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 [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 >
