July 2009 - moab-dev - mailman3.cels.anl.gov

r3087 - MOAB/trunk/parallel
by kraftche＠cae.wisc.edu 31 Jul '09

31 Jul '09

Author: kraftche Date: 2009-07-31 14:20:03 -0500 (Fri, 31 Jul 2009) New Revision: 3087 Modified: MOAB/trunk/parallel/parallel_write_test.cc Log: typo Modified: MOAB/trunk/parallel/parallel_write_test.cc =================================================================== --- MOAB/trunk/parallel/parallel_write_test.cc 2009-07-31 18:31:51 UTC (rev 3086) +++ MOAB/trunk/parallel/parallel_write_test.cc 2009-07-31 19:20:03 UTC (rev 3087) @@ -21,7 +21,7 @@ } const int DEFAULT_INTERVALS = 2; -const char* DEFAULT_FILE_NAME = "paralle_write_test.h5m"; +const char* DEFAULT_FILE_NAME = "parallel_write_test.h5m"; // Create mesh for each processor that is a cube of hexes // with the specified interval count along each edge. Cubes

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r3086 - MOAB/trunk/parallel
by kraftche＠cae.wisc.edu 31 Jul '09

31 Jul '09

Author: kraftche Date: 2009-07-31 13:31:51 -0500 (Fri, 31 Jul 2009) New Revision: 3086 Modified: MOAB/trunk/parallel/parallel_write_test.cc Log: print times Modified: MOAB/trunk/parallel/parallel_write_test.cc =================================================================== --- MOAB/trunk/parallel/parallel_write_test.cc 2009-07-30 23:30:35 UTC (rev 3085) +++ MOAB/trunk/parallel/parallel_write_test.cc 2009-07-31 18:31:51 UTC (rev 3086) @@ -150,6 +150,7 @@ // Create mesh TPRINT("Generating mesh"); + double gen_time = MPI_Wtime(); MBCore mb; MBInterface& moab = mb; MBErrorCode rval = generate_mesh( moab, intervals ); @@ -157,7 +158,8 @@ std::cerr << "Mesh creation failed with error code: " << rval << std::endl; return (int)rval; } - + gen_time = MPI_Wtime() - gen_time; + // Write out local mesh on each processor if requested. if (indiv_file_name) { TPRINT("Writing individual file"); @@ -174,6 +176,7 @@ } TPRINT("Resolving shared entities"); + double res_time = MPI_Wtime(); // Negotiate shared entities using vertex global IDs MBRange hexes; moab.get_entities_by_type( 0, MBHEX, hexes ); @@ -183,8 +186,10 @@ std::cerr << "MBParallelComm::resolve_shared_ents failed" << std::endl; return rval; } + res_time = MPI_Wtime() - res_time; TPRINT("Beginning parallel write"); + double write_time = MPI_Wtime(); // Do parallel write clock_t t = clock(); rval = moab.write_file( output_file_name, "MOAB", "PARALLEL=WRITE_PART" ); @@ -196,7 +201,12 @@ std::cerr << "\t\"" << msg << '"' << std::endl; return (int)rval; } + write_time = MPI_Wtime() - write_time; + double times[3] = { gen_time, res_time, write_time }; + double max[3] = { 0, 0, 0 }; + MPI_Reduce( times, max, 3, MPI_DOUBLE, MPI_MAX, 0, MPI_COMM_WORLD ); + // Clean up and summarize if (0 == rank) { double sec = (double)t / CLOCKS_PER_SEC; @@ -206,6 +216,10 @@ TPRINT("Removing written file"); remove( output_file_name ); } + + std::cout << "Wall time: generate: " << max[0] + << ", resovle shared: " << max[1] + << ", write_file: " << max[2] << std::endl; } TPRINT("Finalizing MPI");

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r3085 - in MOAB/trunk: . parallel
by kraftche＠cae.wisc.edu 30 Jul '09

