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Mesh Oriented datABase
(version 5.5.1)
An array-based unstructured mesh library
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Mesh Oriented datABase
(version 5.5.1)
An array-based unstructured mesh library
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#include <gs.hpp>
Classes | |
| class | crystal_data |
Public Member Functions | |
| gs_data (uint n, const long *label, const Ulong *ulabel, uint maxv, const unsigned int nlabels, const unsigned int nulabels, crystal_data *crystal, ErrorCode &Init_Result) | |
| gs_data () | |
| ~gs_data () | |
| ErrorCode | initialize (uint n, const long *label, const Ulong *ulabel, uint maxv, const unsigned int nlabels, const unsigned int nulabels, crystal_data *crystal) |
| void | reset () |
| void | gs_data_op (realType *u, int op) |
| void | gs_data_op_vec (realType *u, uint n, int op) |
| void | gs_data_op_many (realType **u, uint n, int op) |
Public Attributes | |
| sint * | local_cm |
|
inline |
Constructor for moab_gs_data: takes all arguments and initializes moab_gs_data. If needs_reset is false after calling constructor, initialization has failed.
param n number of tuples in tuple list param label pointer to signed labels param ulabel pointer to unsigned labels param maxv max vector size param nlabels number of signed long labels (not including gid) param nulabels number of unsigned long labels param crystal moab_crystal_data contains MPI_Comm and is used for message passing
Definition at line 199 of file gs.hpp.
207 {
208 Init_Result = this->initialize( n, label, ulabel, maxv, nlabels, nulabels, crystal );
209 };
References initialize().
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inline |
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inline |
| void moab::gs_data::gs_data_op | ( | realType * | u, |
| int | op | ||
| ) |
Definition at line 751 of file gs.cpp.
752 {
753 local_condense( u, op, this->local_cm );
754 #ifdef MOAB_HAVE_MPI
755 this->nlinfo->nonlocal( u, op, _comm );
756 #endif
757 local_uncondense( u, local_cm );
758 }
References local_cm, moab::local_condense(), and moab::local_uncondense().
Definition at line 775 of file gs.cpp.
776 {
777 uint i;
778 #ifdef MOAB_HAVE_MPI
779 if( n > nlinfo->_maxv )
780 moab::fail( "%s: initialized with max vec size = %d,"
781 " but called with vec size = %d\n",
782 __FILE__, nlinfo->_maxv, n );
783 #endif
784 for( i = 0; i < n; ++i )
785 local_condense( u[i], op, local_cm );
786
787 moab::fail( "%s: initialized with max vec size = %d,"
788 " but called with vec size = %d\n",
789 __FILE__, 6, n );
790
791 #ifdef MOAB_HAVE_MPI
792 this->nlinfo->nonlocal_many( u, n, op, _comm );
793 #endif
794 for( i = 0; i < n; ++i )
795 local_uncondense( u[i], local_cm );
796 }
References moab::fail(), local_cm, moab::local_condense(), and moab::local_uncondense().
Definition at line 760 of file gs.cpp.
761 {
762 #ifdef MOAB_HAVE_MPI
763 if( n > nlinfo->_maxv )
764 moab::fail( "%s: initialized with max vec size = %d,"
765 " but called with vec size = %d\n",
766 __FILE__, nlinfo->_maxv, n );
767 #endif
768 local_condense_vec( u, n, op, local_cm );
769 #ifdef MOAB_HAVE_MPI
770 this->nlinfo->nonlocal_vec( u, n, op, _comm );
771 #endif
772 local_uncondense_vec( u, n, local_cm );
773 }
References moab::fail(), local_cm, moab::local_condense_vec(), and moab::local_uncondense_vec().
| ErrorCode moab::gs_data::initialize | ( | uint | n, |
| const long * | label, | ||
| const Ulong * | ulabel, | ||
| uint | maxv, | ||
| const unsigned int | nlabels, | ||
| const unsigned int | nulabels, | ||
| crystal_data * | crystal | ||
| ) |
Sets up the moab_gs_data; see constructor for parameter documentation
Definition at line 802 of file gs.cpp.
