February 2013 - moab-dev - mailman3.cels.anl.gov

MOAB 4.6.0 Released !
by Rajeev Jain 19 Jun '13

19 Jun '13

MOAB version 4.6.0 has been released. Available here: http://ftp.mcs.anl.gov/pub/fathom/moab-4.6.0.tar.gz Notable changes to this version are as follows: * Added new iMeshP extension function iMeshP_getCommunicator, converting fortran integer to MPI C communicator. * Various bug fixes and improvements of mbcoupler (parallel mesh to mesh transfer): handling of spectral elements, works in serial now, better tolerancing for point searches. * Major enhancements, efficiency improvements for NC data reader, including going mostly to a 2.5D representation, addition of a HOMME data reader, bug fixes in representing periodic meshes in parallel. * Added Interface::adjacencies_iterate, whose behavior is much like tag_iterate. * Removed deprecated functions from the Interface: (some overloaded variants of) query_interface, release_interface, tag_get_data, tag_set_data, tag_get_size. * Initial implementation of Damsel reader/writer. * Initial implementation of a GCRM data reader, and a better ReadTemplate class (skeleton for writing new readers). * Add new metadata and properties handling to DAGMC. * Support for 1D in structured mesh interface. * Alternative vtkMOABReaderNew & paraview plugin (in tools directory).

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Would like to go over to BitBucket soon (next week)...
by Tim Tautges 26 Feb '13

26 Feb '13

Hi all, Would anybody have a problem with taking the MOAB repo over to BitBucket next week? From what I've surmised from the various documents out there and talking to the PETSc folks, that seems to be the better way to do things. It also would eliminate the need to have one repo shadowing the other for a time, which would be complicated. Let me know what you think. I'm using BitBucket now for a number of other subprojects, and so far I like the experience, even though I'd call myself still a newbie on git. - tim -- ================================================================ "You will keep in perfect peace him whose mind is steadfast, because he trusts in you." Isaiah 26:3 Tim Tautges Argonne National Laboratory (tautges(a)mcs.anl.gov) (telecommuting from UW-Madison) phone (gvoice): (608) 354-1459 1500 Engineering Dr. fax: (608) 263-4499 Madison, WI 53706

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r6015 - MOAB/trunk/tools/mbcslam
by iulian＠mcs.anl.gov 25 Feb '13

25 Feb '13

Author: iulian Date: 2013-02-25 16:31:50 -0600 (Mon, 25 Feb 2013) New Revision: 6015 Modified: MOAB/trunk/tools/mbcslam/Intx2Mesh.cpp Log: the arrival mesh could be disjoint, so the advancing front strategy might stop after processing each arrival element, remove it from the initial range; stop when the initial range is empty search for a new starting seed within the remaining elements; Modified: MOAB/trunk/tools/mbcslam/Intx2Mesh.cpp =================================================================== --- MOAB/trunk/tools/mbcslam/Intx2Mesh.cpp 2013-02-20 05:37:27 UTC (rev 6014) +++ MOAB/trunk/tools/mbcslam/Intx2Mesh.cpp 2013-02-25 22:31:50 UTC (rev 6015) @@ -162,187 +162,192 @@ Range rs2; mb->get_entities_by_type(mbs1, type, rs1); mb->get_entities_by_type(mbs2, type, rs2); - for (Range::iterator it = rs1.begin(); it != rs1.end(); it++) + while (!rs2.empty()) { - startBlue = *it; - int found = 0; - for (Range::iterator it2 = rs2.begin(); it2 != rs2.end() && !found; it2++) + for (Range::iterator it = rs1.begin(); it != rs1.end(); it++) { - startRed = *it2; - double area = 0; - // if area is > 0 , we have intersections - double P[48]; // max 8 intx points + 8 more in the polygon - // the red quad is convex, always, while the blue can be concave - int nP = 0; - int nb[4], nr[4]; // sides 3 or 4? also, check boxes first - computeIntersectionBetweenRedAndBlue(startRed, startBlue, P, nP, area, nb, nr, true); - if (area > 0) + startBlue = *it; + int found = 0; + for (Range::iterator it2 = rs2.begin(); it2 != rs2.end() && !found; it2++) { - found = 1; - break; // found 2 elements that intersect; these will be the seeds + startRed = *it2; + double area = 0; + // if area is > 0 , we have intersections + double P[48]; // max 8 intx points + 8 more in the polygon + // the red quad is convex, always, while the blue can be concave + int nP = 0; + int nb[4], nr[4]; // sides 3 or 4? also, check boxes first + computeIntersectionBetweenRedAndBlue(startRed, startBlue, P, nP, area, nb, nr, true); + if (area > 0) + { + found = 1; + break; // found 2 elements that intersect; these will be the seeds + } } + if (found) + break; } - if (found) - break; - }

