[petsc-users] killed 9 signal after upgrade from petsc 3.9.4 to 3.12.2
Santiago Andres Triana
repepo at gmail.com
Fri Jan 10 17:04:15 CST 2020
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. <bsmith at mcs.anl.gov> 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 <repepo at gmail.com>
> 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 <dave.mayhem23 at gmail.com>
> 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 <repepo at gmail.com>
> 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 <
> stefano.zampini at gmail.com> 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 <dalcinl at gmail.com>
> > Date: Thu May 9 18:44:10 2019 +0300
> >
> > GKLib: Make FPRFX##randInRange() portable for 32bit/64bit indices
> >
> > commit 2b4afc79a79ef063f369c43da2617fdb64746dd7
> > Author: Lisandro Dalcin <dalcinl at gmail.com>
> > 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 <
> petsc-users at mcs.anl.gov> 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 <repepo at gmail.com>
> 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 <knepley at gmail.com>
> wrote:
> >>> On Mon, Dec 23, 2019 at 3:14 PM Santiago Andres Triana <
> repepo at gmail.com> 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>
>
>
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