809 {
810 nlinfo = NULL;
811 unsigned int j;
812 TupleList nonzero, primary;
813 ErrorCode rval;
814 #ifdef MOAB_HAVE_MPI
815 TupleList shared;
816 #else
817 moab::TupleList::buffer buf;
818 #endif
819 (void)VALGRIND_CHECK_MEM_IS_DEFINED( label, nlabels * sizeof( long ) );
820 (void)VALGRIND_CHECK_MEM_IS_DEFINED( ulabel, nlabels * sizeof( Ulong ) );
821 #ifdef MOAB_HAVE_MPI
822 MPI_Comm_dup( crystal->_comm, &this->_comm );
823 #else
824 buf.buffer_init( 1024 );
825 #endif
826
827 /* construct list of nonzeros: (index ^, label) */
828 nonzero.initialize( 1, nlabels, nulabels, 0, n );
829 nonzero.enableWriteAccess();
830 {
831 uint i;
832 sint* nzi;
833 long* nzl;
834 Ulong* nzul;
835 nzi = nonzero.vi_wr;
836 nzl = nonzero.vl_wr;
837 nzul = nonzero.vul_wr;
838 for( i = 0; i < n; ++i )
839 if( label[nlabels * i] != 0 )
840 {
841 nzi[0] = i;
842 for( j = 0; j < nlabels; j++ )
843 nzl[j] = label[nlabels * i + j];
844 for( j = 0; j < nulabels; j++ )
845 nzul[j] = ulabel[nulabels * i + j];
846 nzi++;
847 nzl += nlabels;
848 nzul += nulabels;
849 nonzero.inc_n();
850 }
851 }
852
853 /* sort nonzeros by label: (index ^2, label ^1) */
854 #ifndef MOAB_HAVE_MPI
855 nonzero.sort( 1, &buf );
856 #else
857 nonzero.sort( 1, &crystal->all->buf );
858 #endif
859
860 /* build list of unique labels w/ lowest associated index:
861 (index in nonzero ^, primary (lowest) index in label, count, label(s),
862 ulabel(s)) */
863 primary.initialize( 3, nlabels, nulabels, 0, nonzero.get_n() );
864 primary.enableWriteAccess();
865 {
866 uint i;
867 sint *nzi = nonzero.vi_wr, *pi = primary.vi_wr;
868 slong *nzl = nonzero.vl_wr, *pl = primary.vl_wr;
869 Ulong *nzul = nonzero.vul_wr, *pul = primary.vul_wr;
870 slong last = -1;
871 for( i = 0; i < nonzero.get_n(); ++i, nzi += 1, nzl += nlabels, nzul += nulabels )
872 {
873 if( nzl[0] == last )
874 {
875 ++pi[-1];
876 continue;
877 }
878 last = nzl[0];
879 pi[0] = i;
880 pi[1] = nzi[0];
881 for( j = 0; j < nlabels; j++ )
882 pl[j] = nzl[j];
883 for( j = 0; j < nulabels; j++ )
884 pul[j] = nzul[j];
885 pi[2] = 1;
886 pi += 3, pl += nlabels;
887 pul += nulabels;
888 primary.inc_n();
889 }
890 }
891
892 /* calculate size of local condense map */
893 {
894 uint i, count = 1;
895 sint* pi = primary.vi_wr;
896 for( i = primary.get_n(); i; --i, pi += 3 )
897 if( pi[2] > 1 ) count += pi[2] + 1;
898 this->local_cm = (sint*)malloc( count * sizeof( sint ) );
899 }
900
901 /* sort unique labels by primary index:
902 (nonzero index ^2, primary index ^1, count, label ^2) */
903 #ifndef MOAB_HAVE_MPI
904 primary.sort( 0, &buf );
905 buf.reset();
906 // buffer_free(&buf);
907 #else
908 primary.sort( 0, &crystal->all->buf );
909 #endif
910
911 /* construct local condense map */
