/test/parallel
by kraftche＠cae.wisc.edu 16 Aug '10

16 Aug '10

Author: kraftche Date: 2010-08-16 12:08:34 -0500 (Mon, 16 Aug 2010) New Revision: 4091 Added: MOAB/trunk/test/parallel/partcheck.cpp Modified: MOAB/trunk/test/parallel/Makefile.am Log: add simple test to load file in parallel, print read time, and call some functions to check consistancy of partitioned data Modified: MOAB/trunk/test/parallel/Makefile.am =================================================================== --- MOAB/trunk/test/parallel/Makefile.am 2010-08-16 17:07:09 UTC (rev 4090) +++ MOAB/trunk/test/parallel/Makefile.am 2010-08-16 17:08:34 UTC (rev 4091) @@ -31,7 +31,7 @@ HDF5_TESTS = endif -check_PROGRAMS = $(TESTS) mbparallelcomm_test +check_PROGRAMS = $(TESTS) mbparallelcomm_test partcheck pcomm_unit_SOURCES = pcomm_unit.cpp parallel_hdf5_test_SOURCES = parallel_hdf5_test.cc @@ -42,6 +42,7 @@ pcomm_serial_SOURCES = pcomm_serial.cpp mbparallelcomm_test_SOURCES = mbparallelcomm_test.cpp scdtest_SOURCES = scdtest.cpp +partcheck_SOURCES = partcheck.cpp # Other files to clean up (e.g. output from tests) MOSTLYCLEANFILES = mhdf_ll.h5m Added: MOAB/trunk/test/parallel/partcheck.cpp =================================================================== --- MOAB/trunk/test/parallel/partcheck.cpp (rev 0) +++ MOAB/trunk/test/parallel/partcheck.cpp 2010-08-16 17:08:34 UTC (rev 4091) @@ -0,0 +1,236 @@ +#include "moab/Core.hpp" +#include "moab/Range.hpp" +#include "moab/ParallelComm.hpp" +#include "moab/Skinner.hpp" +#include "moab/CN.hpp" + +#include <iostream> +#include <sstream> +#include <limits> +#include <string> +#include <time.h> + +#include "moab_mpi.h" + +const char PARTTAG[] = "PARALLEL_PARTITION"; +const char READ_DEL_OPT[] = "READ_DELETE"; +const char BCAST_DEL_OPT[] = "BCAST_DELETE"; +const char READ_PART_OPT[] = "READ_PART"; +const char* const DEFAULT_MODE = READ_PART_OPT; + +const char USAGE[] = " [-v <n>] [-R] [-p <parttag>[=val]] [-D|-B|-P] <input_file>"; + +static void usage( const char* argv0 ) { + std::cerr << "Usage: " << argv0 << USAGE << std::endl

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