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

buildbot failure in moab-par: failed configure
by moab-dev＠mcs.anl.gov 09 Nov '11

09 Nov '11

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r5206 - MOAB/trunk/src/io
by tautges＠mcs.anl.gov 07 Nov '11

07 Nov '11

Author: tautges Date: 2011-11-07 17:20:12 -0600 (Mon, 07 Nov 2011) New Revision: 5206 Modified: MOAB/trunk/src/io/ReadHDF5.cpp Log: Fix problem causing the autotest to fail, putting MPI_Info stuff inside PARALLEL_HDF5 #define block. Modified: MOAB/trunk/src/io/ReadHDF5.cpp =================================================================== --- MOAB/trunk/src/io/ReadHDF5.cpp 2011-11-07 00:58:33 UTC (rev 5205) +++ MOAB/trunk/src/io/ReadHDF5.cpp 2011-11-07 23:20:12 UTC (rev 5206) @@ -330,14 +330,6 @@ return MB_NOT_IMPLEMENTED; } - MPI_Info info = MPI_INFO_NULL; - std::string cb_size; - rval = opts.get_str_option("CB_BUFFER_SIZE", cb_size); - if (MB_SUCCESS == rval) { - MPI_Info_create (&info); - MPI_Info_set (info, "cb_buffer_size", const_cast<char*>(cb_size.c_str())); - } - // This option is intended for testing purposes only, and thus // is not documented anywhere. Decreasing the buffer size can // expose bugs that would otherwise only be seen when reading @@ -378,6 +370,14 @@ return MB_NOT_IMPLEMENTED; #else + MPI_Info info = MPI_INFO_NULL; + std::string cb_size; + rval = opts.get_str_option("CB_BUFFER_SIZE", cb_size); + if (MB_SUCCESS == rval) { + MPI_Info_create (&info); + MPI_Info_set (info, "cb_buffer_size", const_cast<char*>(cb_size.c_str())); + } + int pcomm_no = 0; rval = opts.get_int_option("PARALLEL_COMM", pcomm_no); if (rval == MB_TYPE_OUT_OF_RANGE) {

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r5205 - MOAB/trunk/src/parallel
by tautges＠mcs.anl.gov 06 Nov '11

06 Nov '11

Author: tautges Date: 2011-11-06 18:58:33 -0600 (Sun, 06 Nov 2011) New Revision: 5205 Modified: MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp Log: Add CB_BUFFER_SIZE option for writing too. Modified: MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp =================================================================== --- MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp 2011-11-07 00:51:08 UTC (rev 5204) +++ MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp 2011-11-07 00:58:33 UTC (rev 5205) @@ -316,6 +316,14 @@ pcommAllocated = true; } + MPI_Info info = MPI_INFO_NULL; + std::string cb_size; + rval = opts.get_str_option("CB_BUFFER_SIZE", cb_size); + if (MB_SUCCESS == rval) { + MPI_Info_create (&info); + MPI_Info_set (info, "cb_buffer_size", const_cast<char*>(cb_size.c_str())); + } + dbgOut.set_rank( myPcomm->proc_config().proc_rank() ); dbgOut.limit_output_to_first_N_procs( 32 ); @@ -441,7 +449,7 @@ dbgOut.tprint(1,"(re)opening file in parallel mode\n"); unsigned long junk; hid_t hdf_opt = H5Pcreate( H5P_FILE_ACCESS ); - H5Pset_fapl_mpio( hdf_opt, myPcomm->proc_config().proc_comm(), MPI_INFO_NULL ); + H5Pset_fapl_mpio( hdf_opt, myPcomm->proc_config().proc_comm(), info ); filePtr = mhdf_openFileWithOpt( filename, 1, &junk, id_type, hdf_opt, &status ); H5Pclose( hdf_opt ); if (!filePtr)

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r5204 - MOAB/trunk/src/io
by tautges＠mcs.anl.gov 06 Nov '11

06 Nov '11

Author: tautges Date: 2011-11-06 18:51:08 -0600 (Sun, 06 Nov 2011) New Revision: 5204 Modified: MOAB/trunk/src/io/ReadHDF5.cpp Log: Add option for setting cb_buffer_size. Modified: MOAB/trunk/src/io/ReadHDF5.cpp =================================================================== --- MOAB/trunk/src/io/ReadHDF5.cpp 2011-11-02 21:36:02 UTC (rev 5203) +++ MOAB/trunk/src/io/ReadHDF5.cpp 2011-11-07 00:51:08 UTC (rev 5204) @@ -329,6 +329,14 @@ readUtil->report_error( "'USE_MPIO' option specified w/out 'PARALLEL' option" ); return MB_NOT_IMPLEMENTED; } + + MPI_Info info = MPI_INFO_NULL; + std::string cb_size; + rval = opts.get_str_option("CB_BUFFER_SIZE", cb_size); + if (MB_SUCCESS == rval) { + MPI_Info_create (&info); + MPI_Info_set (info, "cb_buffer_size", const_cast<char*>(cb_size.c_str())); + } // This option is intended for testing purposes only, and thus // is not documented anywhere. Decreasing the buffer size can @@ -439,7 +447,7 @@ } file_prop = H5Pcreate(H5P_FILE_ACCESS); - err = H5Pset_fapl_mpio(file_prop, myPcomm->proc_config().proc_comm(), MPI_INFO_NULL); + err = H5Pset_fapl_mpio(file_prop, myPcomm->proc_config().proc_comm(), info); assert(file_prop >= 0); assert(err >= 0); @@ -720,7 +728,7 @@ Range& file_ids ) { ErrorCode rval; - + for (int i = 0; i < subset_list_length; ++i) { int tag_index;

