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

Best place to find parallel examples?
by Milad Fatenejad 28 Dec '12

28 Dec '12

Hello: I would like to create a mesh which will be decomposed on multiple processors. The mesh will be 1D and I want a layer of ghost cells that is 1 cell thick. What is the best place to find an example which can demonstrate how to do this? Thanks! Milad

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Moab Paraview plugin will not compile
by Cook, Rich 21 Dec '12

21 Dec '12

My apologies for posting here if it's not the right venue. I could not find another resource through Google or locally. BTW, the pointers to the package owners in the README leads to a dead link: "Users are encouraged to check http://cubit.sandia.gov/moab often for news and updates." Riiight. Anyhow, I found you! Ha. A user of our clusters at LLNL has asked if I would compile the MOAB Paraview plugin. So I tried this: tar -xzf moab-4.5.0.tar.gz pushd moab-4.5.0 ./configure --prefix=/nfs/tmp2/rcook/ParaView/moab-plugin/install-dir make -j pushd tools/vtkMOABReader/ cmake -DParaView_DIR=/nfs/tmp2/rcook/ParaView/moab-plugin/Paraview-BuildDir/src/ParaView-3.14.0-Build/ . When I did so, I got the following error. Can someone help me? :-) Thanks! + cmake -DParaView_DIR=/nfs/tmp2/rcook/ParaView/moab-plugin/Paraview-BuildDir/src/ParaView-3.14.0-Build/ . -- The C compiler identification is GNU -- The CXX compiler identification is GNU -- Check for working C compiler: /usr/local/bin/gcc -- Check for working C compiler: /usr/local/bin/gcc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done CMake Error at CMakeLists.txt:8 (INCLUDE): include could not find load file: /tmp/dpkg-mkdeb.eHKBP8GXWA/src/ParaView-3.14.0-Source/ParaViewUse.cmake CMake Error at CMakeLists.txt:9 (ADD_PARAVIEW_PLUGIN): Unknown CMake command "ADD_PARAVIEW_PLUGIN". -- Configuring incomplete, errors occurred! -- ✐Richard Cook ✇ Lawrence Livermore National Laboratory Bldg-453 Rm-4024, Mail Stop L-557 7000 East Avenue, Livermore, CA, 94550, USA ☎ (office) (925) 423-9605 ☎ (fax) (925) 423-6961 --- Information Management & Graphics Grp., Services & Development Div., Integrated Computing & Communications Dept. (opinions expressed herein are mine and not those of LLNL)

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r5930 - MOAB/trunk/src
by tautges＠mcs.anl.gov 18 Dec '12

18 Dec '12

Author: tautges Date: 2012-12-18 16:47:35 -0600 (Tue, 18 Dec 2012) New Revision: 5930 Modified: MOAB/trunk/src/Core.cpp Log: Removing an unaccessed block of code, good spot Iulian. Modified: MOAB/trunk/src/Core.cpp =================================================================== --- MOAB/trunk/src/Core.cpp 2012-12-18 22:08:43 UTC (rev 5929) +++ MOAB/trunk/src/Core.cpp 2012-12-18 22:47:35 UTC (rev 5930) @@ -2900,21 +2900,8 @@ } std::cout << std::endl; - // if negative num_entities, list the set hierarchy too - if (0 > num_entities) { - Range sets; - result = this->get_entities_by_type(0, MBENTITYSET, sets); - if (MB_SUCCESS != result) return result; - for (Range::iterator rit = sets.begin(); rit != sets.end(); rit++) { - this->print(*rit, "", true); - result = this->get_number_entities_by_handle(*rit, num_ents); - std::cout << "(" << num_ents << " total entities)" << std::endl; - } - } - return MB_SUCCESS; } - else if (NULL == entities && num_entities < 0) { // list all entities of all types @@ -2925,7 +2912,6 @@ return list_entities(temp_range); } - else if (NULL == entities && num_entities > 0) { // list all entities of type == num_entities @@ -2934,7 +2920,6 @@ return list_entities(temp_range); } - else { ErrorCode tmp_result; for (int i = 0; i < num_entities; i++) {

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r5929 - MOAB/trunk/doc
by tautges＠mcs.anl.gov 18 Dec '12

