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

r5360 - MOAB/trunk/src/parallel/moab
by nbertram＠wisc.edu 31 Jan '12

31 Jan '12

Author: bertram Date: 2012-01-31 16:34:22 -0600 (Tue, 31 Jan 2012) New Revision: 5360 Modified: MOAB/trunk/src/parallel/moab/TupleList.hpp Log: Adding #include <string> to TupleList.hpp since some compilers were giving an error. Modified: MOAB/trunk/src/parallel/moab/TupleList.hpp =================================================================== --- MOAB/trunk/src/parallel/moab/TupleList.hpp 2012-01-31 21:36:35 UTC (rev 5359) +++ MOAB/trunk/src/parallel/moab/TupleList.hpp 2012-01-31 22:34:22 UTC (rev 5360) @@ -19,6 +19,7 @@ #include <stdlib.h> #include "moab/Types.hpp" +#include <string> /* Integral types defined here to ensure variable type sizes are consistent */ /* integer type to use for everything */

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r5359 - in MOAB/trunk: src/parallel src/parallel/moab test/parallel
by nbertram＠wisc.edu 31 Jan '12

31 Jan '12

Author: bertram Date: 2012-01-31 15:36:35 -0600 (Tue, 31 Jan 2012) New Revision: 5359 Modified: MOAB/trunk/src/parallel/TupleList.cpp MOAB/trunk/src/parallel/moab/ParallelMergeMesh.hpp MOAB/trunk/src/parallel/moab/TupleList.hpp MOAB/trunk/test/parallel/parmerge.cpp Log: Used templates to get rid of duplicated code in TupleList class Modified: MOAB/trunk/src/parallel/TupleList.cpp =================================================================== --- MOAB/trunk/src/parallel/TupleList.cpp 2012-01-31 18:31:42 UTC (rev 5358) +++ MOAB/trunk/src/parallel/TupleList.cpp 2012-01-31 21:36:35 UTC (rev 5359) @@ -7,9 +7,6 @@ #include "moab/TupleList.hpp" -typedef struct {uint v; uint i;} sort_data; -typedef struct { ulong v; uint i;} sort_data_long; - namespace moab { extern void fail(const char *fmt, ...); @@ -414,6 +411,29 @@ n = n_in; } + void TupleList::print(std::string name) const + { + std::cout<<"Printing Tuple " << name << "==================="<<std::endl; + unsigned long i=0,l=0,ul=0,r=0; + for(uint k=0; k<n; k++){ + for(uint j=0; j<mi; j++){ + std::cout<<vi[i++]<<" | "; + } + for(uint j=0; j<ml; j++){ + std::cout<<vl[l++]<<" | "; + } + for(uint j=0; j<mul; j++){ + std::cout<<vul[ul++]<<" | "; + } + for(uint j=0; j<mr; j++){ + std::cout<<vr[r++]<<" | "; + } + std::cout<<std::endl; + } + std::cout<<"======================================="<<std::endl<<std::endl; + } + + void TupleList::permute(uint *perm, void *work) { const unsigned int_size = mi*sizeof(sint), @@ -452,18 +472,20 @@ const unsigned real_size = mr*sizeof(real); const unsigned width = umax_2(umax_2(int_size,long_size), umax_2(ulong_size,real_size)); - //const unsigned data_size = key>=mi ? sizeof(sort_data_long):sizeof(sort_data); - const unsigned data_size = sizeof(sort_data_long); + const unsigned data_size = key>=mi?

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Parallel iZoltan file for MOAB?
by James Porter 31 Jan '12

31 Jan '12

At the ITAPS telecon last week, we discussed the weekly test results (as usual). One thing that came up was the parallel iZoltan tests, which we're currently failing[1]. We think the issue is that we need a file which MOAB can understand. Any ideas on the file we should be using for this? - Jim [1] https://itaps.mcs.anl.gov/resultsp.20120118/IZOLTANP_MOAB.results

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buildbot failure in moab-distcheck: failed compile
by moab-dev＠mcs.anl.gov 31 Jan '12

31 Jan '12

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buildbot failure in moab-par: failed compile
by moab-dev＠mcs.anl.gov 31 Jan '12

31 Jan '12

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r5355 - MOAB/trunk/src/parallel
by nbertram＠wisc.edu 30 Jan '12

