[petsc-users] Problem running geoclaw example with petsc 3.22
Praveen C
cpraveen at gmail.com
Wed Oct 23 21:55:37 CDT 2024
I get very similar error on my mac with
$ gfortran -v
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/opt/homebrew/Caskroom/miniforge/base/envs/claw/libexec/gcc/arm64-apple-darwin20.0.0/13.2.0/lto-wrapper
Target: arm64-apple-darwin20.0.0
Configured with: ../configure --prefix=/opt/homebrew/Caskroom/miniforge/base/envs/claw --build=x86_64-apple-darwin13.4.0 --host=arm64-apple-darwin20.0.0 --target=arm64-apple-darwin20.0.0 --with-libiconv-prefix=/opt/homebrew/Caskroom/miniforge/base/envs/claw --enable-languages=fortran --disable-multilib --enable-checking=release --disable-bootstrap --disable-libssp --with-gmp=/opt/homebrew/Caskroom/miniforge/base/envs/claw --with-mpfr=/opt/homebrew/Caskroom/miniforge/base/envs/claw --with-mpc=/opt/homebrew/Caskroom/miniforge/base/envs/claw --with-isl=/opt/homebrew/Caskroom/miniforge/base/envs/claw --enable-darwin-at-rpath
Thread model: posix
Supported LTO compression algorithms: zlib
gcc version 13.2.0 (GCC)
Before starting
$ ipcs -m
IPC status from <running system> as of Thu Oct 24 08:02:11 IST 2024
T ID KEY MODE OWNER GROUP
Shared Memory:
and when I run the code
Using a PETSc solver
Using Bouss equations from the start
rnode allocated...
node allocated...
listOfGrids allocated...
Storage allocated...
bndList allocated...
Gridding level 1 at t = 0.000000E+00: 4 grids with 10000 cells
Setting initial dt to 2.9999999999999999E-002
max threads set to 1
Done reading data, starting computation ...
Total zeta at initial time: 39269.907650665169
GEOCLAW: Frame 0 output files done at time t = 0.000000D+00
[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[0]PETSC ERROR: Petsc has generated inconsistent data
[0]PETSC ERROR: Unable to locate PCMPI allocated shared address 0x130698000
[0]PETSC ERROR: WARNING! There are unused option(s) set! Could be the program crashed before usage or a spelling mistake, etc!
[0]PETSC ERROR: Option left: name:-ksp_type value: preonly source: file
[0]PETSC ERROR: Option left: name:-mpi_ksp_max_it value: 200 source: file
[0]PETSC ERROR: Option left: name:-mpi_ksp_reuse_preconditioner (no value) source: file
[0]PETSC ERROR: Option left: name:-mpi_ksp_rtol value: 1.e-9 source: file
[0]PETSC ERROR: Option left: name:-mpi_ksp_type value: gmres source: file
[0]PETSC ERROR: Option left: name:-mpi_linear_solver_server_view (no value) source: file
[0]PETSC ERROR: Option left: name:-mpi_pc_gamg_sym_graph value: true source: file
[0]PETSC ERROR: Option left: name:-mpi_pc_gamg_symmetrize_graph value: true source: file
[0]PETSC ERROR: Option left: name:-mpi_pc_type value: gamg source: file
[0]PETSC ERROR: Option left: name:-pc_mpi_minimum_count_per_rank value: 5000 source: file
[0]PETSC ERROR: Option left: name:-pc_type value: mpi source: file
[0]PETSC ERROR: See https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!ZGVQF1mXRVL7_W_U2YYltlhjpJnbZse3y51RCYHH0aJtnt9WRtDMxGfCLD_5ua4VLxp0_IMDDAycDKWb2Yr0Pw$ for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.22.0, Sep 28, 2024