18 Dec '12

Author: tautges Date: 2012-12-18 16:08:43 -0600 (Tue, 18 Dec 2012) New Revision: 5929 Modified: MOAB/trunk/doc/MOAB-UG.doc Log: Updates to the user's guide. Modified: MOAB/trunk/doc/MOAB-UG.doc =================================================================== (Binary files differ)

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r5928 - in MOAB/trunk: src src/moab test
by tautges＠mcs.anl.gov 18 Dec '12

18 Dec '12

Author: tautges Date: 2012-12-18 15:09:41 -0600 (Tue, 18 Dec 2012) New Revision: 5928 Modified: MOAB/trunk/src/BitTag.cpp MOAB/trunk/src/BitTag.hpp MOAB/trunk/src/Core.cpp MOAB/trunk/src/DenseTag.cpp MOAB/trunk/src/DenseTag.hpp MOAB/trunk/src/MeshTag.cpp MOAB/trunk/src/MeshTag.hpp MOAB/trunk/src/SparseTag.cpp MOAB/trunk/src/SparseTag.hpp MOAB/trunk/src/TagInfo.hpp MOAB/trunk/src/VarLenDenseTag.cpp MOAB/trunk/src/VarLenDenseTag.hpp MOAB/trunk/src/VarLenSparseTag.cpp MOAB/trunk/src/VarLenSparseTag.hpp MOAB/trunk/src/moab/Core.hpp MOAB/trunk/src/moab/Interface.hpp MOAB/trunk/test/TagTest.cpp Log: Change to tag_iterate, to allow application to request that tag storage space not be allocated. This commit also modifies interpretation of arguments to the Core::list_entities function, see below for details. Fixes tickets 271 and 268. Passes all tests, serial and parallel. TagTest.cpp: add a test for ticket #271, where apps could change the default value of a tag (that bug is also fixed in this commit) Most tag classes, plus Core and Interface: add an allocate parameter to tag_iterate, allowing applications to request that tag memory not be allocated as a result of calling this function. SparseTag: fix the bug exposing tag default value, along with allocation change above Core: modified meaning of arguments to Core::list_entities(EntityHandle*entities, int num_entities); if entities == NULL, then num_entities < 0 : list the whole database == 0: list the number of entities of each type > 0 : list all entities of type == (EntityType)num_entities This makes debugging significantly easier, since you don't need to assemble an entity range or vector to print e.g. all entity sets Modified: MOAB/trunk/src/BitTag.cpp =================================================================== --- MOAB/trunk/src/BitTag.cpp 2012-12-18 19:23:22 UTC (rev 5927) +++ MOAB/trunk/src/BitTag.cpp 2012-12-18 21:09:41 UTC (rev 5928) @@ -332,7 +332,8 @@ Error* error, Range::iterator&, const Range::iterator&, - void*& ) + void*&, + bool ) { return report_unsupported(error); } template <class Container> inline Modified: MOAB/trunk/src/BitTag.hpp =================================================================== --- MOAB/trunk/src/BitTag.hpp 2012-12-18 19:23:22 UTC (rev 5927) +++ MOAB/trunk/src/BitTag.hpp 2012-12-18 21:09:41 UTC (rev 5928) @@ -292,7 +292,8 @@ Error* error_handler, Range::iterator& iter, const Range::iterator& end, - void*& data_ptr ); + void*& data_ptr, + bool allocate = true); /**\brief Get all tagged entities * Modified: MOAB/trunk/src/Core.cpp =================================================================== --- MOAB/trunk/src/Core.cpp 2012-12-18 19:23:22 UTC (rev 5927) +++ MOAB/trunk/src/Core.cpp 2012-12-18 21:09:41 UTC (rev 5928) @@ -2483,11 +2483,13 @@ Range::const_iterator iter, Range::const_iterator end, int& count, - void*& data_ptr ) + void*& data_ptr, + bool allocate) { Range::const_iterator init = iter; assert(valid_tag_handle( tag_handle )); - ErrorCode result = tag_handle->tag_iterate( sequenceManager, mError, iter, end, data_ptr ); + ErrorCode result = tag_handle->tag_iterate( sequenceManager, mError, iter, end, data_ptr, + allocate); if (MB_SUCCESS == result) count = iter - init; return result; @@ -2887,7 +2889,7 @@

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r5927 - MOAB/trunk/src/io
by iulian＠mcs.anl.gov 18 Dec '12

