[petsc-users] R: PETSc and Windows 10
Matthew Knepley
knepley at gmail.com
Mon Jun 29 12:47:15 CDT 2020
On Mon, Jun 29, 2020 at 1:35 PM Paolo Lampitella <
paololampitella at hotmail.com> wrote:
> Dear Pierre, sorry to bother you, but I already have some issues. What I
> did:
>
>
>
> - pacman -R mingw-w64-x86_64-python mingw-w64-x86_64-gdb (is gdb also
> troublesome?)
> - Followed points 6 and 7 at
> https://doc.freefem.org/introduction/installation.html#compilation-on-windows
>
> I first got a warning on the configure at point 6, as –disable-hips is not
> recognized. Then, on make ‘petsc-slepc’ of point 7 (no SUDO=sudo flag was
> necessary) I got to this point:
>
>
>
> tar xzf ../pkg/petsc-lite-3.13.0.tar.gz
>
> patch -p1 < petsc-suitesparse.patch
>
> patching file
> petsc-3.13.0/config/BuildSystem/config/packages/SuiteSparse.py
>
> touch petsc-3.13.0/tag-tar
>
> cd petsc-3.13.0 && ./configure MAKEFLAGS='' \
>
> --prefix=/home/paolo/freefem/ff-petsc//r \
>
> --with-debugging=0 COPTFLAGS='-O3 -mtune=generic' CXXOPTFLAGS='-O3
> -mtune=generic' FOPTFLAGS='-O3 -mtune=generic' --with-cxx-dialect=C++11
> --with-ssl=0 --with-x=0 --with-fortran-bindings=0 --with-shared-libraries=0
> --with-cc='gcc' --with-cxx='g++' --with-fc='gfortran'
> CXXFLAGS='-fno-stack-protector' CFLAGS='-fno-stack-protector'
> --with-scalar-type=real --with-mpi-lib='/c/Windows/System32/msmpi.dll'
> --with-mpi-include='/home/paolo/FreeFem-sources/3rdparty/include/msmpi'
> --with-mpiexec='/C/Program\ Files/Microsoft\ MPI/Bin/mpiexec'
> --with-blaslapack-include=''
> --with-blaslapack-lib='/mingw64/bin/libopenblas.dll' --download-scalapack
> --download-metis --download-ptscotch --download-mumps --download-hypre
> --download-parmetis --download-superlu --download-suitesparse
> --download-tetgen --download-slepc '--download-metis-cmake-arguments=-G
> "MSYS Makefiles"' '--download-parmetis-cmake-arguments=-G "MSYS Makefiles"'
> '--download-superlu-cmake-arguments=-G "MSYS Makefiles"'
> '--download-hypre-configure-arguments=--build=x86_64-linux-gnu
> --host=x86_64-linux-gnu' PETSC_ARCH=fr
>
>
> ===============================================================================
>
> Configuring PETSc to compile on your system
>
>
> ===============================================================================
>
> TESTING: FortranMPICheck from
> config.packages.MPI(config/BuildSystem/config/pack*******************************************************************************
>
> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for
> details):
>
>
> -------------------------------------------------------------------------------
>
> Fortran error! mpi_init() could not be located!
>
>
> *******************************************************************************
>
>
>
> make: *** [Makefile:210: petsc-3.13.0/tag-conf-real] Errore 1
>
>
>
> Note that I didn’t add anything to any PATH variable, because this is not
> mentioned in your documentation.
>
>
>
> On a side note, this is the same error I got when trying to build PETSc in
> Cygwin with the default OpenMPI available in Cygwin.
>
>
>
> I am attaching the configure.log… it seems to me that the error comes from
> the configure trying to include the mpif.h in your folder and not using the
> -fallow-invalid-boz flag that I had to use, for example, to compile mpi.f90
> into mpi.mod
>
>
>
> But I’m not sure why this is happening
>
Pierre,
Could this be due to gcc 10?
Executing: gfortran -c -o /tmp/petsc-ur0cff6a/config.libraries/conftest.o
-I/tmp/petsc-ur0cff6a/config.compilers
-I/tmp/petsc-ur0cff6a/config.setCompilers
-I/tmp/petsc-ur0cff6a/config.compilersFortran
-I/tmp/petsc-ur0cff6a/config.libraries -Wall -ffree-line-length-0
-Wno-unused-dummy-argument -O3 -mtune=generic
-I/home/paolo/FreeFem-sources/3rdparty/include/msmpi
/tmp/petsc-ur0cff6a/config.libraries/conftest.F90
Possible ERROR while running compiler: exit code 1
stderr:
C:/msys64/home/paolo/FreeFem-sources/3rdparty/include/msmpi/mpif.h:227:36:
227 | PARAMETER (MPI_DATATYPE_NULL=z'0c000000')
| 1
Error: BOZ literal constant at (1) is neither a data-stmt-constant nor an
actual argument to INT, REAL, DBLE, or CMPLX intrinsic function [see
'-fno-allow-invalid-boz']
C:/msys64/home/paolo/FreeFem-sources/3rdparty/include/msmpi/mpif.h:303:27:
303 | PARAMETER (MPI_CHAR=z'4c000101')
| 1
Error: BOZ literal constant at (1) is neither a data-stmt-constant nor an
actual argument to INT, REAL, DBLE, or CMPLX intrinsic function [see
'-fno-allow-invalid-boz']
C:/msys64/home/paolo/FreeFem-sources/3rdparty/include/msmpi/mpif.h:305:36:
305 | PARAMETER (MPI_UNSIGNED_CHAR=z'4c000102')
| 1
Thanks,
Matt
> Thanks
>
>
>
> Paolo
>
>
>
> Inviato da Posta <https://go.microsoft.com/fwlink/?LinkId=550986> per
> Windows 10
>
>
>
> *Da: *Pierre Jolivet <pierre.jolivet at enseeiht.fr>
> *Inviato: *lunedì 29 giugno 2020 18:34
> *A: *Paolo Lampitella <paololampitella at hotmail.com>
> *Cc: *Satish Balay <balay at mcs.anl.gov>; petsc-users
> <petsc-users at mcs.anl.gov>
> *Oggetto: *Re: [petsc-users] PETSc and Windows 10
>
>
>
>
>
>
>
> On 29 Jun 2020, at 6:27 PM, Paolo Lampitella <paololampitella at hotmail.com>
> wrote:
>
>
>
> I think I made the first step of having mingw64 from msys2 working with
> ms-mpi.