[0]PETSC ERROR: /Users/praveen/work/bouss/radial_flat/xgeoclaw with 6 MPI process(es) and PETSC_ARCH on MacMiniHome.local by praveen Thu Oct 24 08:04:27 2024
[0]PETSC ERROR: Configure options: AR=arm64-apple-darwin20.0.0-ar CC=mpicc CXX=mpicxx FC=mpifort CFLAGS="-ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem /opt/homebrew/Caskroom/miniforge/base/envs/claw/include " CPPFLAGS="-D_FORTIFY_SOURCE=2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/claw/include -mmacosx-version-min=11.0 -mmacosx-version-min=11.0" CXXFLAGS="-ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/claw/include " FFLAGS="-march=armv8.3-a -ftree-vectorize -fPIC -fno-stack-protector -O2 -pipe -isystem /opt/homebrew/Caskroom/miniforge/base/envs/claw/include " LDFLAGS="-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/opt/homebrew/Caskroom/miniforge/base/envs/claw/lib -L/opt/homebrew/Caskroom/miniforge/base/envs/claw/lib" LIBS="-Wl,-rpath,/opt/homebrew/Caskroom/miniforge/base/envs/claw/lib -lmpi_mpifh -lgfortran" --COPTFLAGS=-O3 --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 --with-clib-autodetect=0 --with-cxxlib-autodetect=0 --with-fortranlib-autodetect=0 --with-debugging=0 --with-blas-lib=libblas.dylib --with-lapack-lib=liblapack.dylib --with-yaml=1 --with-hdf5=1 --with-fftw=1 --with-hwloc=0 --with-hypre=1 --with-metis=1 --with-mpi=1 --with-mumps=1 --with-parmetis=1 --with-pthread=1 --with-ptscotch=1 --with-shared-libraries --with-ssl=0 --with-scalapack=1 --with-superlu=1 --with-superlu_dist=1 --with-superlu_dist-include=/opt/homebrew/Caskroom/miniforge/base/envs/claw/include/superlu-dist --with-superlu_dist-lib=-lsuperlu_dist --with-suitesparse=1 --with-suitesparse-dir=/opt/homebrew/Caskroom/miniforge/base/envs/claw --with-x=0 --with-scalar-type=real --with-cuda=0 --with-batch --prefix=/opt/homebrew/Caskroom/miniforge/base/envs/claw
[0]PETSC ERROR: #1 PetscShmgetMapAddresses() at /Users/runner/miniforge3/conda-bld/petsc_1728030427805/work/src/sys/utils/server.c:114
[0]PETSC ERROR: #2 PCMPISetMat() at /Users/runner/miniforge3/conda-bld/petsc_1728030427805/work/src/ksp/pc/impls/mpi/pcmpi.c:269
[0]PETSC ERROR: #3 PCSetUp_MPI() at /Users/runner/miniforge3/conda-bld/petsc_1728030427805/work/src/ksp/pc/impls/mpi/pcmpi.c:853
[0]PETSC ERROR: #4 PCSetUp() at /Users/runner/miniforge3/conda-bld/petsc_1728030427805/work/src/ksp/pc/interface/precon.c:1071
[0]PETSC ERROR: #5 KSPSetUp() at /Users/runner/miniforge3/conda-bld/petsc_1728030427805/work/src/ksp/ksp/interface/itfunc.c:415
[0]PETSC ERROR: #6 KSPSolve_Private() at /Users/runner/miniforge3/conda-bld/petsc_1728030427805/work/src/ksp/ksp/interface/itfunc.c:826
[0]PETSC ERROR: #7 KSPSolve() at /Users/runner/miniforge3/conda-bld/petsc_1728030427805/work/src/ksp/ksp/interface/itfunc.c:1075
Code does not progress and I kill it
^CTraceback (most recent call last):
File "/Users/praveen/Applications/clawpack/clawutil/src/python/clawutil/runclaw.py", line 341, in <module>
runclaw(*args)
File "/Users/praveen/Applications/clawpack/clawutil/src/python/clawutil/runclaw.py", line 242, in runclaw
