[petsc-dev] Parmetis bug
Smith, Barry F.
bsmith at mcs.anl.gov
Sun Nov 10 20:28:29 CST 2019
Nice. Anyway to add this exact reproducibility into a PETSc example that runs daily?
The truism: all codes are buggy, even those that haven't been touched in 15 years, is definitely represented here.
Barry
> On Nov 10, 2019, at 7:31 PM, Fande Kong via petsc-dev <petsc-dev at mcs.anl.gov> wrote:
>
> Valgrind info:
>
> ==32155== Invalid read of size 4
> ==32155== at 0x885F62F: libmetis__CreateCoarseGraphNoMask (coarsen.c:879)
> ==32155== by 0x885E2B9: libmetis__CreateCoarseGraph (coarsen.c:636)
> ==32155== by 0x885CA49: libmetis__Match_RM (coarsen.c:262)
> ==32155== by 0x885BFBD: libmetis__CoarsenGraph (coarsen.c:55)
> ==32155== by 0x8869A4C: libmetis__MultilevelBisect (pmetis.c:240)
> ==32155== by 0x88696F6: libmetis__MlevelRecursiveBisection (pmetis.c:183)
> ==32155== by 0x88698D7: libmetis__MlevelRecursiveBisection (pmetis.c:207)
> ==32155== by 0x886951E: METIS_PartGraphRecursive (pmetis.c:133)
> ==32155== by 0x885650B: libmetis__InitKWayPartitioning (kmetis.c:194)
> ==32155== by 0x8856147: libmetis__MlevelKWayPartitioning (kmetis.c:121)
> ==32155== by 0x8855FD3: METIS_PartGraphKway (kmetis.c:71)
> ==32155== by 0x85E7611: libparmetis__PartitionSmallGraph (weird.c:478)
> ==32155== by 0x85D00F3: ParMETIS_V3_PartKway (kmetis.c:91)
> ==32155== by 0x5515C19: MatPartitioningApply_Parmetis_Private (pmetis.c:147)
> ==32155== by 0x5516F7D: MatPartitioningApply_Parmetis (pmetis.c:221)
> ==32155== by 0x550DD7F: MatPartitioningApply (partition.c:332)
> ==32155== by 0x6387033: PCGAMGCreateLevel_GAMG (gamg.c:226)
> ==32155== by 0x638BCA5: PCSetUp_GAMG (gamg.c:593)
> ==32155== by 0x64746B1: PCSetUp (precon.c:894)
> ==32155== by 0x65D388A: KSPSetUp (itfunc.c:377)
> ==32155== Address 0xee2502c is 0 bytes after a block of size 284 alloc'd
> ==32155== at 0x4C2AB80: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
> ==32155== by 0x8820179: gk_malloc (memory.c:147)
> ==32155== by 0x883D92B: libmetis__imalloc (gklib.c:24)
> ==32155== by 0x885BF6A: libmetis__CoarsenGraph (coarsen.c:46)
> ==32155== by 0x8869A4C: libmetis__MultilevelBisect (pmetis.c:240)
> ==32155== by 0x88696F6: libmetis__MlevelRecursiveBisection (pmetis.c:183)
> ==32155== by 0x88698D7: libmetis__MlevelRecursiveBisection (pmetis.c:207)
> ==32155== by 0x886951E: METIS_PartGraphRecursive (pmetis.c:133)
> ==32155== by 0x885650B: libmetis__InitKWayPartitioning (kmetis.c:194)
> ==32155== by 0x8856147: libmetis__MlevelKWayPartitioning (kmetis.c:121)
> ==32155== by 0x8855FD3: METIS_PartGraphKway (kmetis.c:71)
> ==32155== by 0x85E7611: libparmetis__PartitionSmallGraph (weird.c:478)
> ==32155== by 0x85D00F3: ParMETIS_V3_PartKway (kmetis.c:91)
> ==32155== by 0x5515C19: MatPartitioningApply_Parmetis_Private (pmetis.c:147)
> ==32155== by 0x5516F7D: MatPartitioningApply_Parmetis (pmetis.c:221)
