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!aV1t0ykXK5XZXD7-BJX9A_zGNHNR8THmsF66BnZkVDiDJF0FKfSG354RNSvXarj4iea2kTc7lgzUzX55rI7bsw$ > 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 >
