Re: [petsc-users] ex19: Segmentation Violation when run with MUMPS on MacOS (arm64)
The branch with the patched openmpi works fine for me. Thanks for sharing! Best wishes, Zongze > On 4 Apr 2024, at 12: 44, Satish Balay wrote: > > With xcode-15. 3 and branch "barry/2024-04-03/fix-chaco-modern-c/release" ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd The branch with the patched openmpi works fine for me. Thanks for sharing! Best wishes, Zongze > On 4 Apr 2024, at 12:44, Satish Balay wrote: > > With xcode-15.3 and branch "barry/2024-04-03/fix-chaco-modern-c/release" from https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/merge_requests/7433__;!!G_uCfscf7eWS!b2jrTotLzInMflHGijS61VKFqgwsNfFEui4cpKyEgYLspq5b8HyH38UJWxEuke5cGC4RnZf7jdYuh8CtFfZlodjP$ [and a patched openmpi tarball to remove -Wl,-commons,use_dylibs] the following works for me. > > Satish > > > > petsc@mpro petsc.x % ./configure --download-bison --download-chaco --download-ctetgen --download-eigen --download-fftw --download-hdf5 --download-hpddm --download-hwloc --download-hypre --download-libpng --download-metis --download-mmg --download-mumps --download-netcdf --download-openblas --download-openblas-make-options="'USE_THREAD=0 USE_LOCKING=1 USE_OPENMP=0'" --download-p4est --download-parmmg --download-pnetcdf --download-pragmatic --download-ptscotch --download-scalapack --download-slepc --download-suitesparse --download-superlu_dist --download-tetgen --download-triangle --with-c2html=0 --with-debugging=1 --with-fortran-bindings=0 --with-shared-libraries=1 --with-x=0 --with-zlib --download-openmpi=https://urldefense.us/v3/__https://web.cels.anl.gov/projects/petsc/download/externalpackages/openmpi-5.0.2-xcode15.tar.gz__;!!G_uCfscf7eWS!b2jrTotLzInMflHGijS61VKFqgwsNfFEui4cpKyEgYLspq5b8HyH38UJWxEuke5cGC4RnZf7jdYuh8CtFUMGGKvW$ --download-pastix && make && make check > > CC arch-darwin-c-debug/obj/src/lme/interface/lmesolve.o > CLINKER arch-darwin-c-debug/lib/libslepc.3.21.0.dylib >DSYMUTIL arch-darwin-c-debug/lib/libslepc.3.21.0.dylib > Now to install the library do: > make SLEPC_DIR=/Users/petsc/petsc.x/arch-darwin-c-debug/externalpackages/git.slepc PETSC_DIR=/Users/petsc/petsc.x install > = > *** Installing SLEPc *** > *** Installing SLEPc at prefix location: /Users/petsc/petsc.x/arch-darwin-c-debug *** > > Install complete. > Now to check if the libraries are working do (in current directory): > make SLEPC_DIR=/Users/petsc/petsc.x/arch-darwin-c-debug PETSC_DIR=/Users/petsc/petsc.x PETSC_ARCH=arch-darwin-c-debug check > > /usr/bin/make --no-print-directory -f makefile PETSC_ARCH=arch-darwin-c-debug PETSC_DIR=/Users/petsc/petsc.x SLEPC_DIR=/Users/petsc/petsc.x/arch-darwin-c-debug/externalpackages/git.slepc install-builtafterslepc > /usr/bin/make --no-print-directory -f makefile PETSC_ARCH=arch-darwin-c-debug PETSC_DIR=/Users/petsc/petsc.x SLEPC_DIR=/Users/petsc/petsc.x/arch-darwin-c-debug/externalpackages/git.slepc slepc4py-install > make[6]: Nothing to be done for `slepc4py-install'. > *** Building and installing HPDDM *** > = > Now to check if the libraries are working do: > make PETSC_DIR=/Users/petsc/petsc.x PETSC_ARCH=arch-darwin-c-debug check > = > Running PETSc check examples to verify correct installation > Using PETSC_DIR=/Users/petsc/petsc.x and PETSC_ARCH=arch-darwin-c-debug > C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process > C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI processes > C/C++ example src/snes/tutorials/ex19 run successfully with HYPRE > C/C++ example src/snes/tutorials/ex19 run successfully with MUMPS > C/C++ example src/snes/tutorials/ex19 run successfully with SuiteSparse > C/C++ example src/snes/tutorials/ex19 run successfully with SuperLU_DIST > C/C++ example src/vec/vec/tests/ex47 run successfully with HDF5 > Running SLEPc check examples to verify correct installation > Using SLEPC_DIR=/Users/petsc/petsc.x/arch-darwin-c-debug/externalpackages/git.slepc, PETSC_DIR=/Users/petsc/petsc.x, and PETSC_ARCH=arch-darwin-c-debug > C/C++ example src/eps/tests/test10 run successfully with 1 MPI process > C/C++ example src/eps/tests/test10 run successfully with 2 MPI processes > Completed SLEPc check examples > Completed PETSc check examples > petsc@mpro petsc.x % clang --version > Apple clang version 15.0.0 (clang-1500.3.9.4) > Target: arm64-apple-darwin23.4.0 > Thread model: posix > InstalledDir: /Library/Developer/CommandLineTools/usr/bin > petsc@mpro petsc.x % > > > On Tue, 2 Apr 2024, Zongze Yang wrote: > >> Thank you for the suggestion. >> >> I'd like to share some test results using the current Xcode. When I added the flag `LDFLAGS=-Wl,-ld_classic` and configured PETSc
Re: [petsc-users] ex19: Segmentation Violation when run with MUMPS on MacOS (arm64)
