[petsc-users] SuperLU MPI-problem
Mahir.Ulker-Kaustell at tyrens.se
Mahir.Ulker-Kaustell at tyrens.se
Fri Aug 7 04:59:05 CDT 2015
Hong,
Running example 2 with the command line given below gives me two uniprocessor runs!?
$ mpiexec -n 2 ./ex2 -pc_type lu -pc_factor_mat_solver_package superlu_dist -ksp_view
KSP Object: 1 MPI processes
type: gmres
GMRES: restart=30, using Classical (unmodified) Gram-Schmidt Orthogonalization with no iterative refinement
GMRES: happy breakdown tolerance 1e-30
maximum iterations=10000, initial guess is zero
tolerances: relative=0.000138889, absolute=1e-50, divergence=10000
left preconditioning
using PRECONDITIONED norm type for convergence test
PC Object: 1 MPI processes
type: lu
LU: out-of-place factorization
tolerance for zero pivot 2.22045e-14
matrix ordering: nd
factor fill ratio given 0, needed 0
Factored matrix follows:
Mat Object: 1 MPI processes
type: seqaij
rows=56, cols=56
package used to perform factorization: superlu_dist
total: nonzeros=0, allocated nonzeros=0
total number of mallocs used during MatSetValues calls =0
SuperLU_DIST run parameters:
Process grid nprow 1 x npcol 1
Equilibrate matrix TRUE
Matrix input mode 0
Replace tiny pivots TRUE
Use iterative refinement FALSE
Processors in row 1 col partition 1
Row permutation LargeDiag
Column permutation METIS_AT_PLUS_A
Parallel symbolic factorization FALSE
Repeated factorization SamePattern_SameRowPerm
linear system matrix = precond matrix:
Mat Object: 1 MPI processes
type: seqaij
rows=56, cols=56
total: nonzeros=250, allocated nonzeros=280
total number of mallocs used during MatSetValues calls =0
not using I-node routines
Norm of error 5.21214e-15 iterations 1
KSP Object: 1 MPI processes
type: gmres
GMRES: restart=30, using Classical (unmodified) Gram-Schmidt Orthogonalization with no iterative refinement
GMRES: happy breakdown tolerance 1e-30
maximum iterations=10000, initial guess is zero
tolerances: relative=0.000138889, absolute=1e-50, divergence=10000
left preconditioning
using PRECONDITIONED norm type for convergence test
PC Object: 1 MPI processes
type: lu
LU: out-of-place factorization
tolerance for zero pivot 2.22045e-14
matrix ordering: nd
factor fill ratio given 0, needed 0
Factored matrix follows:
Mat Object: 1 MPI processes
type: seqaij
rows=56, cols=56
package used to perform factorization: superlu_dist
total: nonzeros=0, allocated nonzeros=0
total number of mallocs used during MatSetValues calls =0
SuperLU_DIST run parameters:
Process grid nprow 1 x npcol 1
Equilibrate matrix TRUE
Matrix input mode 0
Replace tiny pivots TRUE
Use iterative refinement FALSE
Processors in row 1 col partition 1
Row permutation LargeDiag
Column permutation METIS_AT_PLUS_A
Parallel symbolic factorization FALSE
Repeated factorization SamePattern_SameRowPerm
linear system matrix = precond matrix:
Mat Object: 1 MPI processes
type: seqaij
rows=56, cols=56
total: nonzeros=250, allocated nonzeros=280
total number of mallocs used during MatSetValues calls =0
not using I-node routines
Norm of error 5.21214e-15 iterations 1
Mahir
From: Hong [mailto:hzhang at mcs.anl.gov]
Sent: den 6 augusti 2015 16:36
To: Ülker-Kaustell, Mahir
Cc: Hong; Xiaoye S. Li; PETSc users list
Subject: Re: [petsc-users] SuperLU MPI-problem
Mahir:
I have been using PETSC_COMM_WORLD.
What do you get by running a petsc example, e.g.,
petsc/src/ksp/ksp/examples/tutorials
mpiexec -n 2 ./ex2 -pc_type lu -pc_factor_mat_solver_package superlu_dist -ksp_view
KSP Object: 2 MPI processes
type: gmres
...
Hong
From: Hong [mailto:hzhang at mcs.anl.gov<mailto:hzhang at mcs.anl.gov>]
Sent: den 5 augusti 2015 17:11
To: Ülker-Kaustell, Mahir
Cc: Hong; Xiaoye S. Li; PETSc users list
Subject: Re: [petsc-users] SuperLU MPI-problem
Mahir:
As you noticed, you ran the code in serial mode, not parallel.
Check your code on input communicator, e.g., what input communicator do you use in
KSPCreate(comm,&ksp)?
I have added error flag to superlu_dist interface (released version). When user uses '-mat_superlu_dist_parsymbfact'
in serial mode, this option is ignored with a warning.
Hong
Hong,
If I set parsymbfact:
$ mpiexec -n 2 ./solve -ksp_type preonly -pc_type lu -pc_factor_mat_solver_package superlu_dist -mat_superlu_dist_matinput DISTRIBUTED -mat_superlu_dist_parsymbfact -ksp_view
Invalid ISPEC at line 484 in file get_perm_c.c
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.
-------------------------------------------------------
--------------------------------------------------------------------------
mpiexec detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:
Process name: [[63679,1],0]
Exit code: 255
--------------------------------------------------------------------------
Since the program does not finish the call to KSPSolve(), we do not get any information about the KSP from –ksp_view.