30 Jan '12

Author: bertram Date: 2012-01-30 14:21:58 -0600 (Mon, 30 Jan 2012) New Revision: 5355 Removed: MOAB/trunk/src/parallel/crystal.c MOAB/trunk/src/parallel/crystal.h MOAB/trunk/src/parallel/errmem.c MOAB/trunk/src/parallel/errmem.h MOAB/trunk/src/parallel/fcrystal.c MOAB/trunk/src/parallel/gs.c MOAB/trunk/src/parallel/gs.h MOAB/trunk/src/parallel/minmax.h MOAB/trunk/src/parallel/sort.c MOAB/trunk/src/parallel/sort.h MOAB/trunk/src/parallel/sort_imp.h MOAB/trunk/src/parallel/transfer.c MOAB/trunk/src/parallel/transfer.h MOAB/trunk/src/parallel/tuple_list.c MOAB/trunk/src/parallel/tuple_list.h MOAB/trunk/src/parallel/types.h Log: Removing old C files that are no longer needed because of TupleList.cpp/hpp and gs.cpp/hpp Deleted: MOAB/trunk/src/parallel/crystal.c =================================================================== --- MOAB/trunk/src/parallel/crystal.c 2012-01-30 20:09:58 UTC (rev 5354) +++ MOAB/trunk/src/parallel/crystal.c 2012-01-30 20:21:58 UTC (rev 5355) @@ -1,170 +0,0 @@ -/*------------------------------------------------------------------------------ - - Crystal Router - - Accomplishes all-to-all communication in log P msgs per proc - The routine is low-level; the format of the input/output is an - array of integers, consisting of a sequence of messages with format: - - target proc - source proc - m - integer - integer - ... - integer (m integers in total) - - Before crystal_router is called, the source of each message should be - set to this proc id; upon return from crystal_router, the target of each - message will be this proc id. - - Usage: - - MPI_Comm comm = ... ; - crystal_data crystal; - - crystal_init(&crystal, comm); // initialize the data structure - // now crystal.id = this proc - // and crystal.num = num of procs - - // allocate space for at least MAX ints - buffer_reserve(&crystal->all->buf, MAX*sizeof(uint)); - - // fill up ((uint*)crystal->all->buf.ptr)[0 ... n-1] - // and set crystal->all->n - - crystal_router(&crystal); - - // incoming messages available as - // ((uint*)crystal->all->buf.ptr)[0 ... crystal->all->n-1] - - crystal_free(&crystal); // release acquired memory - - ----------------------------------------------------------------------------*/ -#ifdef USE_MPI - -#include <stdio.h>

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r5354 - in MOAB/trunk: src src/io src/parallel src/parallel/moab test/parallel tools/mbcoupler
by nbertram＠wisc.edu 30 Jan '12

30 Jan '12

Author: bertram Date: 2012-01-30 14:09:58 -0600 (Mon, 30 Jan 2012) New Revision: 5354 Added: MOAB/trunk/src/parallel/TupleList.cpp MOAB/trunk/src/parallel/gs.cpp MOAB/trunk/src/parallel/moab/TupleList.hpp MOAB/trunk/src/parallel/moab/gs.hpp Modified: MOAB/trunk/src/ScdInterface.cpp MOAB/trunk/src/io/WriteHDF5.cpp MOAB/trunk/src/parallel/CMakeLists.txt MOAB/trunk/src/parallel/Makefile.am MOAB/trunk/src/parallel/ParallelComm.cpp MOAB/trunk/src/parallel/ParallelMergeMesh.cpp MOAB/trunk/src/parallel/ProcConfig.cpp MOAB/trunk/src/parallel/WriteHDF5Parallel.cpp MOAB/trunk/src/parallel/moab/ParallelComm.hpp MOAB/trunk/src/parallel/moab/ParallelMergeMesh.hpp MOAB/trunk/src/parallel/moab/ProcConfig.hpp MOAB/trunk/test/parallel/parmerge.cpp MOAB/trunk/tools/mbcoupler/CMakeLists.txt MOAB/trunk/tools/mbcoupler/Coupler.cpp MOAB/trunk/tools/mbcoupler/Coupler.hpp MOAB/trunk/tools/mbcoupler/Makefile.am MOAB/trunk/tools/mbcoupler/errmem.h MOAB/trunk/tools/mbcoupler/ssn_test.cpp Log: Converted tuple_list, gather-scatter, crystal router files from C to C++ files. Modified: MOAB/trunk/src/ScdInterface.cpp =================================================================== --- MOAB/trunk/src/ScdInterface.cpp 2012-01-26 21:22:48 UTC (rev 5353) +++ MOAB/trunk/src/ScdInterface.cpp 2012-01-30 20:09:58 UTC (rev 5354) @@ -7,18 +7,12 @@ #include "ScdVertexData.hpp" #ifdef USE_MPI # include "moab/ParallelComm.hpp" -extern "C" -{ -# include "types.h" -# include "gs.h" -# include "errmem.h" -# include "sort.h" -# include "tuple_list.h" -} #endif #include "assert.h" #include <iostream> #include <functional> +#include "moab/TupleList.hpp" +#include "moab/gs.hpp" #define ERRORR(rval, str) {if (MB_SUCCESS != rval) \ {std::cerr << str; return rval; }} @@ -620,9 +614,11 @@ int incoming = procs.size(); int p, j, k; MPI_Status status; - tuple_list shared_data; - tuple_list_init_max(&shared_data, 1, 0, 2, 0, - shared_indices.size()/2); + TupleList shared_data; + shared_data.initialize(1, 0, 2, 0, + shared_indices.size()/2); + shared_data.enableWriteAccess(); + j = 0; k = 0; while (incoming) { int success = MPI_Waitany(procs.size(), &recv_reqs[0], &p, &status); @@ -630,19 +626,19 @@ unsigned int num_indices = (offsets[p+1]-offsets[p])/2; int *lh = &shared_indices[offsets[p]], *rh = lh + num_indices; for (unsigned int i = 0; i < num_indices; i++) { - shared_data.vi[j++] = procs[p]; - shared_data.vul[k++] = shandles[0] + lh[i]; - shared_data.vul[k++] = rhandles[4*p] + rh[i]; - shared_data.n++; + shared_data.vi_wr[j++] = procs[p]; + shared_data.vul_wr[k++] = shandles[0] + lh[i]; + shared_data.vul_wr[k++] = rhandles[4*p] + rh[i];