> ==32155== by 0x550DD7F: MatPartitioningApply (partition.c:332)
> ==32155== by 0x6387033: PCGAMGCreateLevel_GAMG (gamg.c:226)
> ==32155== by 0x638BCA5: PCSetUp_GAMG (gamg.c:593)
> ==32155== by 0x64746B1: PCSetUp (precon.c:894)
> ==32155== by 0x65D388A: KSPSetUp (itfunc.c:377)
> ==32155==
> ==32155== Conditional jump or move depends on uninitialised value(s)
> ==32155== at 0x885F651: libmetis__CreateCoarseGraphNoMask (coarsen.c:880)
> ==32155== by 0x885E2B9: libmetis__CreateCoarseGraph (coarsen.c:636)
> ==32155== by 0x885CA49: libmetis__Match_RM (coarsen.c:262)
> ==32155== by 0x885BFBD: libmetis__CoarsenGraph (coarsen.c:55)
> ==32155== by 0x8869A4C: libmetis__MultilevelBisect (pmetis.c:240)
> ==32155== by 0x88696F6: libmetis__MlevelRecursiveBisection (pmetis.c:183)
> ==32155== by 0x88698D7: libmetis__MlevelRecursiveBisection (pmetis.c:207)
> ==32155== by 0x886951E: METIS_PartGraphRecursive (pmetis.c:133)
> ==32155== by 0x885650B: libmetis__InitKWayPartitioning (kmetis.c:194)
> ==32155== by 0x8856147: libmetis__MlevelKWayPartitioning (kmetis.c:121)
> ==32155== by 0x8855FD3: METIS_PartGraphKway (kmetis.c:71)
> ==32155== by 0x85E7611: libparmetis__PartitionSmallGraph (weird.c:478)
> ==32155== by 0x85D00F3: ParMETIS_V3_PartKway (kmetis.c:91)
> ==32155== by 0x5515C19: MatPartitioningApply_Parmetis_Private (pmetis.c:147)
> ==32155== by 0x5516F7D: MatPartitioningApply_Parmetis (pmetis.c:221)
> ==32155== by 0x550DD7F: MatPartitioningApply (partition.c:332)
> ==32155== by 0x6387033: PCGAMGCreateLevel_GAMG (gamg.c:226)
> ==32155== by 0x638BCA5: PCSetUp_GAMG (gamg.c:593)
> ==32155== by 0x64746B1: PCSetUp (precon.c:894)
> ==32155== by 0x65D388A: KSPSetUp (itfunc.c:377)
> ==32155==
> ==32155== Use of uninitialised value of size 8
> ==32155== at 0x885F6F2: libmetis__CreateCoarseGraphNoMask (coarsen.c:886)
> ==32155== by 0x885E2B9: libmetis__CreateCoarseGraph (coarsen.c:636)
> ==32155== by 0x885CA49: libmetis__Match_RM (coarsen.c:262)
> ==32155== by 0x885BFBD: libmetis__CoarsenGraph (coarsen.c:55)
> ==32155== by 0x8869A4C: libmetis__MultilevelBisect (pmetis.c:240)
> ==32155== by 0x88696F6: libmetis__MlevelRecursiveBisection (pmetis.c:183)
> ==32155== by 0x88698D7: libmetis__MlevelRecursiveBisection (pmetis.c:207)
> ==32155== by 0x886951E: METIS_PartGraphRecursive (pmetis.c:133)
> ==32155== by 0x885650B: libmetis__InitKWayPartitioning (kmetis.c:194)
> ==32155== by 0x8856147: libmetis__MlevelKWayPartitioning (kmetis.c:121)
> ==32155== by 0x8855FD3: METIS_PartGraphKway (kmetis.c:71)
> ==32155== by 0x85E7611: libparmetis__PartitionSmallGraph (weird.c:478)
> ==32155== by 0x85D00F3: ParMETIS_V3_PartKway (kmetis.c:91)
> ==32155== by 0x5515C19: MatPartitioningApply_Parmetis_Private (pmetis.c:147)
> ==32155== by 0x5516F7D: MatPartitioningApply_Parmetis (pmetis.c:221)
> ==32155== by 0x550DD7F: MatPartitioningApply (partition.c:332)