18 Dec '12

Author: iulian Date: 2012-12-18 13:23:22 -0600 (Tue, 18 Dec 2012) New Revision: 5927 Modified: MOAB/trunk/src/io/ReadHDF5.cpp MOAB/trunk/src/io/ReadNCDF.cpp Log: more warnings Modified: MOAB/trunk/src/io/ReadHDF5.cpp =================================================================== --- MOAB/trunk/src/io/ReadHDF5.cpp 2012-12-18 18:13:29 UTC (rev 5926) +++ MOAB/trunk/src/io/ReadHDF5.cpp 2012-12-18 19:23:22 UTC (rev 5927) @@ -3352,22 +3352,22 @@ public: ErrorCode store_data( EntityHandle file_id, void* data, long count, bool ) { - ErrorCode rval; + ErrorCode rval1; if (isHandle) { assert(readSize == sizeof(EntityHandle)); - rval = readHDF5->convert_id_to_handle( (EntityHandle*)data, count ); - if (MB_SUCCESS != rval) - return error(rval); + rval1 = readHDF5->convert_id_to_handle( (EntityHandle*)data, count ); + if (MB_SUCCESS != rval1) + return error(rval1); } int n = count; return readHDF5->moab()->tag_set_by_ptr( tagHandle, &file_id, 1, &data, &n ); } VTReader( DebugOutput& debug_output, void* buffer, size_t buffer_size, - Tag tag, bool is_handle_tag, size_t read_size, ReadHDF5* owner ) + Tag tag, bool is_handle_tag, size_t read_size1, ReadHDF5* owner ) : ReadHDF5VarLen( debug_output, buffer, buffer_size ), tagHandle(tag), isHandle(is_handle_tag), - readSize(read_size), + readSize(read_size1), readHDF5(owner) {} }; Modified: MOAB/trunk/src/io/ReadNCDF.cpp =================================================================== --- MOAB/trunk/src/io/ReadNCDF.cpp 2012-12-18 18:13:29 UTC (rev 5926) +++ MOAB/trunk/src/io/ReadNCDF.cpp 2012-12-18 19:23:22 UTC (rev 5927) @@ -146,7 +146,7 @@ mGlobalIdTag, MB_TAG_SPARSE|MB_TAG_CREAT, &zero); assert(MB_SUCCESS == result); #ifdef NDEBUG - if (MB_SUCCESS == result); // line to avoid compiler warning about unused variable + if (MB_SUCCESS == result) {}; // line to avoid compiler warning about unused variable #endif ncFile = 0; }

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r5926 - in MOAB/trunk: examples itaps/igeom src/moab test
by iulian＠mcs.anl.gov 18 Dec '12

18 Dec '12

Author: iulian Date: 2012-12-18 12:13:29 -0600 (Tue, 18 Dec 2012) New Revision: 5926 Modified: MOAB/trunk/examples/ObbTree.cpp MOAB/trunk/itaps/igeom/testSmooth2.cc MOAB/trunk/src/moab/SpectralMeshTool.hpp MOAB/trunk/test/TestUtil.hpp Log: eliminate more warnings correct ObbTree example TestUtil should compare double with double, not double with float spectral mesh tool has an unused member data Modified: MOAB/trunk/examples/ObbTree.cpp =================================================================== --- MOAB/trunk/examples/ObbTree.cpp 2012-12-18 15:58:23 UTC (rev 5925) +++ MOAB/trunk/examples/ObbTree.cpp 2012-12-18 18:13:29 UTC (rev 5926) @@ -38,8 +38,7 @@ } // build box - double box_center[3], box_axis1[3], box_axis2[3], box_axis3[3], start_pnt[3], - ray_length; + double box_center[3], box_axis1[3], box_axis2[3], box_axis3[3], pnt_start[3], ray_length; rval = tool.box(tree_root, box_center, box_axis1, box_axis2, box_axis3); if (rval != moab::MB_SUCCESS) { std::cerr << "Couldn't get box for tree root set."; @@ -49,20 +48,27 @@ ray_length = 2.*sqrt(box_axis1[0]*box_axis1[0] + box_axis1[1]*box_axis1[1] + box_axis1[2]*box_axis1[2]); - // do ray-tracing from box center to x direction + // do ray-tracing from box center side to x direction std::vector<double> intersections; std::vector<moab::EntityHandle> intersection_facets; - double dir[3] = {1., 0., 0.}; + + for (int i=0; i<3; i++) + pnt_start[i] = box_center[i]-box_axis1[i]; + + if (ray_length>0) // normalize ray direction + for (int j=0; j<3; j++) + box_axis1[j]=2*box_axis1[j]/ray_length; rval = tool.ray_intersect_triangles(intersections, intersection_facets, - tree_root, 10e-12, box_center, dir, + tree_root, 10e-12, pnt_start, box_axis1, &ray_length); if (rval != moab::MB_SUCCESS) { std::cerr << "Couldn't ray tracing."; return 1; } - std::cout << "ray start point: " << start_pnt[0] << " " - << start_pnt[1] << " " << start_pnt[2] << std::endl; + std::cout << "ray start point: " << pnt_start[0] << " " + << pnt_start[1] << " " << pnt_start[2] << std::endl; + std::cout << " ray direction: " << box_axis1[0] << " " << box_axis1[1] << " " << box_axis1[2] << "\n"; std::cout << "# of intersections : " << intersections.size() << std::endl; std::cout << "intersection distances are on"; for (unsigned int i = 0; i < intersections.size(); i++) { Modified: MOAB/trunk/itaps/igeom/testSmooth2.cc =================================================================== --- MOAB/trunk/itaps/igeom/testSmooth2.cc 2012-12-18 15:58:23 UTC (rev 5925)

