[petsc-users] SuperLU MPI-problem
Matthew Knepley
knepley at gmail.com
Wed Jul 22 16:27:19 CDT 2015
On Wed, Jul 22, 2015 at 4:15 PM, Mahir.Ulker-Kaustell at tyrens.se <
Mahir.Ulker-Kaustell at tyrens.se> wrote:
> So, I tried to use MUMPS instead of SuperLU.
>
>
>
> Still some problems with running out of memory, but I think that Sherry
> and Hong have poked me in an important direction:
>
>
>
> I may have also underestimated the need for matrix reordering when
> computing the LU-factors. I have to look into this…
>
>
>
>
>
> One thing which is puzzling me now is that when I followed Hongs
> suggestion to try an iterative solver, I found that it solved my simple
> test problem after some testing with different settings.
>
> I am solving Ax = b with a sparse, indefinite, symmetric, complex matrix,
> can anything be said about the chances of success in using an iterative
> method?
>
That depends entirely on your problem. It you are solving something that
looks like elasticity, then -pc_type gamg should solve it
fine. However, nothing can be said in general.
Matt
> /Mahir
>
>
>
>
>
> *From:* Matthew Knepley [mailto:knepley at gmail.com]
> *Sent:* den 22 juli 2015 19:17
> *To:* Ülker-Kaustell, Mahir
> *Cc:* Barry Smith; petsc-users
> *Subject:* Re: [petsc-users] SuperLU MPI-problem
>
>
>
> On Wed, Jul 22, 2015 at 11:11 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.
>
>
>
> It is really worth any amount of time and effort to get away from Windows
> if you are doing computational science.
>
>
>
> 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?
>
>
>
> The next step is to run the problem using MUMPS (--download-mumps
> --download-scalapack).
>
>
>
> Thanks,
>
>
>
> Matt
>
>
>
> 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
>
>
>
>
>
> --
>
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
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