[petsc-users] [mumps-dev] MUMPS and PARMETIS: Crashes
Hong
hzhang at mcs.anl.gov
Mon Dec 12 09:27:01 CST 2016
Alfredo,
mpiexec -n 4 ./ex53 -n 10000 -ksp_view -mat_mumps_icntl_28 2
-mat_mumps_icntl_29 2
works well now.
We'll upgrade petsc interface to this mumps-5.0.2.
Hong
On Mon, Dec 12, 2016 at 9:00 AM, Hong <hzhang at mcs.anl.gov> wrote:
> Alfredo:
> Sure, I got the tarball of mumps-5.0.2, and will test it and update
> petsc-mumps interface. I'll let you know if problem remains.
>
> Hong
>
> Dear all,
>> sorry for the late reply. The petsc installation went supersmooth and
>> I could easily reproduce the issue. I dumped the matrix generated by
>> petsc and read it back with a standalone mumps tester in order to
>> confirm the bug. This bug has been already reported by another user,
>> was fixed a few months ago and the fix was included in the 5.0.2
>> release. Could you please check if everything works well with mumps
>> 5.0.2?
>>
>> Kind regards,
>> te MUMPS team
>>
>>
>>
>>
>> On Thu, Oct 20, 2016 at 4:44 PM, Hong <hzhang at mcs.anl.gov> wrote:
>> > Alfredo:
>> > It would be much easier to install petsc with mumps, parmetis, and
>> > debugging this case. Here is what you can do on a linux machine
>> > (see http://www.mcs.anl.gov/petsc/documentation/installation.html):
>> >
>> > 1) get petsc-release:
>> > git clone -b maint https://bitbucket.org/petsc/petsc petsc
>> >
>> > cd petsc
>> > git pull
>> > export PETSC_DIR=$PWD
>> > export PETSC_ARCH=<>
>> >
>> > 2) configure petsc with additional options
>> > '--download-metis --download-parmetis --download-mumps
>> --download-scalapack
>> > --download-ptscotch'
>> > see http://www.mcs.anl.gov/petsc/documentation/installation.html
>> >
>> > 3) build petsc and test
>> > make
>> > make test
>> >
>> > 4) test ex53.c:
>> > cd $PETSC_DIR/src/ksp/ksp/examples/tutorials
>> > make ex53
>> > mpiexec -n 4 ./ex53 -n 10000 -ksp_view -mat_mumps_icntl_28 2
>> > -mat_mumps_icntl_29 2
>> >
>> > 5) debugging ex53.c:
>> > mpiexec -n 4 ./ex53 -n 10000 -ksp_view -mat_mumps_icntl_28 2
>> > -mat_mumps_icntl_29 2 -start_in_debugger
>> >
>> > Give it a try. Contact us if you cannot reproduce this case.
>> >
>> > Hong
>> >
>> >> Dear all,
>> >> this may well be due to a bug in the parallel analysis. Do you think
>> you
>> >> can reproduce the problem in a standalone MUMPS program (i.e., without
>> going
>> >> through PETSc) ? that would save a lot of time to track the bug since
>> we do
>> >> not have a PETSc install at hand. Otherwise we'll give it a shot at
>> >> installing petsc and reproducing the problem on our side.
>> >>
>> >> Kind regards,
>> >> the MUMPS team
>> >>
>> >>
>> >>
>> >> On Wed, Oct 19, 2016 at 8:32 PM, Barry Smith <bsmith at mcs.anl.gov>
>> wrote:
>> >>>
>> >>>
>> >>> Tim,
>> >>>
>> >>> You can/should also run with valgrind to determine exactly the
>> first
>> >>> point with memory corruption issues.
>> >>>
>> >>> Barry
>> >>>
>> >>> > On Oct 19, 2016, at 11:08 AM, Hong <hzhang at mcs.anl.gov> wrote:
>> >>> >
>> >>> > Tim:
>> >>> > With '-mat_mumps_icntl_28 1', i.e., sequential analysis, I can run
>> ex56
>> >>> > with np=3 or larger np successfully.
>> >>> >
>> >>> > With '-mat_mumps_icntl_28 2', i.e., parallel analysis, I can run up
>> to
>> >>> > np=3.
>> >>> >
>> >>> > For np=4:
>> >>> > mpiexec -n 4 ./ex53 -n 10000 -ksp_view -mat_mumps_icntl_28 2
>> >>> > -mat_mumps_icntl_29 2 -start_in_debugger
>> >>> >
>> >>> > code crashes inside mumps:
>> >>> > Program received signal SIGSEGV, Segmentation fault.
>> >>> > 0x00007f33d75857cb in
>> >>> > dmumps_parallel_analysis::dmumps_build_scotch_graph (
>> >>> > id=..., first=..., last=..., ipe=...,
>> >>> > pe=<error reading variable: Cannot access memory at address
>> 0x0>,
>> >>> > work=...)
>> >>> > at dana_aux_par.F:1450
>> >>> > 1450 MAPTAB(J) = I
>> >>> > (gdb) bt
>> >>> > #0 0x00007f33d75857cb in
>> >>> > dmumps_parallel_analysis::dmumps_build_scotch_graph (
>> >>> > id=..., first=..., last=..., ipe=...,
>> >>> > pe=<error reading variable: Cannot access memory at address
>> 0x0>,
>> >>> > work=...)
