[petsc-users] solve problem with pastix

Wed Nov 6 03:40:06 CST 2019

Look into
arch-linux2-cxx-opt/externalpackages/pastix_5.2.3/src/sopalin/src/sopalin_thread.c
I saw something like:

#ifdef HAVE_OLD_SCHED_SETAFFINITY
    if(sched_setaffinity(0,&mask) < 0)
#else /* HAVE_OLD_SCHED_SETAFFINITY */
    if(sched_setaffinity(0,sizeof(mask),&mask) < 0)
#endif /* HAVE_OLD_SCHED_SETAFFINITY */
      {
  perror("sched_setaffinity");
  EXIT(MOD_SOPALIN, INTERNAL_ERR);
      }

Is there possibility that Petsc turn on HAVE_OLD_SCHED_SETAFFINITY during
compilation?

May I know how to trigger re-compilation of external packages with petsc? I
may go in there and check what's going on.

Giang

On Wed, Nov 6, 2019 at 10:12 AM hg <hgbk2008 at gmail.com> wrote:

> sched_setaffinity: Invalid argument only happens when I launch the job
> with sbatch. Running without scheduler is fine. I think this has something
> to do with pastix.
>
> Giang
>
>
> On Wed, Nov 6, 2019 at 4:37 AM Smith, Barry F. <bsmith at mcs.anl.gov> wrote:
>
>>
>>   Google finds this
>> https://gforge.inria.fr/forum/forum.php?thread_id=32824&forum_id=599&group_id=186
>>
>>
>>
>> > On Nov 5, 2019, at 7:01 PM, Matthew Knepley via petsc-users <
>> petsc-users at mcs.anl.gov> wrote:
>> >
>> > I have no idea. That is a good question for the PasTix list.
>> >
>> >   Thanks,
>> >
>> >     Matt
>> >
>> > On Tue, Nov 5, 2019 at 5:32 PM hg <hgbk2008 at gmail.com> wrote:
>> > Should thread affinity be invoked? I set  -mat_pastix_threadnbr 1 and
>> also OMP_NUM_THREADS to 1
>> >
>> > Giang
>> >
>> >
>> > On Tue, Nov 5, 2019 at 10:50 PM Matthew Knepley <knepley at gmail.com>
>> wrote:
>> > On Tue, Nov 5, 2019 at 4:11 PM hg via petsc-users <
>> petsc-users at mcs.anl.gov> wrote:
>> > Hello
>> >
>> > I got crashed when using Pastix as solver for KSP. The error message
>> looks like:
>> >
>> > ....
>> > NUMBER of BUBBLE 1
>> > COEFMAX 1735566 CPFTMAX 0 BPFTMAX 0 NBFTMAX 0 ARFTMAX 0
>> > ** End of Partition & Distribution phase **
>> >    Time to analyze                              0.225 s
>> >    Number of nonzeros in factorized matrix      708784076
>> >    Fill-in                                      12.2337
>> >    Number of operations (LU)                    2.80185e+12
>> >    Prediction Time to factorize (AMD 6180  MKL) 394 s
>> > 0 : SolverMatrix size (without coefficients)    32.4 MB
>> > 0 : Number of nonzeros (local block structure)  365309391
>> >  Numerical Factorization (LU) :
>> > 0 : Internal CSC size                           1.08 GB
>> >    Time to fill internal csc                    6.66 s
>> >    --- Sopalin : Allocation de la structure globale ---
>> >    --- Fin Sopalin Init                             ---
>> >    --- Initialisation des tableaux globaux          ---
>> > sched_setaffinity: Invalid argument
>> > [node083:165071] *** Process received signal ***
>> > [node083:165071] Signal: Aborted (6)
>> > [node083:165071] Signal code:  (-6)
>> > [node083:165071] [ 0] /lib64/libpthread.so.0(+0xf680)[0x2b8081845680]
