[petsc-users] SuperLU MPI-problem
Xiaoye S. Li
xsli at lbl.gov
Mon Aug 3 09:17:54 CDT 2015
I think I know the problem. Since zdistribute.c is called, I guess you
are using the global (replicated) matrix input interface,
pzgssvx_ABglobal(). This interface does not allow you to use parallel
symbolic factorization (since matrix is centralized).
That's why you get the following error:
Invalid ISPEC at line 484 in file get_perm_c.c
You need to use distributed matrix input interface pzgssvx() (without
ABglobal)
Sherry
On Mon, Aug 3, 2015 at 5:02 AM, Mahir.Ulker-Kaustell at tyrens.se <
Mahir.Ulker-Kaustell at tyrens.se> wrote:
> Hong and Sherry,
>
>
>
> I have rebuilt PETSc with SuperLU 4.1. Unfortunately, the problem remains:
>
>
>
> If I use -mat_superlu_dist_parsymbfact, the program crashes with: Invalid
> ISPEC at line 484 in file get_perm_c.c
>
> If I use -mat_superlu_dist_parsymbfact=1 or leave this flag out, the
> program crashes with: Calloc fails for SPA dense[]. at line 438 in file
> zdistribute.c
>
>
>
> Mahir
>
>
>
> *From:* Hong [mailto:hzhang at mcs.anl.gov]
> *Sent:* den 30 juli 2015 02:58
> *To:* Ülker-Kaustell, Mahir
> *Cc:* Xiaoye Li; PETSc users list
>
> *Subject:* Fwd: [petsc-users] SuperLU MPI-problem
>
>
>
> Mahir,
>
>
>
> Sherry fixed several bugs in superlu_dist-v4.1.
>
> The current petsc-release interfaces with superlu_dist-v4.0.
>
> We do not know whether the reported issue (attached below) has been
> resolved or not. If not, can you test it with the latest superlu_dist-v4.1?
>
>
>
> Here is how to do it:
>
> 1. download superlu_dist v4.1
>
> 2. remove existing PETSC_ARCH directory, then configure petsc with
>
> '--download-superlu_dist=superlu_dist_4.1.tar.gz'
>
> 3. build petsc
>
>
>
> Let us know if the issue remains.
>
>
>
> Hong
>
>
>
>
>
> ---------- Forwarded message ----------
> From: *Xiaoye S. Li* <xsli at lbl.gov>
> Date: Wed, Jul 29, 2015 at 2:24 PM
> Subject: Fwd: [petsc-users] SuperLU MPI-problem
> To: Hong Zhang <hzhang at mcs.anl.gov>
>
> Hong,
>
> I am cleaning the mailbox, and saw this unresolved issue. I am not sure
> whether the new fix to parallel symbolic factorization solves the problem.
> What bothers be is that he is getting the following error:
>
> Invalid ISPEC at line 484 in file get_perm_c.c
>
> This has nothing to do with my bug fix.
>
> Shall we ask him to try the new version, or try to get him matrix?
>
> Sherry
>
>
>
>
> ---------- Forwarded message ----------
> From: *Mahir.Ulker-Kaustell at tyrens.se <Mahir.Ulker-Kaustell at tyrens.se>* <
> Mahir.Ulker-Kaustell at tyrens.se>
> Date: Wed, Jul 22, 2015 at 1:32 PM
> Subject: RE: [petsc-users] SuperLU MPI-problem
> To: Hong <hzhang at mcs.anl.gov>, "Xiaoye S. Li" <xsli at lbl.gov>
> Cc: petsc-users <petsc-users at mcs.anl.gov>
>
> The 1000 was just a conservative guess. The number of non-zeros per row is
> in the tens in general but certain constraints lead to non-diagonal streaks
> in the sparsity-pattern.
>
> Is it the reordering of the matrix that is killing me here? How can I set
> options.ColPerm?
>
>
>
> If i use -mat_superlu_dist_parsymbfact the program crashes with
>
>
>
> Invalid ISPEC at line 484 in file get_perm_c.c
>
> -------------------------------------------------------
>
> Primary job terminated normally, but 1 process returned
>
> a non-zero exit code.. Per user-direction, the job has been aborted.
