[petsc-dev] spock

Fri Dec 10 10:08:46 CST 2021

It seems to be hanging on the 2 processor test.
I'll try running jobs manually.

On Fri, Dec 10, 2021 at 9:34 AM Satish Balay <balay at mcs.anl.gov> wrote:

> Merged now. And the following now works [for me].
>
>  1025  git fetch -p
>  1026  git checkout origin/main
>  1027  ./config/examples/arch-olcf-spock.py && make
>  1028  MPIR_CVAR_GPU_EAGER_DEVICE_MEM=0 MPICH_GPU_SUPPORT_ENABLED=1
> MPICH_SMP_SINGLE_COPY_MODE=CMA make check
>
> Satish
>
> On Fri, 10 Dec 2021, Satish Balay via petsc-dev wrote:
>
> > Works for me [per instructions in balay/update-spock,
> config/examples/arch-olcf-spock.py] with main - without these additional
> options
> >
> > I'll go ahead and merge in balay/update-spock
> >
> > Satish
> >
> > -----
> >
> >  1009  git fetch -p
> >  1015  module load emacs
> >  1016  module load rocm/4.3.0
> >  1018  git reset --hard
> >  1019  git checkout origin/main
> >  1020  git merge origin/balay/update-spock
> >  1021  ./config/examples/arch-olcf-spock.py && make
> >
> >
> >
> > [balay at login2.spock petsc]$ MPIR_CVAR_GPU_EAGER_DEVICE_MEM=0
> MPICH_GPU_SUPPORT_ENABLED=1 MPICH_SMP_SINGLE_COPY_MODE=CMA make check
> > Running check examples to verify correct installation
> > Using PETSC_DIR=/autofs/nccs-svm1_home1/balay/petsc and
> PETSC_ARCH=arch-olcf-spock
> > C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process
> > C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI
> processes
> > C/C++ example src/snes/tutorials/ex3k run successfully with
> kokkos-kernels
> > *******************Error detected during compile or
> link!*******************
> > See http://www.mcs.anl.gov/petsc/documentation/faq.html
> > /ccs/home/balay/petsc/src/snes/tutorials ex5f
> > *********************************************************
> > ftn -fPIC   -fPIC    -I/autofs/nccs-svm1_home1/balay/petsc/include
> -I/autofs/nccs-svm1_home1/balay/petsc/arch-olcf-spock/include
> -I/opt/rocm-4.3.0/include     ex5f.F90
> -Wl,-rpath,/autofs/nccs-svm1_home1/balay/petsc/arch-olcf-spock/lib
> -L/autofs/nccs-svm1_home1/balay/petsc/arch-olcf-spock/lib
> -Wl,-rpath,/autofs/nccs-svm1_home1/balay/petsc/arch-olcf-spock/lib
> -L/autofs/nccs-svm1_home1/balay/petsc/arch-olcf-spock/lib
> -Wl,-rpath,/opt/rocm-4.3.0/lib -L/opt/rocm-4.3.0/lib
> -Wl,-rpath,/opt/cray/pe/mpich/8.1.10/gtl/lib
> -L/opt/cray/pe/mpich/8.1.10/gtl/lib
> -Wl,-rpath,/opt/cray/pe/gcc/8.1.0/snos/lib64
> -L/opt/cray/pe/gcc/8.1.0/snos/lib64 -Wl,-rpath,/opt/cray/pe/libsci/
> 21.08.1.2/CRAY/9.0/x86_64/lib -L/opt/cray/pe/libsci/
> 21.08.1.2/CRAY/9.0/x86_64/lib
> -Wl,-rpath,/opt/cray/pe/mpich/8.1.10/ofi/cray/10.0/lib
