[petsc-users] Problem running geoclaw example with petsc 3.22
Praveen C
cpraveen at gmail.com
Thu Oct 31 00:24:29 CDT 2024
Hello Barry
With the extra option
> -mpi_linear_solver_server_use_shared_memory false
I get different error
Thanks
praveen
$ make .output
/Library/Developer/CommandLineTools/usr/bin/make output -f Makefile /Users/praveen/Applications/clawpack/geoclaw/src/2d/bouss/Makefile.bouss /Users/praveen/Applications/clawpack/clawutil/src/Makefile.common
rm -f .output
python /Users/praveen/Applications/clawpack/clawutil/src/python/clawutil/runclaw.py /Users/praveen/Work/bouss/radial_flat/xgeoclaw _output \
True None . False False None "/opt/homebrew/Caskroom/miniforge/base/envs/claw/./bin/mpiexec -n 6"
==> runclaw: Will take data from /Volumes/Samsung_T5/Work/bouss/radial_flat
==> runclaw: Will write output to /Volumes/Samsung_T5/Work/bouss/radial_flat/_output
==> runclaw: Removing all old fort/gauge files in /Volumes/Samsung_T5/Work/bouss/radial_flat/_output
==> Running with command:
/opt/homebrew/Caskroom/miniforge/base/envs/claw/./bin/mpiexec -n 6 /Users/praveen/Work/bouss/radial_flat/xgeoclaw
Reading data file: claw.data
first 5 lines are comments and will be skipped
Reading data file: amr.data
first 5 lines are comments and will be skipped
Running amrclaw ...
Reading data file: geoclaw.data
first 5 lines are comments and will be skipped
Reading data file: refinement.data
first 5 lines are comments and will be skipped
Reading data file: dtopo.data
first 5 lines are comments and will be skipped
Reading data file: topo.data
first 5 lines are comments and will be skipped
converting to topotype > 1 might reduce file size
python tools for converting files are provided
Reading topography file /Volumes/Samsung_T5/Work/bouss/radial_flat/flat100.tt1
Reading data file: qinit.data
first 5 lines are comments and will be skipped
qinit_type = 0, no perturbation
Reading data file: fgout_grids.data
first 5 lines are comments and will be skipped
Reading data file: friction.data
first 5 lines are comments and will be skipped
Reading data file: multilayer.data
first 5 lines are comments and will be skipped
Reading data file: surge.data
first 5 lines are comments and will be skipped
Reading data file: regions.data
first 5 lines are comments and will be skipped
Reading data file: flagregions.data
first 5 lines are comments and will be skipped
+++ rregion bounding box:
0.0000000000000000 5000.0000000000000 0.0000000000000000 5000.0000000000000
+++ i, rr%s(1), rr%ds: 1 0.0000000000000000 5000.0000000000000
+++ Ruled region name: Region_diagonal
+++ Ruled region file_name: /Volumes/Samsung_T5/Work/bouss/radial_flat/RuledRectangle_Diagonal.data
+++ rregion bounding box:
0.0000000000000000 5000.0000000000000 -1000.0000000000000 6000.0000000000000
+++ i, rr%s(1), rr%ds: 2 0.0000000000000000 5000.0000000000000
+++ rregion bounding box:
0.0000000000000000 1000.0000000000000 0.0000000000000000 1000.0000000000000
+++ i, rr%s(1), rr%ds: 3 0.0000000000000000 1000.0000000000000
Reading data file: gauges.data
first 5 lines are comments and will be skipped
Reading data file: fgmax_grids.data
first 5 lines are comments and will be skipped
Reading data file: adjoint.data
first 5 lines are comments and will be skipped
Reading data file: bouss.data
first 5 lines are comments and will be skipped
Using SGN equations
==> Applying Bouss equations to selected grids between levels 1 and 10
==> 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 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: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see https://urldefense.us/v3/__https://petsc.org/release/faq/*valgrind__;Iw!!G_uCfscf7eWS!YfrSA6JCkK1gfGgtTWPw-8jHlRI4KhOjRVRmncpA01ImURbJtFEQuwPz9Y6AYUfTMVo0CPQxqXWVhulpyMltnQ$ and https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!YfrSA6JCkK1gfGgtTWPw-8jHlRI4KhOjRVRmncpA01ImURbJtFEQuwPz9Y6AYUfTMVo0CPQxqXWVhukefFfCQA$
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: Run with -malloc_debug to check if memory corruption is causing the crash.