30 Jul '09

Author: kraftche Date: 2009-07-30 18:30:35 -0500 (Thu, 30 Jul 2009) New Revision: 3085 Modified: MOAB/trunk/RangeMap.hpp MOAB/trunk/ReadHDF5.cpp MOAB/trunk/WriteHDF5.cpp MOAB/trunk/parallel/WriteHDF5Parallel.cpp Log: Fix reoccuring bug using RangeMap the right way. Rather than return end() from insert(..) when the insertion fails, which leads to broken code such as: if (idmap.end() != idmap.insert(..)) instead return std::pair<iterator,bool> where the second value indicates the success of the insertion and the first value is the position of insertion or the conflicting range that prevented the insertion. This is more consistent with STL containers for which insertion can fail (std::set and std::map) and prevents the above coding mistake. Modified: MOAB/trunk/RangeMap.hpp =================================================================== --- MOAB/trunk/RangeMap.hpp 2009-07-30 23:23:13 UTC (rev 3084) +++ MOAB/trunk/RangeMap.hpp 2009-07-30 23:30:35 UTC (rev 3085) @@ -56,9 +56,11 @@ * Insert mapping from [first_key, first_key+count) to [first_val, first_val+count) * * Input range of keys many not overlap any other input range. If it does overlap - * an existing range, end() is returned and the internal map is not changed. + * an existing range, the second value of the pair will be returned as false + * and the iterator will point to (one of) the overlapping ranges. */ - inline iterator insert( KeyType first_key, ValType first_val, KeyType count ); + inline std::pair<iterator,bool> + insert( KeyType first_key, ValType first_val, KeyType count ); /** Find the value corresponding to the specified key. Returns NullVal if not found */ inline ValType find( KeyType key ) const; @@ -110,7 +112,7 @@ }; template <typename KeyType, typename ValType, ValType NullVal> -inline typename RangeMap<KeyType,ValType,NullVal>::iterator +inline std::pair<typename RangeMap<KeyType,ValType,NullVal>::iterator,bool> RangeMap<KeyType,ValType,NullVal>::insert( KeyType first_key, ValType first_val, KeyType count ) { Range block = { first_key, count, first_val }; @@ -122,15 +124,15 @@ if (i->begin + i->count == first_key && i->value + i->count == first_val) { i->count += count; - return i; + return std::pair<iterator,bool>(i,true); } } data.push_back( block ); - return data.end() - 1; + return std::pair<iterator,bool>(data.end() - 1,true); } if (i->begin < first_key + count) - return data.end(); + return std::pair<iterator,bool>(i,false); if (i->begin == first_key + count && i->value == first_val + count) { @@ -148,7 +150,7 @@ --i; } } - return i; + return std::pair<iterator,bool>(i,true); } if (i != data.begin()) { @@ -156,12 +158,12 @@ if (i->begin + i->count == first_key && i->value + i->count == first_val) { i->count += count; - return i; + return std::pair<iterator,bool>(i,true); } ++i; } - return data.insert( i, block ); + return std::pair<iterator,bool>(data.insert( i, block ),true); } Modified: MOAB/trunk/ReadHDF5.cpp =================================================================== --- MOAB/trunk/ReadHDF5.cpp 2009-07-30 23:23:13 UTC (rev 3084) +++ MOAB/trunk/ReadHDF5.cpp 2009-07-30 23:30:35 UTC (rev 3085) @@ -968,8 +968,7 @@ memset( arrays[i], 0, count*sizeof(double) ); arrays[i] += count; } - IDMap::iterator ins = idMap.insert( p->first, handle, count ); - if (ins == idMap.end()) { + if (!idMap.insert( p->first, handle, count ).second) { mhdf_closeData( filePtr, data_id, &status ); return error(MB_FAILURE); } @@ -1034,8 +1033,7 @@ array ); if (MB_SUCCESS != rval) break; - IDMap::iterator ins = idMap.insert( p->first, handle, count ); - if (ins == idMap.end()) + if (!idMap.insert( p->first, handle, count ).second) { rval = MB_FAILURE; break; } mhdf_readConnectivityWithOpt( data_id, p->first - first_id, count, handleType, array, indepIO, &status ); @@ -1145,8 +1143,7 @@ iter += node_per_elem; continue; } - IDMap::iterator ins = idMap.insert( start_id + i, h++, 1 ); - if (ins == idMap.end()) + if (!idMap.insert( start_id + i, h++, 1 ).second) return error(MB_FAILURE); long* const end = iter + node_per_elem; @@ -1236,8 +1233,7 @@ MBErrorCode rval = mb->create_element( type, conn, len, handle ); if (MB_SUCCESS != rval) return error(rval); - IDMap::iterator ins = idMap.insert( file_id, handle, 1 ); - if (ins == idMap.end()) + if (!idMap.insert( file_id, handle, 1 ).second) return error(MB_FAILURE); return MB_SUCCESS; } @@ -2068,8 +2064,7 @@ MBEntityHandle h = start_handle; for (p = file_ids.const_pair_begin(); p != file_ids.const_pair_end(); ++p) { long count = p->second - p->first + 1; - IDMap::iterator ins = idMap.insert( p->first, h, count ); - if (ins == idMap.end()) + if (!idMap.insert( p->first, h, count ).second) return error(MB_FAILURE); h += count; } Modified: MOAB/trunk/WriteHDF5.cpp =================================================================== --- MOAB/trunk/WriteHDF5.cpp 2009-07-30 23:23:13 UTC (rev 3084) +++ MOAB/trunk/WriteHDF5.cpp 2009-07-30 23:30:35 UTC (rev 3085) @@ -251,8 +251,7 @@ (unsigned long)id, (unsigned long)(id+n-1)); #endif - RangeMap<MBEntityHandle,id_t>::iterator it = idMap.insert( pi->first, id, n ); - if (idMap.end() == it) + if (!idMap.insert( pi->first, id, n ).second) return MB_FAILURE; id += n; } Modified: MOAB/trunk/parallel/WriteHDF5Parallel.cpp =================================================================== --- MOAB/trunk/parallel/WriteHDF5Parallel.cpp 2009-07-30 23:23:13 UTC (rev 3084) +++ MOAB/trunk/parallel/WriteHDF5Parallel.cpp 2009-07-30 23:30:35 UTC (rev 3085) @@ -1350,7 +1350,6 @@ if (p == val_id_map.end()) val_id_map[data.all_values[i]] = offset++; } - RangeMap<MBEntityHandle,id_t>::iterator insp; MBRange::const_iterator riter = data.range.begin(); for (size_t i = 0; i < data.local_values.size(); ++i, ++riter) { @@ -1358,8 +1357,7 @@ assert( p != val_id_map.end() ); long id = p->second; - insp = idMap.insert( *riter, id, 1 ); - if (idMap.end() == insp) { + if (!idMap.insert( *riter, id, 1 ).second) { for (unsigned x = 0; x < myPcomm->size(); ++x) { MPI_Barrier( myPcomm->proc_config().proc_comm() ); if (x != myPcomm->rank()) continue; @@ -2121,7 +2119,6 @@ } // store file IDs for remote entities - RangeMap<MBEntityHandle,id_t>::iterator insp; for (proc_iter p = interfaceMesh.begin(); p != interfaceMesh.end(); ++p) { if (p->first == myPcomm->proc_config().proc_rank()) continue; @@ -2141,8 +2138,7 @@ return MB_FAILURE; } else { - insp = idMap.insert( *i, *j, 1 ); - if (insp == idMap.end()) { + if (!idMap.insert( *i, *j, 1 ).second) { iFace->tag_delete( file_id_tag ); return MB_FAILURE; }