proc = subprocess.check_call(cmd_split,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/Caskroom/miniforge/base/envs/claw/lib/python3.12/subprocess.py", line 408, in check_call
retcode = call(*popenargs, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/Caskroom/miniforge/base/envs/claw/lib/python3.12/subprocess.py", line 391, in call
return p.wait(timeout=timeout)
^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/Caskroom/miniforge/base/envs/claw/lib/python3.12/subprocess.py", line 1264, in wait
return self._wait(timeout=timeout)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/homebrew/Caskroom/miniforge/base/envs/claw/lib/python3.12/subprocess.py", line 2053, in _wait
(pid, sts) = self._try_wait(0)
^^^^^^^^^^^^^^^^^
File "/opt/homebrew/Caskroom/miniforge/base/envs/claw/lib/python3.12/subprocess.py", line 2011, in _try_wait
(pid, sts) = os.waitpid(self.pid, wait_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
KeyboardInterrupt
make[1]: *** [output] Interrupt: 2
make: *** [.output] Interrupt: 2
Now it says
$ ipcs -m
IPC status from <running system> as of Thu Oct 24 08:05:06 IST 2024
T ID KEY MODE OWNER GROUP
Shared Memory:
m 720896 0x0000000a --rw-rw-rw- praveen staff
Thanks
praveen
> On 23 Oct 2024, at 8:26 PM, Barry Smith <bsmith at petsc.dev> wrote:
>
>
> Hmm, so it is creating the first shared memory region with ID of 10 (A in hex) puts it in a linked list in PETSc but then when it tries to find it in the linked list it cannot find it.
>
> I don't know how to reproduce this or debug it remotely.
>
> Can you build on a completely different machine or with completely different compilers?
>
> Barry
>
>
>
>
>> On Oct 23, 2024, at 10:31 AM, Praveen C <cpraveen at gmail.com> wrote:
>>
>> I get same error and now it shows
>>
>> $ ipcs -m
>>
>> ------ Shared Memory Segments --------
>> key shmid owner perms bytes nattch status
>> 0x0000000a 32788 praveen 666 240 6
>>
>> Note that the code seems to be still running after printing those error message, but it is not printing any progress which it should do.
>>
>> Thanks
>> praveen
>>
>>> On 23 Oct 2024, at 7:56 PM, Barry Smith <bsmith at petsc.dev> wrote:
>>>
>>>
>>> Try
>>>
>>> ipcrm -m 11
>>>
>>> ipcs -m
>>>
>>> Try running the program again
>>>
>>> If failed check
>>>
>>> ipcs -m
>>>
>>> again
>>>
>>>
>>>
>>>> On Oct 23, 2024, at 10:20 AM, Praveen C <cpraveen at gmail.com> wrote:
>>>>
>>>> Hello Barry
>>>>
>>>> I see this
>>>>
>>>> $ ipcs -m
>>>>
>>>> ------ Shared Memory Segments --------
>>>> key shmid owner perms bytes nattch status
>>>> 0x0000000a 11 praveen 666 240 6
>>>>
>>>> and I am observing same error as below.
>>>>
>>>> Thanks
>>>> praveen
>>>>
>>>>> On 23 Oct 2024, at 7:08 PM, Barry Smith <bsmith at petsc.dev> wrote:
>>>>>
>>>>>
>>>>> Please take a look at the notes in https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscShmgetAllocateArray/__;!!G_uCfscf7eWS!ZGVQF1mXRVL7_W_U2YYltlhjpJnbZse3y51RCYHH0aJtnt9WRtDMxGfCLD_5ua4VLxp0_IMDDAycDKVkQg5Zlw$ For some reason your program is not able to access/use the Unix shared memory; check if you are already using the shared memory (so it is not available for a new run) or the limits are too low to access enough memory.