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Does iMesh_getEntAdj return entities in the canonical connectivity order?
by Stuart Slattery 27 Jan '12

27 Jan '12

Hi all, Say I make a hexahedron element out of 8 vertices in canonical order with iMesh_createEnt. If I call iMesh_getEntAdj on that hexahedron and ask for vertices, should I always get the vertices back in canonical order? Thanks Stuart -- Stuart Slattery Graduate Research Assistant Computational Nuclear Engineering Research Group Department of Engineering Physics University of Wisconsin - Madison 434 Engineering Research Building 1500 Engineering Drive Madison, WI 53706 email : sslattery(a)wisc.edu Phone : 608.263.1709 url : http://cnerg.engr.wisc.edu

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r5353 - MOAB/trunk/src/parallel
by jvporter＠wisc.edu 26 Jan '12

26 Jan '12

Author: jvporter Date: 2012-01-26 15:22:48 -0600 (Thu, 26 Jan 2012) New Revision: 5353 Added: MOAB/trunk/src/parallel/sort_imp.h Removed: MOAB/trunk/src/parallel/sort_imp.c Modified: MOAB/trunk/src/parallel/Makefile.am MOAB/trunk/src/parallel/sort.c Log: Fix build issue with sort_imp.c (autotools treated it as a regular source file rather than an X macro file) Modified: MOAB/trunk/src/parallel/Makefile.am =================================================================== --- MOAB/trunk/src/parallel/Makefile.am 2012-01-26 21:20:31 UTC (rev 5352) +++ MOAB/trunk/src/parallel/Makefile.am 2012-01-26 21:22:48 UTC (rev 5353) @@ -37,7 +37,7 @@ crystal.h \ crystal.c errmem.c \ transfer.c gs.c gs.h tuple_list.c \ - sort.c transfer.h sort_imp.c + sort.c transfer.h sort_imp.h # The list of header files which are to be installed MOAB_PARALLEL_HDRS += \ Modified: MOAB/trunk/src/parallel/sort.c =================================================================== --- MOAB/trunk/src/parallel/sort.c 2012-01-26 21:20:31 UTC (rev 5352) +++ MOAB/trunk/src/parallel/sort.c 2012-01-26 21:22:48 UTC (rev 5353) @@ -9,7 +9,7 @@ #define Value uint #define Data sort_data typedef struct { Value v; Index i; } Data; -#include "sort_imp.c" +#include "sort_imp.h" #undef Value #undef Data @@ -33,6 +33,6 @@ # define merge_index_sort merge_index_sort_long # define sort sort_long # define index_sort index_sort_long -# include "sort_imp.c" +# include "sort_imp.h" #endif Deleted: MOAB/trunk/src/parallel/sort_imp.c =================================================================== --- MOAB/trunk/src/parallel/sort_imp.c 2012-01-26 21:20:31 UTC (rev 5352) +++ MOAB/trunk/src/parallel/sort_imp.c 2012-01-26 21:22:48 UTC (rev 5353) @@ -1,350 +0,0 @@ - -/* this file possibly included multiple times by sort.c - for sorting different integer sizes; - - look in sort.c for some controlling macro definitions, - like Value, Index, Data, and function names */ - -#ifdef Value - -/*------------------------------------------------------------------------------

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r5352 - MOAB/trunk/src/io
by jvporter＠wisc.edu 26 Jan '12

26 Jan '12

Author: jvporter Date: 2012-01-26 15:20:31 -0600 (Thu, 26 Jan 2012) New Revision: 5352 Modified: MOAB/trunk/src/io/ReadHDF5.cpp Log: Eliminate warnings in parallel config Modified: MOAB/trunk/src/io/ReadHDF5.cpp =================================================================== --- MOAB/trunk/src/io/ReadHDF5.cpp 2012-01-26 05:57:04 UTC (rev 5351) +++ MOAB/trunk/src/io/ReadHDF5.cpp 2012-01-26 21:20:31 UTC (rev 5352) @@ -2013,7 +2013,7 @@ bool bcast = false; hid_t ioprop = H5P_DEFAULT; #ifdef USE_MPI - MPI_Comm comm; + MPI_Comm comm = 0; if (nativeParallel) { rank = myPcomm->proc_config().proc_rank(); comm = myPcomm->proc_config().proc_comm(); @@ -2220,7 +2220,7 @@ int rank = 0; bool bcast = false; #ifdef USE_MPI - MPI_Comm comm; + MPI_Comm comm = 0; if (nativeParallel) { rank = myPcomm->proc_config().proc_rank(); comm = myPcomm->proc_config().proc_comm();

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