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clawpack / geoclaw

Version of Clawpack for geophysical waves and flows
http://www.clawpack.org/geoclaw
BSD 3-Clause "New" or "Revised" License
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Error with PETSc options for 2D Boussinesq solver in GeoClaw #606

Open carlosmunozmoncayo opened 6 months ago

carlosmunozmoncayo commented 6 months ago

Hello,

I am having issues running the example in geoclaw/examples/bouss/radial_flat. After setting the environment variables as described in geoclaw/examples/bouss/setenv.sh, and running make .output in geoclaw/examples/bouss/radial_flat, I get the error attached below.
I think the error is caused by the line -pc_type mpi in the PETSc options file geoclaw/examples/bouss/petscMPIoptions. If I don't use that flag, the code runs successfully, but the solution is not the expected radially symmetric one (I guess the linear systems are not solved correctly with the default options):

image

I am using PETSc version 3.21, and it's passing all the installation tests.

Any ideas on what is causing this error? Thank you very much for your help!

`[0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: Null argument, when expecting valid pointer [0]PETSC ERROR: Null Pointer: Parameter 'haystack' # 1 [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 [1]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [1]PETSC ERROR: Null argument, when expecting valid pointer [1]PETSC ERROR: [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: Null Pointer: Parameter 'haystack' # 1 [1]PETSC ERROR: WARNING! There are unused option(s) set! Could be the program crashed before usage or a spelling mistake, etc! [1]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:-ksp_type value: preonly source: file [1]PETSC ERROR: Option left: name:-mpi_ksp_max_it value: 200 source: file [1]PETSC ERROR: Option left: name:-mpi_ksp_reuse_preconditioner (no value) source: file [1]PETSC ERROR: Option left: name:-mpi_ksp_rtol value: 1.e-9 source: file 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 [1]PETSC ERROR: Option left: name:-mpi_ksp_type value: gmres source: file [1]PETSC ERROR: Option left: name:-mpi_linear_solver_server_view (no value) source: file [1]PETSC ERROR: [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.21.0, unknown Option left: name:-mpi_pc_gamg_sym_graph value: true source: file [1]PETSC ERROR: Option left: name:-mpi_pc_gamg_symmetrize_graph value: true source: file [1]PETSC ERROR: [0]PETSC ERROR: /Users/carlos/clawpack/geoclaw/examples/bouss/radial_flat/xgeoclaw on a arch-darwin-c-debug named laptop.local by carlos Mon May 6 20:30:29 2024 [0]PETSC ERROR: Configure options --download-mpich Option left: name:-mpi_pc_type value: gamg source: file [1]PETSC ERROR: Option left: name:-pc_mpi_minimum_count_per_rank value: 5000 source: file [1]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. [0]PETSC ERROR: #1 PetscStrstr() at /Users/carlos/SciSoftware/petsc/include/petscstring.h:402 [0]PETSC ERROR: [1]PETSC ERROR: Petsc Release Version 3.21.0, unknown [1]PETSC ERROR: /Users/carlos/clawpack/geoclaw/examples/bouss/radial_flat/xgeoclaw on a arch-darwin-c-debug named laptop.local by carlos Mon May 6 20:30:29 2024

2 PCCreate_MPI() at /Users/carlos/SciSoftware/petsc/src/ksp/pc/impls/mpi/pcmpi.c:763

[0]PETSC ERROR: #3 PCSetType() at /Users/carlos/SciSoftware/petsc/src/ksp/pc/interface/pcset.c:75 [0]PETSC ERROR: [1]PETSC ERROR: Configure options --download-mpich [1]PETSC ERROR: #1 PetscStrstr() at /Users/carlos/SciSoftware/petsc/include/petscstring.h:402

4 PCSetFromOptions() at /Users/carlos/SciSoftware/petsc/src/ksp/pc/interface/pcset.c:146

[0]PETSC ERROR: #5 KSPSetFromOptions() at /Users/carlos/SciSoftware/petsc/src/ksp/ksp/interface/itcl.c:356 [0]PETSC ERROR: [1]PETSC ERROR: #2 PCCreate_MPI() at /Users/carlos/SciSoftware/petsc/src/ksp/pc/impls/mpi/pcmpi.c:763 [1]PETSC ERROR: #6 PCMPISetMat() at /Users/carlos/SciSoftware/petsc/src/ksp/pc/impls/mpi/pcmpi.c:273 [0]PETSC ERROR: #7 PCSetUp_MPI() at /Users/carlos/SciSoftware/petsc/src/ksp/pc/impls/mpi/pcmpi.c:663

3 PCSetType() at /Users/carlos/SciSoftware/petsc/src/ksp/pc/interface/pcset.c:75

[1]PETSC ERROR: #4 PCSetFromOptions() at /Users/carlos/SciSoftware/petsc/src/ksp/pc/interface/pcset.c:146 [1]PETSC ERROR: [0]PETSC ERROR: #8 PCSetUp() at /Users/carlos/SciSoftware/petsc/src/ksp/pc/interface/precon.c:1079 [0]PETSC ERROR: #9 KSPSetUp() at /Users/carlos/SciSoftware/petsc/src/ksp/ksp/interface/itfunc.c:415 [0]PETSC ERROR: #10 KSPSolve_Private() at /Users/carlos/SciSoftware/petsc/src/ksp/ksp/interface/itfunc.c:831

5 KSPSetFromOptions() at /Users/carlos/SciSoftware/petsc/src/ksp/ksp/interface/itcl.c:356

[1]PETSC ERROR: #6 PCMPISetMat() at /Users/carlos/SciSoftware/petsc/src/ksp/pc/impls/mpi/pcmpi.c:273 [1]PETSC ERROR: #7 PCMPIServerBegin() at /Users/carlos/SciSoftware/petsc/src/ksp/pc/impls/mpi/pcmpi.c:465 [1]PETSC ERROR: #8 PetscInitialize_Common() at /Users/carlos/SciSoftware/petsc/src/sys/objects/pinit.c:1149 [0]PETSC ERROR: #11 KSPSolve() at /Users/carlos/SciSoftware/petsc/src/ksp/ksp/interface/itfunc.c:1078 [1]PETSC ERROR: PetscInitialize:PetscInitialize_Common [1]PETSC ERROR: #9 /Users/carlos/SciSoftware/petsc/src/sys/f90-mod/petscsysmod.F90:387 [1]PETSC ERROR: #10 /Users/carlos/clawpack/geoclaw/src/2d/bouss/amr2.f90:165 application called MPI_Abort(MPI_COMM_SELF, 85) - process 0 Traceback (most recent call last): File "/Users/carlos/clawpack/clawutil/src/python/clawutil/runclaw.py", line 242, in runclaw proc = subprocess.check_call(cmd_split, File "/Users/carlos/.pyenv/versions/3.8.9/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/subprocess.py", line 364, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/Users/carlos/SciSoftware/petsc/arch-darwin-c-debug/bin/mpiexec', '-n', '6', '/Users/carlos/clawpack/geoclaw/examples/bouss/radial_flat/xgeoclaw']' returned non-zero exit status 85.

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/Users/carlos/clawpack/clawutil/src/python/clawutil/runclaw.py", line 341, in runclaw(*args) File "/Users/carlos/clawpack/clawutil/src/python/clawutil/runclaw.py", line 249, in runclaw raise ClawExeError(exe_error_str, cpe.returncode, cpe.cmd, main.ClawExeError:

FORTRAN EXE FAILED

make[1]: [output] Error 1 make: [.output] Error 2 `

renzhy commented 1 month ago

Hi, have you solve this problem?