[petsc-users] SuperLU MPI-problem
Xiaoye S. Li
xsli at lbl.gov
Wed Jul 22 14:19:18 CDT 2015
I am trying to understand your problem. You said you are solving Naviers
equation (elastodynamics) in the frequency domain, using finite element
discretization. I wonder why you have about 1000 nonzeros per row.
Usually in many PDE discretized matrices, the number of nonzeros per row is
in the tens (even for 3D problems), not in the thousands. So, your matrix
is quite a bit denser than many sparse matrices we deal with.
The number of nonzeros in the L and U factors is much more than that in
original matrix A -- typically we see 10-20x fill ratio for 2D, or can be
as bad as 50-100x fill ratio for 3D. But since your matrix starts much
denser (i.e., the underlying graph has many connections), it may not lend
to any good ordering strategy to preserve sparsity of L and U; that is, the
L and U fill ratio may be large.
I don't understand why you get the following error when you use
‘-mat_superlu_dist_parsymbfact’.
Invalid ISPEC at line 484 in file get_perm_c.c
Perhaps Hong Zhang knows; she built the SuperLU_DIST interface for PETSc.
Hong -- in order to use parallel symbolic factorization, is it sufficient
to specify only
‘-mat_superlu_dist_parsymbfact’
? (the default is to use sequential symbolic factorization.)
Sherry
On Wed, Jul 22, 2015 at 9:11 AM, Mahir.Ulker-Kaustell at tyrens.se <
Mahir.Ulker-Kaustell at tyrens.se> wrote:
> Thank you for your reply.
>
> As you have probably figured out already, I am not a computational
> scientist. I am a researcher in civil engineering (railways for high-speed
> traffic), trying to produce some, from my perspective, fairly large
> parametric studies based on finite element discretizations.
>
> I am working in a Windows-environment and have installed PETSc through
> Cygwin.
> Apparently, there is no support for Valgrind in this OS.
>
> If I have understood you correct, the memory issues are related to superLU
> and given my background, there is not much I can do. Is this correct?
>
>
> Best regards,
> Mahir
>
> ______________________________________________
> Mahir Ülker-Kaustell, Kompetenssamordnare, Brokonstruktör, Tekn. Dr,
> Tyréns AB
> 010 452 30 82, Mahir.Ulker-Kaustell at tyrens.se
> ______________________________________________
>
> -----Original Message-----
> From: Barry Smith [mailto:bsmith at mcs.anl.gov]
> Sent: den 22 juli 2015 02:57
> To: Ülker-Kaustell, Mahir
> Cc: Xiaoye S. Li; petsc-users
> Subject: Re: [petsc-users] SuperLU MPI-problem
>
>
> Run the program under valgrind
> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind . When I use
> the option -mat_superlu_dist_parsymbfact I get many scary memory problems
> some involving for example ddist_psymbtonum (pdsymbfact_distdata.c:1332)
>
> Note that I consider it unacceptable for running programs to EVER use
> uninitialized values; until these are all cleaned up I won't trust any runs
> like this.
>
> Barry
>
>
>
>
> ==42050== Conditional jump or move depends on uninitialised value(s)
> ==42050== at 0x10274C436: MPI_Allgatherv (allgatherv.c:1053)
> ==42050== by 0x101557F60: get_perm_c_parmetis
> (get_perm_c_parmetis.c:285)
> ==42050== by 0x101501192: pdgssvx (pdgssvx.c:934)
> ==42050== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST
> (superlu_dist.c:414)
> ==42050== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)
> ==42050== by 0x100F09F2C: PCSetUp_LU (lu.c:152)
> ==42050== by 0x100FF9036: PCSetUp (precon.c:982)
> ==42050== by 0x1010F54EB: KSPSetUp (itfunc.c:332)
> ==42050== by 0x1010F7985: KSPSolve (itfunc.c:546)
> ==42050== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)
> ==42050== by 0x1011C49B7: SNESSolve (snes.c:3906)
> ==42050== by 0x100001B3C: main (in ./ex19)
> ==42050== Uninitialised value was created by a stack allocation
> ==42050== at 0x10155751B: get_perm_c_parmetis (get_perm_c_parmetis.c:96)
> ==42050==
> ==42050== Conditional jump or move depends on uninitialised value(s)
> ==42050== at 0x102851C61: MPIR_Allgatherv_intra (allgatherv.c:651)
> ==42050== by 0x102853EC7: MPIR_Allgatherv (allgatherv.c:903)
> ==42050== by 0x102853F84: MPIR_Allgatherv_impl (allgatherv.c:944)
> ==42050== by 0x10274CA41: MPI_Allgatherv (allgatherv.c:1107)
> ==42050== by 0x101557F60: get_perm_c_parmetis
> (get_perm_c_parmetis.c:285)
> ==42050== by 0x101501192: pdgssvx (pdgssvx.c:934)