>>>>>
>>>>> Barry
>>>>>
>>>>>> On Oct 23, 2024, at 8:23 AM, Praveen C <cpraveen at gmail.com> wrote:
>>>>>>
>>>>>> Dear all
>>>>>>
>>>>>> I am not able to run the boussinesq example from geoclaw using petsc at 3.22.0
>>>>>>
>>>>>> https://urldefense.us/v3/__https://github.com/clawpack/geoclaw/tree/3303883f46572c58130d161986b8a87a57ca7816/examples/bouss__;!!G_uCfscf7eWS!e3VQ4NHKmXGstRsQW5vtI7fmKfUT9zmJkMJcPbcvPyIjicyfJpNoMgx3wZ-qyGcKNSjIkNZkzilec8MnHN6PMw$
>>>>>>
>>>>>> It runs with petsc at 3.21.6
>>>>>>
>>>>>> The error I get is given below. After printing this, the code does not progress.
>>>>>>
>>>>>> I use the following petsc options
>>>>>>
>>>>>> # set min numbers of matrix rows per MPI rank (default is 10000)
>>>>>> -mpi_linear_solve_minimum_count_per_rank 5000
>>>>>>
>>>>>>
>>>>>> # Krylov linear solver:
>>>>>> -mpi_linear_solver_server
>>>>>> -mpi_linear_solver_server_view
>>>>>> -ksp_type gmres
>>>>>> -ksp_max_it 200
>>>>>> -ksp_reuse_preconditioner
>>>>>> -ksp_rtol 1.e-9
>>>>>>
>>>>>> # preconditioner:
>>>>>> -pc_type gamg
>>>>>>
>>>>>> I installed petsc and other dependencies for clawpack using miniforge.
>>>>>>
>>>>>> Thanks
>>>>>> pc
>>>>>>
>>>>>> ==> Use Bouss. in water deeper than 1.0000000000000000 Using a PETSc solver
>>>>>> Using Bouss equations from the start
>>>>>> rnode allocated...
>>>>>> node allocated...
>>>>>> listOfGrids allocated...
>>>>>> Storage allocated...
>>>>>> bndList allocated...
>>>>>> Gridding level 1 at t = 0.000000E+00: 4 grids with 10000 cells
>>>>>> Setting initial dt to 2.9999999999999999E-002
>>>>>> max threads set to 6
>>>>>> Done reading data, starting computation ... Total zeta at initial time: 39269.907650665169 GEOCLAW: Frame 0 output files done at time t = 0.000000D+00
>>>>>>
>>>>>> [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
>>>>>> [0]PETSC ERROR: Petsc has generated inconsistent data
>>>>>> [0]PETSC ERROR: Unable to locate PCMPI allocated shared address 0x55e6d750ae20
>>>>>> [0]PETSC ERROR: WARNING! There are unused option(s) set! Could be the program crashed before usage or a spelling mistake, etc!
>>>>>> [0]PETSC ERROR: Option left: name:-ksp_max_it value: 200 source: file
>>>>>> [0]PETSC ERROR: Option left: name:-ksp_reuse_preconditioner (no value) source: file
>>>>>> [0]PETSC ERROR: Option left: name:-ksp_rtol value: 1.e-9 source: file
>>>>>> [0]PETSC ERROR: Option left: name:-ksp_type value: gmres source: file
>>>>>> [0]PETSC ERROR: Option left: name:-mpi_linear_solve_minimum_count_per_rank value: 5000 source: file
>>>>>> [0]PETSC ERROR: Option left: name:-mpi_linear_solver_server_view (no value) source: file
>>>>>> [0]PETSC ERROR: Option left: name:-pc_type value: gamg source: file
>>>>>> [0]PETSC ERROR: See https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!e3VQ4NHKmXGstRsQW5vtI7fmKfUT9zmJkMJcPbcvPyIjicyfJpNoMgx3wZ-qyGcKNSjIkNZkzilec8MvNjNo7A$ for trouble shooting.