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ANL repos will be moving to git on bitbucket.org
by Tim Tautges 22 Feb '13

22 Feb '13

[Sorry for the duplicate messages for those on all these mailing lists] Hi all, After careful consideration, the ANL team has decided to move the MOAB, CGM*, Lasso, and MeshKit repositories to bitbucket.org. Bitbucket is a public repository hosting site used by a number of well-known projects, including ANL's PETSc project. It provides all the normal repository functions we already use, plus a nice hosted DVCS system that makes it easy for others to interact with. As part of this move we will also move from Subversion to Git, which will additionally simplify branching and merging for subprojects. In preparation for this move, I suggest those wanting write access to the repos above get accounts at bitbucket (if you don't already have one). For those with the possibility, it is advantageous to register under a ".edu" email address; academic users are allowed unlimited "private" repositories on bitbucket (non-academic users have a limit of 5 users for private repos). Note that all the repositories above will be public, as has been the policy up to now on the ANL-hosted system. ONCE YOU HAVE REGISTERED ON BITBUCKET, PLEASE EMAIL ME YOUR USERNAME THERE, AND THE REPOS YOU WOULD LIKE ME TO ADD YOU TO AS WRITERS. If you have no need to have write access, bitbucket will allow anonymous access too, so you shouldn't need a bitbucket account if you only read our repos. As for timing, I'm not sure when the official move will happen. I will be trying to set up mirroring, such that we can try out the git-based access (at least for read) before officially making the move. However, I anticipate moving over for good in the next month or so. If you have any concerns about this, please email me. - tim * - certain parts of the CGM repo are more strictly access controlled; if you don't know which ones, you probably don't need to know. These parts will remain at ANL for now, but we may consider moving these officially to bitbucket too, likely as private repos. All permissions on those parts will maintained as before. -- ================================================================ "You will keep in perfect peace him whose mind is steadfast, because he trusts in you." Isaiah 26:3 Tim Tautges Argonne National Laboratory (tautges(a)mcs.anl.gov) (telecommuting from UW-Madison) phone (gvoice): (608) 354-1459 1500 Engineering Dr. fax: (608) 263-4499 Madison, WI 53706

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r6014 - MOAB/trunk/src/io
by iulian＠mcs.anl.gov 19 Feb '13

