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

r5762 - MOAB/trunk/src/io
by iulian＠mcs.anl.gov 29 Sep '12

29 Sep '12

Author: iulian Date: 2012-09-29 13:44:46 -0500 (Sat, 29 Sep 2012) New Revision: 5762 Modified: MOAB/trunk/src/io/ReadNC.cpp Log: correct reading data to set; new double[] bug too Modified: MOAB/trunk/src/io/ReadNC.cpp =================================================================== --- MOAB/trunk/src/io/ReadNC.cpp 2012-09-28 14:41:33 UTC (rev 5761) +++ MOAB/trunk/src/io/ReadNC.cpp 2012-09-29 18:44:46 UTC (rev 5762) @@ -1222,8 +1222,7 @@ ErrorCode rval = MB_SUCCESS; for (unsigned int i = 0; i < vdatas.size(); ++i) { - if ((std::find(vdatas[i].varDims.begin(), vdatas[i].varDims.end(), tDim) != vdatas[i].varDims.end()) - && (vdatas[i].varDims.size() != 1)) + if ((std::find(vdatas[i].varDims.begin(), vdatas[i].varDims.end(), tDim) != vdatas[i].varDims.end())) vdatas[i].has_t = true; for (unsigned int t = 0; t < tstep_nums.size(); ++t) { @@ -1240,9 +1239,20 @@ ERRORR(MB_INDEX_OUT_OF_RANGE, "Wrong value for timestep number."); // set up the dimensions and counts - // first time - vdatas[i].readDims[t].push_back(tstep_nums[t]); - vdatas[i].readCounts[t].push_back(1); + // first variable dimension is time, if it exists + if (vdatas[i].has_t) + { + if (vdatas[i].varDims.size() != 1) + { + vdatas[i].readDims[t].push_back(tstep_nums[t]); + vdatas[i].readCounts[t].push_back(1); + } + else + { + vdatas[i].readDims[t].push_back(0); + vdatas[i].readCounts[t].push_back(tstep_nums.size()); + } + } // set up other dimensions and counts if (vdatas[i].varDims.empty()) { @@ -1251,9 +1261,12 @@ vdatas[i].readCounts[t].push_back(1); } else { - for (unsigned int idx = 0; idx != vdatas[i].varDims.size(); ++idx) { - vdatas[i].readDims[t].push_back(0); - vdatas[i].readCounts[t].push_back(dimVals[vdatas[i].varDims[idx]]); + for (unsigned int idx = 0; idx != vdatas[i].varDims.size(); ++idx){ + if (tDim != vdatas[i].varDims[idx]){ + // push other variable dimensions, except time, which was already pushed + vdatas[i].readDims[t].push_back(0); + vdatas[i].readCounts[t].push_back(dimVals[vdatas[i].varDims[idx]]); + }

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r5761 - MOAB/trunk/itaps/igeom
by iulian＠mcs.anl.gov 28 Sep '12

28 Sep '12

Author: iulian Date: 2012-09-28 09:41:33 -0500 (Fri, 28 Sep 2012) New Revision: 5761 Modified: MOAB/trunk/itaps/igeom/Makefile.am Log: this caused problems down the line, more exactly in Lasso, mesquite and MeshKit this explicitly defines dependency of FBiGeom to the moab main library Modified: MOAB/trunk/itaps/igeom/Makefile.am =================================================================== --- MOAB/trunk/itaps/igeom/Makefile.am 2012-09-27 23:30:15 UTC (rev 5760) +++ MOAB/trunk/itaps/igeom/Makefile.am 2012-09-28 14:41:33 UTC (rev 5761) @@ -15,7 +15,7 @@ libFBiGeomMOAB_la_includedir = $(includedir) -#libFBiGeomMOAB_la_LIBADD = $(top_builddir)/libMOAB.la +libFBiGeomMOAB_la_LIBADD = $(top_builddir)/src/libMOAB.la libFBiGeomMOAB_la_SOURCES = \ FBiGeom_MOAB.hpp \

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r5758 - MOAB/trunk/src/io
by iulian＠mcs.anl.gov 27 Sep '12