> ==32155== by 0x6387033: PCGAMGCreateLevel_GAMG (gamg.c:226)
> ==32155== by 0x638BCA5: PCSetUp_GAMG (gamg.c:593)
> ==32155== by 0x64746B1: PCSetUp (precon.c:894)
> ==32155== by 0x65D388A: KSPSetUp (itfunc.c:377)
> ==32155==
> ==32155== Use of uninitialised value of size 8
> ==32155== at 0x885F710: libmetis__CreateCoarseGraphNoMask (coarsen.c:886)
> ==32155== by 0x885E2B9: libmetis__CreateCoarseGraph (coarsen.c:636)
> ==32155== by 0x885CA49: libmetis__Match_RM (coarsen.c:262)
> ==32155== by 0x885BFBD: libmetis__CoarsenGraph (coarsen.c:55)
> ==32155== by 0x8869A4C: libmetis__MultilevelBisect (pmetis.c:240)
> ==32155== by 0x88696F6: libmetis__MlevelRecursiveBisection (pmetis.c:183)
> ==32155== by 0x88698D7: libmetis__MlevelRecursiveBisection (pmetis.c:207)
> ==32155== by 0x886951E: METIS_PartGraphRecursive (pmetis.c:133)
> ==32155== by 0x885650B: libmetis__InitKWayPartitioning (kmetis.c:194)
> ==32155== by 0x8856147: libmetis__MlevelKWayPartitioning (kmetis.c:121)
> ==32155== by 0x8855FD3: METIS_PartGraphKway (kmetis.c:71)
> ==32155== by 0x85E7611: libparmetis__PartitionSmallGraph (weird.c:478)
> ==32155== by 0x85D00F3: ParMETIS_V3_PartKway (kmetis.c:91)
> ==32155== by 0x5515C19: MatPartitioningApply_Parmetis_Private (pmetis.c:147)
> ==32155== by 0x5516F7D: MatPartitioningApply_Parmetis (pmetis.c:221)
> ==32155== by 0x550DD7F: MatPartitioningApply (partition.c:332)
> ==32155== by 0x6387033: PCGAMGCreateLevel_GAMG (gamg.c:226)
> ==32155== by 0x638BCA5: PCSetUp_GAMG (gamg.c:593)
> ==32155== by 0x64746B1: PCSetUp (precon.c:894)
> ==32155== by 0x65D388A: KSPSetUp (itfunc.c:377)
> ==32155==
> ==32155== Invalid read of size 4
> ==32155== at 0x885F392: libmetis__CreateCoarseGraphNoMask (coarsen.c:856)
> ==32155== by 0x885E2B9: libmetis__CreateCoarseGraph (coarsen.c:636)
> ==32155== by 0x885CA49: libmetis__Match_RM (coarsen.c:262)
> ==32155== by 0x885BFBD: libmetis__CoarsenGraph (coarsen.c:55)
> ==32155== by 0x8869A4C: libmetis__MultilevelBisect (pmetis.c:240)
> ==32155== by 0x88696F6: libmetis__MlevelRecursiveBisection (pmetis.c:183)
> ==32155== by 0x88698D7: libmetis__MlevelRecursiveBisection (pmetis.c:207)
> ==32155== by 0x886951E: METIS_PartGraphRecursive (pmetis.c:133)
> ==32155== by 0x885650B: libmetis__InitKWayPartitioning (kmetis.c:194)
> ==32155== by 0x8856147: libmetis__MlevelKWayPartitioning (kmetis.c:121)
> ==32155== by 0x8855FD3: METIS_PartGraphKway (kmetis.c:71)
> ==32155== by 0x85E7611: libparmetis__PartitionSmallGraph (weird.c:478)
> ==32155== by 0x85D00F3: ParMETIS_V3_PartKway (kmetis.c:91)
> ==32155== by 0x5515C19: MatPartitioningApply_Parmetis_Private (pmetis.c:147)
> ==32155== by 0x5516F7D: MatPartitioningApply_Parmetis (pmetis.c:221)
> ==32155== by 0x550DD7F: MatPartitioningApply (partition.c:332)
> ==32155== by 0x6387033: PCGAMGCreateLevel_GAMG (gamg.c:226)
> ==32155== by 0x638BCA5: PCSetUp_GAMG (gamg.c:593)