912 {
913 uint i, ln;
914 sint* pi = primary.vi_wr;
915 sint* cm = this->local_cm;
916 for( i = primary.get_n(); i > 0; --i, pi += 3 )
917 if( ( ln = pi[2] ) > 1 )
918 {
919 sint* nzi = nonzero.vi_wr + 1 * pi[0];
920 for( j = ln; j > 0; --j, nzi += 1 )
921 *cm++ = nzi[0];
922 *cm++ = -1;
923 }
924 *cm++ = -1;
925 }
926 nonzero.reset();
927 #ifndef MOAB_HAVE_MPI
928 primary.reset();
929 #else
930 /* assign work proc by label modulo np */
931 {
932 uint i;
933 sint* pi = primary.vi_wr;
934 slong* pl = primary.vl_wr;
935 for( i = primary.get_n(); i; --i, pi += 3, pl += nlabels )
936 pi[0] = pl[0] % crystal->_num;
937 }
938 rval = crystal->gs_transfer( 1, primary, 0 ); /* transfer to work procs */
939 if( rval != MB_SUCCESS ) return rval;
940 /* primary: (source proc, index on src, useless, label) */
941 /* sort by label */
942 primary.sort( 3, &crystal->all->buf );
943 /* add sentinel to primary list */
944 if( primary.get_n() == primary.get_max() )
945 primary.resize( ( primary.get_max() ? primary.get_max() + ( primary.get_max() + 1 ) / 2 + 1 : 2 ) );
946 primary.vl_wr[nlabels * primary.get_n()] = -1;
947 /* construct shared list: (proc1, proc2, index1, label) */
948 #ifdef MOAB_HAVE_MPI
949 shared.initialize( 3, nlabels, nulabels, 0, primary.get_n() );
950 shared.enableWriteAccess();
951 #endif
952 {
953 sint *pi1 = primary.vi_wr, *si = shared.vi_wr;
954 slong lbl, *pl1 = primary.vl_wr, *sl = shared.vl_wr;
955 Ulong *pul1 = primary.vul_wr, *sul = shared.vul_wr;
956 for( ; ( lbl = pl1[0] ) != -1; pi1 += 3, pl1 += nlabels, pul1 += nulabels )
957 {
958 sint* pi2 = pi1 + 3;
959 slong* pl2 = pl1 + nlabels;
960 Ulong* pul2 = pul1 + nulabels;
961 for( ; pl2[0] == lbl; pi2 += 3, pl2 += nlabels, pul2 += nulabels )
962 {
963 if( shared.get_n() + 2 > shared.get_max() )
964 shared.resize( ( shared.get_max() ? shared.get_max() + ( shared.get_max() + 1 ) / 2 + 1 : 2 ) ),
965 si = shared.vi_wr + shared.get_n() * 3;
966 sl = shared.vl_wr + shared.get_n() * nlabels;
967 sul = shared.vul_wr + shared.get_n() * nulabels;
968 si[0] = pi1[0];
969 si[1] = pi2[0];
970 si[2] = pi1[1];
971 for( j = 0; j < nlabels; j++ )
972 sl[j] = pl2[j];
973 for( j = 0; j < nulabels; j++ )
974 sul[j] = pul2[j];
975 si += 3;
976 sl += nlabels;
977 sul += nulabels;
978 shared.inc_n();
979 si[0] = pi2[0];
980 si[1] = pi1[0];
981 si[2] = pi2[1];
982 for( j = 0; j < nlabels; j++ )
983 sl[j] = pl1[j];
984 for( j = 0; j < nulabels; j++ )
985 sul[j] = pul1[j];
986 si += 3;
987 sl += nlabels;
988 sul += nulabels;
989 shared.inc_n();
990 }
991 }
992 }
993 primary.reset();
994 rval = crystal->gs_transfer( 1, shared, 0 ); /* segfaulting transfer to dest procs */
995 if( rval != MB_SUCCESS ) return rval;