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r3084 - MOAB/trunk
by kraftche＠cae.wisc.edu 30 Jul '09

30 Jul '09

Author: kraftche Date: 2009-07-30 18:23:13 -0500 (Thu, 30 Jul 2009) New Revision: 3084 Modified: MOAB/trunk/configure.ac Log: typo in previous checkin Modified: MOAB/trunk/configure.ac =================================================================== --- MOAB/trunk/configure.ac 2009-07-30 23:22:11 UTC (rev 3083) +++ MOAB/trunk/configure.ac 2009-07-30 23:23:13 UTC (rev 3084) @@ -69,7 +69,7 @@ DEFINES="$DEFINES $TEMPLATE_SPECIALIZATION $TEMPLATE_FUNC_SPECIALIZATION" if test "xno" != "x$CONFIGURE_FORTRAN"; then - if text "x" != "FC"; then + if test "x" != "x$FC"; then AC_FC_WRAPPERS fi fi

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r3083 - MOAB/trunk
by kraftche＠cae.wisc.edu 30 Jul '09

30 Jul '09

Author: kraftche Date: 2009-07-30 18:22:11 -0500 (Thu, 30 Jul 2009) New Revision: 3083 Modified: MOAB/trunk/configure.ac Log: don't fail if no FORTRAN compiler Modified: MOAB/trunk/configure.ac =================================================================== --- MOAB/trunk/configure.ac 2009-07-30 20:10:47 UTC (rev 3082) +++ MOAB/trunk/configure.ac 2009-07-30 23:22:11 UTC (rev 3083) @@ -69,7 +69,9 @@ DEFINES="$DEFINES $TEMPLATE_SPECIALIZATION $TEMPLATE_FUNC_SPECIALIZATION" if test "xno" != "x$CONFIGURE_FORTRAN"; then - AC_FC_WRAPPERS + if text "x" != "FC"; then + AC_FC_WRAPPERS + fi fi ################################################################################

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failing tests
by Jed Brown 30 Jul '09

