Send us $PETSC_ARCH/include/petscconf.h
Thanks, Matt On Mon, May 15, 2023 at 12:49 PM Vanella, Marcos (Fed) < marcos.vane...@nist.gov> wrote: > Hi Matt, I configured the lib like this: > > $ ./configure --with-blaslapack-dir=/opt/intel/oneapi/mkl/2022.2.1 > --with-debugging=0 --with-shared-libraries=0 --download-make > > and compiled. I still get some check segfault error. See below: > > $ make PETSC_DIR=/Users/mnv/Documents/Software/petsc-3.19.1 > PETSC_ARCH=arch-darwin-c-opt check > Running check examples to verify correct installation > Using PETSC_DIR=/Users/mnv/Documents/Software/petsc-3.19.1 and > PETSC_ARCH=arch-darwin-c-opt > *******************Error detected during compile or > link!******************* > See https://petsc.org/release/faq/ > /Users/mnv/Documents/Software/petsc-3.19.1/src/snes/tutorials ex19 > > ********************************************************************************* > mpicc -Wl,-bind_at_load -Wl,-multiply_defined,suppress > -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs > -Wl,-search_paths_first -Wl,-no_compact_unwind -fPIC -wd1572 > -Wno-unknown-pragmas -g -O3 > -I/Users/mnv/Documents/Software/petsc-3.19.1/include > -I/Users/mnv/Documents/Software/petsc-3.19.1/arch-darwin-c-opt/include > -I/opt/X11/include -std=c99 ex19.c > -L/Users/mnv/Documents/Software/petsc-3.19.1/arch-darwin-c-opt/lib > -Wl,-rpath,/opt/intel/oneapi/mkl/2022.2.1/lib > -L/opt/intel/oneapi/mkl/2022.2.1/lib -Wl,-rpath,/opt/X11/lib -L/opt/X11/lib > -L/opt/openmpi414_oneapi22u3/lib > -Wl,-rpath,/opt/intel/oneapi/compiler/2022.2.1/mac/compiler/lib > -L/opt/intel/oneapi/tbb/2021.7.1/lib -L/opt/intel/oneapi/ippcp/2021.6.2/lib > -L/opt/intel/oneapi/ipp/2021.6.2/lib > -L/opt/intel/oneapi/dnnl/2022.2.1/cpu_iomp/lib > -L/opt/intel/oneapi/dal/2021.7.1/lib > -L/opt/intel/oneapi/compiler/2022.2.1/mac/compiler/lib > -L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib > -Wl,-rpath,/opt/intel/oneapi/compiler/2022.2.1/mac/bin/intel64/../../compiler/lib > -L/opt/intel/oneapi/compiler/2022.2.1/mac/bin/intel64/../../compiler/lib > -Wl,-rpath,/Library/Developer/CommandLineTools/usr/lib/clang/14.0.3/lib/darwin > -L/Library/Developer/CommandLineTools/usr/lib/clang/14.0.3/lib/darwin > -lpetsc -lmkl_intel_lp64 -lmkl_core -lmkl_sequential -lpthread -lX11 > -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lopen-rte > -lopen-pal -limf -lm -lz -lifport -lifcoremt -lsvml -lipgo -lirc -lpthread > -lclang_rt.osx -lmpi -lopen-rte -lopen-pal -limf -lm -lz -lsvml -lirng > -lc++ -lipgo -ldecimal -lirc -lclang_rt.osx -lmpi -lopen-rte -lopen-pal > -limf -lm -lz -lsvml -lirng -lc++ -lipgo -ldecimal -lirc -lclang_rt.osx -o > ex19 > icc: remark #10441: The Intel(R) C++ Compiler Classic (ICC) is deprecated > and will be removed from product release in the second half of 2023. The > Intel(R) oneAPI DPC++/C++ Compiler (ICX) is the recommended compiler moving > forward. Please transition to use this compiler. Use '-diag-disable=10441' > to disable this message. > In file included from > /Users/mnv/Documents/Software/petsc-3.19.1/include/petscsys.h(44), > from > /Users/mnv/Documents/Software/petsc-3.19.1/include/petscvec.h(9), > from > /Users/mnv/Documents/Software/petsc-3.19.1/include/petscmat.h(7), > from > /Users/mnv/Documents/Software/petsc-3.19.1/include/petscpc.h(7), > from > /Users/mnv/Documents/Software/petsc-3.19.1/include/petscksp.h(7), > from > /Users/mnv/Documents/Software/petsc-3.19.1/include/petscsnes.h(7), > from ex19.c(68): > /Users/mnv/Documents/Software/petsc-3.19.1/include/petscsystypes.h(68): > warning #2621: attribute "warn_unused_result" does not apply here > PETSC_ERROR_CODE_TYPEDEF enum PETSC_ERROR_CODE_NODISCARD { > ^ > > Possible error running C/C++ src/snes/tutorials/ex19 with 1 MPI process > See https://petsc.org/release/faq/ > [excess:37807] *** Process received signal *** > [excess:37807] Signal: Segmentation fault: 11 (11) > [excess:37807] Signal code: Address not mapped (1) > [excess:37807] Failing at address: 0x7f > [excess:37807] *** End of error message *** > -------------------------------------------------------------------------- > Primary job terminated normally, but 1 process returned > a non-zero exit code. Per user-direction, the job has been aborted. > -------------------------------------------------------------------------- > -------------------------------------------------------------------------- > mpiexec noticed that process rank 0 with PID 0 on node excess exited on > signal 11 (Segmentation fault: 11). > -------------------------------------------------------------------------- > Possible error running C/C++ src/snes/tutorials/ex19 with 2 MPI processes > See https://petsc.org/release/faq/ > [excess:37831] *** Process received signal *** > [excess:37831] Signal: Segmentation fault: 11 (11) > [excess:37831] Signal code: Address not mapped (1) > [excess:37831] Failing at address: 0x7f > [excess:37831] *** End of error message *** > [excess:37832] *** Process received signal *** > [excess:37832] Signal: Segmentation fault: 11 (11) > [excess:37832] Signal code: Address not mapped (1) > [excess:37832] Failing at address: 0x7f > [excess:37832] *** End of error message *** > -------------------------------------------------------------------------- > Primary job terminated normally, but 1 process returned > a non-zero exit code. Per user-direction, the job has been aborted. > -------------------------------------------------------------------------- > -------------------------------------------------------------------------- > mpiexec noticed that process rank 1 with PID 0 on node excess exited on > signal 11 (Segmentation fault: 11). > -------------------------------------------------------------------------- > Possible error running Fortran example src/snes/tutorials/ex5f with 1 MPI > process > See https://petsc.org/release/faq/ > forrtl: severe (174): SIGSEGV, segmentation fault occurred > Image PC Routine Line Source > > libifcoremt.dylib 000000010B7F7FE4 for__signal_handl Unknown Unknown > libsystem_platfor 00007FF8024C25ED _sigtramp Unknown Unknown > ex5f 00000001087AFA38 PetscGetArchType Unknown Unknown > ex5f 000000010887913B PetscErrorPrintfI Unknown Unknown > ex5f 000000010878D227 PetscInitialize_C Unknown Unknown > ex5f 000000010879D289 petscinitializef_ Unknown Unknown > ex5f 0000000108713C09 petscsys_mp_petsc Unknown Unknown > ex5f 0000000108710B5D MAIN__ Unknown Unknown > ex5f 0000000108710AEE main Unknown Unknown > dyld 00007FF80213B41F start Unknown Unknown > -------------------------------------------------------------------------- > Primary job terminated normally, but 1 process returned > a non-zero exit code. Per user-direction, the job has been aborted. > -------------------------------------------------------------------------- > -------------------------------------------------------------------------- > mpiexec detected that one or more processes exited with non-zero status, > thus causing > the job to be terminated. The first process to do so was: > > Process name: [[48108,1],0] > Exit code: 174 > -------------------------------------------------------------------------- > Completed test examples > Error while running make check > make[1]: *** [check] Error 1 > make: *** [check] Error 2 > > ------------------------------ > *From:* Vanella, Marcos (Fed) <marcos.vane...@nist.gov> > *Sent:* Monday, May 15, 2023 12:20 PM > *To:* Matthew Knepley <knep...@gmail.com> > *Cc:* petsc-users@mcs.anl.gov <petsc-users@mcs.anl.gov> > *Subject:* Re: [petsc-users] Compiling PETSC with Intel OneAPI compilers > and OpenMPI > > Thank you Matt I'll try this and let you know. > Marcos > ------------------------------ > *From:* Matthew Knepley <knep...@gmail.com> > *Sent:* Monday, May 15, 2023 12:08 PM > *To:* Vanella, Marcos (Fed) <marcos.vane...