> ==42050== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST
> (superlu_dist.c:414)
> ==42050== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)
> ==42050== by 0x100F09F2C: PCSetUp_LU (lu.c:152)
> ==42050== by 0x100FF9036: PCSetUp (precon.c:982)
> ==42050== by 0x1010F54EB: KSPSetUp (itfunc.c:332)
> ==42050== by 0x1010F7985: KSPSolve (itfunc.c:546)
> ==42050== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)
> ==42050== by 0x1011C49B7: SNESSolve (snes.c:3906)
> ==42050== by 0x100001B3C: main (in ./ex19)
> ==42050== Uninitialised value was created by a stack allocation
> ==42050== at 0x10155751B: get_perm_c_parmetis (get_perm_c_parmetis.c:96)
> ==42050==
> ==42049== Syscall param writev(vector[...]) points to uninitialised byte(s)
> ==42049== at 0x102DA1C3A: writev (in
> /usr/lib/system/libsystem_kernel.dylib)
> ==42049== by 0x10296A0DC: MPL_large_writev (mplsock.c:32)
> ==42049== by 0x10295F6AD: MPIDU_Sock_writev (sock_immed.i:610)
> ==42049== by 0x102943FCA: MPIDI_CH3_iSendv (ch3_isendv.c:84)
> ==42049== by 0x102934361: MPIDI_CH3_EagerContigIsend (ch3u_eager.c:556)
> ==42049== by 0x102939531: MPID_Isend (mpid_isend.c:138)
> ==42049== by 0x10277656E: MPI_Isend (isend.c:125)
> ==42049== by 0x102088B66: libparmetis__gkMPI_Isend (gkmpi.c:63)
> ==42049== by 0x10208140F: libparmetis__CommInterfaceData (comm.c:298)
> ==42049== by 0x1020A8758: libparmetis__CompactGraph (ometis.c:553)
> ==42049== by 0x1020A77BB: libparmetis__MultilevelOrder (ometis.c:225)
> ==42049== by 0x1020A7493: ParMETIS_V32_NodeND (ometis.c:151)
> ==42049== by 0x1020A6AFB: ParMETIS_V3_NodeND (ometis.c:34)
> ==42049== by 0x101557CFC: get_perm_c_parmetis
> (get_perm_c_parmetis.c:241)
> ==42049== by 0x101501192: pdgssvx (pdgssvx.c:934)
> ==42049== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST
> (superlu_dist.c:414)
> ==42049== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)
> ==42049== by 0x100F09F2C: PCSetUp_LU (lu.c:152)
> ==42049== by 0x100FF9036: PCSetUp (precon.c:982)
> ==42048== Syscall param writev(vector[...]) points to uninitialised byte(s)
> ==42049== by 0x1010F54EB: KSPSetUp (itfunc.c:332)
> ==42049== Address 0x105edff70 is 1,424 bytes inside a block of size
> 752,720 alloc'd
> ==42049== at 0x1000183B1: malloc (vg_replace_malloc.c:303)
> ==42049== by 0x1020EB90C: gk_malloc (memory.c:147)
> ==42049== by 0x1020EAA28: gk_mcoreCreate (mcore.c:28)
> ==42048== at 0x102DA1C3A: writev (in
> /usr/lib/system/libsystem_kernel.dylib)
> ==42048== by 0x10296A0DC: MPL_large_writev (mplsock.c:32)
> ==42049== by 0x1020BA5CF: libparmetis__AllocateWSpace (wspace.c:23)
> ==42049== by 0x1020A6E84: ParMETIS_V32_NodeND (ometis.c:98)
> ==42048== by 0x10295F6AD: MPIDU_Sock_writev (sock_immed.i:610)
> ==42048== by 0x102943FCA: MPIDI_CH3_iSendv (ch3_isendv.c:84)
> ==42048== by 0x102934361: MPIDI_CH3_EagerContigIsend (ch3u_eager.c:556)
> ==42049== by 0x1020A6AFB: ParMETIS_V3_NodeND (ometis.c:34)
> ==42049== by 0x101557CFC: get_perm_c_parmetis
> (get_perm_c_parmetis.c:241)
> ==42049== by 0x101501192: pdgssvx (pdgssvx.c:934)
> ==42048== by 0x102939531: MPID_Isend (mpid_isend.c:138)
> ==42048== by 0x10277656E: MPI_Isend (isend.c:125)
> ==42049== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST
> (superlu_dist.c:414)
> ==42049== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)
> ==42049== by 0x100F09F2C: PCSetUp_LU (lu.c:152)
> ==42049== by 0x100FF9036: PCSetUp (precon.c:982)
> ==42049== by 0x1010F54EB: KSPSetUp (itfunc.c:332)
> ==42048== by 0x102088B66: libparmetis__gkMPI_Isend (gkmpi.c:63)
> ==42048== by 0x10208140F: libparmetis__CommInterfaceData (comm.c:298)
> ==42049== by 0x1010F7985: KSPSolve (itfunc.c:546)
> ==42049== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)
> ==42048== by 0x1020A8758: libparmetis__CompactGraph (ometis.c:553)
> ==42048== by 0x1020A77BB: libparmetis__MultilevelOrder (ometis.c:225)
> ==42048== by 0x1020A7493: ParMETIS_V32_NodeND (ometis.c:151)
> ==42049== by 0x1011C49B7: SNESSolve (snes.c:3906)
> ==42049== by 0x100001B3C: main (in ./ex19)
> ==42049== Uninitialised value was created by a heap allocation
> ==42049== at 0x1000183B1: malloc (vg_replace_malloc.c:303)
> ==42049== by 0x1020EB90C: gk_malloc (memory.c:147)
> ==42048== by 0x1020A6AFB: ParMETIS_V3_NodeND (ometis.c:34)
> ==42048== by 0x101557CFC: get_perm_c_parmetis
> (get_perm_c_parmetis.c:241)
