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

r4478 - MOAB/trunk/itaps/igeom
by iulian＠mcs.anl.gov 31 Jan '11

31 Jan '11

Author: iulian Date: 2011-01-31 15:34:50 -0600 (Mon, 31 Jan 2011) New Revision: 4478 Modified: MOAB/trunk/itaps/igeom/iGeom.h MOAB/trunk/itaps/igeom/iGeom_MOAB.cpp MOAB/trunk/itaps/igeom/iGeom_MOAB.hpp Log: Change the iGeom.h file to be the one from CGM/itaps folder. One of the changes is that "iGeom_EntityIterator"s are replaced with iBase_EntityIterator's Some other changes in iGeom.h are not clear. Need to investigate more, to see why there are different iGeom.h files in our 2 different implementations of iGeom Modified: MOAB/trunk/itaps/igeom/iGeom.h =================================================================== --- MOAB/trunk/itaps/igeom/iGeom.h 2011-01-31 18:17:23 UTC (rev 4477) +++ MOAB/trunk/itaps/igeom/iGeom.h 2011-01-31 21:34:50 UTC (rev 4478) @@ -1,3283 +1,3789 @@ -#ifndef _ITAPS_iGeom -#define _ITAPS_iGeom - - /** \mainpage The ITAPS Geometry Interface iGeom - * - * The ITAPS Geometry Interface iGeom provides a common interface for - * accessing geometry and data associated with a mesh. Applications written - * to use this interface can use a variety of implementations, choosing - * the one that best meets its needs. They can also use tools written - * to this interface. - * - * \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 model, e.g. vertices, - * edges, faces, regions. \n - * \em Entity \em Set: arbitrary grouping of other entities and sets. - * Entity sets also support parent/child relations with other sets which - * are distinct from entities contained in those sets. Parent/child links - * can be used to embed graph relationships between sets, e.g. to - * represent topological relationships between the sets. \n - * \em Interface: the object with which model is associated and on which - * functions in iGeom are called. \n - * \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 - * Each entity has a specific Entity Type. The Entity - * Type is one of VERTEX, EDGE, FACE, and REGION, and is synonymous with - * the topological dimension of the entity. Entity Type is an enumerated - * type in the iBase_EntityType enumeration. - * - * \section KTAPS Entity-, Array-, and Iterator-Based Access - * - * The iGeom 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 - * - * Many of the functions in iGeom have arguments corresponding to lists of - * objects. In-type arguments for lists consist of a pointer to an array and - * a list size. Lists returned from functions are passed in three arguments, - * a pointer to the array representing the list, and pointers to the - * allocated and occupied lengths of the array. These three arguments are

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buildbot failure in Fathom on moab-par
by moab-dev＠mcs.anl.gov 31 Jan '11

31 Jan '11

The Fathomatic has detected a failed build of moab-par on Fathom. Full details are available at: http://gnep.mcs.anl.gov:8010/builders/moab-par/builds/408 Buildbot URL: http://gnep.mcs.anl.gov:8010/ Buildslave for this Build: gnep Build Reason: The Nightly scheduler named 'nightly' triggered this build Build Source Stamp: None Blamelist: BUILD FAILED: failed test LOG EXCERPT: test_read : success test_read : success PASS: uber_parallel_test PASS: scdtest Warning: acis file has sequence numbers! Warning: acis file has sequence numbers! Warning: acis file has sequence numbers! Warning: acis file has sequence numbers! PASS: pcomm_serial Running test_write_elements ... Running test_write_elements ... Warning: acis file has sequence numbers! Warning: acis file has sequence numbers! Warning: acis file has sequence numbers! Running test_write_shared_sets ... Running test_write_shared_sets ... Warning: acis file has sequence numbers! Warning: acis file has sequence numbers! Warning: acis file has sequence numbers! Running test_var_length_parallel ... Running test_var_length_parallel ... Running test_read_elements ... Running test_read_elements ... Running test_read_elements_by_rank ... Running test_read_elements_by_rank ... Running test_read_tags ... Running test_read_tags ... Running test_read_global_tags ... Running test_read_global_tags ... Running test_read_sets ... Running test_read_sets ... PASS: parallel_hdf5_test PASS: mhdf_parallel Using default interval count: 2 Using default interval count: 2 01: 0.02: Generating mesh 00: 0.01: Generating mesh 00: 0.13: Resolving shared entities 01: 0.14: Resolving shared entities 00: 0.45: Beginning parallel write 01: 0.46: Beginning parallel write Wrote 16 hexes in 0.09 seconds. 01: 0.55: Finalizing MPI 00: 0.54: Removing written file 00: 0.54: Finalizing MPI Wall time: generate: 0.122282, resovle shared: 0.32155, write_file: 0.106157 PASS: parallel_write_test =================== 1 of 8 tests failed =================== sincerely, -The Fathomatic