If I do not set it, I get a serial run even if I specify –n 2:
mpiexec -n 2 ./solve -ksp_type preonly -pc_type lu -pc_factor_mat_solver_package superlu_dist -ksp_view
…
KSP Object: 1 MPI processes
type: preonly
maximum iterations=10000, initial guess is zero
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using NONE norm type for convergence test
PC Object: 1 MPI processes
type: lu
LU: out-of-place factorization
tolerance for zero pivot 2.22045e-14
matrix ordering: nd
factor fill ratio given 0, needed 0
Factored matrix follows:
Mat Object: 1 MPI processes
type: seqaij
rows=954, cols=954
package used to perform factorization: superlu_dist
total: nonzeros=0, allocated nonzeros=0
total number of mallocs used during MatSetValues calls =0
SuperLU_DIST run parameters:
Process grid nprow 1 x npcol 1
Equilibrate matrix TRUE
Matrix input mode 0
Replace tiny pivots TRUE
Use iterative refinement FALSE
Processors in row 1 col partition 1
Row permutation LargeDiag
Column permutation METIS_AT_PLUS_A
Parallel symbolic factorization FALSE
Repeated factorization SamePattern_SameRowPerm
linear system matrix = precond matrix:
Mat Object: 1 MPI processes
type: seqaij
rows=954, cols=954
total: nonzeros=34223, allocated nonzeros=34223
total number of mallocs used during MatSetValues calls =0
using I-node routines: found 668 nodes, limit used is 5
I am running PETSc via Cygwin on a windows machine.
When I installed PETSc the tests with different numbers of processes ran well.
Mahir
From: Hong [mailto:hzhang at mcs.anl.gov<mailto:hzhang at mcs.anl.gov>]
Sent: den 3 augusti 2015 19:06
To: Ülker-Kaustell, Mahir
Cc: Hong; Xiaoye S. Li; PETSc users list
Subject: Re: [petsc-users] SuperLU MPI-problem
Mahir,
I have not used …parsymbfact in sequential runs or set matinput=GLOBAL for parallel runs.
If I use 2 processors, the program runs if I use –mat_superlu_dist_parsymbfact=1:
mpiexec -n 2 ./solve -ksp_type preonly -pc_type lu -pc_factor_mat_solver_package superlu_dist -mat_superlu_dist_matinput GLOBAL -mat_superlu_dist_parsymbfact=1
The incorrect option '-mat_superlu_dist_parsymbfact=1' is not taken, so your code runs well without parsymbfact.
Please run it with '-ksp_view' and see what
'SuperLU_DIST run parameters:' are being used, e.g.
petsc/src/ksp/ksp/examples/tutorials (maint)
$ mpiexec -n 2 ./ex2 -pc_type lu -pc_factor_mat_solver_package superlu_dist -mat_superlu_dist_parsymbfact=1 -ksp_view
...
SuperLU_DIST run parameters:
Process grid nprow 2 x npcol 1
Equilibrate matrix TRUE
Matrix input mode 1
Replace tiny pivots TRUE
Use iterative refinement FALSE
Processors in row 2 col partition 1
Row permutation LargeDiag
Column permutation METIS_AT_PLUS_A
Parallel symbolic factorization FALSE
Repeated factorization SamePattern_SameRowPerm
I do not understand why your code uses matrix input mode = global.
Hong
From: Hong [mailto:hzhang at mcs.anl.gov<mailto:hzhang at mcs.anl.gov>]
Sent: den 3 augusti 2015 16:46
To: Xiaoye S. Li
Cc: Ülker-Kaustell, Mahir; Hong; PETSc users list
Subject: Re: [petsc-users] SuperLU MPI-problem
Mahir,
Sherry found the culprit. I can reproduce it:
petsc/src/ksp/ksp/examples/tutorials
mpiexec -n 2 ./ex2 -pc_type lu -pc_factor_mat_solver_package superlu_dist -mat_superlu_dist_matinput GLOBAL -mat_superlu_dist_parsymbfact
Invalid ISPEC at line 484 in file get_perm_c.c
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.
-------------------------------------------------------
...
PETSc-superlu_dist interface sets matinput=DISTRIBUTED as default when using more than one processes.
Did you either use '-mat_superlu_dist_parsymbfact' for sequential run or set matinput=GLOBAL for parallel run?
I'll add an error flag for these use cases.
Hong
On Mon, Aug 3, 2015 at 9:17 AM, Xiaoye S. Li <xsli at lbl.gov<mailto:xsli at lbl.gov>> wrote:
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<mailto:Mahir.Ulker-Kaustell at tyrens.se> <Mahir.Ulker-Kaustell at tyrens.se<mailto: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<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<mailto: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<mailto: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<mailto:Mahir.Ulker-Kaustell at tyrens.se> <Mahir.Ulker-Kaustell at tyrens.se<mailto: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<mailto:hzhang at mcs.anl.gov>>, "Xiaoye S. Li" <xsli at lbl.gov<mailto:xsli at lbl.gov>>
Cc: petsc-users <petsc-users at mcs.anl.gov<mailto: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<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<mailto: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<mailto:Mahir.Ulker-Kaustell at tyrens.se> <Mahir.Ulker-Kaustell at tyrens.se<mailto: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<mailto:Mahir.Ulker-Kaustell at tyrens.se>
______________________________________________
-----Original Message-----
From: Barry Smith [mailto:bsmith at mcs.anl.gov<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<mailto: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<mailto:Mahir.Ulker-Kaustell at tyrens.se>
>
> From: Xiaoye S. Li [mailto:xsli at lbl.gov<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<mailto:Mahir.Ulker-Kaustell at tyrens.se> <Mahir.Ulker-Kaustell at tyrens.se<mailto: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<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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