30 Jul '09

I don't see the buildbot complaining, but I've got several failing tests. Ignore this if you're already aware of them. Jed $ make check Making check in mhdf make[1]: Entering directory `/home/jed/build/moab/bompi/mhdf' make[1]: Nothing to be done for `check'. make[1]: Leaving directory `/home/jed/build/moab/bompi/mhdf' Making check in parallel make[1]: Entering directory `/home/jed/build/moab/bompi/parallel' make[2]: Entering directory `/home/jed/build/moab/bompi/parallel' make mbparallelcomm_test pcomm_unit parallel_unit_tests parallel_hdf5_test mhdf_parallel parallel_write_test make[3]: Entering directory `/home/jed/build/moab/bompi/parallel' make[3]: `mbparallelcomm_test' is up to date. make[3]: `pcomm_unit' is up to date. make[3]: `parallel_unit_tests' is up to date. make[3]: `parallel_hdf5_test' is up to date. make[3]: `mhdf_parallel' is up to date. make[3]: `parallel_write_test' is up to date. make[3]: Leaving directory `/home/jed/build/moab/bompi/parallel' make check-TESTS make[3]: Entering directory `/home/jed/build/moab/bompi/parallel' Running test_pack_vertices ... Running test_pack_elements ... Running test_pack_higher_order ... Running test_pack_poly ... Running test_pack_sets_simple ... Running test_pack_set_contents ... Running test_pack_sets_of_sets ... Running test_pack_set_parent_child ... Running test_pack_tag_data_sparse ... Running test_pack_tag_data_dense ... Running test_pack_tag_data_default_value ... Running test_pack_variable_length_tag ... Running test_pack_tag_handle_data ... Running test_pack_shared_entities_2d ... Running test_pack_shared_entities_3d ... Running test_pack_vertices ... Running test_pack_elements ... Running test_pack_higher_order ... Running test_pack_poly ... Running test_pack_sets_simple ... Running test_pack_set_contents ... Running test_pack_sets_of_sets ... Running test_pack_set_parent_child ... Running test_pack_tag_data_sparse ... Running test_pack_tag_data_dense ... Running test_pack_tag_data_default_value ... Running test_pack_variable_length_tag ... Running test_pack_tag_handle_data ... Running test_pack_shared_entities_2d ... Running test_pack_shared_entities_3d ... Running test_pack_shared_arbitrary ... HDF5-DIAG: Error detected in HDF5 (1.8.3) MPI-process 1: #000: ../../hdf5-1.8.3/src/H5F.c line 811 in H5Fis_hdf5(): unable to open file major: Low-level I/O minor: Unable to initialize object #001: ../../hdf5-1.8.3/src/H5FD.c line 1083 in H5FD_open(): open failed major: Virtual File Layer minor: Unable to initialize object #002: ../../hdf5-1.8.3/src/H5FDsec2.c line 362 in H5FD_sec2_open(): unable to open file major: File accessability minor: Unable to open file #003: ../../hdf5-1.8.3/src/H5FDsec2.c line 362 in H5FD_sec2_open(): No such file or directory major: Internal error (too specific to document in detail) minor: System error message MBErrorCode Test Failed: MB_SUCCESS == rval at line 1890 of '../../parallel/pcomm_unit.cpp' Expected value: Success (0) Actual value: Failure (14) test_pack_shared_arbitrary: FAILED Running test_filter_pstatus ... Running test_pack_shared_arbitrary ... HDF5-DIAG: Error detected in HDF5 (1.8.3) MPI-process 0: #000: ../../hdf5-1.8.3/src/H5F.c line 811 in H5Fis_hdf5(): unable to open file major: Low-level I/O minor: Unable to initialize object #001: ../../hdf5-1.8.3/src/H5FD.c line 1083 in H5FD_open(): open failed major: Virtual File Layer minor: Unable to initialize object #002: ../../hdf5-1.8.3/src/H5FDsec2.c line 362 in H5FD_sec2_open(): unable to open file major: File accessability minor: Unable to open file #003: ../../hdf5-1.8.3/src/H5FDsec2.c line 362 in H5FD_sec2_open(): No such file or directory major: Internal error (too specific to document in detail) minor: System error message MBErrorCode Test Failed: MB_SUCCESS == rval at line 1890 of '../../parallel/pcomm_unit.cpp' Expected value: Success (0) Actual value: Failure (14) test_pack_shared_arbitrary: FAILED Running test_filter_pstatus ... FAIL: pcomm_unit test_elements_on_several_procs : success test_ghost_elements_3_2_1 : success [brakk:17969] *** Process received signal *** [brakk:17969] Signal: Segmentation fault (11) [brakk:17969] Signal code: Address not mapped (1) [brakk:17969] Failing at address: 0x30111b0e8 [brakk:17969] [ 0] /lib/libpthread.so.0 [0x2b517342a790] [brakk:17969] [ 1] /lib/libc.so.6(memcpy+0x35) [0x2b51736b4335] [brakk:17969] [ 2] /home/jed/build/moab/bompi/.libs/libMOAB.so.0(_ZN14MBParallelComm15unpack_entitiesERPhbibRSt6vectorIS2_ImSaImEESaIS4_EES7_RS2_IS2_IiSaIiEESaIS9_EERS4_SD_RS2_IjSaIjEER7MBRange+0x2b8) [0x2b5170d81884] [brakk:17969] [ 