Error in Running Official GeoClaw Radial Flat Example

[Ren]

Dear All,

I have installed the new version Geoclaw5.11, with petsc 3.21.2. When I test radial flat example, it has some errors. 

Does anyone meet this problem?

Thank you very much!

Zhiyuan

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: 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:-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: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.21.2, May 29, 2024
[0]PETSC ERROR: /home/rzy/rzy/clawpack-v5.11.0/geoclaw/examples/bouss/radial_flat/xgeoclaw on a arch-linux-c-debug named rzy-Tower by rzy Sat Oct 12 10:17:11 2024
[0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-mpich --download-fblaslapack make all check
[0]PETSC ERROR: #1 PetscStrstr() at /home/rzy/rzy/software/petsc-3.21.2/include/petscstring.h:402
[0]PETSC ERROR: #2 PCCreate_MPI() at /home/rzy/rzy/software/petsc-3.21.2/src/ksp/pc/impls/mpi/pcmpi.c:763
[0]PETSC ERROR: #3 PCSetType() at /home/rzy/rzy/software/petsc-3.21.2/src/ksp/pc/interface/pcset.c:75
[0]PETSC ERROR: #4 PCSetFromOptions() at /home/rzy/rzy/software/petsc-3.21.2/src/ksp/pc/interface/pcset.c:146
[0]PETSC ERROR: #5 KSPSetFromOptions() at /home/rzy/rzy/software/petsc-3.21.2/src/ksp/ksp/interface/itcl.c:366
[0]PETSC ERROR: #6 PCMPISetMat() at /home/rzy/rzy/software/petsc-3.21.2/src/ksp/pc/impls/mpi/pcmpi.c:273
[0]PETSC ERROR: #7 PCSetUp_MPI() at /home/rzy/rzy/software/petsc-3.21.2/src/ksp/pc/impls/mpi/pcmpi.c:663
[0]PETSC ERROR: #8 PCSetUp() at /home/rzy/rzy/software/petsc-3.21.2/src/ksp/pc/interface/precon.c:1079
[0]PETSC ERROR: #9 KSPSetUp() at /home/rzy/rzy/software/petsc-3.21.2/src/ksp/ksp/interface/itfunc.c:415
[0]PETSC ERROR: #10 KSPSolve_Private() at /home/rzy/rzy/software/petsc-3.21.2/src/ksp/ksp/interface/itfunc.c:831
[0]PETSC ERROR: [1]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[1]PETSC ERROR: Null argument, when expecting valid pointer
[1]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_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
[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:   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:   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.
[1]PETSC ERROR: Petsc Release Version 3.21.2, May 29, 2024
[1]PETSC ERROR: /home/rzy/rzy/clawpack-v5.11.0/geoclaw/examples/bouss/radial_flat/xgeoclaw on a arch-linux-c-debug named rzy-Tower by rzy Sat Oct 12 10:17:11 2024
[1]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --download-mpich --download-fblaslapack make all check
[1]PETSC ERROR: #1 PetscStrstr() at /home/rzy/rzy/software/petsc-3.21.2/include/petscstring.h:402
[1]PETSC ERROR: #2 PCCreate_MPI() at /home/rzy/rzy/software/petsc-3.21.2/src/ksp/pc/impls/mpi/pcmpi.c:763
[1]PETSC ERROR: #3 PCSetType() at /home/rzy/rzy/software/petsc-3.21.2/src/ksp/pc/interface/pcset.c:75
[1]PETSC ERROR: #4 PCSetFromOptions() at /home/rzy/rzy/software/petsc-3.21.2/src/ksp/pc/interface/pcset.c:146
[1]PETSC ERROR: #5 KSPSetFromOptions() at /home/rzy/rzy/software/petsc-3.21.2/src/ksp/ksp/interface/itcl.c:366
[1]PETSC ERROR: #6 PCMPISetMat() at /home/rzy/rzy/software/petsc-3.21.2/src/ksp/pc/impls/mpi/pcmpi.c:273
[1]PETSC ERROR: #7 PCMPIServerBegin() at /home/rzy/rzy/software/petsc-3.21.2/src/ksp/pc/impls/mpi/pcmpi.c:465
[1]PETSC ERROR: #8 PetscInitialize_Common() at /home/rzy/rzy/software/petsc-3.21.2/src/sys/objects/pinit.c:1149
[1]PETSC ERROR: PetscInitialize:PetscInitialize_Common
[1]PETSC ERROR: #9 /home/rzy/rzy/software/petsc-3.21.2/src/sys/f90-mod/petscsysmod.F90:387
#11 KSPSolve() at /home/rzy/rzy/software/petsc-3.21.2/src/ksp/ksp/interface/itfunc.c:1078
[1]PETSC ERROR: #10 /home/rzy/rzy/clawpack-v5.11.0/geoclaw/src/2d/bouss/amr2.f90:165
application called MPI_Abort(MPI_COMM_SELF, 85) - process 0
Traceback (most recent call last):
  File "/home/rzy/rzy/clawpack-v5.11.0/clawutil/src/python/clawutil/runclaw.py", line 242, in runclaw
    proc = subprocess.check_call(cmd_split,
  File "/usr/lib/python3.10/subprocess.py", line 369, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/home/rzy/rzy/software/petsc-3.21.2/arch-linux-c-debug/bin/mpiexec', '-n', '6', '/home/rzy/rzy/clawpack-v5.11.0/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 "/home/rzy/rzy/clawpack-v5.11.0/clawutil/src/python/clawutil/runclaw.py", line 341, in <module>
    runclaw(*args)
  File "/home/rzy/rzy/clawpack-v5.11.0/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]: *** [/home/rzy/rzy/clawpack-v5.11.0/clawutil/src/Makefile.common:246: output] Error 1
make[1]: Leaving directory '/home/rzy/rzy/clawpack-v5.11.0/geoclaw/examples/bouss/radial_flat'
make: *** [/home/rzy/rzy/clawpack-v5.11.0/clawutil/src/Makefile.common:240: .output] Error 2