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF
Proc: [[5779,1],0]
Errorcode: 59
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
prterun has exited due to process rank 0 with PID 0 on node chandra calling
"abort". This may have caused other processes in the application to be
terminated by signals sent by prterun (as reported here).
--------------------------------------------------------------------------
Traceback (most recent call last):
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 413, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/opt/homebrew/Caskroom/miniforge/base/envs/claw/./bin/mpiexec', '-n', '6', '/Users/praveen/Work/bouss/radial_flat/xgeoclaw']' returned non-zero exit status 59.
During handling of the above exception, another exception occurred:
Traceback (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 249, in runclaw
raise ClawExeError(exe_error_str, cpe.returncode, cpe.cmd,
ClawExeError:
*** FORTRAN EXE FAILED ***
make[1]: *** [output] Error 1
make: *** [.output] Error 2
> On 30 Oct 2024, at 9:33 PM, Barry Smith <bsmith at petsc.dev> wrote:
>
>
> Please put
>
> -mpi_linear_solver_server_use_shared_memory false
>
> into the petscMPIOptions file and see if that changes anything.
>
> Barry
>
>
>> On Oct 30, 2024, at 9:05 AM, Praveen C <cpraveen at gmail.com> wrote:
>>
>> I have attached some files for this
>>
>> cd bouss
>> . setenv.sh # some settings in this file may need to be changed
>>
>> cd radial_flat/1d_radial
>> make .output
>> cd ..
>> make .output
>>
>> Thanks
>> praveen
>>
>> <petscMPIoptions>
>> <setenv.sh>
>>
>>> On 30 Oct 2024, at 6:28 PM, Barry Smith <bsmith at petsc.dev> wrote:
>>>
>>>
>>> Please send me exact instructions on how you are running the geoclaw example, when I run
>>>
>>> geoclaw/examples/bouss/radial_flat
>>>
>>>
>>> it only runs with one level, but never errors, I changed setrun.py to amrdata.amr_levels_max = 5 but it made no difference.
>>>
>>> Thanks
>>>
>>> Barry
>>>
>>>
>>>
>>>> On Oct 24, 2024, at 12:17 PM, Praveen C <cpraveen at gmail.com> wrote:
>>>>
>>>> Hello Barry
>>>>
>>>> I use this script to install clawpack and required dependencies
>>>>
>>>> https://urldefense.us/v3/__https://github.com/cpraveen/cfdlab/blob/master/bin/clawpack.sh__;!!G_uCfscf7eWS!YfrSA6JCkK1gfGgtTWPw-8jHlRI4KhOjRVRmncpA01ImURbJtFEQuwPz9Y6AYUfTMVo0CPQxqXWVhunZ-SMX1Q$
>>>>
>>>> See lines 125-132
>>>>
>>>> You can use it like this
>>>>
>>>> export CLAW=/path/to/where/you/want/clawpack
>>>> bash clawpack.sh v5.11.0
>>>>
>>>> This will git pull clawpack and creates a conda env called “claw” and installs inside that.
>>>>
>>>> I have not specified petsc version in this script, but latest miniforge should install petsc at 3.22
>>>>
>>>> Thank you
>>>> praveen
>>>>
>>>>> On 24 Oct 2024, at 9:37 PM, Barry Smith <bsmith at petsc.dev> wrote:
>>>>>
>>>>>
>>>>> Good, some helpful information with the runs you made.
>>>>>
>>>>> In the crash below it made more progress it was able to allocate multiple regions of shared memory and access them. I don't know why it would crash later.
>>>>>
>>>>> Can you tell me all the steps with miniforge (which seems to be related to the failure) you use? I've never used miniforge.
>>>>>
>>>>> If I can get to an environment that reproduces the problem I can debug it and fix it.