3] /home/jed/build/moab/bompi/.libs/libMOAB.so.0(_ZN14MBParallelComm20exchange_ghost_cellsEiiibb+0x134b) [0x2b5170d97b6d] [brakk:17969] [ 4] /home/jed/build/moab/bompi/.libs/libMOAB.so.0(_ZN12ReadParallel9load_fileEPPKciRmiRSsRSt6vectorIiSaIiEEbS8_RK11FileOptionsS1_PKiiibiiiii+0x76b) [0x2b5170db75fb] [brakk:17969] [ 5] /home/jed/build/moab/bompi/.libs/libMOAB.so.0(_ZN12ReadParallel9load_fileEPPKciRmRK11FileOptionsS1_PKii+0x75b) [0x2b5170db6d93] [brakk:17969] [ 6] /home/jed/build/moab/bompi/parallel/.libs/lt-parallel_unit_tests(_ZN12ReadParallel9load_fileEPKcRmRK11FileOptionsS1_PKii+0x5d) [0x4218d3] [brakk:17969] [ 7] /home/jed/build/moab/bompi/.libs/libMOAB.so.0(_ZN6MBCore9load_fileEPKcRmS1_S1_PKii+0x133) [0x2b5170c5e8e3] [brakk:17969] [ 8] /home/jed/build/moab/bompi/parallel/.libs/lt-parallel_unit_tests(_Z19test_ghost_elementsPKciii+0x14f) [0x41900e] [brakk:17969] [ 9] /home/jed/build/moab/bompi/parallel/.libs/lt-parallel_unit_tests(_Z25test_ghost_elements_3_2_2PKc+0x27) [0x41ac0c] [brakk:17969] [10] /home/jed/build/moab/bompi/parallel/.libs/lt-parallel_unit_tests(_Z8run_testPF11MBErrorCodePKcES1_S1_+0x21) [0x414d50] [brakk:17969] [11] /home/jed/build/moab/bompi/parallel/.libs/lt-parallel_unit_tests(main+0x2d1) [0x4150b6] [brakk:17969] [12] /lib/libc.so.6(__libc_start_main+0xfd) [0x2b51736569ed] [brakk:17969] [13] /home/jed/build/moab/bompi/parallel/.libs/lt-parallel_unit_tests [0x414a99] [brakk:17969] *** End of error message *** -------------------------------------------------------------------------- mpiexec noticed that process rank 1 with PID 17969 on node brakk exited on signal 11 (Segmentation fault). -------------------------------------------------------------------------- FAIL: parallel_unit_tests Running test_write_elements ... Running test_write_elements ... 0: Vertex 2: shared with processor 1 (owned by this processor) 0: Vertex 3: shared with processor 1 (owned by this processor) 0: Vertex 5: shared with processor 1 (owned by this processor) 0: Vertex 8: shared with processor 1 (owned by this processor) 0: Vertex 10: shared with processor 1 (owned by this processor) 0: Vertex 13: shared with processor 1 (owned by this processor) 0: Curve 2: shared with processor 1 (owned by this processor) 0: Curve 8: shared with processor 1 (owned by this processor) 0: Curve 11: shared with processor 1 (owned by this processor) 0: Curve 12: shared with processor 1 (owned by this processor) 0: Curve 14: shared with processor 1 (owned by this processor) 0: Curve 20: shared with processor 1 (owned by this processor) 0: Curve 24: shared with processor 1 (owned by this processor) 0: Surface 5: shared with processor 1 (owned by this processor) 0: Surface 11: shared with processor 1 (owned by this processor) 1: Vertex 2: shared with processor 0 1: Vertex 3: shared with processor 0 1: Vertex 5: shared with processor 0 1: Vertex 8: shared with processor 0 1: Vertex 10: shared with processor 0 1: Vertex 13: shared with processor 0 1: Curve 2: ERROR: 2 of 3 entities owned by this processor 1: Curve 8: ERROR: 2 of 3 entities owned by this processor 1: Curve 11: ERROR: 2 of 3 entities owned by this processor 1: Curve 12: ERROR: 2 of 3 entities owned by this processor 1: Curve 14: ERROR: 2 of 3 entities owned by this processor 1: Curve 20: ERROR: 2 of 3 entities owned by this processor 1: Curve 24: ERROR: 2 of 3 entities owned by this processor 1: Surface 5: ERROR: 8 of 9 entities owned by this processor 1: Surface 11: ERROR: 8 of 9 entities owned by this processor Running test_write_shared_sets ... Equality Test Failed: r1.size() == r2.size() at line 325 of '../../parallel/parallel_hdf5_test.cc' Expected value: 168 Actual value: 146 test_write_elements: FAILED Running test_write_shared_sets ... Running test_var_length_parallel ... Running test_var_length_parallel ... FAIL: parallel_hdf5_test PASS: mhdf_parallel Using default interval count: 2 Using default interval count: 2 00: 0.00: Generating mesh 01: 0.01: Generating mesh 00: 0.00: Resolving shared entities 01: 0.01: Resolving shared entities 00: 0.00: Beginning parallel write 01: 0.01: Beginning parallel write 01: 0.02: Finalizing MPI 00: 0.01: Removing written file Wrote 16 hexes in 0.01 seconds. 00: 0.01: Finalizing MPI PASS: parallel_write_test =================== 3 of 5 tests failed =================== make[3]: *** [check-TESTS] Error 1 make[3]: Leaving directory `/home/jed/build/moab/bompi/parallel' make[2]: *** [check-am] Error 2 make[2]: Leaving directory `/home/jed/build/moab/bompi/parallel' make[1]: *** [check-recursive] Error 1 make[1]: Leaving directory `/home/jed/build/moab/bompi/parallel' make: *** [check-recursive] Error 1