> ==32155== by 0x64746B1: PCSetUp (precon.c:894)
> ==32155== by 0x65D388A: KSPSetUp (itfunc.c:377)
> ==32155== Address 0xee2502c is 0 bytes after a block of size 284 alloc'd
> ==32155== at 0x4C2AB80: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
> ==32155== by 0x8820179: gk_malloc (memory.c:147)
> ==32155== by 0x883D92B: libmetis__imalloc (gklib.c:24)
> ==32155== by 0x885BF6A: libmetis__CoarsenGraph (coarsen.c:46)
> ==32155== by 0x8869A4C: libmetis__MultilevelBisect (pmetis.c:240)
> ==32155== by 0x88696F6: libmetis__MlevelRecursiveBisection (pmetis.c:183)
> ==32155== by 0x88698D7: libmetis__MlevelRecursiveBisection (pmetis.c:207)
> ==32155== by 0x886951E: METIS_PartGraphRecursive (pmetis.c:133)
> ==32155== by 0x885650B: libmetis__InitKWayPartitioning (kmetis.c:194)
> ==32155== by 0x8856147: libmetis__MlevelKWayPartitioning (kmetis.c:121)
> ==32155== by 0x8855FD3: METIS_PartGraphKway (kmetis.c:71)
> ==32155== by 0x85E7611: libparmetis__PartitionSmallGraph (weird.c:478)
> ==32155== by 0x85D00F3: ParMETIS_V3_PartKway (kmetis.c:91)
> ==32155== by 0x5515C19: MatPartitioningApply_Parmetis_Private (pmetis.c:147)
> ==32155== by 0x5516F7D: MatPartitioningApply_Parmetis (pmetis.c:221)
> ==32155== by 0x550DD7F: MatPartitioningApply (partition.c:332)
> ==32155== by 0x6387033: PCGAMGCreateLevel_GAMG (gamg.c:226)
> ==32155== by 0x638BCA5: PCSetUp_GAMG (gamg.c:593)
> ==32155== by 0x64746B1: PCSetUp (precon.c:894)
> ==32155== by 0x65D388A: KSPSetUp (itfunc.c:377)
> ==32155==
> ==32155== Invalid read of size 4
> ==32155== at 0x885F62F: libmetis__CreateCoarseGraphNoMask (coarsen.c:879)
> ==32155== by 0x885E2B9: libmetis__CreateCoarseGraph (coarsen.c:636)
> ==32155== by 0x885D3CC: libmetis__Match_SHEM (coarsen.c:403)
> ==32155== by 0x885BFD2: libmetis__CoarsenGraph (coarsen.c:57)
> ==32155== by 0x8869A4C: libmetis__MultilevelBisect (pmetis.c:240)
> ==32155== by 0x88696F6: libmetis__MlevelRecursiveBisection (pmetis.c:183)
> ==32155== by 0x88698D7: libmetis__MlevelRecursiveBisection (pmetis.c:207)
> ==32155== by 0x886951E: METIS_PartGraphRecursive (pmetis.c:133)
> ==32155== by 0x885650B: libmetis__InitKWayPartitioning (kmetis.c:194)
> ==32155== by 0x8856147: libmetis__MlevelKWayPartitioning (kmetis.c:121)
> ==32155== by 0x8855FD3: METIS_PartGraphKway (kmetis.c:71)
> ==32155== by 0x85E7611: libparmetis__PartitionSmallGraph (weird.c:478)
> ==32155== by 0x85D00F3: ParMETIS_V3_PartKway (kmetis.c:91)
> ==32155== by 0x5515C19: MatPartitioningApply_Parmetis_Private (pmetis.c:147)
> ==32155== by 0x5516F7D: MatPartitioningApply_Parmetis (pmetis.c:221)
> ==32155== by 0x550DD7F: MatPartitioningApply (partition.c:332)
> ==32155== by 0x6387033: PCGAMGCreateLevel_GAMG (gamg.c:226)
> ==32155== by 0x638BCA5: PCSetUp_GAMG (gamg.c:593)
> ==32155== by 0x64746B1: PCSetUp (precon.c:894)
> ==32155== by 0x65D388A: KSPSetUp (itfunc.c:377)
> ==32155== Address 0xee27524 is 8 bytes after a block of size 76 alloc'd