> ==42048== by 0x101501192: pdgssvx (pdgssvx.c:934)
> ==42048== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST
> (superlu_dist.c:414)
> ==42049== by 0x10211C50B: libmetis__imalloc (gklib.c:24)
> ==42049== by 0x1020A8566: libparmetis__CompactGraph (ometis.c:519)
> ==42049== by 0x1020A77BB: libparmetis__MultilevelOrder (ometis.c:225)
> ==42048== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)
> ==42049== by 0x1020A7493: ParMETIS_V32_NodeND (ometis.c:151)
> ==42049== by 0x1020A6AFB: ParMETIS_V3_NodeND (ometis.c:34)
> ==42049== by 0x101557CFC: get_perm_c_parmetis
> (get_perm_c_parmetis.c:241)
> ==42049== by 0x101501192: pdgssvx (pdgssvx.c:934)
> ==42049== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST
> (superlu_dist.c:414)
> ==42049== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)
> ==42048== by 0x100F09F2C: PCSetUp_LU (lu.c:152)
> ==42049== by 0x100F09F2C: PCSetUp_LU (lu.c:152)
> ==42049== by 0x100FF9036: PCSetUp (precon.c:982)
> ==42049== by 0x1010F54EB: KSPSetUp (itfunc.c:332)
> ==42049== by 0x1010F7985: KSPSolve (itfunc.c:546)
> ==42049== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)
> ==42048== by 0x100FF9036: PCSetUp (precon.c:982)
> ==42048== by 0x1010F54EB: KSPSetUp (itfunc.c:332)
> ==42048== Address 0x10597a860 is 1,408 bytes inside a block of size
> 752,720 alloc'd
> ==42049== by 0x1011C49B7: SNESSolve (snes.c:3906)
> ==42049== by 0x100001B3C: main (in ./ex19)
> ==42049==
> ==42048== at 0x1000183B1: malloc (vg_replace_malloc.c:303)
> ==42048== by 0x1020EB90C: gk_malloc (memory.c:147)
> ==42048== by 0x1020EAA28: gk_mcoreCreate (mcore.c:28)
> ==42048== by 0x1020BA5CF: libparmetis__AllocateWSpace (wspace.c:23)
> ==42048== by 0x1020A6E84: ParMETIS_V32_NodeND (ometis.c:98)
> ==42048== by 0x1020A6AFB: ParMETIS_V3_NodeND (ometis.c:34)
> ==42048== by 0x101557CFC: get_perm_c_parmetis
> (get_perm_c_parmetis.c:241)
> ==42048== by 0x101501192: pdgssvx (pdgssvx.c:934)
> ==42048== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST
> (superlu_dist.c:414)
> ==42048== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)
> ==42048== by 0x100F09F2C: PCSetUp_LU (lu.c:152)
> ==42048== by 0x100FF9036: PCSetUp (precon.c:982)
> ==42048== by 0x1010F54EB: KSPSetUp (itfunc.c:332)
> ==42048== by 0x1010F7985: KSPSolve (itfunc.c:546)
> ==42048== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)
> ==42048== by 0x1011C49B7: SNESSolve (snes.c:3906)
> ==42048== by 0x100001B3C: main (in ./ex19)
> ==42048== Uninitialised value was created by a heap allocation
> ==42048== at 0x1000183B1: malloc (vg_replace_malloc.c:303)
> ==42048== by 0x1020EB90C: gk_malloc (memory.c:147)
> ==42048== by 0x10211C50B: libmetis__imalloc (gklib.c:24)
> ==42048== by 0x1020A8566: libparmetis__CompactGraph (ometis.c:519)
> ==42048== by 0x1020A77BB: libparmetis__MultilevelOrder (ometis.c:225)
> ==42048== by 0x1020A7493: ParMETIS_V32_NodeND (ometis.c:151)
> ==42048== by 0x1020A6AFB: ParMETIS_V3_NodeND (ometis.c:34)
> ==42048== by 0x101557CFC: get_perm_c_parmetis
> (get_perm_c_parmetis.c:241)
> ==42048== by 0x101501192: pdgssvx (pdgssvx.c:934)
> ==42048== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST
> (superlu_dist.c:414)
> ==42048== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)
> ==42048== by 0x100F09F2C: PCSetUp_LU (lu.c:152)
> ==42048== by 0x100FF9036: PCSetUp (precon.c:982)
> ==42048== by 0x1010F54EB: KSPSetUp (itfunc.c:332)
> ==42048== by 0x1010F7985: KSPSolve (itfunc.c:546)
> ==42048== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)
> ==42048== by 0x1011C49B7: SNESSolve (snes.c:3906)
> ==42048== by 0x100001B3C: main (in ./ex19)
> ==42048==
> ==42048== Syscall param write(buf) points to uninitialised byte(s)
> ==42048== at 0x102DA1C22: write (in
> /usr/lib/system/libsystem_kernel.dylib)
> ==42048== by 0x10295F5BD: MPIDU_Sock_write (sock_immed.i:525)
> ==42048== by 0x102944839: MPIDI_CH3_iStartMsg (ch3_istartmsg.c:86)
> ==42048== by 0x102933B80: MPIDI_CH3_EagerContigShortSend
> (ch3u_eager.c:257)
> ==42048== by 0x10293ADBA: MPID_Send (mpid_send.c:130)
> ==42048== by 0x10277A1FA: MPI_Send (send.c:127)
> ==42048== by 0x10155802F: get_perm_c_parmetis
> (get_perm_c_parmetis.c:299)
> ==42048== by 0x101501192: pdgssvx (pdgssvx.c:934)
> ==42048== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST
> (superlu_dist.c:414)
> ==42048== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)
