[petsc-users] Problem running geoclaw example with petsc 3.22

Wed Oct 23 09:56:14 CDT 2024

   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!d8hbkBgHfGN-5jZI0yh7_fRBXUe2m7vGeec0JeTo3GvP69O4CajQgQsIdFO7QSfK4ae5V5L0GOBMjnY4xLoT-2U$   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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