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r4475 - MOAB/trunk/src/moab
by tautges＠mcs.anl.gov 28 Jan '11

28 Jan '11

Author: tautges Date: 2011-01-28 17:20:54 -0600 (Fri, 28 Jan 2011) New Revision: 4475 Modified: MOAB/trunk/src/moab/ScdInterface.hpp Log: Redoing comments. Modified: MOAB/trunk/src/moab/ScdInterface.hpp =================================================================== --- MOAB/trunk/src/moab/ScdInterface.hpp 2011-01-28 20:42:48 UTC (rev 4474) +++ MOAB/trunk/src/moab/ScdInterface.hpp 2011-01-28 23:20:54 UTC (rev 4475) @@ -1,5 +1,25 @@ -/** \class ScdInterface - ** \brief An interface for structured mesh +/** \file ScdInterface.hpp + */ +#ifndef SCD_INTERFACE +#define SCD_INTERFACE + +#include <vector> + +#include "moab/Interface.hpp" +#include "moab/HomXform.hpp" + +namespace moab { + +class StructuredElementSeq; +class EntitySequence; +class ScdVertexData; +class EntitySequence; +class ScdBox; +class Core; + +/** \class ScdInterface ScdInterface.hpp "moab/ScdInterface.hpp" + * \brief A structured mesh interface for MOAB-based data + * * Structured mesh in MOAB is created and accessed through the ScdInterface and ScdBox classes. * * \section Construction Construction and Representation @@ -41,24 +61,8 @@ * \section Evaluation Evaluation * The ScdBox class provides functions for evaluating the mesh based on the ijk parameter space. * These functions are inlined where possible, for efficiency. - */ -#ifndef SCD_INTERFACE -#define SCD_INTERFACE +*/ -#include <vector> - -#include "moab/Interface.hpp" -#include "moab/HomXform.hpp" - -namespace moab { - -class StructuredElementSeq; -class EntitySequence; -class ScdVertexData;

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r4474 - in MOAB/trunk: src src/moab src/parallel src/parallel/moab test/parallel
by tautges＠mcs.anl.gov 28 Jan '11

28 Jan '11

Author: tautges Date: 2011-01-28 14:42:48 -0600 (Fri, 28 Jan 2011) New Revision: 4474 Added: MOAB/trunk/src/MergeMesh.cpp MOAB/trunk/src/moab/MergeMesh.hpp MOAB/trunk/src/parallel/ParallelMergeMesh.cpp MOAB/trunk/src/parallel/moab/ParallelMergeMesh.hpp MOAB/trunk/test/parallel/parmerge.cpp Modified: MOAB/trunk/src/Makefile.am MOAB/trunk/src/parallel/Makefile.am MOAB/trunk/src/parallel/moab/ParallelComm.hpp MOAB/trunk/test/parallel/Makefile.am Log: Initial commit of parallel mesh merging. Doesn't pass its test yet, but that test currently connected to make check so auto build/test should work. Modified: MOAB/trunk/src/Makefile.am =================================================================== --- MOAB/trunk/src/Makefile.am 2011-01-26 21:16:35 UTC (rev 4473) +++ MOAB/trunk/src/Makefile.am 2011-01-28 20:42:48 UTC (rev 4474) @@ -65,6 +65,7 @@ Matrix3.cpp \ Matrix3.hpp \ MBCNArrays.hpp \ + MergeMesh.cpp \ MeshSet.cpp \ MeshSet.hpp \ MeshSetSequence.cpp \ @@ -143,6 +144,7 @@ moab/Forward.hpp \ moab/GeomUtil.hpp \ moab/Interface.hpp \ + moab/MergeMesh.hpp \ moab/MeshTopoUtil.hpp \ moab/OrientedBoxTreeTool.hpp \ moab/Range.hpp \ Added: MOAB/trunk/src/MergeMesh.cpp =================================================================== --- MOAB/trunk/src/MergeMesh.cpp (rev 0) +++ MOAB/trunk/src/MergeMesh.cpp 2011-01-28 20:42:48 UTC (rev 4474) @@ -0,0 +1,206 @@ +#include "moab/MergeMesh.hpp" + +#include "moab/Skinner.hpp" +#include "moab/AdaptiveKDTree.hpp" +#include "moab/Range.hpp" +#include "moab/CartVect.hpp" + +#include <algorithm> +#include <string> +#include <vector> +#include <cassert> +#include <iostream> + +namespace moab { + +moab::ErrorCode MergeMesh::merge_entities(moab::EntityHandle *elems, + int elems_size, + const double merge_tol, + const int do_merge, + const int update_sets, + moab::Tag merge_tag) +{ + mergeTol = merge_tol; + mergeTolSq = merge_tol*merge_tol; +

