[petsc-users] Correlation between da_refine and pg_mg_levels
Justin Chang
jychang48 at gmail.com
Mon Apr 3 00:45:26 CDT 2017
So if I begin with a 128x128x8 grid on 1032 procs, it works fine for the
first two levels of da_refine. However, on the third level I get this error:
Level 3 domain size (m) 1e+04 x 1e+04 x 1e+03, num elements 1024 x
1024 x 57 (59768832), size (m) 9.76562 x 9.76562 x 17.8571
Level 2 domain size (m) 1e+04 x 1e+04 x 1e+03, num elements 512 x
512 x 29 (7602176), size (m) 19.5312 x 19.5312 x 35.7143
Level 1 domain size (m) 1e+04 x 1e+04 x 1e+03, num elements 256 x
256 x 15 (983040), size (m) 39.0625 x 39.0625 x 71.4286
Level 0 domain size (m) 1e+04 x 1e+04 x 1e+03, num elements 128 x
128 x 8 (131072), size (m) 78.125 x 78.125 x 142.857
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: Petsc has generated inconsistent data
[0]PETSC ERROR: Eigen estimator failed: DIVERGED_NANORINF at iteration 0
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.
[0]PETSC ERROR: Petsc Development GIT revision: v3.7.5-3418-ge372536 GIT
Date: 2017-03-30 13:35:15 -0500
[0]PETSC ERROR: /scratch2/scratchdirs/jychang/Icesheet/./ex48edison on a
arch-edison-c-opt named nid00865 by jychang Sun Apr 2 21:44:44 2017
[0]PETSC ERROR: Configure options --download-fblaslapack --with-cc=cc
--with-clib-autodetect=0 --with-cxx=CC --with-cxxlib-autodetect=0
--with-debugging=0 --with-fc=ftn --with-fortranlib-autodetect=0
--with-mpiexec=srun --with-64-bit-indices=1 COPTFLAGS=-O3 CXXOPTFLAGS=-O3
FOPTFLAGS=-O3 PETSC_ARCH=arch-edison-c-opt
[0]PETSC ERROR: #1 KSPSolve_Chebyshev() line 380 in
/global/u1/j/jychang/Software/petsc/src/ksp/ksp/impls/cheby/cheby.c
[0]PETSC ERROR: #2 KSPSolve() line 655 in /global/u1/j/jychang/Software/
petsc/src/ksp/ksp/interface/itfunc.c
[0]PETSC ERROR: #3 PCMGMCycle_Private() line 19 in
/global/u1/j/jychang/Software/petsc/src/ksp/pc/impls/mg/mg.c
[0]PETSC ERROR: #4 PCMGMCycle_Private() line 53 in
/global/u1/j/jychang/Software/petsc/src/ksp/pc/impls/mg/mg.c
[0]PETSC ERROR: #5 PCApply_MG() line 331 in /global/u1/j/jychang/Software/
petsc/src/ksp/pc/impls/mg/mg.c
[0]PETSC ERROR: #6 PCApply() line 458 in /global/u1/j/jychang/Software/
petsc/src/ksp/pc/interface/precon.c
[0]PETSC ERROR: #7 KSP_PCApply() line 251 in /global/homes/j/jychang/
Software/petsc/include/petsc/private/kspimpl.h
[0]PETSC ERROR: #8 KSPInitialResidual() line 67 in
/global/u1/j/jychang/Software/petsc/src/ksp/ksp/interface/itres.c
[0]PETSC ERROR: #9 KSPSolve_GMRES() line 233 in
/global/u1/j/jychang/Software/petsc/src/ksp/ksp/impls/gmres/gmres.c
[0]PETSC ERROR: #10 KSPSolve() line 655 in /global/u1/j/jychang/Software/
petsc/src/ksp/ksp/interface/itfunc.c
[0]PETSC ERROR: #11 SNESSolve_NEWTONLS() line 224 in
/global/u1/j/jychang/Software/petsc/src/snes/impls/ls/ls.c
[0]PETSC ERROR: #12 SNESSolve() line 3967 in /global/u1/j/jychang/Software/
petsc/src/snes/interface/snes.c
[0]PETSC ERROR: #13 main() line 1548 in /scratch2/scratchdirs/jychang/
Icesheet/ex48.c
[0]PETSC ERROR: PETSc Option Table entries:
[0]PETSC ERROR: -M 128
[0]PETSC ERROR: -N 128
[0]PETSC ERROR: -P 8
[0]PETSC ERROR: -da_refine 3
[0]PETSC ERROR: -mg_coarse_pc_type gamg
[0]PETSC ERROR: -pc_mg_levels 4
[0]PETSC ERROR: -pc_type mg
[0]PETSC ERROR: -thi_mat_type baij
[0]PETSC ERROR: ----------------End of Error Message -------send entire
error message to petsc-maint at mcs.anl.gov----------
If I changed the coarse grid to 129x129x8, no error whatsoever for up to 4
levels of refinement.