>> >>> > at dana_aux_par.F:1450
>> >>> > #1 0x00007f33d759207c in dmumps_parallel_analysis::dmum
>> ps_parmetis_ord
>> >>> > (
>> >>> > id=..., ord=..., work=...) at dana_aux_par.F:400
>> >>> > #2 0x00007f33d7592d14 in dmumps_parallel_analysis::dmum
>> ps_do_par_ord
>> >>> > (id=...,
>> >>> > ord=..., work=...) at dana_aux_par.F:351
>> >>> > #3 0x00007f33d7593aa9 in dmumps_parallel_analysis::dmum
>> ps_ana_f_par
>> >>> > (id=...,
>> >>> > work1=..., work2=..., nfsiz=...,
>> >>> > fils=<error reading variable: Cannot access memory at address
>> 0x0>,
>> >>> > frere=<error reading variable: Cannot access memory at address
>> >>> > 0x0>)
>> >>> > at dana_aux_par.F:98
>> >>> > #4 0x00007f33d74c622a in dmumps_ana_driver (id=...) at
>> >>> > dana_driver.F:563
>> >>> > #5 0x00007f33d747706b in dmumps (id=...) at dmumps_driver.F:1108
>> >>> > #6 0x00007f33d74721b5 in dmumps_f77 (job=1, sym=0, par=1,
>> >>> > comm_f77=-2080374779, n=10000, icntl=..., cntl=..., keep=...,
>> >>> > dkeep=...,
>> >>> > keep8=..., nz=0, irn=..., irnhere=0, jcn=..., jcnhere=0, a=...,
>> >>> > ahere=0,
>> >>> > nz_loc=7500, irn_loc=..., irn_lochere=1, jcn_loc=...,
>> >>> > jcn_lochere=1,
>> >>> > a_loc=..., a_lochere=1, nelt=0, eltptr=..., eltptrhere=0,
>> >>> > eltvar=...,
>> >>> > eltvarhere=0, a_elt=..., a_elthere=0, perm_in=...,
>> perm_inhere=0,
>> >>> > rhs=...,
>> >>> > rhshere=0, redrhs=..., redrhshere=0, info=..., rinfo=...,
>> >>> > infog=...,
>> >>> > rinfog=..., deficiency=0, lwk_user=0, size_schur=0,
>> >>> > listvar_schur=...,
>> >>> > ---Type <return> to continue, or q <return> to quit---
>> >>> > ar_schurhere=0, schur=..., schurhere=0, wk_user=...,
>> wk_userhere=0,
>> >>> > colsca=...,
>> >>> > colscahere=0, rowsca=..., rowscahere=0, instance_number=1,
>> nrhs=1,
>> >>> > lrhs=0, lredrhs=0,
>> >>> > rhs_sparse=..., rhs_sparsehere=0, sol_loc=..., sol_lochere=0,
>> >>> > irhs_sparse=...,
>> >>> > irhs_sparsehere=0, irhs_ptr=..., irhs_ptrhere=0, isol_loc=...,
>> >>> > isol_lochere=0,
>> >>> > nz_rhs=0, lsol_loc=0, schur_mloc=0, schur_nloc=0, schur_lld=0,
>> >>> > mblock=0, nblock=0,
>> >>> > nprow=0, npcol=0, ooc_tmpdir=..., ooc_prefix=...,
>> >>> > write_problem=..., tmpdirlen=20,
>> >>> > prefixlen=20, write_problemlen=20) at dmumps_f77.F:260
>> >>> > #7 0x00007f33d74709b1 in dmumps_c (mumps_par=0x16126f0) at
>> >>> > mumps_c.c:415
>> >>> > #8 0x00007f33d68408ca in MatLUFactorSymbolic_AIJMUMPS (F=0x1610280,
>> >>> > A=0x14bafc0,
>> >>> > r=0x160cc30, c=0x1609ed0, info=0x15c6708)
>> >>> > at /scratch/hzhang/petsc/src/mat/impls/aij/mpi/mumps/mumps.c:14
>> 87
>> >>> >
>> >>> > -mat_mumps_icntl_29 = 0 or 1 give same error.
>> >>> > I'm cc'ing this email to mumps developer, who may help to resolve
>> this
>> >>> > matter.
>> >>> >
>> >>> > Hong
>> >>> >
>> >>> >
>> >>> > Hi all,
>> >>> >
>> >>> > I have some problems with PETSc using MUMPS and PARMETIS.
>> >>> > In some cases it works fine, but in some others it doesn't, so I am
>> >>> > trying to understand what is happening.