>
> -------------------------------------------------------
>
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
>
> [0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the
> batch system) has told this process to end
>
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>
> [0]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
>
> [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS
> X to find memory corruption errors
>
> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
> run
>
> [0]PETSC ERROR: to get more information on the crash.
>
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
>
> [0]PETSC ERROR: Signal received
>
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
>
> [0]PETSC ERROR: Petsc Release Version 3.6.0, Jun, 09, 2015
>
> [0]PETSC ERROR: ./solve on a cygwin-complex-nodebug named CZC5202SM2 by
> muk Wed Jul 22 21:59:23 2015
>
> [0]PETSC ERROR: Configure options PETSC_DIR=/packages/petsc-3.6.0
> PETSC_ARCH=cygwin-complex-nodebug --with-cc=gcc --with-cxx=g++
> --with-fc=gfortran --with-debugging=0 --with-fortran-kernels=1
> --with-scalar-type=complex --download-fblaspack --download-mpich
> --download-scalapack --download-mumps --download-metis --download-parmetis
> --download-superlu --download-superlu_dist --download-fftw
>
> [0]PETSC ERROR: #1 User provided function() line 0 in unknown file
>
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>
> [unset]: aborting job:
>
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
>
>
>
> If i use -mat_superlu_dist_parsymbfact=1 the program crashes (somewhat
> later) with
>
>
>
> Malloc fails for Lnzval_bc_ptr[*][] at line 626 in file zdistribute.c
>
> col block 3006 -------------------------------------------------------
>
> Primary job terminated normally, but 1 process returned
>
> a non-zero exit code.. Per user-direction, the job has been aborted.
>
> -------------------------------------------------------
>
> col block 1924 [0]PETSC ERROR:
> ------------------------------------------------------------------------
>
> [0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the
> batch system) has told this process to end
>
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>
> [0]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
>
> [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS
> X to find memory corruption errors
>
> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
> run
>
> [0]PETSC ERROR: to get more information on the crash.
>
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
>
> [0]PETSC ERROR: Signal received
>
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
>
> [0]PETSC ERROR: Petsc Release Version 3.6.0, Jun, 09, 2015
>
> [0]PETSC ERROR: ./solve on a cygwin-complex-nodebug named CZC5202SM2 by
> muk Wed Jul 22 21:59:58 2015
>
> [0]PETSC ERROR: Configure options PETSC_DIR=/packages/petsc-3.6.0
> PETSC_ARCH=cygwin-complex-nodebug --with-cc=gcc --with-cxx=g++
> --with-fc=gfortran --with-debugging=0 --with-fortran-kernels=1
> --with-scalar-type=complex --download-fblaspack --download-mpich
> --download-scalapack --download-mumps --download-metis --download-parmetis
> --download-superlu --download-superlu_dist --download-fftw
>
> [0]PETSC ERROR: #1 User provided function() line 0 in unknown file
>
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>
> [unset]: aborting job:
>
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
>
>
>
>
>
> /Mahir
>
>
>
>
>
> *From:* Hong [mailto:hzhang at mcs.anl.gov]
>
> *Sent:* den 22 juli 2015 21:34
> *To:* Xiaoye S. Li
> *Cc:* Ülker-Kaustell, Mahir; petsc-users
>
>
> *Subject:* Re: [petsc-users] SuperLU MPI-problem
>
>
>
> In Petsc/superlu_dist interface, we set default
>
>
>
> options.ParSymbFact = NO;
>
>
>
> When user raises the flag "-mat_superlu_dist_parsymbfact",
>
> we set
>
>
>
> options.ParSymbFact = YES;
>
> options.ColPerm = PARMETIS; /* in v2.2, PARMETIS is forced for
> ParSymbFact regardless of user ordering setting */
>
>
>
> We do not change anything else.
>
>
>
> Hong
>
>
>
> On Wed, Jul 22, 2015 at 2:19 PM, Xiaoye S. Li <xsli at lbl.gov> wrote:
>
> 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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