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r3082 - MOAB/trunk/parallel
by kraftche＠cae.wisc.edu 30 Jul '09

30 Jul '09

Author: kraftche Date: 2009-07-30 15:10:47 -0500 (Thu, 30 Jul 2009) New Revision: 3082 Modified: MOAB/trunk/parallel/WriteHDF5Parallel.cpp Log: Fix bug causing parallel read failure when compiled with Intel compiler (and potentially many others): Do not do: "if (rangemap.end() == rangemap.insert(a,b,c))" because the order in which the two sides are evaluated is undefined, and the value of end() may change after insert(). Modified: MOAB/trunk/parallel/WriteHDF5Parallel.cpp =================================================================== --- MOAB/trunk/parallel/WriteHDF5Parallel.cpp 2009-07-30 20:03:05 UTC (rev 3081) +++ MOAB/trunk/parallel/WriteHDF5Parallel.cpp 2009-07-30 20:10:47 UTC (rev 3082) @@ -228,7 +228,7 @@ #endif -void range_remove( MBRange& from, const MBRange& removed ) +static void range_remove( MBRange& from, const MBRange& removed ) { /* The following should be more efficient, but isn't due @@ -1006,7 +1006,7 @@ for (i = 0; i < numtypes; i++) { long prev = 0; - for (unsigned j = 0; j <= myPcomm->proc_config().proc_size(); j++) + for (j = 0; j <= myPcomm->proc_config().proc_size(); j++) { long tmp = all[j*numtypes + i]; all[j*numtypes+i] = prev; @@ -1135,22 +1135,22 @@ if (data.filter_tag) mb->tag_get_name( data.filter_tag, n2 ); - std::cerr << pfx << "data_tag: " << n1 << std::endl - << pfx << "filter_tag: " << n2 << std::endl - << pfx << "filter_value: " << data.filter_value << std::endl - << pfx << "range: " << data.range << std::endl - << pfx << "counts: "; + s << pfx << "data_tag: " << n1 << std::endl + << pfx << "filter_tag: " << n2 << std::endl + << pfx << "filter_value: " << data.filter_value << std::endl + << pfx << "range: " << data.range << std::endl + << pfx << "counts: "; std::copy( data.counts.begin(), data.counts.end(), - std::ostream_iterator<int>(std::cerr,",") ); - std::cerr << std::endl << pfx << "displs: "; + std::ostream_iterator<int>(s,",") ); + s << std::endl << pfx << "displs: "; std::copy( data.displs.begin(), data.displs.end(), - std::ostream_iterator<int>(std::cerr,",") ); - std::cerr << std::endl << pfx << "all_values: "; + std::ostream_iterator<int>(s,",") ); + s << std::endl << pfx << "all_values: "; std::copy( data.all_values.begin(), data.all_values.end(), - std::ostream_iterator<int>(std::cerr,",") ); - std::cerr << std::endl << pfx << "local_values:"; + std::ostream_iterator<int>(s,",") ); + s << std::endl << pfx << "local_values:"; std::copy( data.local_values.begin(), data.local_values.end(), - std::ostream_iterator<int>(std::cerr,",") ); + std::ostream_iterator<int>(s,",") ); std::cerr << std::endl; } @@ -1350,6 +1350,7 @@ if (p == val_id_map.end()) val_id_map[data.all_values[i]] = offset++; } + RangeMap<MBEntityHandle,id_t>::iterator insp; MBRange::const_iterator riter = data.range.begin(); for (size_t i = 0; i < data.local_values.size(); ++i, ++riter) { @@ -1357,7 +1358,8 @@ assert( p != val_id_map.end() ); long id = p->second; - if (idMap.end() == idMap.insert( *riter, id, 1 )) { + insp = idMap.insert( *riter, id, 1 ); + if (idMap.end() == insp) { for (unsigned x = 0; x < myPcomm->size(); ++x) { MPI_Barrier( myPcomm->proc_config().proc_comm() ); if (x != myPcomm->rank()) continue; @@ -2061,9 +2063,8 @@ bool TagNameCompare::operator() (const WriteHDF5::SparseTag& t1, const WriteHDF5::SparseTag& t2) { - MBErrorCode rval; - rval = iFace->tag_get_name( t1.tag_id, name1 ); - rval = iFace->tag_get_name( t2.tag_id, name2 ); + iFace->tag_get_name( t1.tag_id, name1 ); + iFace->tag_get_name( t2.tag_id, name2 ); return name1 < name2; } @@ -2120,6 +2121,7 @@ } // store file IDs for remote entities + RangeMap<MBEntityHandle,id_t>::iterator insp; for (proc_iter p = interfaceMesh.begin(); p != interfaceMesh.end(); ++p) { if (p->first == myPcomm->proc_config().proc_rank()) continue; @@ -2134,10 +2136,17 @@ j = file_id_vect.begin(); for (i = p->second.begin(); i != p->second.end(); ++i, ++j) { - if (*j == 0 || idMap.insert( *i, *j, 1 ) == idMap.end()) { + if (*j == 0) { iFace->tag_delete( file_id_tag ); return MB_FAILURE; } + else { + insp = idMap.insert( *i, *j, 1 ); + if (insp == idMap.end()) { + iFace->tag_delete( file_id_tag ); + return MB_FAILURE; + } + } } }

