On Mon, Apr 3, 2017 at 6:11 AM, Jed Brown <[email protected]> wrote: > Justin Chang <[email protected]> writes: > > > 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 > > Building with debugging and adding -fp_trap to get a stack trace would > be really useful. Or reproducing at smaller scale.
I can't think why it would fail there, but DMDA really likes old numbers of vertices, because it wants to take every other point, 129 seems good. I will see if I can reproduce once I get a chance. And now you see why it almost always takes a full-time person just to run jobs on one of these machines. Horrible design flaws never get fixed. Matt > > [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 > > Why are levels 1 and 0 printed above, then 2,1,0 below. > > > makefile:25: recipe for target 'runcori' failed > > What is this makefile message doing? > > > 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 > >> > -- 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