> -L/opt/cray/pe/mpich/8.1.10/ofi/cray/10.0/lib
> -Wl,-rpath,/opt/cray/pe/dsmml/0.2.2/dsmml/lib
> -L/opt/cray/pe/dsmml/0.2.2/dsmml/lib -Wl,-rpath,/opt/cray/pe/pmi/6.0.14/lib
> -L/opt/cray/pe/pmi/6
> >  .0.14/li
> >  b -Wl,-rpath,/opt/cray/pe/cce/12.0.3/cce/x86_64/lib
> -L/opt/cray/pe/cce/12.0.3/cce/x86_64/lib
> -Wl,-rpath,/opt/cray/xpmem/2.2.40-2.1_2.44__g3cf3325.shasta/lib64
> -L/opt/cray/xpmem/2.2.40-2.1_2.44__g3cf3325.shasta/lib64
> -Wl,-rpath,/opt/cray/pe/cce/12.0.3/cce-clang/x86_64/lib/clang/12.0.0/lib/linux
> -L/opt/cray/pe/cce/12.0.3/cce-clang/x86_64/lib/clang/12.0.0/lib/linux
> -Wl,-rpath,/opt/cray/pe/gcc/8.1.0/snos/lib/gcc/x86_64-suse-linux/8.1.0
> -L/opt/cray/pe/gcc/8.1.0/snos/lib/gcc/x86_64-suse-linux/8.1.0
> -Wl,-rpath,/opt/cray/pe/cce/12.0.3/binutils/x86_64/x86_64-unknown-linux-gnu/lib
> -L/opt/cray/pe/cce/12.0.3/binutils/x86_64/x86_64-unknown-linux-gnu/lib
> -lpetsc -lmagma -lkokkoskernels -lkokkoscontainers -lkokkoscore -lhipsparse
> -lhipblas -lrocsparse -lrocsolver -lrocblas -lrocrand -lamdhip64 -lstdc++
> -ldl -lmpi_gtl_hsa -lmpifort_cray -lmpi_cray -ldsmml -lpmi -lpmi2 -lxpmem
> -lpgas-shmem -lquadmath -lmodules -lfi -lcraymath -lf -lu -lcsup -lgfortran
> -lpthread -lgcc_eh -lm -lclang_rt.craypg
> >  o-x86_64
> >   -lclang_rt.builtins-x86_64 -lquadmath -lstdc++ -ldl -lmpi_gtl_hsa -o
> ex5f/opt/cray/pe/cce/12.0.3/binutils/x86_64/x86_64-pc-linux-gnu/bin/ld:
> warning: alignment 128 of symbol
> `$host_init$$runtime_init_for_iso_c_binding$iso_c_binding_' in
> /opt/cray/pe/cce/12.0.3/cce/x86_64/lib/libmodules.so is smaller than 256 in
> /tmp/pe_202599/ex5f_1.o
> > /opt/cray/pe/cce/12.0.3/binutils/x86_64/x86_64-pc-linux-gnu/bin/ld:
> warning: alignment 64 of symbol `$data_init$iso_c_binding_' in
> /opt/cray/pe/cce/12.0.3/cce/x86_64/lib/libmodules.so is smaller than 256 in
> /tmp/pe_202599/ex5f_1.o
> > Fortran example src/snes/tutorials/ex5f run successfully with 1 MPI
> process
> > Completed test examples
> > [balay at login2.spock petsc]$
> >
> >
> > On Fri, 10 Dec 2021, Mark Adams wrote:
> >
> > > FWIW,  here is my current status.
> > >
> > > 08:08 main= spock:/gpfs/alpine/csc314/scratch/adams/petsc$ make
> > > PETSC_DIR=/gpfs/alpine/csc314/scratch/adams/petsc
> > > PETSC_ARCH=arch-olcf-spock check
> > > Running check examples to verify correct installation
> > > Using PETSC_DIR=/gpfs/alpine/csc314/scratch/adams/petsc and
> > > PETSC_ARCH=arch-olcf-spock
> > > Possible error running C/C++ src/snes/tutorials/ex19 with 1 MPI process
> > > See http://www.mcs.anl.gov/petsc/documentation/faq.html
> > > lid velocity = 0.0016, prandtl # = 1., grashof # = 1.