> ==42048== by 0x100F09F2C: PCSetUp_LU (lu.c:152)
> ==42048== by 0x100FF9036: PCSetUp (precon.c:982)
> ==42048== by 0x1010F54EB: KSPSetUp (itfunc.c:332)
> ==42048== by 0x1010F7985: KSPSolve (itfunc.c:546)
> ==42048== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)
> ==42048== by 0x1011C49B7: SNESSolve (snes.c:3906)
> ==42048== by 0x100001B3C: main (in ./ex19)
> ==42048== Address 0x104810704 is on thread 1's stack
> ==42048== in frame #3, created by MPIDI_CH3_EagerContigShortSend
> (ch3u_eager.c:218)
> ==42048== Uninitialised value was created by a heap allocation
> ==42048== at 0x1000183B1: malloc (vg_replace_malloc.c:303)
> ==42048== by 0x10153B704: superlu_malloc_dist (memory.c:108)
> ==42048== by 0x101557AB9: get_perm_c_parmetis
> (get_perm_c_parmetis.c:185)
> ==42048== by 0x101501192: pdgssvx (pdgssvx.c:934)
> ==42048== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST
> (superlu_dist.c:414)
> ==42048== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)
> ==42048== by 0x100F09F2C: PCSetUp_LU (lu.c:152)
> ==42048== by 0x100FF9036: PCSetUp (precon.c:982)
> ==42048== by 0x1010F54EB: KSPSetUp (itfunc.c:332)
> ==42048== by 0x1010F7985: KSPSolve (itfunc.c:546)
> ==42048== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)
> ==42048== by 0x1011C49B7: SNESSolve (snes.c:3906)
> ==42048== by 0x100001B3C: main (in ./ex19)
> ==42048==
> ==42050== Conditional jump or move depends on uninitialised value(s)
> ==42050== at 0x102744CB8: MPI_Alltoallv (alltoallv.c:480)
> ==42050== by 0x101510B3E: dist_symbLU (pdsymbfact_distdata.c:539)
> ==42050== by 0x10150A5C6: ddist_psymbtonum (pdsymbfact_distdata.c:1275)
> ==42050== by 0x1015018C2: pdgssvx (pdgssvx.c:1057)
> ==42050== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST
> (superlu_dist.c:414)
> ==42050== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)
> ==42050== by 0x100F09F2C: PCSetUp_LU (lu.c:152)
> ==42050== by 0x100FF9036: PCSetUp (precon.c:982)
> ==42050== by 0x1010F54EB: KSPSetUp (itfunc.c:332)
> ==42050== by 0x1010F7985: KSPSolve (itfunc.c:546)
> ==42050== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)
> ==42050== by 0x1011C49B7: SNESSolve (snes.c:3906)
> ==42050== by 0x100001B3C: main (in ./ex19)
> ==42050== Uninitialised value was created by a stack allocation
> ==42050== at 0x10150E4C4: dist_symbLU (pdsymbfact_distdata.c:96)
> ==42050==
> ==42050== Conditional jump or move depends on uninitialised value(s)
> ==42050== at 0x102744E43: MPI_Alltoallv (alltoallv.c:490)
> ==42050== by 0x101510B3E: dist_symbLU (pdsymbfact_distdata.c:539)
> ==42050== by 0x10150A5C6: ddist_psymbtonum (pdsymbfact_distdata.c:1275)
> ==42050== by 0x1015018C2: pdgssvx (pdgssvx.c:1057)
> ==42050== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST
> (superlu_dist.c:414)
> ==42050== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)
> ==42050== by 0x100F09F2C: PCSetUp_LU (lu.c:152)
> ==42050== by 0x100FF9036: PCSetUp (precon.c:982)
> ==42050== by 0x1010F54EB: KSPSetUp (itfunc.c:332)
> ==42050== by 0x1010F7985: KSPSolve (itfunc.c:546)
> ==42050== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)
> ==42050== by 0x1011C49B7: SNESSolve (snes.c:3906)
> ==42050== by 0x100001B3C: main (in ./ex19)
> ==42050== Uninitialised value was created by a stack allocation
> ==42050== at 0x10150E4C4: dist_symbLU (pdsymbfact_distdata.c:96)
> ==42050==
> ==42050== Conditional jump or move depends on uninitialised value(s)
> ==42050== at 0x102744EBF: MPI_Alltoallv (alltoallv.c:497)
> ==42050== by 0x101510B3E: dist_symbLU (pdsymbfact_distdata.c:539)
> ==42050== by 0x10150A5C6: ddist_psymbtonum (pdsymbfact_distdata.c:1275)
> ==42050== by 0x1015018C2: pdgssvx (pdgssvx.c:1057)
> ==42050== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST
> (superlu_dist.c:414)
> ==42050== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)
> ==42050== by 0x100F09F2C: PCSetUp_LU (lu.c:152)
> ==42050== by 0x100FF9036: PCSetUp (precon.c:982)
> ==42050== by 0x1010F54EB: KSPSetUp (itfunc.c:332)
> ==42050== by 0x1010F7985: KSPSolve (itfunc.c:546)
> ==42050== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)
> ==42050== by 0x1011C49B7: SNESSolve (snes.c:3906)
> ==42050== by 0x100001B3C: main (in ./ex19)
> ==42050== Uninitialised value was created by a stack allocation
> ==42050== at 0x10150E4C4: dist_symbLU (pdsymbfact_distdata.c:96)
> ==42050==