With xcode-15.3 and branch "barry/2024-04-03/fix-chaco-modern-c/release" from https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/merge_requests/7433__;!!G_uCfscf7eWS!YJPSyG4qeGbCKYRp9y16HJgjw7AOrQ0mL0QWb_XcKYZ17UwK2GtURGMpkyi4TctAY-8XqSvQUFmyCQFNnKy75fI$ [and a patched openmpi tarball to remove -Wl,-commons,use_dylibs] the following works for me. Satish petsc@mpro petsc.x % ./configure --download-bison --download-chaco --download-ctetgen --download-eigen --download-fftw --download-hdf5 --download-hpddm --download-hwloc --download-hypre --download-libpng --download-metis --download-mmg --download-mumps --download-netcdf --download-openblas --download-openblas-make-options="'USE_THREAD=0 USE_LOCKING=1 USE_OPENMP=0'" --download-p4est --download-parmmg --download-pnetcdf --download-pragmatic --download-ptscotch --download-scalapack --download-slepc --download-suitesparse --download-superlu_dist --download-tetgen --download-triangle --with-c2html=0 --with-debugging=1 --with-fortran-bindings=0 --with-shared-libraries=1 --with-x=0 --with-zlib --download-openmpi=https://urldefense.us/v3/__https://web.cels.anl.gov/projects/petsc/download/externalpackages/openmpi-5.0.2-xcode15.tar.gz__;!!G_uCfscf7eWS!YJPSyG4qeGbCKYRp9y16HJgjw7AOrQ0mL0QWb_XcKYZ17UwK2GtURGMpkyi4TctAY-8XqSvQUFmyCQFNvoG1gVM$ --download-pastix && make && make check CC arch-darwin-c-debug/obj/src/lme/interface/lmesolve.o CLINKER arch-darwin-c-debug/lib/libslepc.3.21.0.dylib DSYMUTIL arch-darwin-c-debug/lib/libslepc.3.21.0.dylib Now to install the library do: make SLEPC_DIR=/Users/petsc/petsc.x/arch-darwin-c-debug/externalpackages/git.slepc PETSC_DIR=/Users/petsc/petsc.x install = *** Installing SLEPc *** *** Installing SLEPc at prefix location: /Users/petsc/petsc.x/arch-darwin-c-debug *** Install complete. Now to check if the libraries are working do (in current directory): make SLEPC_DIR=/Users/petsc/petsc.x/arch-darwin-c-debug PETSC_DIR=/Users/petsc/petsc.x PETSC_ARCH=arch-darwin-c-debug check /usr/bin/make --no-print-directory -f makefile PETSC_ARCH=arch-darwin-c-debug PETSC_DIR=/Users/petsc/petsc.x SLEPC_DIR=/Users/petsc/petsc.x/arch-darwin-c-debug/externalpackages/git.slepc install-builtafterslepc /usr/bin/make --no-print-directory -f makefile PETSC_ARCH=arch-darwin-c-debug PETSC_DIR=/Users/petsc/petsc.x SLEPC_DIR=/Users/petsc/petsc.x/arch-darwin-c-debug/externalpackages/git.slepc slepc4py-install make[6]: Nothing to be done for `slepc4py-install'. *** Building and installing HPDDM *** = Now to check if the libraries are working do: make PETSC_DIR=/Users/petsc/petsc.x PETSC_ARCH=arch-darwin-c-debug check = Running PETSc check examples to verify correct installation Using PETSC_DIR=/Users/petsc/petsc.x and PETSC_ARCH=arch-darwin-c-debug C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI processes C/C++ example src/snes/tutorials/ex19 run successfully with HYPRE C/C++ example src/snes/tutorials/ex19 run successfully with MUMPS C/C++ example src/snes/tutorials/ex19 run successfully with SuiteSparse C/C++ example src/snes/tutorials/ex19 run successfully with SuperLU_DIST C/C++ example src/vec/vec/tests/ex47 run successfully with HDF5 Running SLEPc check examples to verify correct installation Using SLEPC_DIR=/Users/petsc/petsc.x/arch-darwin-c-debug/externalpackages/git.slepc, PETSC_DIR=/Users/petsc/petsc.x, and PETSC_ARCH=arch-darwin-c-debug C/C++ example src/eps/tests/test10 run successfully with 1 MPI process C/C++ example src/eps/tests/test10 run successfully with 2 MPI processes Completed SLEPc check examples Completed PETSc check examples petsc@mpro petsc.x % clang --version Apple clang version 15.0.0 (clang-1500.3.9.4) Target: arm64-apple-darwin23.4.0 Thread model: posix InstalledDir: /Library/Developer/CommandLineTools/usr/bin petsc@mpro petsc.x % On Tue, 2 Apr 2024, Zongze Yang wrote: > Thank you for the suggestion. > > I'd like to share some test results using the current Xcode. When I added the > flag `LDFLAGS=-Wl,-ld_classic` and configured PETSc with OpenMPI, the tests > with the latest Xcode seemed okay, except for some link warnings. The > configure > command is > ``` > ./configure \ > PETSC_ARCH=arch-darwin-c-debug-openmpi \ > LDFLAGS=-Wl,-ld_classic \ > > --download-openmpi=https://urldefense.us/v3/__https://download.open-mpi.org/release/open-mpi/v5.0/openmpi-5.0.3rc1.tar.bz2__;!!G_uCfscf7eWS!eGiVH2meEkLSEHvkY6Y-m7U1wPG4ZDxHod7lLZI3HTu6itzNEDm7n3cz4GNly925EEHvVRnyNQYn2aAt0ewiXz99$ > > \ > --download-mumps --download-scalapack \ > --with-clean \ > && make && make check > ```
Re: [petsc-users] ex19: Segmentation Violation when run with MUMPS on MacOS (arm64)
On Mon, 1 Apr 2024, Zongze Yang wrote: > Thank you for your update. > > I found some links that suggest this issue is related to the Apple linker, > which is causing problems with Fortran linking. > > 1. > https://urldefense.us/v3/__https://github.com/open-mpi/ompi/issues/12427__;!!G_uCfscf7eWS!bHY4uqpTfwl0jKopATQs3gw--TZSBmDp0Lb1gzDBeEu4ZB_zTph-jfw49yIr3jvPx0YEhQbk1PjYbGYVpjjms6Wb$ > > 2. > https://urldefense.us/v3/__https://x.com/science_dot/status/1768667417553547635?s=46__;!!G_uCfscf7eWS!bHY4uqpTfwl0jKopATQs3gw--TZSBmDp0Lb1gzDBeEu4ZB_zTph-jfw49yIr3jvPx0YEhQbk1PjYbGYVptASYXS2$ > https://urldefense.us/v3/__https://github.com/Homebrew/homebrew-core/issues/162714__;!!G_uCfscf7eWS!chekWa3R3JhHB1MVv33Oqj9fPFhbnx9sm7cm7Lk5-n7PHicsVkY0n7XoSkWmk259VLNjTzEus6xBpRL20MmLo1g$ recommends "downgrade CLT (or xcode?) to 15.1" Satish
Re: [petsc-users] ex19: Segmentation Violation when run with MUMPS on MacOS (arm64)
