[petsc-users] solve problem with pastix
Matthew Knepley
knepley at gmail.com
Wed Nov 6 04:02:58 CST 2019
On Wed, Nov 6, 2019 at 4:40 AM hg <hgbk2008 at gmail.com> wrote:
> 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.
>
If we built it during configure, then you can just go to
$PETSC_DIR/$PETSC_ARCH/externalpackages/*pastix*/
and rebuild/install it to test. If you want configure to do it, you have to
delete
$PETSC_DIR/$PETSC_ARCH/lib/petsc/conf/pkg.conf.pastix
and reconfigure.
Thanks,
Matt
> 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/
>>>
>>>
--
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/ <http://www.cse.buffalo.edu/~knepley/>
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