On 23 Oct 2024, at 8:26 PM, Barry Smith <bsmith@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@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@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@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@petsc.dev> wrote:

  Please take a look at the notes in https://petsc.org/release/manualpages/Sys/PetscShmgetAllocateArray/  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@gmail.com> wrote:

Dear all

I am not able to run the boussinesq example from geoclaw using petsc@3.22.0

https://urldefense.us/v3/__https://github.com/clawpack/geoclaw/tree/3303883f46572c58130d161986b8a87a57ca7816/examples/bouss__;!!G_uCfscf7eWS!e3VQ4NHKmXGstRsQW5vtI7fmKfUT9zmJkMJcPbcvPyIjicyfJpNoMgx3wZ-qyGcKNSjIkNZkzilec8MnHN6PMw$

It runs with petsc@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