27 Sep '12

Author: iulian Date: 2012-09-27 15:29:19 -0500 (Thu, 27 Sep 2012) New Revision: 5758 Modified: MOAB/trunk/src/io/ReadNC.cpp MOAB/trunk/src/io/ReadNC.hpp Log: correct reading data in parallel for Homme grids, considering the local range of the global id, for vertices. Still, it does not work yet in parallel. Also, reformat the code, I could not read it, it had lots of tabs (so replace tabs with 2 spaces, and indentation is now at 2 spaces) Modified: MOAB/trunk/src/io/ReadNC.cpp =================================================================== --- MOAB/trunk/src/io/ReadNC.cpp 2012-09-27 16:41:29 UTC (rev 5757) +++ MOAB/trunk/src/io/ReadNC.cpp 2012-09-27 20:29:19 UTC (rev 5758) @@ -22,26 +22,23 @@ #define ERRORR(rval, str) \ if (MB_SUCCESS != rval) {readMeshIface->report_error("%s", str); return rval;} - + #define ERRORS(err, str) \ if (err) {readMeshIface->report_error("%s", str); return MB_FAILURE;} - + namespace moab { -ReaderIface* ReadNC::factory( Interface* iface ) - { return new ReadNC( iface ); } +ReaderIface* ReadNC::factory(Interface* iface) { + return new ReadNC(iface); +} -ReadNC::ReadNC(Interface* impl) - : mbImpl(impl), CPU_WORD_SIZE(-1), IO_WORD_SIZE(-1), fileId(-1), - tMin(-1), tMax(-1), - iDim(-1), jDim(-1), tDim(-1), iCDim(-1), jCDim(-1), - numUnLim(-1), mCurrentMeshHandle(0), - startVertex(0), startElem(0), mGlobalIdTag(0), - max_line_length(-1), max_str_length(-1), vertexOffset(0), dbgOut(stderr), - isParallel(false), partMethod(-1), ucdMesh(false) +ReadNC::ReadNC(Interface* impl) : + mbImpl(impl), CPU_WORD_SIZE(-1), IO_WORD_SIZE(-1), fileId(-1), tMin(-1), tMax(-1), iDim(-1), jDim(-1), tDim(-1), iCDim(-1), + jCDim(-1), numUnLim(-1), mCurrentMeshHandle(0), startVertex(0), startElem(0), mGlobalIdTag(0), max_line_length(-1), + max_str_length(-1), vertexOffset(0), dbgOut(stderr), isParallel(false), partMethod(-1), ucdMesh(false) #ifdef USE_MPI - , myPcomm(NULL) +, myPcomm(NULL) #endif { assert(impl != NULL); @@ -52,15 +49,14 @@ gCDims[i] = -1; lCDims[i] = -1; } - + locallyPeriodic[0] = locallyPeriodic[1] = 0; globallyPeriodic[0] = globallyPeriodic[1] = 0; - +

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r5752 - MOAB/trunk/tools/mbcoupler
by jain＠mcs.anl.gov 25 Sep '12

25 Sep '12

Author: jain Date: 2012-09-25 13:33:05 -0500 (Tue, 25 Sep 2012) New Revision: 5752 Modified: MOAB/trunk/tools/mbcoupler/mbcoupler_test.cpp Log: Adding extra option PARALLEL_COMM= for write_file, gets rid of error - not receive valid id handle for shared Vertex. All test cases with mbcoupler_test now work. Modified: MOAB/trunk/tools/mbcoupler/mbcoupler_test.cpp =================================================================== --- MOAB/trunk/tools/mbcoupler/mbcoupler_test.cpp 2012-09-25 17:53:15 UTC (rev 5751) +++ MOAB/trunk/tools/mbcoupler/mbcoupler_test.cpp 2012-09-25 18:33:05 UTC (rev 5752) @@ -185,7 +185,11 @@ Range partSets; // only save the target mesh partSets.insert((EntityHandle)roots[1]); - result = mbImpl->write_file(outFile.c_str(), NULL, writeOpts.c_str(), partSets); + std::string newwriteOpts; + std::ostringstream extraOpt; + extraOpt << ";PARALLEL_COMM=" << 1; + newwriteOpts = writeOpts+extraOpt.str(); + result = mbImpl->write_file(outFile.c_str(), NULL, newwriteOpts.c_str(), partSets); PRINT_LAST_ERROR; std::cout << "Wrote " << outFile << std::endl; std::cout << "mbcoupler_test complete." << std::endl;

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r5749 - MOAB/trunk/tools/mbcoupler
by iulian＠mcs.anl.gov 25 Sep '12