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r5925 - MOAB/trunk/src/io
by tautges＠mcs.anl.gov 18 Dec '12

18 Dec '12

Author: tautges Date: 2012-12-18 09:58:23 -0600 (Tue, 18 Dec 2012) New Revision: 5925 Modified: MOAB/trunk/src/io/WriteNCDF.cpp Log: Fixing potential buffer overflow pointed out by Klokworks. Modified: MOAB/trunk/src/io/WriteNCDF.cpp =================================================================== --- MOAB/trunk/src/io/WriteNCDF.cpp 2012-12-18 05:58:06 UTC (rev 5924) +++ MOAB/trunk/src/io/WriteNCDF.cpp 2012-12-18 15:58:23 UTC (rev 5925) @@ -1674,10 +1674,8 @@ /* store element type as attribute of connectivity variable */ - char element_type_string[ExoIIInterface::MAX_STR_LENGTH+1]; - strcpy(element_type_string, ExoIIUtil::ElementTypeNames[ block.element_type ]); - - if (NC_NOERR != nc_put_att_text(ncFile, connect, "elem_type", strlen(element_type_string), element_type_string)) + std::string element_type_string(ExoIIUtil::ElementTypeNames[ block.element_type ]); + if (NC_NOERR != nc_put_att_text(ncFile, connect, "elem_type", element_type_string.length(), element_type_string.c_str())) { mWriteIface->report_error("WriteNCDF: failed to store element type name %d", (int)block.element_type); return (MB_FAILURE);

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r5923 - in MOAB/trunk/src: io parallel
by iulian＠mcs.anl.gov 17 Dec '12