> ==32155== at 0x4C2AB80: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
> ==32155== by 0x8820179: gk_malloc (memory.c:147)
> ==32155== by 0x883D92B: libmetis__imalloc (gklib.c:24)
> ==32155== by 0x88607CF: libmetis__SetupCoarseGraph (coarsen.c:1107)
> ==32155== by 0x885F16A: libmetis__CreateCoarseGraphNoMask (coarsen.c:826)
> ==32155== by 0x885E2B9: libmetis__CreateCoarseGraph (coarsen.c:636)
> ==32155== by 0x885D3CC: libmetis__Match_SHEM (coarsen.c:403)
> ==32155== by 0x885BFD2: libmetis__CoarsenGraph (coarsen.c:57)
> ==32155== by 0x8869A4C: libmetis__MultilevelBisect (pmetis.c:240)
> ==32155== by 0x88696F6: libmetis__MlevelRecursiveBisection (pmetis.c:183)
> ==32155== by 0x88698D7: libmetis__MlevelRecursiveBisection (pmetis.c:207)
> ==32155== by 0x886951E: METIS_PartGraphRecursive (pmetis.c:133)
> ==32155== by 0x885650B: libmetis__InitKWayPartitioning (kmetis.c:194)
> ==32155== by 0x8856147: libmetis__MlevelKWayPartitioning (kmetis.c:121)
> ==32155== by 0x8855FD3: METIS_PartGraphKway (kmetis.c:71)
> ==32155== by 0x85E7611: libparmetis__PartitionSmallGraph (weird.c:478)
> ==32155== by 0x85D00F3: ParMETIS_V3_PartKway (kmetis.c:91)
> ==32155== by 0x5515C19: MatPartitioningApply_Parmetis_Private (pmetis.c:147)
> ==32155== by 0x5516F7D: MatPartitioningApply_Parmetis (pmetis.c:221)
> ==32155== by 0x550DD7F: MatPartitioningApply (partition.c:332)
> ==32155==
> ==32155== Invalid read of size 4
> ==32155== at 0x885F392: libmetis__CreateCoarseGraphNoMask (coarsen.c:856)
> ==32155== by 0x885E2B9: libmetis__CreateCoarseGraph (coarsen.c:636)
> ==32155== by 0x885D3CC: libmetis__Match_SHEM (coarsen.c:403)
> ==32155== by 0x885BFD2: libmetis__CoarsenGraph (coarsen.c:57)
> ==32155== by 0x8869A4C: libmetis__MultilevelBisect (pmetis.c:240)
> ==32155== by 0x88696F6: libmetis__MlevelRecursiveBisection (pmetis.c:183)
> ==32155== by 0x88698D7: libmetis__MlevelRecursiveBisection (pmetis.c:207)
> ==32155== by 0x886951E: METIS_PartGraphRecursive (pmetis.c:133)
> ==32155== by 0x885650B: libmetis__InitKWayPartitioning (kmetis.c:194)
> ==32155== by 0x8856147: libmetis__MlevelKWayPartitioning (kmetis.c:121)
> ==32155== by 0x8855FD3: METIS_PartGraphKway (kmetis.c:71)
> ==32155== by 0x85E7611: libparmetis__PartitionSmallGraph (weird.c:478)
> ==32155== by 0x85D00F3: ParMETIS_V3_PartKway (kmetis.c:91)
> ==32155== by 0x5515C19: MatPartitioningApply_Parmetis_Private (pmetis.c:147)
> ==32155== by 0x5516F7D: MatPartitioningApply_Parmetis (pmetis.c:221)
> ==32155== by 0x550DD7F: MatPartitioningApply (partition.c:332)
> ==32155== by 0x6387033: PCGAMGCreateLevel_GAMG (gamg.c:226)
> ==32155== by 0x638BCA5: PCSetUp_GAMG (gamg.c:593)
> ==32155== by 0x64746B1: PCSetUp (precon.c:894)
> ==32155== by 0x65D388A: KSPSetUp (itfunc.c:377)
> ==32155== Address 0xee274cc is 4 bytes before a block of size 76 alloc'd