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r4473 - MOAB/trunk/src
by kraftche＠cae.wisc.edu 26 Jan '11

26 Jan '11

Author: kraftche Date: 2011-01-26 15:16:35 -0600 (Wed, 26 Jan 2011) New Revision: 4473 Modified: MOAB/trunk/src/SequenceManager.cpp Log: increase default sequence sizes Modified: MOAB/trunk/src/SequenceManager.cpp =================================================================== --- MOAB/trunk/src/SequenceManager.cpp 2011-01-26 20:35:48 UTC (rev 4472) +++ MOAB/trunk/src/SequenceManager.cpp 2011-01-26 21:16:35 UTC (rev 4473) @@ -19,9 +19,9 @@ namespace moab { -const EntityID DEFAULT_VERTEX_SEQUENCE_SIZE = 4096; +const EntityID DEFAULT_VERTEX_SEQUENCE_SIZE = 1024*1024; const EntityID DEFAULT_ELEMENT_SEQUENCE_SIZE = DEFAULT_VERTEX_SEQUENCE_SIZE; -const EntityID DEFAULT_POLY_SEQUENCE_SIZE = 4 * DEFAULT_ELEMENT_SEQUENCE_SIZE; +const EntityID DEFAULT_POLY_SEQUENCE_SIZE = 16*1024; const EntityID DEFAULT_MESHSET_SEQUENCE_SIZE = DEFAULT_VERTEX_SEQUENCE_SIZE; const int UNUSED_SIZE = 0;

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r4472 - MOAB/trunk/src
by kraftche＠cae.wisc.edu 26 Jan '11

26 Jan '11

Author: kraftche Date: 2011-01-26 14:35:48 -0600 (Wed, 26 Jan 2011) New Revision: 4472 Modified: MOAB/trunk/src/AffineXform.cpp MOAB/trunk/src/AffineXform.hpp Log: fix bug in AffineXform && add regression test Modified: MOAB/trunk/src/AffineXform.cpp =================================================================== --- MOAB/trunk/src/AffineXform.cpp 2011-01-25 21:09:54 UTC (rev 4471) +++ MOAB/trunk/src/AffineXform.cpp 2011-01-26 20:35:48 UTC (rev 4472) @@ -358,8 +358,14 @@ { CartVect output; + AffineXform scale = AffineXform::scale( 1.0 ); + ASSERT(!scale.scale()); + scale = AffineXform::scale( -1.0 ); + ASSERT(!scale.scale()); + //scale in X only - AffineXform scale = AffineXform::scale( CartVect(2,1,1).array() ); + scale = AffineXform::scale( CartVect(2,1,1).array() ); + ASSERT(scale.scale()); scale.xform_point( point1.array(), output.array() ); ASSERT_VECTORS_EQUAL( output, CartVect(2*point1[0],point1[1],point1[2]) ); scale.xform_point( point2.array(), output.array() ); @@ -371,6 +377,7 @@ // scale in all scale = AffineXform::scale( CartVect(0.5,0.5,0.5).array() ); + ASSERT(scale.scale()); scale.xform_point( point1.array(), output.array() ); ASSERT_VECTORS_EQUAL( output, 0.5*point1 ); scale.xform_point( point2.array(), output.array() ); Modified: MOAB/trunk/src/AffineXform.hpp =================================================================== --- MOAB/trunk/src/AffineXform.hpp 2011-01-25 21:09:54 UTC (rev 4471) +++ MOAB/trunk/src/AffineXform.hpp 2011-01-26 20:35:48 UTC (rev 4472) @@ -243,7 +243,7 @@ inline bool AffineXform::scale() const { - return fabs(fabs(mMatrix.determinant()) - 1) < std::numeric_limits<double>::epsilon(); + return fabs(fabs(mMatrix.determinant()) - 1) > std::numeric_limits<double>::epsilon(); } } // namespace moab