> > >     0 KSP Residual norm 0.0406612
> > >     1 KSP Residual norm 0.036923
> > >     2 KSP Residual norm 0.0191849
> > >     3 KSP Residual norm 0.00201589
> > >     4 KSP Residual norm 0.000376045
> > >     5 KSP Residual norm 4.2974e-05
> > >     6 KSP Residual norm 5.96585e-06
> > >     7 KSP Residual norm 4.5398e-07
> > >     8 KSP Residual norm 6.30474e-08
> > >     9 KSP Residual norm 5.55518e-09
> > >    10 KSP Residual norm 6.180e-10
> > >    11 KSP Residual norm 6.211e-11
> > >   Linear solve converged due to CONVERGED_RTOL iterations 11
> > >     0 KSP Residual norm 3.32845e-06
> > >     1 KSP Residual norm 9.0003e-07
> > >     2 KSP Residual norm 1.32594e-07
> > >     3 KSP Residual norm 1.49857e-08
> > >     4 KSP Residual norm 1.31887e-09
> > >     5 KSP Residual norm 2.105e-10
> > >     6 KSP Residual norm 2.827e-11
> > >     7 KSP Residual norm < 1.e-11
> > >     8 KSP Residual norm < 1.e-11
> > >     9 KSP Residual norm < 1.e-11
> > >    10 KSP Residual norm < 1.e-11
> > >   Linear solve converged due to CONVERGED_RTOL iterations 10
> > > Number of SNES iterations = 2
> > > Possible error running C/C++ src/snes/tutorials/ex19 with 2 MPI
> processes
> > > See http://www.mcs.anl.gov/petsc/documentation/faq.html
> > > lid velocity = 0.0016, prandtl # = 1., grashof # = 1.
> > >     0 KSP Residual norm 0.0406612
> > >     1 KSP Residual norm 0.0281101
> > >     2 KSP Residual norm 0.00773873
> > >     3 KSP Residual norm 0.00165731
> > >     4 KSP Residual norm 0.000395614
> > >     5 KSP Residual norm 8.67655e-05
> > >     6 KSP Residual norm 1.69495e-05
> > >     7 KSP Residual norm 3.70051e-06
> > >     8 KSP Residual norm 5.97067e-07
> > >     9 KSP Residual norm 1.02242e-07
> > >    10 KSP Residual norm 1.75727e-08
> > >    11 KSP Residual norm 3.84826e-09
> > >    12 KSP Residual norm 6.414e-10
> > >    13 KSP Residual norm 1.380e-10
> > >   Linear solve converged due to CONVERGED_RTOL iterations 13
> > >     0 KSP Residual norm 3.32846e-06
> > >     1 KSP Residual norm 8.99139e-07
> > >     2 KSP Residual norm 1.72893e-07
> > >     3 KSP Residual norm 3.733e-08
> > >     4 KSP Residual norm 6.67427e-09
> > >     5 KSP Residual norm 1.22785e-09
> > >     6 KSP Residual norm 2.551e-10
> > >     7 KSP Residual norm 5.458e-11
> > >     8 KSP Residual norm 1.050e-11
> > >     9 KSP Residual norm < 1.e-11
> > >    10 KSP Residual norm < 1.e-11
> > >    11 KSP Residual norm < 1.e-11
> > >    12 KSP Residual norm < 1.e-11
> > >   Linear solve converged due to CONVERGED_RTOL iterations 12
> > > Number of SNES iterations = 2
> > > 3,5c3,14
> > > <   1 SNES Function norm 4.12227e-06
> > > <   2 SNES Function norm 6.098e-11
> > > < Number of SNES iterations = 2
> > > ---
> > > >     0 KSP Residual norm 0.0406612
> > > >     1 KSP Residual norm 0.21263
> > > >     2 KSP Residual norm 1.09192
> > > >     3 KSP Residual norm 6.9087
> > > >     4 KSP Residual norm 23.4292
> > > >     5 KSP Residual norm 57.7558
> > > >     6 KSP Residual norm 118.076
> > > >     7 KSP Residual norm 213.527
> > > >     8 KSP Residual norm 354.101
> > > >     9 KSP Residual norm 550.58
> > > >   Linear solve did not converge due to DIVERGED_DTOL iterations 9
> > > > Number of SNES iterations = 0
> > > /gpfs/alpine/csc314/scratch/adams/petsc/src/snes/tutorials
> > > Possible problem with ex19 running with hypre, diffs above
> > > =========================================
> > > gmake[3]: [makefile:115: runex3k_kokkos] Error 134 (ignored)
> > > 21,25c21,26
> > > <   1 SNES Function norm 2.952582418265e-01
> > > <   2 SNES Function norm 4.502293658739e-04
> > > <   3 SNES Function norm 1.389665806646e-09
> > > < Number of SNES iterations = 3
> > > < Norm of error 1.49752e-10 Iterations 3
> > > ---
> > > > Memory access fault by GPU node-4 (Agent handle: 0xb08c90) on address
> > > 0xe17000. Reason: Page not present or supervisor privilege.
