[petsc-users] Solver compilation with 64-bit version of PETSc under Windows 10 using Cygwin

Mon Jan 20 05:24:18 CST 2020

On Mon, Jan 20, 2020 at 5:43 AM Дмитрий Мельничук <
dmitry.melnichuk at geosteertech.com> wrote:

> Thank you so much for your assistance!
>
> As far as I have been able to find out, the errors * "Type mismatch in
> argument ‘ierr’"* have been successfully fixed.
> But execution of command "*make PETSC_DIR=/cygdrive/d/...
> PETSC_ARCH=arch-mswin-c-debug check" *leads to the appereance of
> Segmantation Violation error.
>
> I compiled PETSc with Microsoft MPI v10.
> Does it make sense to compile PETSc with another MPI implementation (such
> as MPICH) in order to resolve the issue?
>

Its not MPI. The problem appears to be your BLAS.

Barry, is this a mismatch with BLAS ints?

   Matt

> Error message:
> *Running test examples to verify correct installation*
> *Using
> PETSC_DIR=/cygdrive/d/Computational_geomechanics/installation/petsc-barry
> and PETSC_ARCH=arch-mswin-c-debug*
> *Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1 MPI
> process*
> *See http://www.mcs.anl.gov/petsc/documentation/faq.html
> <http://www.mcs.anl.gov/petsc/documentation/faq.html>*
> *C:/MPI/Bin/mpiexec.exe: error while loading shared libraries: ?: cannot
> open shared object file: No such file or directory*
> *Possible error running C/C++ src/snes/examples/tutorials/ex19 with 2 MPI
> processes*
> *See http://www.mcs.anl.gov/petsc/documentation/faq.html
> <http://www.mcs.anl.gov/petsc/documentation/faq.html>*
> *C:/MPI/Bin/mpiexec.exe: error while loading shared libraries: ?: cannot
> open shared object file: No such file or directory*
> *Possible error running Fortran example src/snes/examples/tutorials/ex5f
> with 1 MPI process*
> *See http://www.mcs.anl.gov/petsc/documentation/faq.html
> <http://www.mcs.anl.gov/petsc/documentation/faq.html>*
> *[0]PETSC ERROR:
> ------------------------------------------------------------------------*
> *[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range*
> *[0]PETSC ERROR: Try option -start_in_debugger or
> -on_error_attach_debugger*
> *[0]PETSC ERROR: or see
> https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
> <https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind>*
> *[0]PETSC ERROR: or try http://valgrind.org <http://valgrind.org> on
> GNU/linux and Apple Mac OS X to find memory corruption errors*
> *[0]PETSC ERROR: likely location of problem given in stack below*
> *[0]PETSC ERROR: ---------------------  Stack Frames
> ------------------------------------*
> *[0]PETSC ERROR: Note: The EXACT line numbers in the stack are not
> available,*
> *[0]PETSC ERROR:       INSTEAD the line number of the start of the
> function*
> *[0]PETSC ERROR:       is given.*
> *[0]PETSC ERROR: [0] VecNorm_Seq line 221
> /cygdrive/d/Computational_geomechanics/installation/petsc-barry/src/vec/vec/impls/seq/bvec2.c*
> *[0]PETSC ERROR: [0] VecNorm line 213
> /cygdrive/d/Computational_geomechanics/installation/petsc-barry/src/vec/vec/interface/rvector.c*
> *[0]PETSC ERROR: [0] SNESSolve_NEWTONLS line 144
> /cygdrive/d/Computational_geomechanics/installation/petsc-barry/src/snes/impls/ls/ls.c*
> *[0]PETSC ERROR: [0] SNESSolve line 4375
> /cygdrive/d/Computational_geomechanics/installation/petsc-barry/src/snes/interface/snes.c*
> *[0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------*
> *[0]PETSC ERROR: Signal received*
> *[0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html
> <https://www.mcs.anl.gov/petsc/documentation/faq.html> for trouble
> shooting.*
> *[0]PETSC ERROR: Petsc Development GIT revision: unknown  GIT Date:
> unknown*
> *[0]PETSC ERROR: ./ex5f on a arch-mswin-c-debug named DESKTOP-R88IMOB by
> useruser Mon Jan 20 09:18:34 2020*
> *[0]PETSC ERROR: Configure options --with-cc=x86_64-w64-mingw32-gcc
> --with-cxx=x86_64-w64-mingw32-g++ --with-fc=x86_64-w64-mingw32-gfortran
> --with-mpi-include=/cygdrive/c/MPISDK/Include
> --with-mpi-lib=/cygdrive/c/MPISDK/Lib/libmsmpi.a
> --with-mpi-mpiexec=/cygdrive/c/MPI/Bin/mpiexec.exe --with-debugging=yes
> -CFLAGS=-O2 -CXXFLAGS=-O2 -FFLAGS="-O2 -static-libgfortran -static
> -lpthread -fno-range-check -fdefault-integer-8" --download-fblaslapack
> --with-shared-libraries=no --with-64-bit-indices --force*
> *[0]PETSC ERROR: #1 User provided function() line 0 in  unknown file*
>
> *job aborted:*
> *[ranks] message*
>
> *[0] application aborted*
> *aborting MPI_COMM_WORLD (comm=0x44000000), error 50152059, comm rank 0*