Thank you for your update. I found some links that suggest this issue is related to the Apple linker, which is causing problems with Fortran linking. 1. https://urldefense.us/v3/__https://github.com/open-mpi/ompi/issues/12427__;!!G_uCfscf7eWS!bHY4uqpTfwl0jKopATQs3gw--TZSBmDp0Lb1gzDBeEu4ZB_zTph-jfw49yIr3jvPx0YEhQbk1PjYbGYVpjjms6Wb$ 2. https://urldefense.us/v3/__https://x.com/science_dot/status/1768667417553547635?s=46__;!!G_uCfscf7eWS!bHY4uqpTfwl0jKopATQs3gw--TZSBmDp0Lb1gzDBeEu4ZB_zTph-jfw49yIr3jvPx0YEhQbk1PjYbGYVptASYXS2$ Best wishes, Zongze > On 2 Apr 2024, at 01:15, Satish Balay wrote: > > On Mon, 1 Apr 2024, Zongze Yang wrote: > >> >> I noticed this in the config.log of OpenMPI: >> ``` >> configure:30230: checking to see if mpifort compiler needs additional linker >> flags >> configure:30247: gfortran -o conftest -fPIC -ffree-line-length-none >> -ffree-line-length-0 -Wno-lto-type-mismatch -g -O0 -fallow-argument-mismatch >> -Wl,-flat_namespace -Wl,-commons,use_dylibs conftest.f90 >&5 >> ld: warning: -commons use_dylibs is no longer supported, using error >> treatment instead >> configure:30247: $? = 0 >> configure:30299: result: -Wl,-commons,use_dylibs >> ``` >> So, I find it odd that this flag isn't picked up on your platform, as it >> only checked the exit value. > > I get: > > configure:30247: gfortran -o conftest -fPIC -ffree-line-length-none > -ffree-line-length-0 -Wno-lto-type-mismatch -g -O0 -fallow-argument-mismatch > -Wl,-flat_namespace -Wl,-commons,use_dylibs conftest.f90 >&5 > ld: unknown options: -commons > collect2: error: ld returned 1 exit status > configure:30247: $? = 1 > configure: failed program was: > | program test > | integer :: i > | end program > configure:30299: result: none > > Note, I have and older xcode-15/CLT version: > > petsc@npro ~ % clang --version > Apple clang version 15.0.0 (clang-1500.1.0.2.5) > Target: arm64-apple-darwin23.3.0 > Thread model: posix > InstalledDir: /Library/Developer/CommandLineTools/usr/bin > > Satish
Re: [petsc-users] ex19: Segmentation Violation when run with MUMPS on MacOS (arm64)
On Mon, 1 Apr 2024, Zongze Yang wrote: > > I noticed this in the config.log of OpenMPI: > ``` > configure:30230: checking to see if mpifort compiler needs additional linker > flags > configure:30247: gfortran -o conftest -fPIC -ffree-line-length-none > -ffree-line-length-0 -Wno-lto-type-mismatch -g -O0 -fallow-argument-mismatch > -Wl,-flat_namespace -Wl,-commons,use_dylibs conftest.f90 >&5 > ld: warning: -commons use_dylibs is no longer supported, using error > treatment instead > configure:30247: $? = 0 > configure:30299: result: -Wl,-commons,use_dylibs > ``` > So, I find it odd that this flag isn't picked up on your platform, as it only > checked the exit value. I get: configure:30247: gfortran -o conftest -fPIC -ffree-line-length-none -ffree-line-length-0 -Wno-lto-type-mismatch -g -O0 -fallow-argument-mismatch -Wl,-flat_namespace -Wl,-commons,use_dylibs conftest.f90 >&5 ld: unknown options: -commons collect2: error: ld returned 1 exit status configure:30247: $? = 1 configure: failed program was: | program test | integer :: i | end program configure:30299: result: none Note, I have and older xcode-15/CLT version: petsc@npro ~ % clang --version Apple clang version 15.0.0 (clang-1500.1.0.2.5) Target: arm64-apple-darwin23.3.0 Thread model: posix InstalledDir: /Library/Developer/CommandLineTools/usr/bin Satish
Re: [petsc-users] ex19: Segmentation Violation when run with MUMPS on MacOS (arm64)
> On 1 Apr 2024, at 23: 38, Satish Balay wrote: > > On Sun, 31 Mar 2024, Zongze Yang wrote: >>> --- >>> petsc@ npro petsc % ./configure --download-bison --download-chaco --download-ctetgen ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd > On 1 Apr 2024, at 23:38, Satish Balay wrote: > > On Sun, 31 Mar 2024, Zongze Yang wrote: >>> --- >>> petsc@npro petsc % ./configure --download-bison --download-chaco --download-ctetgen --download-eigen --download-fftw --download-hdf5 --download-hpddm --download-hwloc --download-hypre --download-libpng --download-metis --download-mmg --download-mumps --download-netcdf --download-openblas >> --download-openblas-make-options="'USE_THREAD=0 USE_LOCKING=1 USE_OPENMP=0'" --download-p4est --download-parmmg --download-pnetcdf --download-pragmatic --download-ptscotch --download-scalapack --download-slepc --download-suitesparse --download-superlu_dist --download-tetgen --download-tri >> angle --with-c2html=0 --with-debugging=1 --with-fortran-bindings=0 --with-shared-libraries=1 --with-x=0 --with-zlib --download-openmpi=https://urldefense.us/v3/__https://download.open-mpi.org/release/open-mpi/v5.0/openmpi-5.0.3rc1.tar.bz2__;!!G_uCfscf7eWS!aCLPUhLfLFG5UwNlUWgGGhXZlw905gJwDd >>AryIrltDIXJcdmOP6Is44FzBVrY5ndwzmIqMhI515mnNjTuHoR-tzq$ --download-pastix=https://urldefense.us/v3/__https://web.cels.anl.gov/projects/petsc/download/externalpackages/pastix_5.2.3-p1.tar.bz2__;!!G_uCfscf7eWS!aCLPUhLfLFG5UwNlUWgGGhXZlw905gJwDdAryIrltDIXJcdmOP6Is44FzBVrY5ndwzmIqMhI515mnNjTuA >>fJ49xl$ && make && make check >> >> There's an error encountered during configuration with the above options: >> ``` >> TESTING: FortranMPICheck from config.packages.MPI(config/BuildSystem/config/packages/MPI.py:676) >> * >> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): >> - >> Fortran error! mpi_init() could not be located! >> * >> ``` >> Please refer to the attached file for further information. > > So I'm getting: > >>> > *** Fortran