> ==32155== at 0x4C2AB80: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
> ==32155== by 0x8820179: gk_malloc (memory.c:147)
> ==32155== by 0x883D92B: libmetis__imalloc (gklib.c:24)
> ==32155== by 0x88607CF: libmetis__SetupCoarseGraph (coarsen.c:1107)
> ==32155== by 0x885F16A: libmetis__CreateCoarseGraphNoMask (coarsen.c:826)
> ==32155== by 0x885E2B9: libmetis__CreateCoarseGraph (coarsen.c:636)
> ==32155== by 0x885D3CC: libmetis__Match_SHEM (coarsen.c:403)
> ==32155== by 0x885BFD2: libmetis__CoarsenGraph (coarsen.c:57)
> ==32155== by 0x8869A4C: libmetis__MultilevelBisect (pmetis.c:240)
> ==32155== by 0x88696F6: libmetis__MlevelRecursiveBisection (pmetis.c:183)
> ==32155== by 0x88698D7: libmetis__MlevelRecursiveBisection (pmetis.c:207)
> ==32155== by 0x886951E: METIS_PartGraphRecursive (pmetis.c:133)
> ==32155== by 0x885650B: libmetis__InitKWayPartitioning (kmetis.c:194)
> ==32155== by 0x8856147: libmetis__MlevelKWayPartitioning (kmetis.c:121)
> ==32155== by 0x8855FD3: METIS_PartGraphKway (kmetis.c:71)
> ==32155== by 0x85E7611: libparmetis__PartitionSmallGraph (weird.c:478)
> ==32155== by 0x85D00F3: ParMETIS_V3_PartKway (kmetis.c:91)
> ==32155== by 0x5515C19: MatPartitioningApply_Parmetis_Private (pmetis.c:147)
> ==32155== by 0x5516F7D: MatPartitioningApply_Parmetis (pmetis.c:221)
> ==32155== by 0x550DD7F: MatPartitioningApply (partition.c:332)
> ==32155==
>
>
> On Sun, Nov 10, 2019 at 2:24 PM Mark Adams <mfadams at lbl.gov> wrote:
> Fande, It looks to me like this branch in ParMetis must be taken to trigger this error. First Match_SHEM and then CreateCoarseGraphNoMask.
>
> /* determine which matching scheme you will use */
> switch (ctrl->ctype) {
> case METIS_CTYPE_RM:
> Match_RM(ctrl, graph);
> break;
> case METIS_CTYPE_SHEM:
> if (eqewgts || graph->nedges == 0)
> Match_RM(ctrl, graph);
> else
> Match_SHEM(ctrl, graph);
> break;
> default:
> gk_errexit(SIGERR, "Unknown ctype: %d\n", ctrl->ctype);
> }
>
> -----------------------
>
> /* Check if the mask-version of the code is a good choice */
> mask = HTLENGTH;
> if (cnvtxs < 2*mask || graph->nedges/graph->nvtxs > mask/20) {
> CreateCoarseGraphNoMask(ctrl, graph, cnvtxs, match);
> return;
> }
>
> ------------
>
> The actual error is in CreateCoarseGraphNoMask, graph->cmap is too small and this gets garbage. parmetis coarsen.c:856:
>
> istart = xadj[v];
> iend = xadj[v+1];
> for (j=istart; j<iend; j++) {
> k = cmap[adjncy[j]];
> if ((m = htable[k]) == -1) {
> cadjncy[nedges] = k;
>
> Anyway, this is what I have so far,
> Mark
>
>
> On Sun, Nov 10, 2019 at 10:34 AM Mark Adams <mfadams at lbl.gov> wrote:
> Fande, the problem is k below seems to index beyond the end of htable, resulting in a crazy m and a segv on the last line below.
>
> I don't have a clean valgrind machine now, that is what is needed if no one has seen anything like this. I could add a test in a MR and get the pipeline to do it.
