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 <bsm...@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 <cprav...@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 <bsm...@petsc.dev> wrote: >>> >>> >>> Please take a look at the notes in >>> https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscShmgetAllocateArray/__;!!G_uCfscf7eWS!fpsbNP5z6XCWQ6tD3oyfDrMPZn-6CqXz9A-Lqv4A0-ss21oyjEdcRNGSEw8Kl1XFP9QBS7Iz3yheqkQrhkRkEg$ >>> 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 <cprav...@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 >>> >> >