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!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 <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 >> >