> ==42050== Conditional jump or move depends on uninitialised value(s)
> ==42050== at 0x1027450B1: MPI_Alltoallv (alltoallv.c:512)
> ==42050== by 0x101510B3E: dist_symbLU (pdsymbfact_distdata.c:539)
> ==42050== by 0x10150A5C6: ddist_psymbtonum (pdsymbfact_distdata.c:1275)
> ==42050== by 0x1015018C2: pdgssvx (pdgssvx.c:1057)
> ==42050== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST
> (superlu_dist.c:414)
> ==42050== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)
> ==42050== by 0x100F09F2C: PCSetUp_LU (lu.c:152)
> ==42050== by 0x100FF9036: PCSetUp (precon.c:982)
> ==42050== by 0x1010F54EB: KSPSetUp (itfunc.c:332)
> ==42050== by 0x1010F7985: KSPSolve (itfunc.c:546)
> ==42050== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)
> ==42050== by 0x1011C49B7: SNESSolve (snes.c:3906)
> ==42050== by 0x100001B3C: main (in ./ex19)
> ==42050== Uninitialised value was created by a stack allocation
> ==42050== at 0x10150E4C4: dist_symbLU (pdsymbfact_distdata.c:96)
> ==42050==
> ==42050== Conditional jump or move depends on uninitialised value(s)
> ==42050== at 0x10283FB06: MPIR_Alltoallv_intra (alltoallv.c:92)
> ==42050== by 0x1028407B6: MPIR_Alltoallv (alltoallv.c:343)
> ==42050== by 0x102840884: MPIR_Alltoallv_impl (alltoallv.c:380)
> ==42050== by 0x10274541B: MPI_Alltoallv (alltoallv.c:531)
> ==42050== by 0x101510B3E: dist_symbLU (pdsymbfact_distdata.c:539)
> ==42050== by 0x10150A5C6: ddist_psymbtonum (pdsymbfact_distdata.c:1275)
> ==42050== by 0x1015018C2: pdgssvx (pdgssvx.c:1057)
> ==42050== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST
> (superlu_dist.c:414)
> ==42050== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)
> ==42050== by 0x100F09F2C: PCSetUp_LU (lu.c:152)
> ==42050== by 0x100FF9036: PCSetUp (precon.c:982)
> ==42050== by 0x1010F54EB: KSPSetUp (itfunc.c:332)
> ==42050== by 0x1010F7985: KSPSolve (itfunc.c:546)
> ==42050== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)
> ==42050== by 0x1011C49B7: SNESSolve (snes.c:3906)
> ==42050== by 0x100001B3C: main (in ./ex19)
> ==42050== Uninitialised value was created by a stack allocation
> ==42050== at 0x10150E4C4: dist_symbLU (pdsymbfact_distdata.c:96)
> ==42050==
> ==42050== Syscall param writev(vector[...]) points to uninitialised byte(s)
> ==42050== at 0x102DA1C3A: writev (in
> /usr/lib/system/libsystem_kernel.dylib)
> ==42050== by 0x10296A0DC: MPL_large_writev (mplsock.c:32)
> ==42050== by 0x10295F6AD: MPIDU_Sock_writev (sock_immed.i:610)
> ==42050== by 0x102943FCA: MPIDI_CH3_iSendv (ch3_isendv.c:84)
> ==42050== by 0x102934361: MPIDI_CH3_EagerContigIsend (ch3u_eager.c:556)
> ==42050== by 0x102939531: MPID_Isend (mpid_isend.c:138)
> ==42050== by 0x10277656E: MPI_Isend (isend.c:125)
> ==42050== by 0x101524C41: pdgstrf2_trsm (pdgstrf2.c:201)
> ==42050== by 0x10151ECBF: pdgstrf (pdgstrf.c:1082)
> ==42050== by 0x1015019A5: pdgssvx (pdgssvx.c:1069)
> ==42050== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST
> (superlu_dist.c:414)
> ==42050== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)
> ==42050== by 0x100F09F2C: PCSetUp_LU (lu.c:152)
> ==42050== by 0x100FF9036: PCSetUp (precon.c:982)
> ==42050== by 0x1010F54EB: KSPSetUp (itfunc.c:332)
> ==42050== by 0x1010F7985: KSPSolve (itfunc.c:546)
> ==42050== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)
> ==42050== by 0x1011C49B7: SNESSolve (snes.c:3906)
> ==42050== by 0x100001B3C: main (in ./ex19)
> ==42050== Address 0x1060144d0 is 1,168 bytes inside a block of size
> 131,072 alloc'd
> ==42050== at 0x1000183B1: malloc (vg_replace_malloc.c:303)
> ==42050== by 0x10153B704: superlu_malloc_dist (memory.c:108)
> ==42050== by 0x1014FD7AD: doubleMalloc_dist (dmemory.c:145)
> ==42050== by 0x10151DA7D: pdgstrf (pdgstrf.c:735)
> ==42050== by 0x1015019A5: pdgssvx (pdgssvx.c:1069)
> ==42050== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST
> (superlu_dist.c:414)
> ==42050== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)
> ==42050== by 0x100F09F2C: PCSetUp_LU (lu.c:152)
> ==42050== by 0x100FF9036: PCSetUp (precon.c:982)
> ==42050== by 0x1010F54EB: KSPSetUp (itfunc.c:332)
> ==42050== by 0x1010F7985: KSPSolve (itfunc.c:546)
> ==42050== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)
> ==42050== by 0x1011C49B7: SNESSolve (snes.c:3906)
> ==42050== by 0x100001B3C: main (in ./ex19)
> ==42050== Uninitialised value was created by a heap allocation