1 0

r3081 - MOAB/trunk
by kraftche＠cae.wisc.edu 30 Jul '09

30 Jul '09

Author: kraftche Date: 2009-07-30 15:03:05 -0500 (Thu, 30 Jul 2009) New Revision: 3081 Modified: MOAB/trunk/MBCN.hpp MOAB/trunk/MBRange.hpp MOAB/trunk/TagServer.hpp Log: fix some warnings encountered when compiling with icc Modified: MOAB/trunk/MBCN.hpp =================================================================== --- MOAB/trunk/MBCN.hpp 2009-07-30 20:02:35 UTC (rev 3080) +++ MOAB/trunk/MBCN.hpp 2009-07-30 20:03:05 UTC (rev 3081) @@ -141,49 +141,56 @@ static void SetBasis(const int in_basis); //! return the string type name for this type - static const char *EntityTypeName(const MBEntityType this_type); + static inline + const char *EntityTypeName(const MBEntityType this_type); //! given a name, find the corresponding entity type static MBEntityType EntityTypeFromName(const char *name); //! return the topological entity dimension - static short int Dimension(const MBEntityType t); + static inline + short int Dimension(const MBEntityType t); //! return the number of (corner) vertices contained in the specified type. - static short int VerticesPerEntity(const MBEntityType t); + static inline + short int VerticesPerEntity(const MBEntityType t); //! return the number of sub-entities bounding the entity. - static short int NumSubEntities(const MBEntityType t, const int d); + static inline + short int NumSubEntities(const MBEntityType t, const int d); //! return the type of a particular sub-entity. //! \param this_type Type of entity for which sub-entity type is being queried //! \param sub_dimension Topological dimension of sub-entity whose type is being queried //! \param index Index of sub-entity whose type is being queried //! \return type Entity type of sub-entity with specified dimension and index - static MBEntityType SubEntityType(const MBEntityType this_type, - const int sub_dimension, - const int index); + static inline + MBEntityType SubEntityType(const MBEntityType this_type, + const int sub_dimension, + const int index); //! return the vertex indices of the specified sub-entity. //! \param this_type Type of entity for which sub-entity connectivity is being queried //! \param sub_dimension Dimension of sub-entity //! \param sub_index Index of sub-entity //! \param sub_entity_conn Connectivity of sub-entity (returned to calling function) - static void SubEntityVertexIndices(const MBEntityType this_type, - const int sub_dimension, - const int sub_index, - int sub_entity_conn[]); + static inline + void SubEntityVertexIndices(const MBEntityType this_type, + const int sub_dimension, + const int sub_index, + int sub_entity_conn[]); //! return the vertex indices of the specified sub-entity. //! \param this_type Type of entity for which sub-entity connectivity is being queried //! \param sub_dimension Dimension of sub-entity //! \param sub_index Index of sub-entity //! \param num_sub_ent_vertices the number of vertices in the sub-entity - static const short* SubEntityVertexIndices( const MBEntityType this_type, - const int sub_dimension, - const int sub_index, - MBEntityType& sub_type, - int& num_sub_ent_vertices ); + static inline + const short* SubEntityVertexIndices( const MBEntityType this_type, + const int sub_dimension, + const int sub_index, + MBEntityType& sub_type, + int& num_sub_ent_vertices ); //! return the node indices of the specified sub-entity. //! \param this_topo The topology of the queried element type @@ -336,13 +343,15 @@ //! \param pvec Permutation array //! \param num_entries Number of indicies in permutation array //! \param is_reverse Array is reverse permutation - static void setPermutation(const MBEntityType t, const int dim, int *pvec, const int num_entries, - const bool is_reverse = false); + static inline + void setPermutation(const MBEntityType t, const int dim, int *pvec, + const int num_entries, const bool is_reverse = false); //! Reset permutation or reverse permutation vector //! \param t EntityType whose permutation vector is being reset //! \param dim Dimension of facets being reset; if -1 is input, all dimensions are reset - static void resetPermutation(const MBEntityType t, const int dim); + static inline + void resetPermutation(const MBEntityType t, const int dim); //! Permute a handle array according to permutation vector set with setPermute; //! permutation is done in-place @@ -381,24 +390,27 @@ //! \param num_verts Number of nodes defining entity //! \return bool Returns true if this_type combined with num_nodes indicates //! mid-edge nodes are likely - static bool HasMidEdgeNodes(const MBEntityType this_type, - const int num_verts); + static inline + bool HasMidEdgeNodes(const MBEntityType this_type, + const int num_verts); //! true if entities of a given type and number of nodes indicates mid face nodes are present. //! \param this_type Type of entity for which sub-entity connectivity is being queried //! \param num_verts Number of nodes defining entity //! \return bool Returns true if this_type combined with num_nodes indicates //! mid-face nodes are likely - static bool HasMidFaceNodes(const MBEntityType this_type, - const int num_verts); + static inline + bool HasMidFaceNodes(const MBEntityType this_type, + const int num_verts); //! true if entities of a given type and number of nodes indicates mid region nodes are present. //! \param this_type Type of entity for which sub-entity connectivity is being queried //! \param num_verts Number of nodes defining entity //! \return bool Returns true if this_type combined with num_nodes indicates //! mid-region nodes are likely - static bool HasMidRegionNodes(const MBEntityType this_type, - const int num_verts); + static inline + bool HasMidRegionNodes(const MBEntityType this_type, + const int num_verts); //! true if entities of a given type and number of nodes indicates mid edge/face/region nodes //! are present. @@ -406,15 +418,17 @@ //! \param num_verts Number of nodes defining entity //! \param mid_nodes If mid_nodes[i], i=1..2 is non-zero, indicates that mid-edge //! (i=1), mid-face (i=2), and/or mid-region (i=3) nodes are likely - static void HasMidNodes(const MBEntityType this_type, - const int num_verts, - int mid_nodes[4]); + static inline + void HasMidNodes(const MBEntityType this_type, + const int num_verts, + int mid_nodes[4]); //! Same as above, except returns a single integer with the bits, from //! least significant to most significant set to one if the corresponding //! mid nodes on sub entities of the least dimension (0) to the highest //! dimension (3) are present in the elment type. - static int HasMidNodes( const MBEntityType this_type, const int num_verts ); + static inline + int HasMidNodes( const MBEntityType this_type, const int num_verts ); //! given data about an element and a vertex in that element, return the dimension //! and index of the sub-entity that the vertex resolves. If it does not resolve a Modified: MOAB/trunk/MBRange.hpp =================================================================== --- MOAB/trunk/MBRange.hpp 2009-07-30 20:02:35 UTC (rev 3080) +++ MOAB/trunk/MBRange.hpp 2009-07-30 20:03:05 UTC (rev 3081) @@ -220,16 +220,16 @@ ~MBRange(); //! return the beginning const iterator of this range - const_iterator begin() const; + inline const_iterator begin() const; //! return the beginning const reverse iterator of this range - const_reverse_iterator rbegin() const; + inline const_reverse_iterator rbegin() const; //! return the ending const iterator for this range - const_iterator end() const; + inline const_iterator end() const; //! return the ending const reverse iterator for this range - const_reverse_iterator rend() const; + inline const_reverse_iterator rend() const; //! return the number of values this Ranges represents MBEntityHandle size() const; @@ -239,7 +239,7 @@ //! return whether empty or not //! always use "if(!Ranges::empty())" instead of "if(Ranges::size())" - bool empty() const; + inline bool empty() const; //! insert an item into the list and return the iterator for the inserted item iterator insert(MBEntityHandle val); @@ -255,12 +255,12 @@ iterator erase( iterator iter1, iterator iter2); //! erases a value from this container - iterator erase(MBEntityHandle val); + inline iterator erase(MBEntityHandle val); //! get first entity in range - const MBEntityHandle& front() const; + inline const MBEntityHandle& front() const; //! get last entity in range - const MBEntityHandle& back() const; + inline const MBEntityHandle& back() const; //! remove first entity from range MBEntityHandle pop_front(); //! remove last entity from range Modified: MOAB/trunk/TagServer.hpp =================================================================== --- MOAB/trunk/TagServer.hpp 2009-07-30 20:02:35 UTC (rev 3080) +++ MOAB/trunk/TagServer.hpp 2009-07-30 20:03:05 UTC (rev 3081) @@ -304,11 +304,11 @@ MBErrorCode get_default_data_ref(const MBTag tag_handle, const void *& data, int& size); //! get information about a tag - const TagInfo* get_tag_info(const char *tag_name ) const; - const TagInfo* get_tag_info( MBTag tag_handle ) const; - TagInfo* get_tag_info( MBTag tag_handle ); - const TagInfo* get_tag_info( MBTagId id, MBTagType storage ) const; - TagInfo* get_tag_info( MBTagId id, MBTagType storage ); + inline const TagInfo* get_tag_info(const char *tag_name ) const; + inline const TagInfo* get_tag_info( MBTag tag_handle ) const; + inline TagInfo* get_tag_info( MBTag tag_handle ); + inline const TagInfo* get_tag_info( MBTagId id, MBTagType storage ) const; + inline TagInfo* get_tag_info( MBTagId id, MBTagType storage ); unsigned long get_memory_use( MBTag tag_handle ) const;