>
> *---- error analysis -----*
>
> *[0] on DESKTOP-R88IMOB*
> *./ex5f aborted the job. abort code 50152059*
>
> *---- error analysis -----*
> *Completed test examples*
>
> Kind regards,
> Dmitry Melnichuk
>
> 19.01.2020, 07:47, "Smith, Barry F." <bsmith at mcs.anl.gov>:
>
>
>    Dmitry,
>
>    I have completed and tested the branch
> barry/2020-01-15/support-default-integer-8 it is undergoing testing now
> https://gitlab.com/petsc/petsc/merge_requests/2456
>
>    Please give it a try. Note that MPI has no support for integer
> promotion so YOU must insure that any MPI calls from Fortran pass 4 byte
> integers not promoted 8 byte integers.
>
>    I have tested it with recent versions of MPICH and OpenMPI, it is
> fragile at compile time and may fail to compile with different versions of
> MPI.
>
>     Good luck,
>
>    Barry
>
>     I do not recommend this approach for integer promotion in Fortran.
> Just blindly promoting all integers can often lead to problems. I recommend
> using the kind mechanism of
> Fortran to insure that each variable is the type you want, you can
> recompile with different options to promote the kind declared variables you
> wish. Of course this is more intrusive and requires changes to the Fortran
> code.
>
>
>  On Jan 15, 2020, at 7:00 AM, Дмитрий Мельничук <
> dmitry.melnichuk at geosteertech.com> wrote:
>
>  Hello all!
>
>  At present time I need to compile solver called Defmod (
> https://bitbucket.org/stali/defmod/wiki/Home), which is written in
> Fortran 95.
>  Defmod uses PETSc for solving linear algebra system.
>  Solver compilation with 32-bit version of PETSc does not cause any
> problem.
>  But solver compilation with 64-bit version of PETSc produces an error
> with size of ierr PETSc variable.
>
>  1. For example, consider the following statements written in Fortran:
>
>
>  PetscErrorCode :: ierr_m
>  PetscInt :: ierr
>  ...
>  ...
>  call VecDuplicate(Vec_U,Vec_Um,ierr)
>  call VecCopy(Vec_U,Vec_Um,ierr)
>  call VecGetLocalSize(Vec_U,j,ierr)
>  call VecGetOwnershipRange(Vec_U,j1,j2,ierr_m)
>
>
>  As can be seen first three subroutunes require ierr to be size of
> INTEGER(8), while the last subroutine (VecGetOwnershipRange) requires ierr
> to be size of INTEGER(4).
>  Using the same integer format gives an error:
>
>  There is no specific subroutine for the generic ‘vecgetownershiprange’ at
> (1)
>
>  2. Another example is:
>
>
>  call MatAssemblyBegin(Mat_K,Mat_Final_Assembly,ierr)
>  CHKERRA(ierr)
>  call MatAssemblyEnd(Mat_K,Mat_Final_Assembly,ierr)
>
>
>  I am not able to define an appropriate size if ierr in CHKERRA(ierr). If
> I choose INTEGER(8), the error "Type mismatch in argument ‘ierr’ at (1);
> passed INTEGER(8) to INTEGER(4)" occurs.
>  If I define ierr as INTEGER(4), the error "Type mismatch in argument
> ‘ierr’ at (1); passed INTEGER(4) to INTEGER(8)" appears.
>
>
>  3. If I change the sizes of ierr vaiables as error messages require, the
> compilation completed successfully, but an error occurs when calculating
> the RHS vector with following message:
>
>  [0]PETSC ERROR: Out of range index value -4 cannot be negative
>
>
>  Command to configure 32-bit version of PETSc under Windows 10 using
> Cygwin:
>  ./configure --with-cc=x86_64-w64-mingw32-gcc
> --with-cxx=x86_64-w64-mingw32-g++ --with-fc=x86_64-w64-mingw32-gfortran
> --download-fblaslapack --with-mpi-include=/cygdrive/c/MPISDK/Include
> --with-mpi-lib=/cygdrive/c/MPISDK/Lib/libmsmpi.a
> --with-mpi-mpiexec=/cygdrive/c/MPI/Bin/mpiexec.exe --with-debugging=yes
> -CFLAGS='-O2' -CXXFLAGS='-O2' -FFLAGS='-O2 -static-libgfortran -static
> -lpthread -fno-range-check' --with-shared-libraries=no
>
>  Command to configure 64-bit version of PETSc under Windows 10 using
> Cygwin:
>  ./configure --with-cc=x86_64-w64-mingw32-gcc
> --with-cxx=x86_64-w64-mingw32-g++ --with-fc=x86_64-w64-mingw32-gfortran
> --download-fblaslapack --with-mpi-include=/cygdrive/c/MPISDK/Include
> --with-mpi-lib=/cygdrive/c/MPISDK/Lib/libmsmpi.a
> --with-mpi-mpiexec=/cygdrive/c/MPI/Bin/mpiexec.exe --with-debugging=yes
> -CFLAGS='-O2' -CXXFLAGS='-O2' -FFLAGS='-O2 -static-libgfortran -static
> -lpthread -fno-range-check -fdefault-integer-8' --with-shared-libraries=no
> --with-64-bit-indices --known-64-bit-blas-indices
>
>
>  Kind regards,
>  Dmitry Melnichuk
>
>
>
>

-- 
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/>
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