> ==42050== at 0x1000183B1: malloc (vg_replace_malloc.c:303)
> ==42050== by 0x10153B704: superlu_malloc_dist (memory.c:108)
> ==42050== by 0x1014FD7AD: doubleMalloc_dist (dmemory.c:145)
> ==42050== by 0x10151DA7D: pdgstrf (pdgstrf.c:735)
> ==42050== by 0x1015019A5: pdgssvx (pdgssvx.c:1069)
> ==42050== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST
> (superlu_dist.c:414)
> ==42050== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)
> ==42050== by 0x100F09F2C: PCSetUp_LU (lu.c:152)
> ==42050== by 0x100FF9036: PCSetUp (precon.c:982)
> ==42050== by 0x1010F54EB: KSPSetUp (itfunc.c:332)
> ==42050== by 0x1010F7985: KSPSolve (itfunc.c:546)
> ==42050== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)
> ==42050== by 0x1011C49B7: SNESSolve (snes.c:3906)
> ==42050== by 0x100001B3C: main (in ./ex19)
> ==42050==
> ==42048== Conditional jump or move depends on uninitialised value(s)
> ==42048== at 0x10151F141: pdgstrf (pdgstrf.c:1139)
> ==42048== by 0x1015019A5: pdgssvx (pdgssvx.c:1069)
> ==42048== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST
> (superlu_dist.c:414)
> ==42048== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)
> ==42048== by 0x100F09F2C: PCSetUp_LU (lu.c:152)
> ==42048== by 0x100FF9036: PCSetUp (precon.c:982)
> ==42048== by 0x1010F54EB: KSPSetUp (itfunc.c:332)
> ==42048== by 0x1010F7985: KSPSolve (itfunc.c:546)
> ==42048== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)
> ==42048== by 0x1011C49B7: SNESSolve (snes.c:3906)
> ==42048== by 0x100001B3C: main (in ./ex19)
> ==42048== Uninitialised value was created by a heap allocation
> ==42048== at 0x1000183B1: malloc (vg_replace_malloc.c:303)
> ==42048== by 0x10153B704: superlu_malloc_dist (memory.c:108)
> ==42048== by 0x10150ABE2: ddist_psymbtonum (pdsymbfact_distdata.c:1332)
> ==42048== by 0x1015018C2: pdgssvx (pdgssvx.c:1057)
> ==42048== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST
> (superlu_dist.c:414)
> ==42048== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)
> ==42048== by 0x100F09F2C: PCSetUp_LU (lu.c:152)
> ==42048== by 0x100FF9036: PCSetUp (precon.c:982)
> ==42048== by 0x1010F54EB: KSPSetUp (itfunc.c:332)
> ==42048== by 0x1010F7985: KSPSolve (itfunc.c:546)
> ==42048== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)
> ==42048== by 0x1011C49B7: SNESSolve (snes.c:3906)
> ==42048== by 0x100001B3C: main (in ./ex19)
> ==42048==
> ==42049== Conditional jump or move depends on uninitialised value(s)
> ==42049== at 0x10151F141: pdgstrf (pdgstrf.c:1139)
> ==42049== by 0x1015019A5: pdgssvx (pdgssvx.c:1069)
> ==42049== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST
> (superlu_dist.c:414)
> ==42049== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)
> ==42049== by 0x100F09F2C: PCSetUp_LU (lu.c:152)
> ==42049== by 0x100FF9036: PCSetUp (precon.c:982)
> ==42049== by 0x1010F54EB: KSPSetUp (itfunc.c:332)
> ==42049== by 0x1010F7985: KSPSolve (itfunc.c:546)
> ==42049== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)
> ==42049== by 0x1011C49B7: SNESSolve (snes.c:3906)
> ==42049== by 0x100001B3C: main (in ./ex19)
> ==42049== Uninitialised value was created by a heap allocation
> ==42049== at 0x1000183B1: malloc (vg_replace_malloc.c:303)
> ==42049== by 0x10153B704: superlu_malloc_dist (memory.c:108)
> ==42049== by 0x10150ABE2: ddist_psymbtonum (pdsymbfact_distdata.c:1332)
> ==42049== by 0x1015018C2: pdgssvx (pdgssvx.c:1057)
> ==42049== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST
> (superlu_dist.c:414)
> ==42049== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)
> ==42049== by 0x100F09F2C: PCSetUp_LU (lu.c:152)
> ==42049== by 0x100FF9036: PCSetUp (precon.c:982)
> ==42049== by 0x1010F54EB: KSPSetUp (itfunc.c:332)
> ==42049== by 0x1010F7985: KSPSolve (itfunc.c:546)
> ==42049== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)
> ==42049== by 0x1011C49B7: SNESSolve (snes.c:3906)
> ==42049== by 0x100001B3C: main (in ./ex19)
> ==42049==
> ==42048== Conditional jump or move depends on uninitialised value(s)
> ==42048== at 0x101520054: pdgstrf (pdgstrf.c:1429)
> ==42048== by 0x1015019A5: pdgssvx (pdgssvx.c:1069)
> ==42048== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST
> (superlu_dist.c:414)
> ==42048== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)
> ==42048== by 0x100F09F2C: PCSetUp_LU (lu.c:152)
> ==42048== by 0x100FF9036: PCSetUp (precon.c:982)
