I get very similar error on my mac with $ gfortran -v Using built-in specs. COLLECT_GCC=gfortran COLLECT_LTO_WRAPPER=/opt/homebrew/Caskroom/miniforge/base/envs/claw/libexec/gcc/arm64-apple-darwin20.0.0/13.2.0/lto-wrapper Target: arm64-apple-darwin20.0.0 Configured with: ../configure --prefix=/opt/homebrew/Caskroom/miniforge/base/envs/claw --build=x86_64-apple-darwin13.4.0 --host=arm64-apple-darwin20.0.0 --target=arm64-apple-darwin20.0.0 --with-libiconv-prefix=/opt/homebrew/Caskroom/miniforge/base/envs/claw --enable-languages=fortran --disable-multilib --enable-checking=release --disable-bootstrap --disable-libssp --with-gmp=/opt/homebrew/Caskroom/miniforge/base/envs/claw --with-mpfr=/opt/homebrew/Caskroom/miniforge/base/envs/claw --with-mpc=/opt/homebrew/Caskroom/miniforge/base/envs/claw --with-isl=/opt/homebrew/Caskroom/miniforge/base/envs/claw --enable-darwin-at-rpath Thread model: posix Supported LTO compression algorithms: zlib gcc version 13.2.0 (GCC)
Before starting $ ipcs -m IPC status from <running system> as of Thu Oct 24 08:02:11 IST 2024 T ID KEY MODE OWNER GROUP Shared Memory: and when I run the code 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 1 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 0x130698000 [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_type value: preonly source: file [0]PETSC ERROR: Option left: name:-mpi_ksp_max_it value: 200 source: file [0]PETSC ERROR: Option left: name:-mpi_ksp_reuse_preconditioner (no value) source: file [0]PETSC ERROR: Option left: name:-mpi_ksp_rtol value: 1.e-9 source: file [0]PETSC ERROR: Option left: name:-mpi_ksp_type value: gmres source: file [0]PETSC ERROR: Option left: name:-mpi_linear_solver_server_view (no value) source: file [0]PETSC ERROR: Option left: name:-mpi_pc_gamg_sym_graph value: true source: file [0]PETSC ERROR: Option left: name:-mpi_pc_gamg_symmetrize_graph value: true source: file [0]PETSC ERROR: Option left: name:-mpi_pc_type value: gamg source: file [0]PETSC ERROR: Option left: name:-pc_mpi_minimum_count_per_rank value: 5000 source: file [0]PETSC ERROR: Option left: name:-pc_type value: mpi source: file [0]PETSC ERROR: See https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!ZGVQF1mXRVL7_W_U2YYltlhjpJnbZse3y51RCYHH0aJtnt9WRtDMxGfCLD_5ua4VLxp0_IMDDAycDKWb2Yr0Pw$ for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.22.0, Sep 28, 2024 [0]PETSC ERROR: /Users/praveen/work/bouss/radial_flat/xgeoclaw with 6 MPI process(es) and PETSC_ARCH on MacMiniHome.local by praveen Thu Oct 24 08:04:27 2024 [0]PETSC ERROR: Configure options: AR=arm64-apple-darwin20.0.0-ar CC=mpicc CXX=mpicxx FC=mpifort CFLAGS="-ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem /opt/homebrew/Caskroom/miniforge/base/envs/claw/include " CPPFLAGS="-D_FORTIFY_SOURCE=2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/claw/include -mmacosx-version-min=11.0 -mmacosx-version-min=11.0" CXXFLAGS="-ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/claw/include " FFLAGS="-march=armv8.3-a -ftree-vectorize -fPIC -fno-stack-protector -O2 -pipe -isystem /opt/homebrew/Caskroom/miniforge/base/envs/claw/include " LDFLAGS="-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/opt/homebrew/Caskroom/miniforge/base/envs/claw/lib -L/opt/homebrew/Caskroom/miniforge/base/envs/claw/lib" LIBS="-Wl,-rpath,/opt/homebrew/Caskroom/miniforge/base/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.dylib --with-lapack-lib=liblapack.dylib --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/homebrew/Caskroom/miniforge/base/envs/claw/include/superlu-dist --with-superlu_dist-lib=-lsuperlu_dist --with-suitesparse=1 --with-suitesparse-dir=/opt/homebrew/Caskroom/miniforge/base/envs/claw --with-x=0 --with-scalar-type=real --with-cuda=0 --with-batch --prefix=/opt/homebrew/Caskroom/miniforge/base/envs/claw [0]PETSC ERROR: #1 PetscShmgetMapAddresses() at /Users/runner/miniforge3/conda-bld/petsc_1728030427805/work/src/sys/utils/server.c:114 [0]PETSC ERROR: #2 PCMPISetMat() at /Users/runner/miniforge3/conda-bld/petsc_1728030427805/work/src/ksp/pc/impls/mpi/pcmpi.c:269 [0]PETSC ERROR: #3 PCSetUp_MPI() at /Users/runner/miniforge3/conda-bld/petsc_1728030427805/work/src/ksp/pc/impls/mpi/pcmpi.c:853 [0]PETSC ERROR: #4 PCSetUp() at /Users/runner/miniforge3/conda-bld/petsc_1728030427805/work/src/ksp/pc/interface/precon.c:1071 [0]PETSC ERROR: #5 KSPSetUp() at /Users/runner/miniforge3/conda-bld/petsc_1728030427805/work/src/ksp/ksp/interface/itfunc.c:415 [0]PETSC ERROR: #6 KSPSolve_Private() at /Users/runner/miniforge3/conda-bld/petsc_1728030427805/work/src/ksp/ksp/interface/itfunc.c:826 [0]PETSC ERROR: #7 KSPSolve() at /Users/runner/miniforge3/conda-bld/petsc_1728030427805/work/src/ksp/ksp/interface/itfunc.c:1075 Code does not progress and I kill it ^CTraceback (most recent call last): File "/Users/praveen/Applications/clawpack/clawutil/src/python/clawutil/runclaw.py", line 341, in <module> runclaw(*args) File "/Users/praveen/Applications/clawpack/clawutil/src/python/clawutil/runclaw.py", line 242, in runclaw proc = subprocess.check_call(cmd_split, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/homebrew/Caskroom/miniforge/base/envs/claw/lib/python3.12/subprocess.py", line 408, in check_call retcode = call(*popenargs, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/homebrew/Caskroom/miniforge/base/envs/claw/lib/python3.12/subprocess.py", line 391, in call return p.wait(timeout=timeout) ^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/homebrew/Caskroom/miniforge/base/envs/claw/lib/python3.12/subprocess.py", line 1264, in wait return self._wait(timeout=timeout) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/homebrew/Caskroom/miniforge/base/envs/claw/lib/python3.12/subprocess.py", line 2053, in _wait (pid, sts) = self._try_wait(0) ^^^^^^^^^^^^^^^^^ File "/opt/homebrew/Caskroom/miniforge/base/envs/claw/lib/python3.12/subprocess.py", line 2011, in _try_wait (pid, sts) = os.waitpid(self.pid, wait_flags) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ KeyboardInterrupt make[1]: *** [output] Interrupt: 2 make: *** [.output] Interrupt: 2 Now it says $ ipcs -m IPC status from <running system> as of Thu Oct 24 08:05:06 IST 2024 T ID KEY MODE OWNER GROUP Shared Memory: m 720896 0x0000000a --rw-rw-rw- praveen staff Thanks praveen > On 23 Oct 2024, at 8:26 PM, Barry Smith <bsm...@petsc.dev> wrote: > > > 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 <cprav...@gmail.com> 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 <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!ZGVQF1mXRVL7_W_U2YYltlhjpJnbZse3y51RCYHH0aJtnt9WRtDMxGfCLD_5ua4VLxp0_IMDDAycDKVkQg5Zlw$ >>>>> 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 >>>>> >>>> >>> >> >