19 Feb '13

Author: iulian Date: 2013-02-19 23:37:27 -0600 (Tue, 19 Feb 2013) New Revision: 6014 Modified: MOAB/trunk/src/io/ReadHDF5.cpp Log: resolves ticket 273 the bug was in intersecting the subranges. For a partial read (that appears in parallel), the id_map between file ids and local entity handles is fragmented, in terms of file ids. When we populate the local sets, we are reading "complete" sets from the file, on each processor, and we have to carefully fish out only the file entities that are found in the id_map (and exist on the local processor) Because of efficiency, we are doing this intersection of subranges using 2 advancing pointers; the construct that crashed was this: hint = merge.insert( hint, it->value + off, it->value + off + count - 1 ); for some low values of it->value, and negative count, this number it->value + off + count - 1 was actually negative, but because it is an EntityHandle, it is an unsigned long int; it became something like 0xfffff...fffd which is valid :( positive, very large. the set blowed up really bad, because this range that was added was ridiculously large. two fixes (redundant, in a way): 1) break out when count becomes negative, and treat the next range in the ranged set. 2) when advance to a next subrange in id_map, check if we passed the "end", and break out if yes passes make check in parallel, but I should add a test to capture this bug it showed up only at reading in parallel, I need to find out how to exercise the partial read of a file in serial and manufacture a simpler test Modified: MOAB/trunk/src/io/ReadHDF5.cpp =================================================================== --- MOAB/trunk/src/io/ReadHDF5.cpp 2013-02-19 19:41:19 UTC (rev 6013) +++ MOAB/trunk/src/io/ReadHDF5.cpp 2013-02-20 05:37:27 UTC (rev 6014) @@ -608,7 +608,7 @@ } - dbgOut.tprint( 1, "Cleaining up\n" ); + dbgOut.tprint( 1, "Cleaning up\n" ); ErrorCode rval2 = clean_up_read( opts ); if (rval == MB_SUCCESS && rval2 != MB_SUCCESS) rval = rval2; @@ -3449,11 +3449,20 @@ if (id < it->begin) id = it->begin; const long off = id - it->begin; long count = std::min( it->count - off, end - id ); + // it is possible that this new subrange is starting after the end + // it will result in negative count, which does not make sense + // we are done with this range, go to the next one + if (count <= 0) + break; hint = merge.insert( hint, it->value + off, it->value + off + count - 1 ); id += count; if (id < end) + { if (++it == id_map.end()) break; + if (it->begin > end) + break; // + } } } }

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r6008 - in MOAB/branches/Version4.6: . src/io
by tautges＠mcs.anl.gov 15 Feb '13

15 Feb '13

Author: tautges Date: 2013-02-15 16:22:31 -0600 (Fri, 15 Feb 2013) New Revision: 6008 Modified: MOAB/branches/Version4.6/MOABConfig.cmake.in MOAB/branches/Version4.6/src/io/WriteAns.hpp MOAB/branches/Version4.6/src/io/WriteCCMIO.hpp MOAB/branches/Version4.6/src/io/WriteDamsel.hpp MOAB/branches/Version4.6/src/io/WriteGMV.hpp MOAB/branches/Version4.6/src/io/WriteGmsh.hpp MOAB/branches/Version4.6/src/io/WriteSLAC.hpp MOAB/branches/Version4.6/src/io/WriteSmf.hpp MOAB/branches/Version4.6/src/io/WriteTemplate.hpp MOAB/branches/Version4.6/src/io/WriteVtk.hpp Log: Back-porting r6007. Modified: MOAB/branches/Version4.6/MOABConfig.cmake.in =================================================================== --- MOAB/branches/Version4.6/MOABConfig.cmake.in 2013-02-15 22:13:04 UTC (rev 6007) +++ MOAB/branches/Version4.6/MOABConfig.cmake.in 2013-02-15 22:22:31 UTC (rev 6008) @@ -1,4 +1,6 @@ -# Config file for MOAB +# Config file for MOAB; use the CMake find_package() function to pull this into +# your own CMakeLists.txt file. +# # This file defines the following variables: # MOAB_FOUND - boolean indicating that MOAB is found # MOAB_INCLUDE_DIRS - include directories from which to pick up MOAB includes Modified: MOAB/branches/Version4.6/src/io/WriteAns.hpp =================================================================== --- MOAB/branches/Version4.6/src/io/WriteAns.hpp 2013-02-15 22:13:04 UTC (rev 6007) +++ MOAB/branches/Version4.6/src/io/WriteAns.hpp 2013-02-15 22:22:31 UTC (rev 6008) @@ -65,9 +65,9 @@ const EntityHandle *output_list, const int num_sets, const std::vector<std::string>& qa_list, - const Tag* tag_list, - int num_tags, - int export_dimension); + const Tag* tag_list = NULL, + int num_tags = 0, + int export_dimension = 3); //! struct used to hold data for each block to be output; used by //! initialize_file to initialize the file header for increased speed Modified: MOAB/branches/Version4.6/src/io/WriteCCMIO.hpp =================================================================== --- MOAB/branches/Version4.6/src/io/WriteCCMIO.hpp 2013-02-15 22:13:04 UTC (rev 6007) +++ MOAB/branches/Version4.6/src/io/WriteCCMIO.hpp 2013-02-15 22:22:31 UTC (rev 6008) @@ -67,9 +67,9 @@ const EntityHandle *output_list, const int num_sets, const std::vector<std::string>& qa_list, - const Tag* tag_list, - int num_tags, - int export_dimension); + const Tag* tag_list = NULL, + int num_tags = 0, + int export_dimension = 3); protected: Modified: MOAB/branches/Version4.6/src/io/WriteDamsel.hpp ===================================================================