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r4470 - in MOAB/trunk: . src src/moab tools/refiner tools/vtkMOABReader
by tautges＠mcs.anl.gov 25 Jan '11

25 Jan '11

Author: tautges Date: 2011-01-25 15:05:19 -0600 (Tue, 25 Jan 2011) New Revision: 4470 Modified: MOAB/trunk/configure.ac MOAB/trunk/src/GeomTopoTool.cpp MOAB/trunk/src/MBTagConventions.hpp MOAB/trunk/src/moab/GeomTopoTool.hpp MOAB/trunk/tools/refiner/Makefile.am MOAB/trunk/tools/refiner/test_mesh_refiner.cpp MOAB/trunk/tools/vtkMOABReader/vtkMOABReader.cxx Log: - Adding more functionality in GeomTopoTool - Including parallel tags in MBTagConventions, sometimes we want these even from serial code - more search paths for vtk - a bit more testing of refiner Modified: MOAB/trunk/configure.ac =================================================================== --- MOAB/trunk/configure.ac 2011-01-25 19:33:28 UTC (rev 4469) +++ MOAB/trunk/configure.ac 2011-01-25 21:05:19 UTC (rev 4470) @@ -716,7 +716,7 @@ x?*) VTK_LIB_DIR= VTK_INC_DIR= - for dir in ${WITH_VTK}/include/vtk ${VTK_DIR}/include/vtk/Rendering ${WITH_VTK}/include ${WITH_VTK}; do + for dir in ${WITH_VTK}/include/vtk ${VTK_DIR}/include/vtk/Rendering ${WITH_VTK}/include ${WITH_VTK}/include/paraview-* ${WITH_VTK}; do if test "x" = "x$VTK_INC_DIR"; then AC_CHECK_FILE([${dir}/vtkRenderer.h],[VTK_INC_DIR="-I$dir"]) fi Modified: MOAB/trunk/src/GeomTopoTool.cpp =================================================================== --- MOAB/trunk/src/GeomTopoTool.cpp 2011-01-25 19:33:28 UTC (rev 4469) +++ MOAB/trunk/src/GeomTopoTool.cpp 2011-01-25 21:05:19 UTC (rev 4470) @@ -31,489 +31,546 @@ // forward and reverse volumes, respectively. If a surface // is non-manifold in a single volume, the same volume will // be listed for both the forward and reverse slots. -const char GEOM_SENSE_2_TAG_NAME[] = "GEOM_SENSE_2"; + const char GEOM_SENSE_2_TAG_NAME[] = "GEOM_SENSE_2"; -const char GEOM_SENSE_N_ENTS_TAG_NAME[] = "GEOM_SENSE_N_ENTS"; -const char GEOM_SENSE_N_SENSES_TAG_NAME[] = "GEOM_SENSE_N_SENSES"; + const char GEOM_SENSE_N_ENTS_TAG_NAME[] = "GEOM_SENSE_N_ENTS"; + const char GEOM_SENSE_N_SENSES_TAG_NAME[] = "GEOM_SENSE_N_SENSES"; -GeomTopoTool::GeomTopoTool(Interface *impl, bool find_geoments) - : mdbImpl(impl), - sense2Tag(0), - senseNEntsTag(0), - senseNSensesTag(0), - obbTree(impl), - contiguous(true), - oneVolRootSet(0) -{ - ErrorCode result = mdbImpl->tag_create(GEOM_DIMENSION_TAG_NAME, 4, - MB_TAG_SPARSE, geomTag, NULL); - if (MB_SUCCESS != result && MB_ALREADY_ALLOCATED != result) { - std::cerr << "Error: Failed to create geometry dimension tag." - << std::endl; - } + GeomTopoTool::GeomTopoTool(Interface *impl, bool find_geoments) + : mdbImpl(impl), + sense2Tag(0), + senseNEntsTag(0), + senseNSensesTag(0), + obbTree(impl),

