Hi Barry, petsc-users: Just updated to petsc-3.12.3 and the performance is about the same as 3.12.2, i.e. about 2x the memory use of petsc-3.9.4
petsc-3.12.3 (uses superlu_dist-6.2.0) Summary of Memory Usage in PETSc Maximum (over computational time) process memory: total 2.9368e+10 max 1.2922e+09 min 1.1784e+09 Current process memory: total 2.8192e+10 max 1.2263e+09 min 1.1456e+09 Maximum (over computational time) space PetscMalloc()ed: total 2.7619e+09 max 1.4339e+08 min 8.6494e+07 Current space PetscMalloc()ed: total 3.6127e+06 max 1.5053e+05 min 1.5053e+05 petsc-3.9.4 Summary of Memory Usage in PETSc Maximum (over computational time) process memory: total 1.5695e+10 max 7.1985e+08 min 6.0131e+08 Current process memory: total 1.3186e+10 max 6.9240e+08 min 4.2821e+08 Maximum (over computational time) space PetscMalloc()ed: total 3.1290e+09 max 1.5869e+08 min 1.0179e+08 Current space PetscMalloc()ed: total 1.8808e+06 max 7.8368e+04 min 7.8368e+04 However, it seems that the culprit is superlu_dist: I recompiled current petsc/slepc with superlu_dist-5.4.0 (used option --download-superlu_dist=/home/spin/superlu_dist-5.4.0.tar.gz) and the result is this: petsc-3.12.3 with superlu_dist-5.4.0: Summary of Memory Usage in PETSc Maximum (over computational time) process memory: total 1.5636e+10 max 7.1217e+08 min 5.9963e+08 Current process memory: total 1.3401e+10 max 6.5498e+08 min 4.2626e+08 Maximum (over computational time) space PetscMalloc()ed: total 2.7619e+09 max 1.4339e+08 min 8.6494e+07 Current space PetscMalloc()ed: total 3.6127e+06 max 1.5053e+05 min 1.5053e+05 I could not compile petsc-3.12.3 with the exact superlu_dist version that petsc-3.9.4 uses (5.3.0), but will try newer versions to see how they perform ... I guess I should address this issue to the superlu mantainers? Thanks! Santiago On Fri, Jan 10, 2020 at 9:19 PM Smith, Barry F. <[email protected]> wrote: > > Can you please try v3.12.3 There was some funky business mistakenly > added related to partitioning that has been fixed in 3.12.3 > > Barry > > > > On Jan 10, 2020, at 1:57 PM, Santiago Andres Triana <[email protected]> > wrote: > > > > Dear all, > > > > I ran the program with valgrind --tool=massif, the results are cryptic > to me ... not sure who's the memory hog! the logs are attached. > > > > The command I used is: > > mpiexec -n 24 valgrind --tool=massif --num-callers=20 > --log-file=valgrind.log.%p ./ex7 -f1 A.petsc -f2 B.petsc -eps_nev 1 $opts > -eps_target -4.008e-3+1.57142i -eps_target_magnitude -eps_tol 1e-14 > > > > Is there any possibility to install a version of superlu_dist (or mumps) > different from what the petsc version automatically downloads? > > > > Thanks! > > Santiago > > > > > > On Thu, Jan 9, 2020 at 10:04 PM Dave May <[email protected]> > wrote: > > This kind of issue is difficult to untangle because you have potentially > three pieces of software which might have changed between v3.9 and v3.12, > namely > > PETSc, SLEPC and SuperLU_dist. > > You need to isolate which software component is responsible for the 2x > increase in memory. > > > > When I look at the memory usage in the log files, things look very very > similar for the raw PETSc objects. > > > > [v3.9] > > --- Event Stage 0: Main Stage > > > > Viewer 4 3 2520 0. > > Matrix 15 15 125236536 0. > > Vector 22 22 19713856 0. > > Index Set 10 10 995280 0. > > Vec Scatter 4 4 4928 0. > > EPS Solver 1 1 2276 0. > > Spectral Transform 1 1 848 0. > > Basis Vectors 1 1 2168 0. > > PetscRandom 1 1 662 0. > > Region 1 1 672 0. > > Direct Solver 1 1 17440 0. > > Krylov Solver 1 1 1176 0. > > Preconditioner 1 1 1000 0. > > > > versus > > > > [v3.12] > > --- Event Stage 0: Main Stage > > > > Viewer 4 3 2520 0. > > Matrix 15 15 125237144 0. > > Vector 22 22 19714528 0. > > Index Set 10 10 995096 