>> >>> >
>> >>> > I just picked the following example:
>> >>> >
>> >>> > http://www.mcs.anl.gov/petsc/petsc-current/src/ksp/ksp/examp
>> les/tutorials/ex53.c.html
>> >>> >
>> >>> > Now, when I start it with less than 4 processes it works as
>> expected:
>> >>> > mpirun -n 3 ./ex53 -n 10000 -ksp_view -mat_mumps_icntl_28 1
>> >>> > -mat_mumps_icntl_29 2
>> >>> >
>> >>> > But with 4 or more processes, it crashes, but only when I am using
>> >>> > Parmetis:
>> >>> > mpirun -n 4 ./ex53 -n 10000 -ksp_view -mat_mumps_icntl_28 1
>> >>> > -mat_mumps_icntl_29 2
>> >>> >
>> >>> > Metis worked in every case I tried without any problems.
>> >>> >
>> >>> > I wonder if I am doing something wrong or if this is a general
>> problem
>> >>> > or even a bug? Is Parmetis supposed to work with that example with 4
>> >>> > processes?
>> >>> >
>> >>> > Thanks a lot and kind regards.
>> >>> >
>> >>> > Volker
>> >>> >
>> >>> >
>> >>> > Here is the error log of process 0:
>> >>> >
>> >>> > Entering DMUMPS 5.0.1 driver with JOB, N = 1 10000
>> >>> > =================================================
>> >>> > MUMPS compiled with option -Dmetis
>> >>> > MUMPS compiled with option -Dparmetis
>> >>> > =================================================
>> >>> > L U Solver for unsymmetric matrices
>> >>> > Type of parallelism: Working host
>> >>> >
>> >>> > ****** ANALYSIS STEP ********
>> >>> >
>> >>> > ** Max-trans not allowed because matrix is distributed
>> >>> > Using ParMETIS for parallel ordering.
>> >>> > [0]PETSC ERROR:
>> >>> >
>> >>> > ------------------------------------------------------------
>> ------------
>> >>> > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation
>> Violation,
>> >>> > probably memory access out of range
>> >>> > [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: likely location of problem given in stack below
>> >>> > [0]PETSC ERROR: --------------------- Stack Frames
>> >>> > ------------------------------------
>> >>> > [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not
>> >>> > available,
>> >>> > [0]PETSC ERROR: INSTEAD the line number of the start of the
>> >>> > function
>> >>> > [0]PETSC ERROR: is given.
>> >>> > [0]PETSC ERROR: [0] MatLUFactorSymbolic_AIJMUMPS line 1395
>> >>> >
>> >>> > /fsgarwinhpc/133/petsc/sources/petsc-3.7.4a/src/mat/impls/ai
>> j/mpi/mumps/mumps.c
>> >>> > [0]PETSC ERROR: [0] MatLUFactorSymbolic line 2927
>> >>> > /fsgarwinhpc/133/petsc/sources/petsc-3.7.4a/src/mat/interfac
>> e/matrix.c
>> >>> > [0]PETSC ERROR: [0] PCSetUp_LU line 101
>> >>> >
>> >>> > /fsgarwinhpc/133/petsc/sources/petsc-3.7.4a/src/ksp/pc/impls
>> /factor/lu/lu.c
>> >>> > [0]PETSC ERROR: [0] PCSetUp line 930
>> >>> >
>> >>> > /fsgarwinhpc/133/petsc/sources/petsc-3.7.4a/src/ksp/pc/inter
>> face/precon.c
>> >>> > [0]PETSC ERROR: [0] KSPSetUp line 305
>> >>> >
>> >>> > /fsgarwinhpc/133/petsc/sources/petsc-3.7.4a/src/ksp/ksp/inte
>> rface/itfunc.c
>> >>> > [0]PETSC ERROR: [0] KSPSolve line 563
>> >>> >
>> >>> > /fsgarwinhpc/133/petsc/sources/petsc-3.7.4a/src/ksp/ksp/inte
>> rface/itfunc.c
>> >>> > [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 3.7.4, Oct, 02, 2016
>> >>> > [0]PETSC ERROR: ./ex53 on a linux-manni-mumps named manni by 133 Wed
>> >>> > Oct 19 16:39:49 2016
>> >>> > [0]PETSC ERROR: Configure options --with-cc=mpiicc
>> --with-cxx=mpiicpc
>> >>> > --with-fc=mpiifort --with-shared-libraries=1
>> >>> > --with-valgrind-dir=~/usr/valgrind/
>> >>> >
>> >>> > --with-mpi-dir=/home/software/intel/Intel-2016.4/compilers_a
>> nd_libraries_2016.4.258/linux/mpi
>> >>> > --download-scalapack --download-mumps --download-metis
>> >>> > --download-metis-shared=0 --download-parmetis
>> >>> > --download-parmetis-shared=0
>> >>> > [0]PETSC ERROR: #1 User provided function() line 0 in unknown file
>> >>> > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>> >>> >
>> >>>
>> >>
>> >>
>> >>
>> >> --
>> >> -----------------------------------------
>> >> Alfredo Buttari, PhD
>> >> CNRS-IRIT
>> >> 2 rue Camichel, 31071 Toulouse, France
>> >> http://buttari.perso.enseeiht.fr
>> >
>> >
>>
>>
>>
>> --
>> -----------------------------------------
>> Alfredo Buttari, PhD
>> CNRS-IRIT
>> 2 rue Camichel, 31071 Toulouse, France
>> http://buttari.perso.enseeiht.fr
>>
>
>
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