@nist.gov> > *Cc:* petsc-users@mcs.anl.gov <petsc-users@mcs.anl.gov> > *Subject:* Re: [petsc-users] Compiling PETSC with Intel OneAPI compilers > and OpenMPI > > On Mon, May 15, 2023 at 11:19 AM Vanella, Marcos (Fed) via petsc-users < > petsc-users@mcs.anl.gov> wrote: > > Hello, I'm trying to compile the PETSc library version 3.19.1 with OpenMPI > 4.1.4 and the OneAPI 2022 Update 2 Intel Compiler suite on a Mac with OSX > Ventura 13.3.1. > I can compile PETSc in debug mode with this configure and make lines. I > can run the PETSC tests, which seem fine. > When I compile the library in optimized mode, either using -O3 or O1, for > example configuring with: > > > I hate to yell "compiler bug" when this happens, but it sure seems like > one. Can you just use > > --with-debugging=0 > > without the custom COPTFLAGS, CXXOPTFLAGS, FOPTFLAGS? If that works, it is > almost > certainly a compiler bug. If not, then we can go in the debugger and see > what is failing. > > Thanks, > > Matt > > > $ ./configure --prefix=/opt/petsc-oneapi22u3 > --with-blaslapack-dir=/opt/intel/oneapi/mkl/2022.2.1 COPTFLAGS='-m64 -O1 -g > -diag-disable=10441' CXXOPTFLAGS='-m64 -O1 -g -diag-disable=10441' > FOPTFLAGS='-m64 -O1 -g' LDFLAGS='-m64' --with-debugging=0 > --with-shared-libraries=0 --download-make > > and using mpicc (icc), mpif90 (ifort) from Open MPI, the static lib > compiles. Yet, I see right off the bat this segfault error in the first > PETSc example: > > $ make PETSC_DIR=/Users/mnv/Documents/Software/petsc-3.19.1 > PETSC_ARCH=arch-darwin-c-opt test > /Users/mnv/Documents/Software/petsc-3.19.1/arch-darwin-c-opt/bin/make > --no-print-directory -f > /Users/mnv/Documents/Software/petsc-3.19.1/gmakefile.test > PETSC_ARCH=arch-darwin-c-opt > PETSC_DIR=/Users/mnv/Documents/Software/petsc-3.19.1 test > /opt/intel/oneapi/intelpython/latest/bin/python3 > /Users/mnv/Documents/Software/petsc-3.19.1/config/gmakegentest.py > --petsc-dir=/Users/mnv/Documents/Software/petsc-3.19.1 > --petsc-arch=arch-darwin-c-opt --testdir=./arch-darwin-c-opt/tests > Using MAKEFLAGS: --no-print-directory -- PETSC_ARCH=arch-darwin-c-opt > PETSC_DIR=/Users/mnv/Documents/Software/petsc-3.19.1 > CC arch-darwin-c-opt/tests/sys/classes/draw/tests/ex1.o > In file included from > /Users/mnv/Documents/Software/petsc-3.19.1/include/petscsys.h(44), > from > /Users/mnv/Documents/Software/petsc-3.19.1/src/sys/classes/draw/tests/ex1.c(4): > /Users/mnv/Documents/Software/petsc-3.19.1/include/petscsystypes.h(68): > warning #2621: attribute "warn_unused_result" does not apply here > PETSC_ERROR_CODE_TYPEDEF enum PETSC_ERROR_CODE_NODISCARD { > ^ > > CLINKER arch-darwin-c-opt/tests/sys/classes/draw/tests/ex1 > TEST > arch-darwin-c-opt/tests/counts/sys_classes_draw_tests-ex1_1.counts > not ok sys_classes_draw_tests-ex1_1 *# Error code: 139* > *# [excess:98681] *** Process received signal **** > *# [excess:98681] Signal: Segmentation fault: 11 (11)* > *# [excess:98681] Signal code: Address not mapped (1)* > *# [excess:98681] Failing at address: 0x7f* > *# [excess:98681] *** End of error message **** > # > -------------------------------------------------------------------------- > # Primary job terminated normally, but 1 process returned > # a non-zero exit code. Per user-direction, the job has been aborted. > # > -------------------------------------------------------------------------- > # > -------------------------------------------------------------------------- > # mpiexec noticed that process rank 0 with PID 0 on node excess exited on > signal 11 (Segmentation fault: 11). > # > -------------------------------------------------------------------------- > ok sys_classes_draw_tests-ex1_1 # SKIP Command failed so no diff > > I see the same segfault error in all PETSc examples. > Any help is mostly appreciated, I'm starting to work with PETSc. Our plan > is to use the linear solver from PETSc for the Poisson equation on our > numerical scheme and test this on a GPU cluster. So also, any guideline on > how to interface PETSc with a fortran code and personal experience is also > most appreciated! > > Marcos > > > > > > -- > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > https://www.cse.buffalo.edu/~knepley/ > <http://www.cse.buffalo.edu/~knepley/> > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>