However, I am having trouble getting this started up on Cori's KNL...
I am using a coarse grid 136x136x8 across 1088 cores, and slurm is simply
cancelling the job. No other PETSc error was given. This is literally what
my log files say:
Level 1 domain size (m) 1e+04 x 1e+04 x 1e+03, num elements 272 x
272 x 15 (1109760), size (m) 36.7647 x 36.7647 x 71.4286
Level 0 domain size (m) 1e+04 x 1e+04 x 1e+03, num elements 136 x
136 x 8 (147968), size (m) 73.5294 x 73.5294 x 142.857
makefile:25: recipe for target 'runcori' failed
Level 2 domain size (m) 1e+04 x 1e+04 x 1e+03, num elements 544 x
544 x 29 (8582144), size (m) 18.3824 x 18.3824 x 35.7143
Level 1 domain size (m) 1e+04 x 1e+04 x 1e+03, num elements 272 x
272 x 15 (1109760), size (m) 36.7647 x 36.7647 x 71.4286
Level 0 domain size (m) 1e+04 x 1e+04 x 1e+03, num elements 136 x
136 x 8 (147968), size (m) 73.5294 x 73.5294 x 142.857
srun: error: nid04139: task 480: Killed
srun: Terminating job step 4387719.0
srun: Job step aborted: Waiting up to 32 seconds for job step to finish.
slurmstepd: error: *** STEP 4387719.0 ON nid03873 CANCELLED AT
2017-04-02T22:21:21 ***
srun: error: nid03960: task 202: Killed
srun: error: nid04005: task 339: Killed
srun: error: nid03873: task 32: Killed
srun: error: nid03960: task 203: Killed
srun: error: nid03873: task 3: Killed
srun: error: nid03960: task 199: Killed
srun: error: nid04004: task 264: Killed
srun: error: nid04141: task 660: Killed
srun: error: nid04139: task 539: Killed
srun: error: nid03873: task 63: Killed
srun: error: nid03960: task 170: Killed
srun: error: nid08164: task 821: Killed
srun: error: nid04139: task 507: Killed
srun: error: nid04005: task 299: Killed
srun: error: nid03960: tasks 136-169,171-198,200-201: Killed
srun: error: nid04005: task 310: Killed
srun: error: nid08166: task 1008: Killed
srun: error: nid04141: task 671: Killed
srun: error: nid03873: task 18: Killed
srun: error: nid04139: tasks 476-479,481-506,508-538,540-543: Killed
srun: error: nid04005: tasks 272-298,300-309,311-338: Killed
srun: error: nid04140: tasks 544-611: Killed
srun: error: nid04142: tasks 680-747: Killed
srun: error: nid04138: tasks 408-475: Killed
srun: error: nid04006: tasks 340-407: Killed
srun: error: nid08163: tasks 748-815: Killed
srun: error: nid08166: tasks 952-1007,1009-1019: Killed
srun: error: nid03873: tasks 0-2,4-17,19-31,33-62,64-67: Killed
srun: error: nid08165: tasks 884-951: Killed
srun: error: nid03883: tasks 68-135: Killed
srun: error: nid08164: tasks 816-820,822-883: Killed
srun: error: nid08167: tasks 1020-1087: Killed
srun: error: nid04141: tasks 612-659,661-670,672-679: Killed
srun: error: nid04004: tasks 204-263,265-271: Killed
make: [runcori] Error 137 (ignored)
[257]PETSC ERROR:
------------------------------------------------------------------------
[257]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the
batch system) has told this process to end
[257]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[257]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[257]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS
X to find memory corruption errors
[257]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
and run
[257]PETSC ERROR: to get more information on the crash.