> ==42048== by 0x1010F54EB: KSPSetUp (itfunc.c:332)
> ==42048== by 0x1010F7985: KSPSolve (itfunc.c:546)
> ==42049== Conditional jump or move depends on uninitialised value(s)
> ==42048== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)
> ==42048== by 0x1011C49B7: SNESSolve (snes.c:3906)
> ==42048== by 0x100001B3C: main (in ./ex19)
> ==42048== Uninitialised value was created by a heap allocation
> ==42049== at 0x101520054: pdgstrf (pdgstrf.c:1429)
> ==42048== at 0x1000183B1: malloc (vg_replace_malloc.c:303)
> ==42048== by 0x10153B704: superlu_malloc_dist (memory.c:108)
> ==42049== by 0x1015019A5: pdgssvx (pdgssvx.c:1069)
> ==42049== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST
> (superlu_dist.c:414)
> ==42048== by 0x10150ABE2: ddist_psymbtonum (pdsymbfact_distdata.c:1332)
> ==42048== by 0x1015018C2: pdgssvx (pdgssvx.c:1057)
> ==42048== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST
> (superlu_dist.c:414)
> ==42049== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)
> ==42049== by 0x100F09F2C: PCSetUp_LU (lu.c:152)
> ==42048== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)
> ==42048== by 0x100F09F2C: PCSetUp_LU (lu.c:152)
> ==42049== by 0x100FF9036: PCSetUp (precon.c:982)
> ==42049== by 0x1010F54EB: KSPSetUp (itfunc.c:332)
> ==42049== by 0x1010F7985: KSPSolve (itfunc.c:546)
> ==42048== by 0x100FF9036: PCSetUp (precon.c:982)
> ==42048== by 0x1010F54EB: KSPSetUp (itfunc.c:332)
> ==42048== by 0x1010F7985: KSPSolve (itfunc.c:546)
> ==42049== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)
> ==42049== by 0x1011C49B7: SNESSolve (snes.c:3906)
> ==42048== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)
> ==42048== by 0x1011C49B7: SNESSolve (snes.c:3906)
> ==42049== by 0x100001B3C: main (in ./ex19)
> ==42049== Uninitialised value was created by a heap allocation
> ==42049== at 0x1000183B1: malloc (vg_replace_malloc.c:303)
> ==42048== by 0x100001B3C: main (in ./ex19)
> ==42048==
> ==42049== by 0x10153B704: superlu_malloc_dist (memory.c:108)
> ==42049== by 0x10150ABE2: ddist_psymbtonum (pdsymbfact_distdata.c:1332)
> ==42049== by 0x1015018C2: pdgssvx (pdgssvx.c:1057)
> ==42049== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST
> (superlu_dist.c:414)
> ==42049== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)
> ==42049== by 0x100F09F2C: PCSetUp_LU (lu.c:152)
> ==42049== by 0x100FF9036: PCSetUp (precon.c:982)
> ==42049== by 0x1010F54EB: KSPSetUp (itfunc.c:332)
> ==42049== by 0x1010F7985: KSPSolve (itfunc.c:546)
> ==42049== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)
> ==42049== by 0x1011C49B7: SNESSolve (snes.c:3906)
> ==42049== by 0x100001B3C: main (in ./ex19)
> ==42049==
> ==42050== Conditional jump or move depends on uninitialised value(s)
> ==42050== at 0x10151FDE6: pdgstrf (pdgstrf.c:1382)
> ==42050== by 0x1015019A5: pdgssvx (pdgssvx.c:1069)
> ==42050== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST
> (superlu_dist.c:414)
> ==42050== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)
> ==42050== by 0x100F09F2C: PCSetUp_LU (lu.c:152)
> ==42050== by 0x100FF9036: PCSetUp (precon.c:982)
> ==42050== by 0x1010F54EB: KSPSetUp (itfunc.c:332)
> ==42050== by 0x1010F7985: KSPSolve (itfunc.c:546)
> ==42050== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)
> ==42050== by 0x1011C49B7: SNESSolve (snes.c:3906)
> ==42050== by 0x100001B3C: main (in ./ex19)
> ==42050== Uninitialised value was created by a heap allocation
> ==42050== at 0x1000183B1: malloc (vg_replace_malloc.c:303)
> ==42050== by 0x10153B704: superlu_malloc_dist (memory.c:108)
> ==42050== by 0x10150B241: ddist_psymbtonum (pdsymbfact_distdata.c:1389)
> ==42050== by 0x1015018C2: pdgssvx (pdgssvx.c:1057)
> ==42050== by 0x1009CFE7A: MatLUFactorNumeric_SuperLU_DIST
> (superlu_dist.c:414)
> ==42050== by 0x10046CC5C: MatLUFactorNumeric (matrix.c:2946)
> ==42050== by 0x100F09F2C: PCSetUp_LU (lu.c:152)
> ==42050== by 0x100FF9036: PCSetUp (precon.c:982)
> ==42050== by 0x1010F54EB: KSPSetUp (itfunc.c:332)
> ==42050== by 0x1010F7985: KSPSolve (itfunc.c:546)
> ==42050== by 0x10125541E: SNESSolve_NEWTONLS (ls.c:233)
> ==42050== by 0x1011C49B7: SNESSolve (snes.c:3906)
> ==42050== by 0x100001B3C: main (in ./ex19)
> ==42050==
>
>
> > On Jul 20, 2015, at 12:03 PM, Mahir.Ulker-Kaustell at tyrens.se wrote:
> >
> > Ok. So I have been creating the full factorization on each process. That
> gives me some hope!
