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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> wrote:
>>>>
>>>>
>>>> Please take a look at the notes in
>>>> https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscShmgetAllocateArray/__;!!G_uCfscf7eWS!bQF1Ha5L7JIXTnw9qnMNuyiV_XldBWdWhmzhKBu5P99ZZNiosqJx6XbzQab2pfjMrRYRfp2qnm25RDoEeefcAbM$
>>>> 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 <[email protected]> wrote:
>>>>>
>>>>> Dear all
>>>>>
>>>>> I am not able to run the boussinesq example from geoclaw using
>>>>> [email protected]
>>>>>
>>>>> https://urldefense.us/v3/__https://github.com/clawpack/geoclaw/tree/3303883f46572c58130d161986b8a87a57ca7816/examples/bouss__;!!G_uCfscf7eWS!e3VQ4NHKmXGstRsQW5vtI7fmKfUT9zmJkMJcPbcvPyIjicyfJpNoMgx3wZ-qyGcKNSjIkNZkzilec8MnHN6PMw$
>>>>>
>>>>>
>>>>> It runs with [email protected]
>>>>>
>>>>> 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
>>>>
>>>
>>
>