compiler > checking whether the compiler supports GNU Fortran... yes > checking whether gfortran accepts -g... yes > checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B > checking the name lister (/usr/bin/nm -B) interface... BSD nm > checking whether ln -s works... yes > checking if Fortran compiler works... yes > checking for extra arguments to build a shared library... impossible -- -static > checking for gfortran warnings flags... none > checking for Fortran flag to compile .f files... none > checking for Fortran flag to compile .f90 files... none > checking if Fortran compilers preprocess .F90 files without additional flag... yes > checking to see if Fortran compilers need additional linker flags... -Wl,-flat_namespace > checking external symbol convention... single underscore > checking if C and Fortran are link compatible... yes > checking to see if Fortran compiler likes the C++ exception flags... skipped (no C++ exceptions flags) > checking to see if mpifort compiler needs additional linker flags... none > > > However you are getting: > > > *** Fortran compiler > checking whether the compiler supports GNU Fortran... yes > checking whether gfortran accepts -g... yes > checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B > checking the name lister (/usr/bin/nm -B) interface... BSD nm > checking whether ln -s works... yes > checking if Fortran compiler works... yes > checking for extra arguments to build a shared library... impossible -- -static > checking for gfortran warnings flags... none > checking for Fortran flag to compile .f files... none > checking for Fortran flag to compile .f90 files... none > checking if Fortran compilers preprocess .F90 files without additional flag... yes > checking to see if Fortran compilers need additional linker flags... -Wl,-flat_namespace > checking external symbol convention... single underscore > checking if C and Fortran are link compatible... yes > checking to see if Fortran compiler likes the C++ exception flags... skipped (no C++ exceptions flags) > checking to see if mpifort compiler needs additional linker flags... -Wl,-commons,use_dylibs > > > So gfortran [or ld from this newer xcode?] is behaving differently - and openmpi is picking up and using this broken/unsupported option - and likely triggering subsequent errors. I noticed this in the config.log of OpenMPI: ``` configure:30230: checking to see if mpifort compiler needs additional linker flags configure:30247: gfortran -o conftest
Re: [petsc-users] ex19: Segmentation Violation when run with MUMPS on MacOS (arm64)
On Sun, 31 Mar 2024, Zongze Yang wrote: > > --- > > petsc@npro petsc % ./configure --download-bison --download-chaco > > --download-ctetgen --download-eigen --download-fftw --download-hdf5 > > --download-hpddm --download-hwloc --download-hypre --download-libpng > > --download-metis --download-mmg --download-mumps --download-netcdf > > --download-openblas > --download-openblas-make-options="'USE_THREAD=0 USE_LOCKING=1 USE_OPENMP=0'" > --download-p4est --download-parmmg --download-pnetcdf --download-pragmatic > --download-ptscotch --download-scalapack --download-slepc > --download-suitesparse --download-superlu_dist --download-tetgen > --download-tri > angle --with-c2html=0 --with-debugging=1 --with-fortran-bindings=0 > --with-shared-libraries=1 --with-x=0 --with-zlib > --download-openmpi=https://urldefense.us/v3/__https://download.open-mpi.org/release/open-mpi/v5.0/openmpi-5.0.3rc1.tar.bz2__;!!G_uCfscf7eWS!aCLPUhLfLFG5UwNlUWgGGhXZlw905gJwDd > AryIrltDIXJcdmOP6Is44FzBVrY5ndwzmIqMhI515mnNjTuHoR-tzq$ > --download-pastix=https://urldefense.us/v3/__https://web.cels.anl.gov/projects/petsc/download/externalpackages/pastix_5.2.3-p1.tar.bz2__;!!G_uCfscf7eWS!aCLPUhLfLFG5UwNlUWgGGhXZlw905gJwDdAryIrltDIXJcdmOP6Is44FzBVrY5ndwzmIqMhI515mnNjTuA > fJ49xl$ && make && make check > > There's an error encountered during configuration with the above options: > ``` > TESTING: FortranMPICheck from > config.packages.MPI(config/BuildSystem/config/packages/MPI.py:676) > * >UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for > details): > - >Fortran error! mpi_init() could not be located! > * > ``` > Please refer to the attached file for further information. So I'm getting: >> *** Fortran compiler checking whether the compiler supports GNU Fortran... yes checking whether gfortran accepts -g... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking if Fortran compiler works... yes checking for extra arguments to build a shared library... impossible -- -static checking for gfortran warnings flags... none checking for Fortran flag to compile .f files... none checking for Fortran flag to compile .f90 files... none checking if Fortran compilers preprocess .F90 files without additional flag... yes checking to see if Fortran compilers need additional linker flags... -Wl,-flat_namespace checking external symbol convention... single underscore checking if C and Fortran are link compatible... yes checking to see if Fortran compiler likes the C++ exception flags... skipped (no C++ exceptions flags) checking to see if mpifort compiler needs additional linker flags... none However you are getting: *** Fortran compiler checking whether the compiler supports GNU Fortran... yes checking whether gfortran accepts -g... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking if Fortran compiler works... yes checking for extra arguments to build a shared library... impossible -- -static checking for gfortran warnings flags... none checking for Fortran flag to compile .f files... none checking for Fortran flag to compile .f90 files... none checking if Fortran compilers preprocess .F90 files without additional flag... yes checking to see if Fortran compilers need additional linker flags... -Wl,-flat_namespace checking external symbol convention... single underscore checking if C and Fortran are link compatible... yes checking to see if Fortran compiler likes the C++ exception flags... skipped (no C++ exceptions flags) checking to see if mpifort compiler needs additional linker flags... -Wl,-commons,use_dylibs So gfortran [or ld from this newer xcode?] is behaving differently - and openmpi is picking up and using this broken/unsupported option - and likely triggering subsequent errors. >>> ld: warning: -commons use_dylibs is no longer supported, using error treatment instead ld: common symbol '_mpi_fortran_argv_null_' from '/private/var/folders/tf/v4zjvtw12yb3tszk813gmnvwgn/T/petsc-xyn64q55/config.libraries/conftest.o' conflicts with definition from dylib '_mpi_fortran_argv_null_' from '/Users/zzyang/workspace/repos/petsc/arch-darwin-c-debug/lib/libmpi_usempif08.40.dylib' <<< Or perhaps openmpi configure is affected by this new warning that this newer xcode spews >>> ld: warning: duplicate -rpath '/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc' ignored <<< I'm not sure what to suggest here [other than using Linux - and
Re: [petsc-users] ex19: Segmentation Violation when run with MUMPS on MacOS (arm64)
> On 31 Mar 2024, at 02: 59, Satish Balay via petsc-users wrote: > > I'll just note - I can reproduce with: > > petsc@ npro petsc. x % ./configure --download-mpich --download-mumps --download-scalapack ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd > On 31 Mar 2024, at 02:59, Satish Balay via petsc-users wrote: > > I'll just note - I can reproduce with: > > petsc@npro petsc.x % ./configure --download-mpich --download-mumps --download-scalapack && make && make check > > And then - the following work fine for me: > > petsc@npro petsc.x % ./configure --download-mpich --download-mumps --download-scalapack COPTFLAGS=-O0 FOPTFLAGS=-O0 LDFLAGS=-Wl,-ld_classic && make && make check Hello, I've encountered the same issue. Even after building PETSc with the aforementioned configuration, the error persists. Apart from the segmentation fault, occasionally the following error arises: ``` > === > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > = PID 47531 RUNNING AT yzzs-mac.local > = EXIT CODE: 6 > = CLEANING UP REMAINING PROCESSES > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES > === > YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Terminated: 15 (signal 15) > This typically refers to a problem with your application. > Please see the FAQ page for debugging suggestions /Users/zzyang/workspace/repos/petsc/src/snes/tutorials Possible problem with ex19 running with MUMPS, diffs above ``` Is there a possibility that this is related to the Fortran bindings of MPICH? Best wishes, Zongze > >CLINKER arch-darwin-c-debug/lib/libpetsc.3.021.0.dylib > DSYMUTIL arch-darwin-c-debug/lib/libpetsc.3.021.0.dylib > = > Now to check if the libraries are working do: > make PETSC_DIR=/Users/petsc/petsc.x PETSC_ARCH=arch-darwin-c-debug check > = > Running PETSc check examples to verify correct installation > Using PETSC_DIR=/Users/petsc/petsc.x and PETSC_ARCH=arch-darwin-c-debug > C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process > C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI processes > C/C++ example src/snes/tutorials/ex19 run successfully with MUMPS > Fortran example src/snes/tutorials/ex5f run successfully with 1 MPI process > Completed PETSc check examples > petsc@npro petsc.x % > > petsc@npro petsc.z % ./configure --download-openmpi=https://urldefense.us/v3/__https://download.open-mpi.org/release/open-mpi/v5.0/openmpi-5.0.3rc1.tar.bz2__;!!G_uCfscf7eWS!adsQx6TTtuIrMPz2ZorSv0iNPff5Fm5aFUi4i9n_E7v3GfAc8XCDtrlfVFyfPEgDFe4lKLL1XzkJ3c_97YoeukE$ --download-mumps --download-scalapack && make && make check > > DSYMUTIL arch-darwin-c-debug/lib/libpetsc.3.021.0.dylib > = > Now to check if the libraries are working do: > make PETSC_DIR=/Users/petsc/petsc.z PETSC_ARCH=arch-darwin-c-debug check > = > Running PETSc check examples to verify correct installation > Using PETSC_DIR=/Users/petsc/petsc.z and PETSC_ARCH=arch-darwin-c-debug > C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process > C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI processes > C/C++ example src/snes/tutorials/ex19 run successfully with MUMPS > Fortran example src/snes/tutorials/ex5f run successfully with 1 MPI process > Completed PETSc check examples > petsc@npro petsc.z % > > [however parmmg and pastix are failing to build with openmpi] > > And I thought this worked for me yesterday - but I see failures now. > > ./configure --download-bison --download-chaco --download-ctetgen --download-eigen --download-fftw --download-hdf5 --download-hpddm --download-hwloc --download-hwloc-configure-arguments=--disable-opencl --download-hypre --download-libpng --download-metis --download-mmg --download-mpich --download-mpich-configure-arguments=--disable-opencl --download-mumps --download-netcdf --download-openblas --download-openblas-make-options="'USE_THREAD=0 USE_LOCKING=1 USE_OPENMP=0'" --download-parmmg --download-pastix --download-pnetcdf --download-pragmatic --download-ptscotch --download-scalapack --download-slepc --download-suitesparse --download-superlu_dist --download-tetgen --download-triangle --with-c2html=0 --with-debugging=1 --with-fortran-bindings=0 --with-shared-libraries=1 --with-x=0 --with-zlib --COPTFLAGS=-O0 --FOPTFLAGS=-O0 --LDFLAGS=-Wl,-ld_classic --with-clean > > Satish > > On Sat, 30 Mar 2024, Barry Smith wrote: > >> >> Can you check the value of IRHSCOMP in the debugger? Using gdb as the debugger may work better for this. >> >> Barry >> >> >>> On Mar
Re: [petsc-users] ex19: Segmentation Violation when run with MUMPS on MacOS (arm64)
On my Mac at configure time I get clang: error: linker command failed with exit code 1 (use -v to see invocation) Possible ERROR while running linker: exit code 1 when trying to link a test case against the lapack libraries. I cannot generate ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd On my Mac at configure time I get clang: error: linker command failed with exit code 1 (use -v to see invocation) Possible ERROR while running linker: exit code 1 when trying to link a test case against the lapack libraries. I cannot generate an error message showing what error has occurred > On Mar 30, 2024, at 2:59 PM, Satish Balay wrote: > > I'll just note - I can reproduce with: > > petsc@npro petsc.x % ./configure --download-mpich --download-mumps --download-scalapack && make && make check > > And then - the following work fine for me: > > petsc@npro petsc.x % ./configure --download-mpich --download-mumps --download-scalapack COPTFLAGS=-O0 FOPTFLAGS=-O0 LDFLAGS=-Wl,-ld_classic && make && make check > >CLINKER arch-darwin-c-debug/lib/libpetsc.3.021.0.dylib > DSYMUTIL arch-darwin-c-debug/lib/libpetsc.3.021.0.dylib > = > Now to check if the libraries are working do: > make PETSC_DIR=/Users/petsc/petsc.x PETSC_ARCH=arch-darwin-c-debug check > = > Running PETSc check examples to verify correct installation > Using PETSC_DIR=/Users/petsc/petsc.x and PETSC_ARCH=arch-darwin-c-debug > C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process > C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI processes > C/C++ example src/snes/tutorials/ex19 run successfully with MUMPS > Fortran example src/snes/tutorials/ex5f run successfully with 1 MPI process > Completed PETSc check examples > petsc@npro petsc.x % > > petsc@npro petsc.z % ./configure --download-openmpi=https://urldefense.us/v3/__https://download.open-mpi.org/release/open-mpi/v5.0/openmpi-5.0.3rc1.tar.bz2__;!!G_uCfscf7eWS!ZCdX8VX2WwwopcGzGQq5RpwHmqiuIiIb1r4zByAJVKyH9howYTVO-FFqVMGMbc8fUX6bC9Jsln49TEDpvn4TyIo$ --download-mumps --download-scalapack && make && make check > > DSYMUTIL arch-darwin-c-debug/lib/libpetsc.3.021.0.dylib > = > Now to check if the libraries are working do: > make PETSC_DIR=/Users/petsc/petsc.z PETSC_ARCH=arch-darwin-c-debug check > = > Running PETSc check examples to verify correct installation > Using PETSC_DIR=/Users/petsc/petsc.z and PETSC_ARCH=arch-darwin-c-debug > C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process > C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI processes > C/C++ example src/snes/tutorials/ex19 run successfully with MUMPS > Fortran example src/snes/tutorials/ex5f run successfully with 1 MPI process > Completed PETSc check examples > petsc@npro petsc.z % > > [however parmmg and pastix are failing to build with openmpi] > > And I thought this worked for me yesterday - but I see failures now. > > ./configure --download-bison --download-chaco --download-ctetgen --download-eigen --download-fftw --download-hdf5 --download-hpddm --download-hwloc --download-hwloc-configure-arguments=--disable-opencl --download-hypre --download-libpng --download-metis --download-mmg --download-mpich --download-mpich-configure-arguments=--disable-opencl --download-mumps --download-netcdf --download-openblas --download-openblas-make-options="'USE_THREAD=0 USE_LOCKING=1 USE_OPENMP=0'" --download-parmmg --download-pastix --download-pnetcdf --download-pragmatic --download-ptscotch --download-scalapack --download-slepc --download-suitesparse --download-superlu_dist --download-tetgen --download-triangle --with-c2html=0 --with-debugging=1 --with-fortran-bindings=0 --with-shared-libraries=1 --with-x=0 --with-zlib --COPTFLAGS=-O0 --FOPTFLAGS=-O0 --LDFLAGS=-Wl,-ld_classic --with-clean > > Satish > > On Sat, 30 Mar 2024, Barry Smith wrote: > >> >> Can you check the value of IRHSCOMP in the debugger? Using gdb as the debugger may work better for this. >> >> Barry >> >> >>> On Mar 30, 2024, at 3:46 AM, zeyu xia wrote: >>> >>> This Message Is From an External Sender >>> This message came from outside your organization. >>> Hi! Thanks for your reply. >>> >>> There still exist some problems, as seen in the files 'configure.log', 'make check3.txt', and 'debug.txt' in the attachment. Particularly, the file 'debug.txt' contains the output of bt command of lldb. >>> >>> Thanks for your attention. >>> >>> Best regards, >>> Zeyu Xia >>> >>> >>> Satish Balay > 于2024年3月30日周六 02:52写道： I'm able to reproduce this error on a slightly older xcode [but don't know why this issue comes up] > Apple clang version 15.0.0