> > > > Memory access fault by GPU node-5 (Agent handle: 0xb0d3c0) on address
> > > 0xe11000. Reason: Page not present or supervisor privilege.
> > > > srun: error: spock25: task 0: Aborted
> > > > srun: launch/slurm: _step_signal: Terminating StepId=304034.3
> > > > slurmstepd: error: *** STEP 304034.3 ON spock25 CANCELLED AT
> > > 2021-12-10T08:08:40 ***
> > > > srun: error: spock25: task 1: Aborted (core dumped)
> > > /gpfs/alpine/csc314/scratch/adams/petsc/src/snes/tutorials
> > > Possible problem with ex3k running with kokkos-kernels, diffs above
> > > =========================================
> > > *******************Error detected during compile or
> link!*******************
> > > See http://www.mcs.anl.gov/petsc/documentation/faq.html
> > > /gpfs/alpine/csc314/scratch/adams/petsc/src/snes/tutorials ex5f
> > > *********************************************************
> > > ftn -fPIC   -fPIC    -I/gpfs/alpine/csc314/scratch/adams/petsc/include
> > > -I/gpfs/alpine/csc314/scratch/adams/petsc/arch-olcf-spock/include
> > >
> -I/gpfs/alpine/geo127/proj-shared/spock/petsc/current/arch-opt-cray/include
> > > -I/opt/rocm-4.3.0/include     ex5f.F90
> > >  -Wl,-rpath,/gpfs/alpine/csc314/scratch/adams/petsc/arch-olcf-spock/lib
> > > -L/gpfs/alpine/csc314/scratch/adams/petsc/arch-olcf-spock/lib
> > >
> -Wl,-rpath,/gpfs/alpine/geo127/proj-shared/spock/petsc/current/arch-opt-cray/lib
> > > -L/gpfs/alpine/geo127/proj-shared/spock/petsc/current/arch-opt-cray/lib
> > > -Wl,-rpath,/opt/rocm-4.3.0/lib -L/opt/rocm-4.3.0/lib
> > > -Wl,-rpath,/opt/cray/pe/mpich/8.1.10/gtl/lib
> > > -L/opt/cray/pe/mpich/8.1.10/gtl/lib
> > > -Wl,-rpath,/opt/cray/pe/gcc/8.1.0/snos/lib64
> > > -L/opt/cray/pe/gcc/8.1.0/snos/lib64 -Wl,-rpath,/opt/cray/pe/libsci/
> > > 21.08.1.2/CRAY/9.0/x86_64/lib -L/opt/cray/pe/libsci/
> > > 21.08.1.2/CRAY/9.0/x86_64/lib
> > > -Wl,-rpath,/opt/cray/pe/mpich/8.1.10/ofi/cray/10.0/lib
> > > -L/opt/cray/pe/mpich/8.1.10/ofi/cray/10.0/lib
> > > -Wl,-rpath,/opt/cray/pe/dsmml/0.2.2/dsmml/lib
> > > -L/opt/cray/pe/dsmml/0.2.2/dsmml/lib
> -Wl,-rpath,/opt/cray/pe/pmi/6.0.14/lib
> > > -L/opt/cray/pe/pmi/6.0.14/lib
> > > -Wl,-rpath,/opt/cray/pe/cce/12.0.3/cce/x86_64/lib
> > > -L/opt/cray/pe/cce/12.0.3/cce/x86_64/lib
> > > -Wl,-rpath,/opt/cray/xpmem/2.2.40-2.1_2.44__g3cf3325.shasta/lib64
> > > -L/opt/cray/xpmem/2.2.40-2.1_2.44__g3cf3325.shasta/lib64
> > >
> -Wl,-rpath,/opt/cray/pe/cce/12.0.3/cce-clang/x86_64/lib/clang/12.0.0/lib/linux