17 Dec '12

Author: iulian Date: 2012-12-17 23:51:44 -0600 (Mon, 17 Dec 2012) New Revision: 5923 Modified: MOAB/trunk/src/io/ReadCGM.cpp MOAB/trunk/src/parallel/ProcConfig.cpp Log: eliminate some more warnings from moab build with cgm Modified: MOAB/trunk/src/io/ReadCGM.cpp =================================================================== --- MOAB/trunk/src/io/ReadCGM.cpp 2012-12-18 05:49:44 UTC (rev 5922) +++ MOAB/trunk/src/io/ReadCGM.cpp 2012-12-18 05:51:44 UTC (rev 5923) @@ -77,7 +77,7 @@ ErrorCode rval; // get some tag handles - int negone = -1, zero = 0, negonearr[] = {-1, -1, -1, -1}; + int negone = -1, zero = 0 /*, negonearr[] = {-1, -1, -1, -1}*/; rval = mdbImpl->tag_get_handle( GEOM_DIMENSION_TAG_NAME, 1, MB_TYPE_INTEGER, geom_tag, MB_TAG_SPARSE|MB_TAG_CREAT, &negone); assert(!rval); @@ -122,7 +122,7 @@ const EntityHandle* file_set, const FileOptions& opts, const ReaderIface::SubsetList* subset_list, - const Tag* file_id_tag) + const Tag* /*file_id_tag*/) { // blocks_to_load and num_blocks are ignored. ErrorCode rval; @@ -331,7 +331,7 @@ if (name_list.size() == 0) continue; name_list.reset(); - CubitString name = *name_list.get(); + CubitString name1 = *name_list.get(); EntityHandle h; rval = mdbImpl->create_meshset( MESHSET_SET, h ); @@ -340,9 +340,9 @@ char namebuf[NAME_TAG_SIZE]; memset( namebuf, '\0', NAME_TAG_SIZE ); - strncpy( namebuf, name.c_str(), NAME_TAG_SIZE - 1 ); - if (name.length() >= (unsigned)NAME_TAG_SIZE) - std::cout << "WARNING: group name '" << name.c_str() + strncpy( namebuf, name1.c_str(), NAME_TAG_SIZE - 1 ); + if (name1.length() >= (unsigned)NAME_TAG_SIZE) + std::cout << "WARNING: group name '" << name1.c_str() << "' truncated to '" << namebuf << "'" << std::endl; rval = mdbImpl->tag_set_data( name_tag, &h, 1, namebuf ); if (MB_SUCCESS != rval) @@ -367,11 +367,11 @@ } for (int j = 0; j < name_list.size(); ++j) { - name = *name_list.get_and_step(); + name1 = *name_list.get_and_step(); memset( namebuf, '\0', NAME_TAG_SIZE );

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r5921 - MOAB/trunk/itaps/igeom
by iulian＠mcs.anl.gov 17 Dec '12

17 Dec '12

Author: iulian Date: 2012-12-17 18:37:02 -0600 (Mon, 17 Dec 2012) New Revision: 5921 Modified: MOAB/trunk/itaps/igeom/FBiGeom_MOAB.cpp Log: eliminate warnings; usually the "size" variables were not returned before the allocation happens either in each function (see CHECK_SIZE macro), or the user allocates it in advance Modified: MOAB/trunk/itaps/igeom/FBiGeom_MOAB.cpp =================================================================== --- MOAB/trunk/itaps/igeom/FBiGeom_MOAB.cpp 2012-12-17 21:59:54 UTC (rev 5920) +++ MOAB/trunk/itaps/igeom/FBiGeom_MOAB.cpp 2012-12-18 00:37:02 UTC (rev 5921) @@ -387,6 +387,8 @@ index1 += index1_step; index2 += index2_step; } + // it is now safe to set the size + *is_adjacent_info_size = count; RETURN(iBase_SUCCESS); } @@ -410,21 +412,22 @@ int* on_coordinates_allocated, int* on_coordinates_size, int* err) { CHECK_SIZE(*on_coordinates, *on_coordinates_allocated, near_coordinates_size, double, NULL); + for (int i = 0; i < entity_handles_size; i++) { if (storage_order == iBase_INTERLEAVED) { - FBiGeom_getEntClosestPt(instance, entity_handles[i], near_coordinates[3 - * i], near_coordinates[3 * i + 1], near_coordinates[3 * i + 2], - on_coordinates[3 * i], on_coordinates[3 * i + 1], - on_coordinates[3 * i + 2], err); + FBiGeom_getEntClosestPt(instance, entity_handles[i], + near_coordinates[3*i], near_coordinates[3*i+1], near_coordinates[3*i+2], + on_coordinates[3*i], on_coordinates[3*i+1], on_coordinates[3*i+2], + err); } else if (storage_order == iBase_BLOCKED) { FBiGeom_getEntClosestPt(instance, entity_handles[i], - near_coordinates[i], near_coordinates[i + entity_handles_size], - near_coordinates[i + 2 * entity_handles_size], - on_coordinates[i], on_coordinates[i + entity_handles_size], - on_coordinates[i + 2 * entity_handles_size], err); + near_coordinates[i], near_coordinates[i+entity_handles_size], near_coordinates[i+2*entity_handles_size], + on_coordinates[i], on_coordinates[i+entity_handles_size], on_coordinates[i+2*entity_handles_size], + err); } FWDERR(); } + *on_coordinates_size = near_coordinates_size; RETURN(iBase_SUCCESS); } @@ -503,7 +506,7 @@ norm_y += norm_step; norm_z += norm_step; } - + *normals_size = count; RETURN(iBase_SUCCESS);

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