I fixed the KNL issue - apparently "larger" jobs need to have the executable copied into the /tmp directory to speedup loading/startup time so I did that instead of executing the program via makefile.
On Mon, Apr 3, 2017 at 12:45 AM, Justin Chang <[email protected]> wrote: > 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/Softwa > re/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 [email protected] > > 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 [email protected] > #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 <[email protected]> wrote: > >> On Sun, Apr 2, 2017 at 2:13 PM, Barry Smith <[email protected]> wrote: >> >>> >>> > On Apr 2, 2017, at 9:25 AM, Justin Chang <[email protected]> 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 <[email protected]> >>> wrote: >>> > >>> > > On Mar 31, 2017, at 10:00 AM, Jed Brown <[email protected]> wrote: >>> > > >>> > > Justin Chang <[email protected]> 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 >> > >