996 /* shared list: (useless, proc2, index, label) */
997 /* sort by label */
998 shared.sort( 3, &crystal->all->buf );
999 /* sort by partner proc */
1000 shared.sort( 1, &crystal->all->buf );
1001 /* count partner procs */
1002 {
1003 uint i, count = 0;
1004 sint proc = -1, *si = shared.vi_wr;
1005 for( i = shared.get_n(); i; --i, si += 3 )
1006 if( si[1] != proc )
1007 {
1008 ++count;
1009 proc = si[1];
1010 }
1011 // this->nlinfo = new nonlocal_info();
1012 // this->nlinfo->initialize(count,shared.get_n(),
1013 // nlabels, nulabels, maxv);
1014 this->nlinfo = new nonlocal_info( count, shared.get_n(), nlabels, nulabels, maxv );
1015 }
1016 /* construct non-local info */
1017 {
1018 uint i;
1019 sint proc = -1, *si = shared.vi_wr;
1020 slong* sl = shared.vl_wr;
1021 Ulong* ul = shared.vul_wr;
1022 uint* target = this->nlinfo->_target;
1023 uint* nshared = this->nlinfo->_nshared;
1024 uint* sh_ind = this->nlinfo->_sh_ind;
1025 slong* slabels = this->nlinfo->_slabels;
1026 Ulong* ulabels = this->nlinfo->_ulabels;
1027 for( i = shared.get_n(); i; --i, si += 3 )
1028 {
1029 if( si[1] != proc )
1030 {
1031 proc = si[1];
1032 *target++ = proc;
1033 *nshared++ = 0;
1034 }
1035 ++nshared[-1];
1036 *sh_ind++ = si[2];
1037 // don't store 1st slabel
1038 sl++;
1039 for( j = 0; j < nlabels - 1; j++ )
1040 slabels[j] = sl[j];
1041 for( j = 0; j < nulabels; j++ )
1042 ulabels[j] = ul[j];
1043 slabels += nlabels - 1;
1044 ulabels += nulabels;
1045 sl += nlabels - 1;
1046 ul += nulabels;
1047 }
1048 }
1049 shared.reset();
1050 #endif
1051 return MB_SUCCESS;
1052 }
References moab::TupleList::enableWriteAccess(), ErrorCode, moab::TupleList::get_max(), moab::TupleList::get_n(), moab::TupleList::inc_n(), moab::TupleList::initialize(), local_cm, MB_SUCCESS, moab::TupleList::buffer::reset(), moab::TupleList::reset(), moab::TupleList::resize(), moab::TupleList::sort(), VALGRIND_CHECK_MEM_IS_DEFINED, moab::TupleList::vi_wr, moab::TupleList::vl_wr, and moab::TupleList::vul_wr.
Referenced by gs_data(), moab::ParallelComm::resolve_shared_ents(), and moab::ParallelComm::resolve_shared_sets().
| void moab::gs_data::reset | ( | ) |
Definition at line 1054 of file gs.cpp.
1055 {
1056 free( local_cm );
1057 local_cm = NULL;
1058 #ifdef MOAB_HAVE_MPI
1059 if( nlinfo != NULL )
1060 {
1061 nlinfo->nlinfo_free();
1062 delete this->nlinfo;
1063 MPI_Comm_free( &_comm );
1064 nlinfo = NULL;
1065 }
1066 #endif
1067 }
References local_cm.
Referenced by moab::ParallelComm::resolve_shared_ents(), moab::ParallelComm::resolve_shared_sets(), and ~gs_data().
| sint* moab::gs_data::local_cm |
Definition at line 180 of file gs.hpp.
Referenced by gs_data_op(), gs_data_op_many(), gs_data_op_vec(), initialize(), and reset().
1.9.1.