Please take a look at the notes in https://urldefense.us/v3/__https://petsc.org/release/manualpages/Sys/PetscShmgetAllocateArray/__;!!G_uCfscf7eWS!fTBuqCCGHRprXT35JlP-Fm7YsLqOM33bEFcdtlsJEH1q0worVtAiE6xo-LviQiuClRi9lhg4z48P1hVdAp7sD5E$ 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