> > > -L/opt/cray/pe/cce/12.0.3/cce-clang/x86_64/lib/clang/12.0.0/lib/linux
> > > -Wl,-rpath,/opt/cray/pe/gcc/8.1.0/snos/lib/gcc/x86_64-suse-linux/8.1.0
> > > -L/opt/cray/pe/gcc/8.1.0/snos/lib/gcc/x86_64-suse-linux/8.1.0
> > >
> -Wl,-rpath,/opt/cray/pe/cce/12.0.3/binutils/x86_64/x86_64-unknown-linux-gnu/lib
> > > -L/opt/cray/pe/cce/12.0.3/binutils/x86_64/x86_64-unknown-linux-gnu/lib
> > > -lpetsc -lHYPRE -lkokkoskernels -lkokkoscontainers -lkokkoscore
> -lhipsparse
> > > -lhipblas -lrocsparse -lrocsolver -lrocblas -lrocrand -lamdhip64
> -lstdc++
> > > -ldl -lmpi_gtl_hsa -lmpifort_cray -lmpi_cray -ldsmml -lpmi -lpmi2
> -lxpmem
> > > -lpgas-shmem -lquadmath -lmodules -lfi -lcraymath -lf -lu -lcsup
> -lgfortran
> > > -lpthread -lgcc_eh -lm -lclang_rt.craypgo-x86_64
> -lclang_rt.builtins-x86_64
> > > -lquadmath -lstdc++ -ldl -lmpi_gtl_hsa -o ex5f
> > > /opt/cray/pe/cce/12.0.3/binutils/x86_64/x86_64-pc-linux-gnu/bin/ld:
> > > warning: alignment 128 of symbol
> > > `$host_init$$runtime_init_for_iso_c_binding$iso_c_binding_' in
> > > /opt/cray/pe/cce/12.0.3/cce/x86_64/lib/libmodules.so is smaller than
> 256 in
> > > /tmp/pe_46424/ex5f_1.o
> > > /opt/cray/pe/cce/12.0.3/binutils/x86_64/x86_64-pc-linux-gnu/bin/ld:
> > > warning: alignment 64 of symbol `$data_init$iso_c_binding_' in
> > > /opt/cray/pe/cce/12.0.3/cce/x86_64/lib/libmodules.so is smaller than
> 256 in
> > > /tmp/pe_46424/ex5f_1.o
> > > Possible error running Fortran example src/snes/tutorials/ex5f with 1
> MPI
> > > process
> > > See http://www.mcs.anl.gov/petsc/documentation/faq.html
> > >     0 KSP Residual norm < 1.e-11
> > >   Linear solve converged due to CONVERGED_ATOL iterations 0
> > >
> > > On Fri, Dec 10, 2021 at 8:07 AM Mark Adams <mfadams at lbl.gov> wrote:
> > >
> > > > I am trying to get Spock working (again) and am having problems.
> > > >
> > > > * make check seems to fail but it is hard to see what is going on.
> Maybe
> > > > we should start here, but let me continue.
> > > >
> > > > * GAMG seems to work on the CPU
> > > >
> > > > * I have this for configuring with Kokkos. I am guessing these
> versions
> > > > are out of data. What is current practice:
> > > >     '--with-kokkos-hip-arch=VEGA908',
> > > >     '--download-kokkos-commit=3.4.01',
> > > >     '--download-kokkos-kernels-commit=3.4.01',
> > > >
> > > > * Should I hold off (and tell my eager user to do same)?
> > > >
> > > > Thanks,
> > > > Mark
> > > >
> > >
> >
>
>
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