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r5203 - MOAB/trunk/src
by tautges＠mcs.anl.gov 02 Nov '11

02 Nov '11

Author: tautges Date: 2011-11-02 16:36:02 -0500 (Wed, 02 Nov 2011) New Revision: 5203 Modified: MOAB/trunk/src/FBEngine.cpp Log: Removing ^M's, and fixing warning about not returning anything. Modified: MOAB/trunk/src/FBEngine.cpp =================================================================== --- MOAB/trunk/src/FBEngine.cpp 2011-11-01 03:56:14 UTC (rev 5202) +++ MOAB/trunk/src/FBEngine.cpp 2011-11-02 21:36:02 UTC (rev 5203) @@ -1,3440 +1,3441 @@ -#include <iostream> -#include <map> - -#include "moab/FBEngine.hpp" -#include "moab/Interface.hpp" -#include "moab/GeomTopoTool.hpp" -#include "moab/OrientedBoxTreeTool.hpp" - -#include <stdlib.h> -#include <cstring> -#include <map> -#include <set> -#include <queue> -#include <algorithm> -#include "assert.h" - -#include "SmoothCurve.hpp" -#include "SmoothFace.hpp" - -// this is just to replace MBI with moab interface, which is _mbImpl in this class -#define MBI _mbImpl -#define MBERRORR(rval, STR) { if (MB_SUCCESS != rval) { \ - std::cout<<STR<<std::endl; \ - return rval; } } - -namespace moab { - -// some tolerances for ray tracing and geometry intersections -// these are involved in ray tracing, at least - -unsigned min_tolerace_intersections = 1000; -double tolerance = 0.01; // TODO: how is this used ???? -double tolerance_segment = 0.01; // for segments intersection, points collapse, area coordinates for triangles -// it should be a relative, not an absolute value -// as this splitting operation can create small edges, it should be relatively high -// or, it should be coordinated with the decimation errors -// we really just want to preserve the integrity of the mesh, we should avoid creating small edges or angles -const bool Debug_surf_eval = false; -bool debug_splits = false; - -// will compute intersection between a segment and slice of a plane -// output is the intersection point -bool intersect_segment_and_plane_slice(CartVect & from, CartVect & to, - CartVect & p1, CartVect & p2, CartVect & Dir, CartVect & normPlane, - CartVect & intx_point, double & parPos) -{

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r5202 - MOAB/trunk/src
by iulian＠mcs.anl.gov 31 Oct '11

31 Oct '11

Author: iulian Date: 2011-10-31 22:56:14 -0500 (Mon, 31 Oct 2011) New Revision: 5202 Modified: MOAB/trunk/src/FBEngine.cpp Log: bug in get adjacencies for mesh based geometry in moab::Interface, the number of hops in children/parent relations is not exact, it means "up to"; so, if number of hops is 2, direct children (or parents) will be returned too, not only the grand-children (or grand-parents) so, subtract those with a hop number smaller by 1, to get the "exact" desired number of hops. Modified: MOAB/trunk/src/FBEngine.cpp =================================================================== --- MOAB/trunk/src/FBEngine.cpp 2011-10-26 17:39:44 UTC (rev 5201) +++ MOAB/trunk/src/FBEngine.cpp 2011-11-01 03:56:14 UTC (rev 5202) @@ -810,17 +810,26 @@ ErrorCode rval; adjs.clear(); if (to_dim > this_dim) { - int number; - rval = MBI->num_parent_meshsets(from, &number, 0); - rval = MBI->get_parent_meshsets(from, adjs); - adjs.clear(); - rval = MBI->get_parent_meshsets(from, adjs, to_dim - this_dim); + int diffDim = to_dim-this_dim; + rval = MBI->get_parent_meshsets(from, adjs, diffDim); + if (diffDim>1) + { + // subtract the parents that come with diffDim-1 hops + Range extra; + rval = MBI->get_parent_meshsets(from, extra, diffDim-1); + adjs = subtract(adjs, extra); + } + } else { - int number; - rval = MBI->num_child_meshsets(from, &number, 0); - rval = MBI->get_child_meshsets(from, adjs); - adjs.clear(); - rval = MBI->get_child_meshsets(from, adjs, this_dim - to_dim); + int diffDim = this_dim - to_dim; + rval = MBI->get_child_meshsets(from, adjs, diffDim); + if (diffDim > 1) + { + // subtract the children that come with diffDim-1 hops + Range extra; + rval = MBI->get_child_meshsets(from, extra, diffDim-1); + adjs = subtract(adjs, extra); + } } return MB_SUCCESS;

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