25 Sep '12

Author: iulian Date: 2012-09-25 01:25:55 -0500 (Tue, 25 Sep 2012) New Revision: 5749 Modified: MOAB/trunk/tools/mbcoupler/Coupler.cpp MOAB/trunk/tools/mbcoupler/mbcoupler_test.cpp Log: the initial box test needs to have the same absolute epsilon, otherwise some points might be left out. Vijay asked about it at some point today, but I, of course, dismissed the question. still, some problems appear later, but at least there are no missing points now, when we increase the number of processors also, I am printing more things in the coupler, maybe these should be removed when we fix the other problems that appear. Modified: MOAB/trunk/tools/mbcoupler/Coupler.cpp =================================================================== --- MOAB/trunk/tools/mbcoupler/Coupler.cpp 2012-09-24 17:25:39 UTC (rev 5748) +++ MOAB/trunk/tools/mbcoupler/Coupler.cpp 2012-09-25 06:25:55 UTC (rev 5749) @@ -291,9 +291,9 @@ if (j == my_rank) continue; // test if point is in proc's box - if (allBoxes[6*j] <= xyz[i] && xyz[i] <= allBoxes[6*j+3] && - allBoxes[6*j+1] <= xyz[i+1] && xyz[i+1] <= allBoxes[6*j+4] && - allBoxes[6*j+2] <= xyz[i+2] && xyz[i+2] <= allBoxes[6*j+5]) + if ( (allBoxes[6*j] <= xyz[i]+abs_eps) && ( xyz[i] <= allBoxes[6*j+3]+abs_eps) && + (allBoxes[6*j+1] <= xyz[i+1]+abs_eps) && (xyz[i+1] <= allBoxes[6*j+4]+abs_eps) && + (allBoxes[6*j+2] <= xyz[i+2]+abs_eps) && (xyz[i+2] <= allBoxes[6*j+5]+abs_eps)) { // if in this proc's box, will send to proc to test further // check size, grow if we're at max @@ -311,10 +311,14 @@ } } + printf("rank: %d local points: %d, nb sent target pts: %d mappedPts: %d \n", + my_rank, num_points, target_pts.get_n(), mappedPts->get_n()); // perform scatter/gather, to gather points to source mesh procs if (myPc) { (myPc->proc_config().crystal_router())->gs_transfer(1, target_pts, 0); + printf("rank: %d after first gs nb received_pts: %d\n", + my_rank, target_pts.get_n()); // after scatter/gather: // target_pts.set_n( # points local proc has to map ); // target_pts.vi_wr[2*i] = proc sending point i @@ -344,8 +348,13 @@ // no longer need target_pts target_pts.reset(); + printf("rank: %d nb sent source pts: %d, mappedPts now: %d\n", + my_rank, source_pts.get_n(), mappedPts->get_n()); // send target points back to target procs (myPc->proc_config().crystal_router())->gs_transfer(1, source_pts, 0); + + printf("rank: %d nb received source pts: %d\n", + my_rank, source_pts.get_n()); } // store proc/index tuples in targetPts, and/or pass back to application; @@ -380,9 +389,9 @@ int locIndex = source_pts.vi_rd[3*i+1]; if(located_pts[locIndex]){ - //asked 2+ procs if they have point p, they both said yes, we'll keep the one with lowest rank

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r5747 - MOAB/trunk/tools/vtkMOABReader
by obara＠mcs.anl.gov 23 Sep '12