>
> void CreateCoarseGraphNoMask(ctrl_t *ctrl, graph_t *graph, idx_t cnvtxs,
> idx_t *match)
> {
> idx_t j, k, m, istart, iend, nvtxs, nedges, ncon, cnedges, v, u, dovsize;
> idx_t *xadj, *vwgt, *vsize, *adjncy, *adjwgt;
> idx_t *cmap, *htable;
> idx_t *cxadj, *cvwgt, *cvsize, *cadjncy, *cadjwgt;
> graph_t *cgraph;
> ine
> WCOREPUSH;
>
> dovsize = (ctrl->objtype == METIS_OBJTYPE_VOL ? 1 : 0);
>
> IFSET(ctrl->dbglvl, METIS_DBG_TIME, gk_startcputimer(ctrl->ContractTmr));
>
> nvtxs = graph->nvtxs;
> ncon = graph->ncon;
> xadj = graph->xadj;
> vwgt = graph->vwgt;
> vsize = graph->vsize;
> adjncy = graph->adjncy;
> adjwgt = graph->adjwgt;
> cmap = graph->cmap;
>
>
> /* Initialize the coarser graph */
> cgraph = SetupCoarseGraph(graph, cnvtxs, dovsize);
> cxadj = cgraph->xadj;
> cvwgt = cgraph->vwgt;
> cvsize = cgraph->vsize;
> cadjncy = cgraph->adjncy;
> cadjwgt = cgraph->adjwgt;
>
> htable = iset(cnvtxs, -1, iwspacemalloc(ctrl, cnvtxs));
>
> cxadj[0] = cnvtxs = cnedges = 0;
> for (v=0; v<nvtxs; v++) {
> if ((u = match[v]) < v)
> continue;
>
> ASSERT(cmap[v] == cnvtxs);
> ASSERT(cmap[match[v]] == cnvtxs);
>
> if (ncon == 1)
> cvwgt[cnvtxs] = vwgt[v];
> else
> icopy(ncon, vwgt+v*ncon, cvwgt+cnvtxs*ncon);
>
> if (dovsize)
> cvsize[cnvtxs] = vsize[v];
>
> nedges = 0;
>
> istart = xadj[v];
> iend = xadj[v+1];
> for (j=istart; j<iend; j++) {
> k = cmap[adjncy[j]];
> if ((m = htable[k]) == -1) {
> cadjncy[nedges] = k;
> cadjwgt[nedges] = adjwgt[j];
> htable[k] = nedges++;
> }
> else {
> cadjwgt[m] += adjwgt[j];
>
> On Sun, Nov 10, 2019 at 1:35 AM Mark Adams <mfadams at lbl.gov> wrote:
>
>
> On Sat, Nov 9, 2019 at 10:51 PM Fande Kong <fdkong.jd at gmail.com> wrote:
> Hi Mark,
>
> Thanks for reporting this bug. I was surprised because we have sufficient heavy tests in moose using partition weights and do not have any issue so far.
>
>
> I have been pounding on this code with elasticity and have not seen this issue. I am now looking at Lapacianas and I only see it with pretty large problems. The example below is pretty minimal (eg, it works with 16 cores and it works with -dm_refine 4). I have reproduced this on Cori, SUMMIT and my laptop.
>
> I will take a shot on this.
>
> Thanks, I'll try to take a look at it also. I have seen it in DDT, but did not dig further. It looked like a typical segv in ParMetis.
>
>
> Fande,
>
> On Sat, Nov 9, 2019 at 3:08 PM Mark Adams <mfadams at lbl.gov> wrote:
> snes/ex13 is getting a ParMetis segv with GAMG and coarse grid repartitioning. Below shows the branch and how to run it.
>
> I've tried valgrind on Cori but it gives a lot of false positives. I've seen this error in DDT but I have not had a chance to dig and try to fix it. At least I know it has something to do with weights.
>
> If anyone wants to take a shot at it feel free. This bug rarely happens.
>
> The changes use weights and are just a few lines of code (from 1.5 years ago):
>
> 12:08 (0455fb9fec...)|BISECTING ~/Codes/petsc$ git bisect bad
> 0455fb9fecf69cf5cf35948c84d3837e5a427e2e is the first bad commit
> commit 0455fb9fecf69cf5cf35948c84d3837e5a427e2e
> Author: Fande Kong <fdkong.jd at gmail.com>
> Date: Thu Jun 21 18:21:19 2018 -0600
>
> Let parmetis and ptsotch take edge weights and vertex weights
>
> src/mat/partition/impls/pmetis/pmetis.c | 7 +++++++
> src/mat/partition/impls/scotch/scotch.c | 6 +++---
> 2 files changed, 10 insertions(+), 3 deletions(-)
>
> > mpiexec -n 32 ./ex13 -cells 2,4,4, -dm_refine 5 -simplex 0 -dim 3 -potential_petscspace_degree 1 -potential_petscspace_order 1 -pc_type gamg -petscpartitioner_type simple -pc_gamg_repartition true -check_pointer_intensity 0
More information about the petsc-dev
mailing list