[petsc-users] Problem running geoclaw example with petsc 3.22
Barry Smith
bsmith at petsc.dev
Wed Oct 23 09:26:21 CDT 2024
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!aFrFZtkivHqm4h8CCjiTYRVosesIL2-ZKUsQYJczi7-l8ZEO2G1Hnn1WpIl76gLAKbAzDIJeAaKXAudi5UARJTU$ 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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