23 Sep '12

Author: obara Date: 2012-09-23 19:27:43 -0500 (Sun, 23 Sep 2012) New Revision: 5747 Added: MOAB/trunk/tools/vtkMOABReader/TestMOABModelReader.cxx Modified: MOAB/trunk/tools/vtkMOABReader/CMakeLists.txt.in MOAB/trunk/tools/vtkMOABReader/vtkMOABReader.cxx MOAB/trunk/tools/vtkMOABReader/vtkMOABReader.h Log: Adding an updated version of the vtkMOABReader and an additional test Modified: MOAB/trunk/tools/vtkMOABReader/CMakeLists.txt.in =================================================================== --- MOAB/trunk/tools/vtkMOABReader/CMakeLists.txt.in 2012-09-21 17:40:02 UTC (rev 5746) +++ MOAB/trunk/tools/vtkMOABReader/CMakeLists.txt.in 2012-09-24 00:27:43 UTC (rev 5747) @@ -1,3 +1,4 @@ +CMAKE_MINIMUM_REQUIRED(VERSION 2.8.2 FATAL_ERROR) SET(MOAB_DIR "@abs_builddir@/../.." CACHE PATH "MOAB base directory") if (MOAB_DIR) INCLUDE_DIRECTORIES(${MOAB_DIR}/include @srcdir@) @@ -3,10 +4,46 @@ LINK_DIRECTORIES(${MOAB_DIR}/lib) LINK_LIBRARIES(MOAB) -CMAKE_MINIMUM_REQUIRED(VERSION 2.6.3) -FIND_PACKAGE(ParaView REQUIRED) -INCLUDE(${PARAVIEW_USE_FILE}) - ADD_PARAVIEW_PLUGIN(vtkMOABReader "4.0" - SERVER_MANAGER_XML @srcdir@/vtkMOABReader.xml - SERVER_MANAGER_SOURCES @srcdir@/vtkMOABReader.cxx - GUI_RESOURCE_FILES @srcdir@/vtkMOABReaderGUI.xml) + + FIND_PACKAGE (ParaView REQUIRED) + IF(ParaView_FOUND) + include (${PARAVIEW_USE_FILE}) + ELSE(ParaView_FOUND) + message(FATAL_ERROR "Please set the path to ParaView build") + ENDIF(ParaView_FOUND) + + if(APPLE) + ADD_EXECUTABLE(TestMOABModelReader MACOSX_BUNDLE + TestMOABModelReader.cxx + vtkMOABReader.cxx) + else(APPLE) + ADD_EXECUTABLE(TestMOABModelReader + TestMOABModelReader.cxx + vtkMOABReader.cxx) + endif(APPLE) + + if(VTK_LIBRARIES) + SET(VTK_LIBS ${VTK_LIBRARIES}) + else(VTK_LIBRARIES) + SET(VTK_LIBS + vtkHybrid + vtkRendering) + endif(VTK_LIBRARIES) + + ADD_PARAVIEW_PLUGIN(vtkMOABReader "4.0" + SERVER_MANAGER_XML @srcdir@/vtkMOABReader.xml + SERVER_MANAGER_SOURCES @srcdir@/vtkMOABReader.cxx + GUI_RESOURCE_FILES @srcdir@/vtkMOABReaderGUI.xml) + + FIND_LIBRARY(MOAB_LIBRARY MOAB)

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r5739 - in MOAB/trunk/src: . io
by tautges＠mcs.anl.gov 14 Sep '12

14 Sep '12

Author: tautges Date: 2012-09-14 12:35:14 -0500 (Fri, 14 Sep 2012) New Revision: 5739 Modified: MOAB/trunk/src/FBEngine.cpp MOAB/trunk/src/io/ReadCCMIO.cpp Log: Removing some compiler warnings. Modified: MOAB/trunk/src/FBEngine.cpp =================================================================== --- MOAB/trunk/src/FBEngine.cpp 2012-09-14 14:20:05 UTC (rev 5738) +++ MOAB/trunk/src/FBEngine.cpp 2012-09-14 17:35:14 UTC (rev 5739) @@ -822,32 +822,36 @@ return MB_FAILURE; } - ErrorCode rval; + ErrorCode rval = MB_SUCCESS; adjs.clear(); if (to_dim > this_dim) { int diffDim = to_dim-this_dim; rval = MBI->get_parent_meshsets(from, adjs, diffDim); + if (MB_SUCCESS != rval) return rval; if (diffDim>1) { // subtract the parents that come with diffDim-1 hops Range extra; rval = MBI->get_parent_meshsets(from, extra, diffDim-1); + if (MB_SUCCESS != rval) return rval; adjs = subtract(adjs, extra); } } else { int diffDim = this_dim - to_dim; rval = MBI->get_child_meshsets(from, adjs, diffDim); + if (MB_SUCCESS != rval) return rval; if (diffDim > 1) { // subtract the children that come with diffDim-1 hops Range extra; rval = MBI->get_child_meshsets(from, extra, diffDim-1); + if (MB_SUCCESS != rval) return rval; adjs = subtract(adjs, extra); } } - return MB_SUCCESS; + return rval; } // so far, this one is @@ -2216,6 +2220,7 @@ MBERRORR(MB_FAILURE, " can't get third node"); CartVect Pt[3]; rval = _mbImpl->get_coords(conn3, 3, (double*) &Pt[0]); + MBERRORR(rval, "Failed to get coords"); int indexFirst = (thirdIndex + 1) % 3; int indexSecond = (thirdIndex + 2) % 3; int index[2] = { indexFirst, indexSecond };

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buildbot failure in moab-occ-par: failed compile
by moab-dev＠mcs.anl.gov 14 Sep '12

14 Sep '12

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buildbot failure in moab-occ-par: failed compile
by moab-dev＠mcs.anl.gov 14 Sep '12

14 Sep '12

1 0

buildbot failure in moab-cub-par-sha: failed compile
by moab-dev＠mcs.anl.gov 14 Sep '12

14 Sep '12

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