>>>>>
>>>>> Barry
>>>>>
>>>>>
>>>>>> On Oct 24, 2024, at 11:49 AM, Praveen C <cpraveen at gmail.com> wrote:
>>>>>>
>>>>>> I get this
>>>>>>
>>>>>> $ mpiexec -n 3 ./ex89f -n 20 -mpi_linear_solver_server -mpi_linear_solver_server -mpi_linear_solver_server_ksp_view -ksp_monitor -ksp_converged_reason -ksp_view -mpi_linear_solver_server_minimum_count_per_rank 5
>>>>>> [0]PETSC ERROR: ------------------------------------------------------------------------
>>>>>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
>>>>>> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>>>>>> [0]PETSC ERROR: or see https://urldefense.us/v3/__https://petsc.org/release/faq/*valgrind__;Iw!!G_uCfscf7eWS!YfrSA6JCkK1gfGgtTWPw-8jHlRI4KhOjRVRmncpA01ImURbJtFEQuwPz9Y6AYUfTMVo0CPQxqXWVhulpyMltnQ$ and https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!YfrSA6JCkK1gfGgtTWPw-8jHlRI4KhOjRVRmncpA01ImURbJtFEQuwPz9Y6AYUfTMVo0CPQxqXWVhukefFfCQA$
>>>>>> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
>>>>>> [0]PETSC ERROR: to get more information on the crash.
>>>>>> [0]PETSC ERROR: Run with -malloc_debug to check if memory corruption is causing the crash.
>>>>>> --------------------------------------------------------------------------
>>>>>> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF
>>>>>> Proc: [[47380,1],0]
>>>>>> Errorcode: 59
>>>>>>
>>>>>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>>>>>> You may or may not see output from other processes, depending on
>>>>>> exactly when Open MPI kills them.
>>>>>> --------------------------------------------------------------------------
>>>>>> --------------------------------------------------------------------------
>>>>>> prterun has exited due to process rank 0 with PID 0 on node MacMiniHome calling
>>>>>> "abort". This may have caused other processes in the application to be
>>>>>> terminated by signals sent by prterun (as reported here).
>>>>>> —————————————————————————————————————
>>>>>>
>>>>>> and I have this after the code exits
>>>>>>
>>>>>> $ ipcs -m
>>>>>> IPC status from <running system> as of Thu Oct 24 21:17:39 IST 2024
>>>>>> T ID KEY MODE OWNER GROUP
>>>>>> Shared Memory:
>>>>>> m 1572864 0x0000000b --rw-rw-rw- praveen staff
>>>>>> m 524289 0x0000000c --rw-rw-rw- praveen staff
>>>>>> m 655362 0x0000000d --rw-rw-rw- praveen staff
>>>>>> m 262147 0x0000000e --rw-rw-rw- praveen staff
>>>>>> m 262148 0x0000000f --rw-rw-rw- praveen staff
>>>>>> m 393221 0x0000000a --rw-rw-rw- praveen staff
>>>>>>
>>>>>> This is with petsc installed with miniforge, which I also use with clawpack. With spack installed petsc, I can run the ex89f example.
>>>>>>
>>>>>> Thanks
>>>>>> praveen
>>>>>>
>>>>>>> On 24 Oct 2024, at 7:55 PM, Barry Smith <bsmith at petsc.dev> wrote:
>>>>>>>
>>>>>>>
>>>>>>> Ok, super strange, I've run many times on my Mac
>>>>>>>
>>>>>>> Can you please try to remove that allocated memory with ipcrm and then
>>>>>>>
>>>>>>> cd $PETSC_DIR/src/ksp/ksp/tutorials
>>>>>>> make ex89f
>>>>>>> mpiexec -n 3 ./ex89f -n 20 -mpi_linear_solver_server -mpi_linear_solver_server -mpi_linear_solver_server_ksp_view -ksp_monitor -ksp_converged_reason -ksp_view -mpi_linear_solver_server_minimum_count_per_rank 5
>>>>>>>
>>>>>>> This does the same thing as the GeoClaw code but is much simpler.
>>>>>>>
>>>>>>> Barry
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>> On Oct 23, 2024, at 10:55 PM, Praveen C <cpraveen at gmail.com> wrote:
>>>>>>>>
>>>>>>>> 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!YfrSA6JCkK1gfGgtTWPw-8jHlRI4KhOjRVRmncpA01ImURbJtFEQuwPz9Y6AYUfTMVo0CPQxqXWVhukefFfCQA$ 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!YfrSA6JCkK1gfGgtTWPw-8jHlRI4KhOjRVRmncpA01ImURbJtFEQuwPz9Y6AYUfTMVo0CPQxqXWVhumk7U9-wA$ 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
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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