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r6007 - in MOAB/trunk: . src/io
by tautges＠mcs.anl.gov 15 Feb '13

15 Feb '13

Author: tautges Date: 2013-02-15 16:13:04 -0600 (Fri, 15 Feb 2013) New Revision: 6007 Modified: MOAB/trunk/MOABConfig.cmake.in MOAB/trunk/src/io/WriteAns.hpp MOAB/trunk/src/io/WriteCCMIO.hpp MOAB/trunk/src/io/WriteDamsel.hpp MOAB/trunk/src/io/WriteGMV.hpp MOAB/trunk/src/io/WriteGmsh.hpp MOAB/trunk/src/io/WriteSLAC.hpp MOAB/trunk/src/io/WriteSmf.hpp MOAB/trunk/src/io/WriteTemplate.hpp MOAB/trunk/src/io/WriteVtk.hpp Log: MOABConfig.cmake.in: a few more comments on how to use this. Others: add/make default args to write_file consistent across file writers. Passes make check, serial and parallel. Modified: MOAB/trunk/MOABConfig.cmake.in =================================================================== --- MOAB/trunk/MOABConfig.cmake.in 2013-02-15 19:46:42 UTC (rev 6006) +++ MOAB/trunk/MOABConfig.cmake.in 2013-02-15 22:13:04 UTC (rev 6007) @@ -1,4 +1,6 @@ -# Config file for MOAB +# Config file for MOAB; use the CMake find_package() function to pull this into +# your own CMakeLists.txt file. +# # This file defines the following variables: # MOAB_FOUND - boolean indicating that MOAB is found # MOAB_INCLUDE_DIRS - include directories from which to pick up MOAB includes Modified: MOAB/trunk/src/io/WriteAns.hpp =================================================================== --- MOAB/trunk/src/io/WriteAns.hpp 2013-02-15 19:46:42 UTC (rev 6006) +++ MOAB/trunk/src/io/WriteAns.hpp 2013-02-15 22:13:04 UTC (rev 6007) @@ -65,9 +65,9 @@ const EntityHandle *output_list, const int num_sets, const std::vector<std::string>& qa_list, - const Tag* tag_list, - int num_tags, - int export_dimension); + const Tag* tag_list = NULL, + int num_tags = 0, + int export_dimension = 3); //! struct used to hold data for each block to be output; used by //! initialize_file to initialize the file header for increased speed Modified: MOAB/trunk/src/io/WriteCCMIO.hpp =================================================================== --- MOAB/trunk/src/io/WriteCCMIO.hpp 2013-02-15 19:46:42 UTC (rev 6006) +++ MOAB/trunk/src/io/WriteCCMIO.hpp 2013-02-15 22:13:04 UTC (rev 6007) @@ -67,9 +67,9 @@ const EntityHandle *output_list, const int num_sets, const std::vector<std::string>& qa_list, - const Tag* tag_list, - int num_tags, - int export_dimension); + const Tag* tag_list = NULL, + int num_tags = 0, + int export_dimension = 3); protected: Modified: MOAB/trunk/src/io/WriteDamsel.hpp ===================================================================

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r6003 - MOAB/trunk/src/io
by iulian＠mcs.anl.gov 14 Feb '13