0. > > Vec Scatter 4 4 3168 0. > > Star Forest Graph 4 4 3936 0. > > EPS Solver 1 1 2292 0. > > Spectral Transform 1 1 848 0. > > Basis Vectors 1 1 2184 0. > > PetscRandom 1 1 662 0. > > Region 1 1 672 0. > > Direct Solver 1 1 17456 0. > > Krylov Solver 1 1 1400 0. > > Preconditioner 1 1 1000 0. > > > > Certainly there is no apparent factor 2x increase in memory usage in the > underlying petsc objects themselves. > > Furthermore, the counts of creations of petsc objects in toobig.log and > justfine.log match, indicating that none of the implementations used in > either PETSc or SLEPc have fundamentally changed wrt the usage of the > native petsc objects. > > > > It is also curious that VecNorm is called 3 times in "justfine.log" and > 19 times in "toobig.log" - although I don't see how that could be related > to you problem... > > > > The above at least gives me the impression that issue of memory increase > is likely not coming from PETSc. > > I just read Barry's useful email which is even more compelling and also > indicates SLEPc is not the likely culprit either as it uses PetscMalloc() > internally. > > > > Some options to identify the problem: > > > > 1/ Eliminate SLEPc as a possible culprit by not calling EPSSolve() and > rather just call KSPSolve() with some RHS vector. > > * If you still see a 2x increase, switch the preconditioner to using > -pc_type bjacobi -ksp_max_it 10 rather than superlu_dist. > > If the memory usage is good, you can be pretty certain the issue arises > internally to superl_dist. > > > > 2/ Leave your code as is and perform your profiling using mumps rather > than superlu_dist. > > This is a less reliable test than 1/ since the mumps implementation used > with v3.9 and v3.12 may differ... > > > > Thanks > > Dave > > > > On Thu, 9 Jan 2020 at 20:17, Santiago Andres Triana <[email protected]> > wrote: > > Dear all, > > > > I think parmetis is not involved since I still run out of memory if I > use the following options: > > export opts='-st_type sinvert -st_ksp_type preonly -st_pc_type lu > -st_pc_factor_mat_solver_type superlu_dist -eps_true_residual 1' > > and issuing: > > mpiexec -n 24 ./ex7 -f1 A.petsc -f2 B.petsc -eps_nev 1 -eps_target > -4.008e-3+1.57142i $opts -eps_target_magnitude -eps_tol 1e-14 -memory_view > > > > Bottom line is that the memory usage of petsc-3.9.4 / slepc-3.9.2 is > much lower than current version. I can only solve relatively small problems > using the 3.12 series :( > > I have an example with smaller matrices that will likely fail in a 32 Gb > ram machine with petsc-3.12 but runs just fine with petsc-3.9. The > -memory_view output is > > > > with petsc-3.9.4: (log 'justfine.log' attached) > > > > Summary of Memory Usage in PETSc > > Maximum (over computational time) process memory: total > 1.6665e+10 max 7.5674e+08 min 6.4215e+08 > > Current process memory: total > 1.5841e+10 max 7.2881e+08 min 6.0905e+08 > > Maximum (over computational time) space PetscMalloc()ed: total > 3.1290e+09 max 1.5868e+08 min 1.0179e+08 > > Current space PetscMalloc()ed: total > 1.8808e+06 max 7.8368e+04 min 7.8368e+04 > > > > > > with petsc-3.12.2: (log 'toobig.log' attached) > > > > Summary of Memory Usage in PETSc > > Maximum (over computational time) process memory: total > 3.1564e+10 max 1.3662e+09 min 1.2604e+09 > > Current process memory: total > 3.0355e+10 max 1.3082e+09 min 1.2254e+09 > > Maximum (over computational time) space PetscMalloc()ed: total > 2.7618e+09 max 1.4339e+08 min 8.6493e+07 > > Current space PetscMalloc()ed: total > 3.6127e+06 max 1.5053e+05 min 1.5053e+05 > > > > Strangely, monitoring with 'top' I can see *appreciably higher* peak > memory use, usually twice what -memory_view ends up reporting, both for > petsc-3.9.4 and current. Program fails usually at this peak if not enough > ram available > > > > The matrices for the example quoted above can be downloaded here (I use > slepc's tutorial ex7.c to solve the problem): > > https://www.dropbox.com/s/as9bec9iurjra6r/A.petsc?dl=0 (about 600 Mb) > > https://www.dropbox.com/s/u2bbmng23rp8l91/B.petsc?dl=0 (about 210 Mb) > > > > I haven't been able to use a debugger successfully since I am using a > compute node without the possibility of an xterm ... note that I have no > experience using a debugger so any help on that will also be appreciated! > > Hope I can switch to the current petsc/slepc version for my production > runs soon... > > > > Thanks again! > > Santiago > > > > > > > > On Thu, Jan 9, 2020 at 4:25 PM Stefano Zampini < > [email protected]> wrote: > > Can you reproduce the issue with smaller matrices? Or with a debug build > (i.e. using —with-debugging=1 and compilation flags -02 -g)? > > > > The only changes in parmetis between the two PETSc releases are these > below, but I don’t see how they could cause issues > > > > kl-18448:pkg-parmetis szampini$ git log -2 > > commit ab4fedc6db1f2e3b506be136e3710fcf89ce16ea (HEAD -> master, tag: > v4.0.3-p5, origin/master, origin/dalcinl/random, origin/HEAD) > > Author: Lisandro Dalcin <[email protected]> > > Date: Thu May 9 18:44:10 2019 +0300 > > > > GKLib: Make FPRFX##randInRange() portable for 32bit/64bit indices > > > > commit 2b4afc79a79ef063f369c43da2617fdb64746dd7 > > Author: Lisandro Dalcin <[email protected]> > > Date: Sat May 4 17:22:19 2019 +0300 > > > > GKlib: Use gk_randint32() to define the RandomInRange() macro > > > > > > > >> On Jan 9, 2020, at 4:31 AM, Smith, Barry F. via petsc-users < > [email protected]> wrote: > >> > >> > >> This is extremely worrisome: > >> > >> ==23361== Use of uninitialised value of size 8 > >> ==23361== at 0x847E939: gk_randint64 (random.c:99) > >> ==23361== by 0x847EF88: gk_randint32 (random.c:128) > >> ==23361== by 0x81EBF0B: libparmetis__Match_Global (in > /space/hpc-home/trianas/petsc-3.12.3/arch-linux2-c-debug/lib/libparmetis.so) > >> > >> do you get that with PETSc-3.9.4 or only with 3.12.3? > >> > >> This may result in Parmetis using non-random numbers and then giving > back an inappropriate ordering that requires more memory for SuperLU_DIST. > >> > >> Suggest looking at the code, or running in the debugger to see what is > going on there. We use parmetis all the time and don't see this. > >> > >> Barry > >> > >> > >> > >> > >> > >> > >>> On Jan 8, 2020, at 4:34 PM, Santiago Andres Triana <[email protected]> > wrote: > >>> > >>> Dear Matt, petsc-users: > >>> > >>> Finally back after the holidays to try to solve this issue, thanks for > your patience! > >>> I compiled the latest petsc (3.12.3) with debugging enabled, the same > problem appears: relatively large matrices result in out of memory errors. > This is not the case for petsc-3.9.4, all fine there. > >>> This is a non-hermitian, generalized eigenvalue problem, I generate > the A and B matrices myself and then I use example 7 (from the slepc > tutorial at $SLEPC_DIR/src/eps/examples/tutorials/ex7.c ) to solve the > problem: > >>> > >>> mpiexec -n 24 valgrind --tool=memcheck -q --num-callers=20 > --log-file=valgrind.log.%p ./ex7 -malloc off -f1 A.petsc -f2 B.petsc > -eps_nev 1 -eps_target -2.5e-4+1.56524i -eps_target_magnitude -eps_tol > 1e-14 $opts > >>> > >>> where the $opts variable is: > >>> export opts='-st_type sinvert -st_ksp_type preonly -st_pc_type lu > -eps_error_relative ::ascii_info_detail -st_pc_factor_mat_solver_type > superlu_dist -mat_superlu_dist_iterrefine 1 -mat_superlu_dist_colperm > PARMETIS -mat_superlu_dist_parsymbfact 1 -eps_converged_reason > -eps_conv_rel -eps_monitor_conv -eps_true_residual 1' > >>> > >>> the output from valgrind (sample from one processor) and from the > program