Re: [petsc-users] ex19: Segmentation Violation when run with MUMPS on MacOS (arm64)
I'll just note - I can reproduce with: petsc@npro petsc.x % ./configure --download-mpich --download-mumps --download-scalapack && make && make check And then - the following work fine for me: petsc@npro petsc.x % ./configure --download-mpich --download-mumps --download-scalapack COPTFLAGS=-O0 FOPTFLAGS=-O0 LDFLAGS=-Wl,-ld_classic && make && make check CLINKER arch-darwin-c-debug/lib/libpetsc.3.021.0.dylib DSYMUTIL arch-darwin-c-debug/lib/libpetsc.3.021.0.dylib = Now to check if the libraries are working do: make PETSC_DIR=/Users/petsc/petsc.x PETSC_ARCH=arch-darwin-c-debug check = Running PETSc check examples to verify correct installation Using PETSC_DIR=/Users/petsc/petsc.x and PETSC_ARCH=arch-darwin-c-debug C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI processes C/C++ example src/snes/tutorials/ex19 run successfully with MUMPS Fortran example src/snes/tutorials/ex5f run successfully with 1 MPI process Completed PETSc check examples petsc@npro petsc.x % petsc@npro petsc.z % ./configure --download-openmpi=https://urldefense.us/v3/__https://download.open-mpi.org/release/open-mpi/v5.0/openmpi-5.0.3rc1.tar.bz2__;!!G_uCfscf7eWS!adsQx6TTtuIrMPz2ZorSv0iNPff5Fm5aFUi4i9n_E7v3GfAc8XCDtrlfVFyfPEgDFe4lKLL1XzkJ3c_97YoeukE$ --download-mumps --download-scalapack && make && make check DSYMUTIL arch-darwin-c-debug/lib/libpetsc.3.021.0.dylib = Now to check if the libraries are working do: make PETSC_DIR=/Users/petsc/petsc.z PETSC_ARCH=arch-darwin-c-debug check = Running PETSc check examples to verify correct installation Using PETSC_DIR=/Users/petsc/petsc.z and PETSC_ARCH=arch-darwin-c-debug C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI processes C/C++ example src/snes/tutorials/ex19 run successfully with MUMPS Fortran example src/snes/tutorials/ex5f run successfully with 1 MPI process Completed PETSc check examples petsc@npro petsc.z % [however parmmg and pastix are failing to build with openmpi] And I thought this worked for me yesterday - but I see failures now. ./configure --download-bison --download-chaco --download-ctetgen --download-eigen --download-fftw --download-hdf5 --download-hpddm --download-hwloc --download-hwloc-configure-arguments=--disable-opencl --download-hypre --download-libpng --download-metis --download-mmg --download-mpich --download-mpich-configure-arguments=--disable-opencl --download-mumps --download-netcdf --download-openblas --download-openblas-make-options="'USE_THREAD=0 USE_LOCKING=1 USE_OPENMP=0'" --download-parmmg --download-pastix --download-pnetcdf --download-pragmatic --download-ptscotch --download-scalapack --download-slepc --download-suitesparse --download-superlu_dist --download-tetgen --download-triangle --with-c2html=0 --with-debugging=1 --with-fortran-bindings=0 --with-shared-libraries=1 --with-x=0 --with-zlib --COPTFLAGS=-O0 --FOPTFLAGS=-O0 --LDFLAGS=-Wl,-ld_classic --with-clean Satish On Sat, 30 Mar 2024, Barry Smith wrote: > > Can you check the value of IRHSCOMP in the debugger? Using gdb as the > debugger may work better for this. > > Barry > > > > On Mar 30, 2024, at 3:46 AM, zeyu xia wrote: > > > > This Message Is From an External Sender > > This message came from outside your organization. > > Hi! Thanks for your reply. > > > > There still exist some problems, as seen in the files 'configure.log', > > 'make check3.txt', and 'debug.txt' in the attachment. Particularly, the > > file 'debug.txt' contains the output of bt command of lldb. > > > > Thanks for your attention. > > > > Best regards, > > Zeyu Xia > > > > > > Satish Balay mailto:ba...@mcs.anl.gov>> 于2024年3月30日周六 > > 02:52写道： > >> I'm able to reproduce this error on a slightly older xcode [but don't know > >> why this issue comes up] > >> > >> > Apple clang version 15.0.0 (clang-1500.1.0.2.5) > >> > >> Can you try using the additional configure options (along with > >> LDFLAGS=-Wl,-ld_classic) and see if it works? > >> > >> COPTFLAGS=-O0 FOPTFLAGS=-O0 > >> > >> Satish > >> > >> On Fri, 29 Mar 2024, zeyu xia wrote: > >> > >> > Hi! I am grateful for your prompt response. > >> > > >> > I follow your suggestions, and however, it still does not work. For the > >> > related information please find the files 'make check2.txt' and > >> > 'configure.log' in the attachment. > >> > > >> > If possible, please do me a favor again. Thanks for your patience. > >> > > >> > Best wishes, > >> > Zeyu Xia > >> > > >> > > >> > Satish Balay mailto:ba...@mcs.anl.gov>> > >> > 于2024年3月29日周五 23:48写道： > >> > > >> > > Could you: > >> > > > >> > > - reinstall brew after the xcode upgrade (not just update) > >> > >
Re: [petsc-users] ex19: Segmentation Violation when run with MUMPS on MacOS (arm64)