[878]PETSC ERROR:
------------------------------------------------------------------------
[878]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the
batch system) has told this process to end
[878]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[878]PETSC ERROR: or see
http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[878]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS
X to find memory corruption errors
[878]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
and run
[878]PETSC ERROR: to get more information on the crash.
....
[clipped]
....
my job script for KNL looks like this:
#!/bin/bash
#SBATCH -N 16
#SBATCH -C knl,quad,cache
#SBATCH -p regular
#SBATCH -J knl1024
#SBATCH -L SCRATCH
#SBATCH -o knl1088.o%j
#SBATCH -e knl1088.e%j
#SBATCH --mail-type=ALL
#SBATCH --mail-user=jychang48 at gmail.com
#SBATCH -t 00:20:00
srun -n 1088 -c 4 --cpu_bind=cores ./ex48 ....
Any ideas why this is happening? Or do I need to contact the NERSC folks?
Thanks,
Justin
On Sun, Apr 2, 2017 at 2:15 PM, Matthew Knepley <knepley at gmail.com> wrote:
> On Sun, Apr 2, 2017 at 2:13 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>
>>
>> > On Apr 2, 2017, at 9:25 AM, Justin Chang <jychang48 at gmail.com> wrote:
>> >
>> > Thanks guys,
>> >
>> > So I want to run SNES ex48 across 1032 processes on Edison, but I keep
>> getting segmentation violations. These are the parameters I am trying:
>> >
>> > srun -n 1032 -c 2 ./ex48 -M 80 -N 80 -P 9 -da_refine 1 -pc_type mg
>> -thi_mat_type baij -mg_coarse_pc_type gamg
>> >
>> > The above works perfectly fine if I used 96 processes. I also tried to
>> use a finer coarse mesh on 1032 but the error persists.
>> >
>> > Any ideas why this is happening? What are the ideal parameters to use
>> if I want to use 1k+ cores?
>> >
>>
>> Hmm, one should never get segmentation violations. You should only get
>> not completely useful error messages about incompatible sizes etc. Send an
>> example of the segmentation violations. (I sure hope you are checking the
>> error return codes for all functions?).
>
>
> He is just running SNES ex48.
>
> Matt
>
>
>>
>> Barry
>>
>> > Thanks,
>> > Justin
>> >
>> > On Fri, Mar 31, 2017 at 12:47 PM, Barry Smith <bsmith at mcs.anl.gov>
>> wrote:
>> >
>> > > On Mar 31, 2017, at 10:00 AM, Jed Brown <jed at jedbrown.org> wrote:
>> > >
>> > > Justin Chang <jychang48 at gmail.com> writes:
>> > >
>> > >> Yeah based on my experiments it seems setting pc_mg_levels to
>> $DAREFINE + 1
>> > >> has decent performance.
>> > >>
>> > >> 1) is there ever a case where you'd want $MGLEVELS <= $DAREFINE? In
>> some of
>> > >> the PETSc tutorial slides (e.g., http://www.mcs.anl.gov/
>> > >> petsc/documentation/tutorials/TutorialCEMRACS2016.pdf on slide
>> 203/227)
>> > >> they say to use $MGLEVELS = 4 and $DAREFINE = 5, but when I ran
>> this, it
>> > >> was almost twice as slow as if $MGLEVELS >= $DAREFINE
>> > >
>> > > Smaller coarse grids are generally more scalable -- when the problem
>> > > data is distributed, multigrid is a good solution algorithm. But if
>> > > multigrid stops being effective because it is not preserving
>> sufficient
>> > > coarse grid accuracy (e.g., for transport-dominated problems in
>> > > complicated domains) then you might want to stop early and use a more
>> > > robust method (like direct solves).
>> >
>> > Basically for symmetric positive definite operators you can make the
>> coarse problem as small as you like (even 1 point) in theory. For
>> indefinite and non-symmetric problems the theory says the "coarse grid must
>> be sufficiently fine" (loosely speaking the coarse grid has to resolve the
>> eigenmodes for the eigenvalues to the left of the x = 0).
>> >
>> > https://www.jstor.org/stable/2158375?seq=1#page_scan_tab_contents
>> >
>> >
>> >
>>
>>
>
>
> --
> 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
>
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