>>>>>> [0]PETSC ERROR: Petsc Release Version 3.22.0, Sep 28, 2024 [0]PETSC ERROR: /home/praveen/bouss/radial_flat/xgeoclaw with 6 MPI process(es) and PETSC_ARCH on euler by praveen Thu Oct 17 21:49:54 2024
>>>>>> [0]PETSC ERROR: Configure options: AR=${PREFIX}/bin/x86_64-conda-linux-gnu-ar CC=mpicc CXX=mpicxx FC=mpifort CFLAGS="-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/miniforge/envs/claw/include " CPPFLAGS="-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/miniforge/envs/claw/include" CXXFLAGS="-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/miniforge/envs/claw/include " FFLAGS="-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/miniforge/envs/claw/include -Wl,--no-as-needed" LDFLAGS="-pthread -fopenmp -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/miniforge/envs/claw/lib -Wl,-rpath-link,/opt/miniforge/envs/claw/lib -L/opt/miniforge/envs/claw/lib -Wl,-rpath-link,/opt/miniforge/envs/claw/lib" LIBS="-Wl,-rpath,/opt/miniforge/envs/claw/lib -lmpi_mpifh -lgfortran" --COPTFLAGS=-O3 --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 --with-clib-autodetect=0 --with-cxxlib-autodetect=0 --with-fortranlib-autodetect=0 --with-debugging=0 --with-blas-lib=libblas.so --with-lapack-lib=liblapack.so --with-yaml=1 --with-hdf5=1 --with-fftw=1 --with-hwloc=0 --with-hypre=1 --with-metis=1 --with-mpi=1 --with-mumps=1 --with-parmetis=1 --with-pthread=1 --with-ptscotch=1 --with-shared-libraries --with-ssl=0 --with-scalapack=1 --with-superlu=1 --with-superlu_dist=1 --with-superlu_dist-include=/opt/miniforge/envs/claw/include/superlu-dist --with-superlu_dist-lib=-lsuperlu_dist --with-suitesparse=1 --with-suitesparse-dir=/opt/miniforge/envs/claw --with-x=0 --with-scalar-type=real --with-cuda=0 --prefix=/opt/miniforge/envs/claw
>>>>>> [0]PETSC ERROR: #1 PetscShmgetMapAddresses() at /home/conda/feedstock_root/build_artifacts/petsc_1728030599661/work/src/sys/utils/server.c:114
>>>>>> [0]PETSC ERROR: #2 PCMPISetMat() at /home/conda/feedstock_root/build_artifacts/petsc_1728030599661/work/src/ksp/pc/impls/mpi/pcmpi.c:269
>>>>>> [0]PETSC ERROR: #3 PCSetUp_MPI() at /home/conda/feedstock_root/build_artifacts/petsc_1728030599661/work/src/ksp/pc/impls/mpi/pcmpi.c:853
>>>>>> [0]PETSC ERROR: #4 PCSetUp() at /home/conda/feedstock_root/build_artifacts/petsc_1728030599661/work/src/ksp/pc/interface/precon.c:1071
>>>>>> [0]PETSC ERROR: #5 KSPSetUp() at /home/conda/feedstock_root/build_artifacts/petsc_1728030599661/work/src/ksp/ksp/interface/itfunc.c:415
>>>>>> [0]PETSC ERROR: #6 KSPSolve_Private() at /home/conda/feedstock_root/build_artifacts/petsc_1728030599661/work/src/ksp/ksp/interface/itfunc.c:826
>>>>>> [0]PETSC ERROR: #7 KSPSolve() at /home/conda/feedstock_root/build_artifacts/petsc_1728030599661/work/src/ksp/ksp/interface/itfunc.c:1075
>>>>>
>>>>
>>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20241024/2f8ba5e0/attachment-0001.html>
More information about the petsc-users
mailing list