Can you check the value of IRHSCOMP in the debugger? Using gdb as the debugger may work better for this. Barry > On Mar 30, 2024, at 3:46 AM, zeyu xia wrote: > > This Message Is From an External Sender > This message came from outside your organization. > Hi! Thanks for your reply. > > There still exist some problems, as seen in the files 'configure.log', 'make > check3.txt', and 'debug.txt' in the attachment. Particularly, the file > 'debug.txt' contains the output of bt command of lldb. > > Thanks for your attention. > > Best regards, > Zeyu Xia > > > Satish Balay mailto:ba...@mcs.anl.gov>> 于2024年3月30日周六 > 02:52写道： >> I'm able to reproduce this error on a slightly older xcode [but don't know >> why this issue comes up] >> >> > Apple clang version 15.0.0 (clang-1500.1.0.2.5) >> >> Can you try using the additional configure options (along with >> LDFLAGS=-Wl,-ld_classic) and see if it works? >> >> COPTFLAGS=-O0 FOPTFLAGS=-O0 >> >> Satish >> >> On Fri, 29 Mar 2024, zeyu xia wrote: >> >> > Hi! I am grateful for your prompt response. >> > >> > I follow your suggestions, and however, it still does not work. For the >> > related information please find the files 'make check2.txt' and >> > 'configure.log' in the attachment. >> > >> > If possible, please do me a favor again. Thanks for your patience. >> > >> > Best wishes, >> > Zeyu Xia >> > >> > >> > Satish Balay mailto:ba...@mcs.anl.gov>> 于2024年3月29日周五 >> > 23:48写道： >> > >> > > Could you: >> > > >> > > - reinstall brew after the xcode upgrade (not just update) >> > > https://urldefense.us/v3/__https://petsc.org/main/install/install/*installing-on-macos__;Iw!!G_uCfscf7eWS!dGItos-D58VSJn4kOlKy2TEX-PWhflbWfNuM0zqhEXbGniD5S13iWCxgBmg9wYk4OrSwaP6jjzANIHN1ZHATKXE$ >> > > - not use --LDFLAGS=-Wl,-ld_classic >> > > >> > > And see if the problem persists? >> > > >> > > Satish >> > > >> > > On Fri, 29 Mar 2024, zeyu xia wrote: >> > > >> > > > Dear PETSc team: >> > > > >> > > > Recently I installed firedrake on MacOS (arm64) with the latest >> > > > Xcode, and there seems some error with mumps. I ran two times of the >> > > > command `make check`. The first time it just output wrong results, and >> > > the >> > > > second time it raised an error with Segmentation Violation. Please see >> > > the >> > > > files “make check.txt” and “configure.log” in the attachment. >> > > > >> > > > I will certainly be happy and grateful if you can take some >> > > > time >> > > to >> > > > deal with this problem. Thanks for your patience. >> > > > >> > > > Best wishes, >> > > > Zeyu Xia >> > > > >> > > >> > >
Re: [petsc-users] ex19: Segmentation Violation when run with MUMPS on MacOS (arm64)
I'm able to reproduce this error on a slightly older xcode [but don't know why this issue comes up] > Apple clang version 15.0.0 (clang-1500.1.0.2.5) Can you try using the additional configure options (along with LDFLAGS=-Wl,-ld_classic) and see if it works? COPTFLAGS=-O0 FOPTFLAGS=-O0 Satish On Fri, 29 Mar 2024, zeyu xia wrote: > Hi! I am grateful for your prompt response. > > I follow your suggestions, and however, it still does not work. For the > related information please find the files 'make check2.txt' and > 'configure.log' in the attachment. > > If possible, please do me a favor again. Thanks for your patience. > > Best wishes, > Zeyu Xia > > > Satish Balay 于2024年3月29日周五 23:48写道： > > > Could you: > > > > - reinstall brew after the xcode upgrade (not just update) > > https://urldefense.us/v3/__https://petsc.org/main/install/install/*installing-on-macos__;Iw!!G_uCfscf7eWS!dGItos-D58VSJn4kOlKy2TEX-PWhflbWfNuM0zqhEXbGniD5S13iWCxgBmg9wYk4OrSwaP6jjzANIHN1ZHATKXE$ > > > > - not use --LDFLAGS=-Wl,-ld_classic > > > > And see if the problem persists? > > > > Satish > > > > On Fri, 29 Mar 2024, zeyu xia wrote: > > > > > Dear PETSc team: > > > > > > Recently I installed firedrake on MacOS (arm64) with the latest > > > Xcode, and there seems some error with mumps. I ran two times of the > > > command `make check`. The first time it just output wrong results, and > > the > > > second time it raised an error with Segmentation Violation. Please see > > the > > > files “make check.txt” and “configure.log” in the attachment. > > > > > > I will certainly be happy and grateful if you can take some time > > to > > > deal with this problem. Thanks for your patience. > > > > > > Best wishes, > > > Zeyu Xia > > > > > >
Re: [petsc-users] ex19: Segmentation Violation when run with MUMPS on MacOS (arm64)
Could you: - reinstall brew after the xcode upgrade (not just update) https://urldefense.us/v3/__https://petsc.org/main/install/install/*installing-on-macos__;Iw!!G_uCfscf7eWS!fr-mLHdhIQgT2IBZhK9C2IQMUAmTmneTF38VsNLrywxooidf1uunovfx8qJrr8-Y73tICazCqyaZ6SJ6ca6JXnQ$ - not use --LDFLAGS=-Wl,-ld_classic And see if the problem persists? Satish On Fri, 29 Mar 2024, zeyu xia wrote: > Dear PETSc team: > > Recently I installed firedrake on MacOS (arm64) with the latest > Xcode, and there seems some error with mumps. I ran two times of the > command `make check`. The first time it just output wrong results, and the > second time it raised an error with Segmentation Violation. Please see the > files “make check.txt” and “configure.log” in the attachment. > > I will certainly be happy and grateful if you can take some time to > deal with this problem. Thanks for your patience. > > Best wishes, > Zeyu Xia >