are attached. > >>> If it's of any use the matrices are here (might need at least 180 Gb > of ram to solve the problem succesfully under petsc-3.9.4): > >>> > >>> https://www.dropbox.com/s/as9bec9iurjra6r/A.petsc?dl=0 > >>> https://www.dropbox.com/s/u2bbmng23rp8l91/B.petsc?dl=0 > >>> > >>> WIth petsc-3.9.4 and slepc-3.9.2 I can use matrices up to 10Gb (with > 240 Gb ram), but only up to 3Gb with the latest petsc/slepc. > >>> Any suggestions, comments or any other help are very much appreciated! > >>> > >>> Cheers, > >>> Santiago > >>> > >>> > >>> > >>> On Mon, Dec 23, 2019 at 11:19 PM Matthew Knepley <[email protected]> > wrote: > >>> On Mon, Dec 23, 2019 at 3:14 PM Santiago Andres Triana < > [email protected]> wrote: > >>> Dear all, > >>> > >>> After upgrading to petsc 3.12.2 my solver program crashes > consistently. Before the upgrade I was using petsc 3.9.4 with no problems. > >>> > >>> My application deals with a complex-valued, generalized eigenvalue > problem. The matrices involved are relatively large, typically 2 to 10 Gb > in size, which is no problem for petsc 3.9.4. > >>> > >>> Are you sure that your indices do not exceed 4B? If so, you need to > configure using > >>> > >>> --with-64-bit-indices > >>> > >>> Also, it would be nice if you ran with the debugger so we can get a > stack trace for the SEGV. > >>> > >>> Thanks, > >>> > >>> Matt > >>> > >>> However, after the upgrade I can only obtain solutions when the > matrices are small, the solver crashes when the matrices' size exceed about > 1.5 Gb: > >>> > >>> [0]PETSC ERROR: > ------------------------------------------------------------------------ > >>> [0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or > the batch system) has told this process to end > >>> [0]PETSC ERROR: Try option -start_in_debugger or > -on_error_attach_debugger > >>> [0]PETSC ERROR: or see > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind > >>> [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac > OS X to find memory corruption errors > >>> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, > and run > >>> [0]PETSC ERROR: to get more information on the crash. > >>> > >>> and so on for each cpu. > >>> > >>> > >>> I tried using valgrind and this is the typical output: > >>> > >>> ==2874== Conditional jump or move depends on uninitialised value(s) > >>> ==2874== at 0x4018178: index (in /lib64/ld-2.22.so) > >>> ==2874== by 0x400752D: expand_dynamic_string_token (in /lib64/ > ld-2.22.so) > >>> ==2874== by 0x4008009: _dl_map_object (in /lib64/ld-2.22.so) > >>> ==2874== by 0x40013E4: map_doit (in /lib64/ld-2.22.so) > >>> ==2874== by 0x400EA53: _dl_catch_error (in /lib64/ld-2.22.so) > >>> ==2874== by 0x4000ABE: do_preload (in /lib64/ld-2.22.so) > >>> ==2874== by 0x4000EC0: handle_ld_preload (in /lib64/ld-2.22.so) > >>> ==2874== by 0x40034F0: dl_main (in /lib64/ld-2.22.so) > >>> ==2874== by 0x4016274: _dl_sysdep_start (in /lib64/ld-2.22.so) > >>> ==2874== by 0x4004A99: _dl_start (in /lib64/ld-2.22.so) > >>> ==2874== by 0x40011F7: ??? (in /lib64/ld-2.22.so) > >>> ==2874== by 0x12: ??? > >>> ==2874== > >>> > >>> > >>> These are my configuration options. Identical for both petsc 3.9.4 and > 3.12.2: > >>> > >>> ./configure --with-scalar-type=complex --download-mumps > --download-parmetis --download-metis --download-scalapack=1 > --download-fblaslapack=1 --with-debugging=0 --download-superlu_dist=1 > --download-ptscotch=1 CXXOPTFLAGS='-O3 -march=native' FOPTFLAGS='-O3 > -march=native' COPTFLAGS='-O3 -march=native' > >>> > >>> > >>> Thanks in advance for any comments or ideas! > >>> > >>> Cheers, > >>> Santiago > >>> > >>> > >>> -- > >>> 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/ > >>> <test1.e6034496><valgrind.log.23361> > >> > > > > <massif.out.petsc-3.9><massif.out.petsc-3.12> > >