1 0

r3080 - MOAB/trunk/m4
by kraftche＠cae.wisc.edu 30 Jul '09

30 Jul '09

Author: kraftche Date: 2009-07-30 15:02:35 -0500 (Thu, 30 Jul 2009) New Revision: 3080 Modified: MOAB/trunk/m4/compiler.m4 Log: suppress excessive noise from intel compiler Modified: MOAB/trunk/m4/compiler.m4 =================================================================== --- MOAB/trunk/m4/compiler.m4 2009-07-30 19:11:03 UTC (rev 3079) +++ MOAB/trunk/m4/compiler.m4 2009-07-30 20:02:35 UTC (rev 3080) @@ -255,6 +255,8 @@ # Autoconf does G++ for us if test x$GXX = xyes; then cxx_compiler=GNU + # Intel claims to be GCC, check for it here + SNL_TRY_COMPILER_DEFINE([__INTEL_COMPILER],[cxx_compiler=Intel]) # Search for other compiler types # For efficiency, limit checks to relevant OSs else @@ -326,6 +328,11 @@ GNU:*) SNL_CXX_SPECIAL="$EXTRA_GNU_FLAGS" ;; + Intel:*) + SNL_CXX_32BIT=-m32 + SNL_CXX_64BIT=-m64 + SNL_CXX_SPECIAL="$EXTRA_GNU_FLAGS -wd981 -wd383" + ;; VisualAge:*) SNL_CXX_32BIT=-q32 SNL_CXX_64BIT=-q64 @@ -381,6 +388,8 @@ # Autoconf does gcc for us if test x$GCC = xyes; then cc_compiler=GNU + # Intel claims to be GCC, check for it here + SNL_TRY_COMPILER_DEFINE([__INTEL_COMPILER],[cc_compiler=Intel]) # Search for other compiler types # For efficiency, limit checks to relevant OSs else @@ -442,6 +451,11 @@ SNL_CC_64BIT=-m64 SNL_CC_SPECIAL="$EXTRA_GNU_FLAGS" ;; + Intel:*) + SNL_CC_32BIT=-m32 + SNL_CC_64BIT=-m64 + SNL_CC_SPECIAL="$EXTRA_GNU_FLAGS -wd981 -wd383" + ;; GNU:mips*) SNL_CC_32BIT="-mips32 -mabi=32" SNL_CC_64BIT="-mips64 -mabi=64"

1 0

r3079 - MOAB/trunk/parallel
by tautges＠mcs.anl.gov 30 Jul '09

30 Jul '09

Author: tautges Date: 2009-07-30 14:11:03 -0500 (Thu, 30 Jul 2009) New Revision: 3079 Modified: MOAB/trunk/parallel/MBParallelComm.cpp Log: Fixing a buffer size under-estimate when packing remote handles. Modified: MOAB/trunk/parallel/MBParallelComm.cpp =================================================================== --- MOAB/trunk/parallel/MBParallelComm.cpp 2009-07-30 18:51:22 UTC (rev 3078) +++ MOAB/trunk/parallel/MBParallelComm.cpp 2009-07-30 19:11:03 UTC (rev 3079) @@ -4223,7 +4223,8 @@ { // 2 vectors of handles plus ints CHECK_BUFF_SPACE(buff, buff_ptr, ((L1p.size()+1)*sizeof(int) + - L1hloc.size()*sizeof(MBEntityHandle))); + (L1hloc.size()+1)*sizeof(MBEntityHandle) + + (L1hrem.size()+1)*sizeof(MBEntityHandle))); // should be in pairs of handles PACK_INT(buff_ptr, L1hloc.size());

1 0