> >
> > I followed your suggestion and tried to use the runtime option
> ‘-mat_superlu_dist_parsymbfact’.
> > However, now the program crashes with:
> >
> > Invalid ISPEC at line 484 in file get_perm_c.c
> >
> > And so on…
> >
> > From the SuperLU manual; I should give the option either YES or NO,
> however -mat_superlu_dist_parsymbfact YES makes the program crash in the
> same way as above.
> > Also I can’t find any reference to -mat_superlu_dist_parsymbfact in the
> PETSc documentation
> >
> > Mahir
> >
> > Mahir Ülker-Kaustell, Kompetenssamordnare, Brokonstruktör, Tekn. Dr,
> Tyréns AB
> > 010 452 30 82, Mahir.Ulker-Kaustell at tyrens.se
> >
> > From: Xiaoye S. Li [mailto:xsli at lbl.gov]
> > Sent: den 20 juli 2015 18:12
> > To: Ülker-Kaustell, Mahir
> > Cc: Hong; petsc-users
> > Subject: Re: [petsc-users] SuperLU MPI-problem
> >
> > The default SuperLU_DIST setting is to serial symbolic factorization.
> Therefore, what matters is how much memory do you have per MPI task?
> >
> > The code failed to malloc memory during redistribution of matrix A to
> {L\U} data struction (using result of serial symbolic factorization.)
> >
> > You can use parallel symbolic factorization, by runtime option:
> '-mat_superlu_dist_parsymbfact'
> >
> > Sherry Li
> >
> >
> > On Mon, Jul 20, 2015 at 8:59 AM, Mahir.Ulker-Kaustell at tyrens.se <
> Mahir.Ulker-Kaustell at tyrens.se> wrote:
> > Hong:
> >
> > Previous experiences with this equation have shown that it is very
> difficult to solve it iteratively. Hence the use of a direct solver.
> >
> > The large test problem I am trying to solve has slightly less than 10^6
> degrees of freedom. The matrices are derived from finite elements so they
> are sparse.
> > The machine I am working on has 128GB ram. I have estimated the memory
> needed to less than 20GB, so if the solver needs twice or even three times
> as much, it should still work well. Or have I completely misunderstood
> something here?
> >
> > Mahir
> >
> >
> >
> > From: Hong [mailto:hzhang at mcs.anl.gov]
> > Sent: den 20 juli 2015 17:39
> > To: Ülker-Kaustell, Mahir
> > Cc: petsc-users
> > Subject: Re: [petsc-users] SuperLU MPI-problem
> >
> > Mahir:
> > Direct solvers consume large amount of memory. Suggest to try followings:
> >
> > 1. A sparse iterative solver if [-omega^2M + K] is not too
> ill-conditioned. You may test it using the small matrix.
> >
> > 2. Incrementally increase your matrix sizes. Try different matrix
> orderings.
> > Do you get memory crash in the 1st symbolic factorization?
> > In your case, matrix data structure stays same when omega changes, so
> you only need to do one matrix symbolic factorization and reuse it.
> >
> > 3. Use a machine that gives larger memory.
> >
> > Hong
> >
> > Dear Petsc-Users,
> >
> > I am trying to use PETSc to solve a set of linear equations arising from
> Naviers equation (elastodynamics) in the frequency domain.
> > The frequency dependency of the problem requires that the system
> >
> > [-omega^2M + K]u = F
> >
> > where M and K are constant, square, positive definite matrices (mass and
> stiffness respectively) is solved for each frequency omega of interest.
> > K is a complex matrix, including material damping.
> >
> > I have written a PETSc program which solves this problem for a small
> (1000 degrees of freedom) test problem on one or several processors, but it
> keeps crashing when I try it on my full scale (in the order of 10^6 degrees
> of freedom) problem.
> >
> > The program crashes at KSPSetUp() and from what I can see in the error
> messages, it appears as if it consumes too much memory.
> >
> > I would guess that similar problems have occurred in this mail-list, so
> I am hoping that someone can push me in the right direction…
> >
> > Mahir
>
>
>
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