>> > [node083:165071] [ 1] /lib64/libc.so.6(gsignal+0x37)[0x2b8082191207]
>> > [node083:165071] [ 2] /lib64/libc.so.6(abort+0x148)[0x2b80821928f8]
>> > [node083:165071] [ 3]
>> /sdhome/bui/opt/petsc-3.11.0_ompi-3.0.0/lib/libpetsc.so.3.11(sopalin_launch_comm+0x0)[0x2b80a4124c9d]
>> > [node083:165071] [ 4] Launching 1 threads (1 commputation, 0
>> communication, 0 out-of-core)
>> >    --- Sopalin : Local structure allocation         ---
>> >
>> /sdhome/bui/opt/petsc-3.11.0_ompi-3.0.0/lib/libpetsc.so.3.11(D_sopalin_init_smp+0x29b)[0x2b80a40c39d2]
>> > [node083:165071] [ 5]
>> /sdhome/bui/opt/petsc-3.11.0_ompi-3.0.0/lib/libpetsc.so.3.11(D_ge_sopalin_smp+0x68)[0x2b80a40cf4c2]
>> > [node083:165071] [ 6]
>> /sdhome/bui/opt/petsc-3.11.0_ompi-3.0.0/lib/libpetsc.so.3.11(sopalin_launch_thread+0x4ba)[0x2b80a4124a31]
>> > [node083:165071] [ 7]
>> /sdhome/bui/opt/petsc-3.11.0_ompi-3.0.0/lib/libpetsc.so.3.11(D_ge_sopalin_thread+0x94)[0x2b80a40d6170]
>> > [node083:165071] [ 8]
>> /sdhome/bui/opt/petsc-3.11.0_ompi-3.0.0/lib/libpetsc.so.3.11(D_pastix_task_sopalin+0x5ad)[0x2b80a40b09a2]
>> > [node083:165071] [ 9]
>> /sdhome/bui/opt/petsc-3.11.0_ompi-3.0.0/lib/libpetsc.so.3.11(d_pastix+0xa8a)[0x2b80a40b2325]
>> > [node083:165071] [10]
>> /sdhome/bui/opt/petsc-3.11.0_ompi-3.0.0/lib/libpetsc.so.3.11(+0x63927b)[0x2b80a35bf27b]
>> > [node083:165071] [11]
>> /sdhome/bui/opt/petsc-3.11.0_ompi-3.0.0/lib/libpetsc.so.3.11(MatLUFactorNumeric+0x19a)[0x2b80a32c7552]
>> > [node083:165071] [12]
>> /sdhome/bui/opt/petsc-3.11.0_ompi-3.0.0/lib/libpetsc.so.3.11(+0xa46c09)[0x2b80a39ccc09]
>> > [node083:165071] [13]
>> /sdhome/bui/opt/petsc-3.11.0_ompi-3.0.0/lib/libpetsc.so.3.11(PCSetUp+0x311)[0x2b80a3a8f1a9]
>> > [node083:165071] [14]
>> /sdhome/bui/opt/petsc-3.11.0_ompi-3.0.0/lib/libpetsc.so.3.11(KSPSetUp+0xbf7)[0x2b80a3b46e81]
>> > [node083:165071] [15]
>> /sdhome/bui/opt/petsc-3.11.0_ompi-3.0.0/lib/libpetsc.so.3.11(KSPSolve+0x210)[0x2b80a3b4746e]
>> >
>> > Does anyone have an idea what is the problem and how to fix it? The
>> PETSc parameters I used are as below:
>> >
>> > It looks like PasTix is having trouble setting the thread affinity:
>> >
>> > sched_setaffinity: Invalid argument
>> >
>> > so it may be your build of PasTix.
>> >
>> >   Thanks,
>> >
>> >      Matt
>> >
>> > -pc_type lu
>> > -pc_factor_mat_solver_package pastix
>> > -mat_pastix_verbose 2
>> > -mat_pastix_threadnbr 1
>> >
>> > Giang
>> >
>> >
>> >
>> > --
>> > What most experimenters take for granted before they begin their
>> experiments is infinitely more interesting than any results to which their
>> experiments lead.
>> > -- Norbert Wiener
>> >
>> > https://www.cse.buffalo.edu/~knepley/
>> >
>> >
>> > --
>> > What most experimenters take for granted before they begin their
>> experiments is infinitely more interesting than any results to which their
>> experiments lead.
>> > -- Norbert Wiener
>> >
>> > https://www.cse.buffalo.edu/~knepley/
>>
>>
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