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r4468 - MOAB/trunk/itaps/imesh
by jvporter＠wisc.edu 24 Jan '11

24 Jan '11

Author: jvporter Date: 2011-01-24 14:16:57 -0600 (Mon, 24 Jan 2011) New Revision: 4468 Modified: MOAB/trunk/itaps/imesh/iMesh_MOAB.cpp Log: Fix iMesh_areEHValid Modified: MOAB/trunk/itaps/imesh/iMesh_MOAB.cpp =================================================================== --- MOAB/trunk/itaps/imesh/iMesh_MOAB.cpp 2011-01-24 19:39:31 UTC (rev 4467) +++ MOAB/trunk/itaps/imesh/iMesh_MOAB.cpp 2011-01-24 20:16:57 UTC (rev 4468) @@ -402,12 +402,7 @@ int* areHandlesInvarient, int* err ) { - MBiMesh* mbi = dynamic_cast<MBiMesh*>(MOABI); - if (!mbi) { - RETURN(iBase_FAILURE); - } - - *areHandlesInvarient = !mbi->have_deleted_ents( !!doReset ); + *areHandlesInvarient = !MBIMESHI->have_deleted_ents( !!doReset ); RETURN(iBase_SUCCESS); }

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r4464 - MOAB/trunk/tools
by kraftche＠cae.wisc.edu 24 Jan '11

24 Jan '11

Author: kraftche Date: 2011-01-24 09:31:21 -0600 (Mon, 24 Jan 2011) New Revision: 4464 Modified: MOAB/trunk/tools/ Log: update svn:ignore property for tools/ Property changes on: MOAB/trunk/tools ___________________________________________________________________ Modified: svn:ignore - mbdepth mbsize mbtagprop mbgsets hexmodops spheredecomp mbskin mbsurfplot mbconvert Makefile Makefile.in .deps .libs + mbdepth mbperf mbsize mbtagprop mbgsets hexmodops spheredecomp mbskin mbsurfplot mbconvert Makefile Makefile.in .deps .libs

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r4463 - MOAB/trunk/src/io/mhdf/src
by kraftche＠cae.wisc.edu 21 Jan '11

21 Jan '11

Author: kraftche Date: 2011-01-21 14:16:03 -0600 (Fri, 21 Jan 2011) New Revision: 4463 Modified: MOAB/trunk/src/io/mhdf/src/file.c Log: Some versions of HDF5 library (e.g. 1.8.4p2) segfault if asked to open some random non-hdf5 binary file. The normal work-around for this is to call H5Fis_hdf5 to check the file type first. However, that call has no option to open the file in parallel, causing hacks like prefixing the filename with bglockless: in Blue Gene machines to fail the test. As an incomplete compromise, only call H5Fis_hdf5 if compiled with an HDF5 library w/out support for MPI-IO. Modified: MOAB/trunk/src/io/mhdf/src/file.c =================================================================== --- MOAB/trunk/src/io/mhdf/src/file.c 2011-01-21 20:13:06 UTC (rev 4462) +++ MOAB/trunk/src/io/mhdf/src/file.c 2011-01-21 20:16:03 UTC (rev 4463) @@ -290,12 +290,13 @@ /* Check if file is HDF5 */ /* Don't do this because it can't handle MPI-IO driver code that - passes options via prefixes on the file name. + passes options via prefixes on the file name. */ +#ifndef HDF5_PARALLEL if (H5Fis_hdf5( filename ) <= 0) { mhdf_setFail( status, "%s: File is not HDF5", filename ); return NULL; } - */ +#endif /* Create struct to hold working data */ file_ptr = mhdf_alloc_FileHandle( 0, status );

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