14 Feb '13

Author: iulian Date: 2013-02-14 11:20:57 -0600 (Thu, 14 Feb 2013) New Revision: 6003 Modified: MOAB/trunk/src/io/ReadNC.cpp Log: mbsize and mbconvert for NC files worked only if READ_PART was passed as an option now, check more carefully for USE_MPI and isParallel flag; local member data myPcomm is not initialized, except if the READ_PART option is used so do not use myPcomm if isParallel is false Modified: MOAB/trunk/src/io/ReadNC.cpp =================================================================== --- MOAB/trunk/src/io/ReadNC.cpp 2013-02-14 17:04:34 UTC (rev 6002) +++ MOAB/trunk/src/io/ReadNC.cpp 2013-02-14 17:20:57 UTC (rev 6003) @@ -488,7 +488,10 @@ if (!isParallel) // return success here, since rval still has _NOT_FOUND from not finding option + // in this case, myPcomm will be NULL, so it can never be used; always check for isParallel + // before any use for myPcomm return MB_SUCCESS; + int pcomm_no = 0; rval = opts.get_int_option("PARALLEL_COMM", pcomm_no); @@ -724,7 +727,8 @@ // in one shot bool create_gathers = true; #ifdef USE_MPI - if (myPcomm->proc_config().proc_rank() != 0) create_gathers = false; + if (isParallel) + if (myPcomm->proc_config().proc_rank() != 0) create_gathers = false; #endif // compute the number of local quads, accounting for coarse or fine representation @@ -866,7 +870,7 @@ // if (gatherOpt) { #ifdef USE_MPI - if (myPcomm->proc_config().proc_rank() == 0) { + if (isParallel && myPcomm->proc_config().proc_rank() == 0) { #endif EntityHandle gather_set; rval = mbImpl->create_meshset(MESHSET_SET, gather_set); @@ -1986,7 +1990,7 @@ #ifdef USE_MPI // if serial, use a locally-periodic representation only if local mesh is periodic, otherwise don't - if ((myPcomm->proc_config().proc_size() == 1) && globallyPeriodic[0]) + if ((isParallel && myPcomm->proc_config().proc_size() == 1) && globallyPeriodic[0]) locallyPeriodic[0] = 1; #else if (globallyPeriodic[0]) @@ -3335,9 +3339,16 @@ std::size_t numOwnedEnts = 0; #ifdef USE_MPI Range ents_owned; - rval = myPcomm->filter_pstatus(ents, PSTATUS_NOT_OWNED, PSTATUS_NOT, -1, &ents_owned); - ERRORR(rval, "Trouble getting owned QUAD entity."); - numOwnedEnts = ents_owned.size(); + if (isParallel){

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r6002 - MOAB/trunk/src/io
by iulian＠mcs.anl.gov 14 Feb '13

14 Feb '13

Author: iulian Date: 2013-02-14 11:04:34 -0600 (Thu, 14 Feb 2013) New Revision: 6002 Modified: MOAB/trunk/src/io/ReadCGM.cpp Log: remove reference to CUBIT_12, it is not needed anymore, because we are not going to support cubit 10 anymore, and cubit 13 has the same signature for the import_solid_model and export_... methods (as cubit 12) Modified: MOAB/trunk/src/io/ReadCGM.cpp =================================================================== --- MOAB/trunk/src/io/ReadCGM.cpp 2013-02-13 17:19:42 UTC (rev 6001) +++ MOAB/trunk/src/io/ReadCGM.cpp 2013-02-14 17:04:34 UTC (rev 6002) @@ -41,9 +41,7 @@ #include "moab/GeomTopoTool.hpp" -#ifdef CUBIT_12 # include "CubitCompat.hpp" -#endif #include <stdio.h> #include <algorithm> @@ -193,11 +191,7 @@ if (!file_type || !strcmp(file_type ,"CUBIT")) return MB_FAILURE; -#ifndef CUBIT_12 - s = GeometryQueryTool::instance()->import_solid_model( cgm_file_name, file_type ); -#else s = CubitCompat_import_solid_model( cgm_file_name, file_type ); -#endif if (CUBIT_SUCCESS != s) { readUtilIface->report_error( "%s: Failed to read file of type \"%s\"", cgm_file_name, file_type ); return MB_FAILURE;

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buildbot failure in moab-cub-par-tru: failed shell test install
by moab-dev＠mcs.anl.gov 14 Feb '13

14 Feb '13

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