>
>
>
> I found that the issue I was having was related to:
>
>
>
> https://gcc.gnu.org/bugzilla/show_bug.cgi?id=91556
>
>
>
> and, probably (but impossible to check now), I was using an msys2 and/or
> mingw mpi package before this fix:
>
>
>
>
> https://github.com/msys2/MINGW-packages/commit/11b4cff3d2ec7411037b692b0ad5a9f3e9b9978d#diff-eac59989e3096be97d940c8f47b50fba
>
>
>
> Admittedly, I never used gcc 10 before on any machine. Still, I feel that
> reporting that sort of error in that way is,
>
> at least, misleading (I would have preferred the initial implementation as
> mentioned in the gcc bug track).
>
>
>
> A second thing that I was not used to, and made me more uncertain of the
> procedure I was following, is having to compile myself the mpi module.
> There are several version of this out there, but I decided to stick with
> this one:
>
>
>
> https://www.scivision.dev/windows-mpi-msys2/
>
>
>
> even if there seems to be no need to include -fno-range-check and the
> current mpi.f90 version is different from the mpif.h as reported here:
>
>
>
> https://github.com/microsoft/Microsoft-MPI/issues/33
>
>
>
> which, to me, are both signs of lack of attention on the fortran side by
> those that maintain this thing.
>
>
>
> In summary, this is the procedure I followed so far (on a 64 bit machine
> with Windows 10):
>
>
>
> - Install MSYS2 from https://www.msys2.org/ and just follow the
> install wizard
> - Open the MSYS2 terminal and execute: pacman -Syuu
> - Close the terminal when asked and reopen it
> - Keep executing ‘pacman -Syuu’ until nothing else needs to be updated
> - Close the MSYS2 terminal and reopen it (I guess because was in
> paranoid mode), then install packages with:
>
>
>
> pacman -S base-devel git gcc gcc-fortran bsdcpio lndir pax-git unzip
>
> pacman -S mingw-w64-x86_64-toolchain
>
> pacman -S mingw-w64-x86_64-msmpi
>
> pacman -S mingw-w64-x86_64-cmake
>
> pacman -S mingw-w64-x86_64-freeglut
>
> pacman -S mingw-w64-x86_64-gsl
>
> pacman -S mingw-w64-x86_64-libmicroutils
>
> pacman -S mingw-w64-x86_64-hdf5
>
> pacman -S mingw-w64-x86_64-openblas
>
> pacman -S mingw-w64-x86_64-arpack
>
> pacman -S mingw-w64-x86_64-jq
>
>
>
> This set should include all the libraries mentioned by Pierre and/or used
> by his Jenkins, as the final scope here is to have PETSc and dependencies
> working. But I think that for pure MPI one could stop to msmpi (even,
> maybe, just install msmpi and have the dependencies figured out by pacman).
> Honestly, I don’t remember the exact order I used to install the packages,
> but this should not affect things. Also, as I was still in paranoid mode, I
> kept executing ‘pacman -Syuu’ after each package was installed. After this,
> close the MSYS2 terminal.
>
>
>
> - Open the MINGW64 terminal and create the .mod file out of the
> mpi.f90 file, as mentioned here
> https://www.scivision.dev/windows-mpi-msys2/, with:
>
>
>
> cd /mingw64/include
>
> gfortran mpif90 -c -fno-range-check -fallow-invalid-boz
>
>
>
> Ah, yes, that’s new to gfortran 10 (we use gfortran 9 on our workers),
> which is now what’s ship with MSYS2 (we haven’t updated yet). Sorry that I
> forgot about that.
>
>
>
> This is needed to ‘USE mpi’ (as opposed to INCLUDE ‘mpif.h’)
>
>
>
> - Install the latest MS-MPI (both sdk and setup) from
> https://www.microsoft.com/en-us/download/details.aspx?id=100593
>
>
>
> At this point I’ve been able to compile (using the MINGW64 terminal)
> different mpi test programs and they run as expected in the classical
> Windows prompt. I added this function to my .bashrc in MSYS2 in order to
> easily copy the required dependencies out of MSYS:
>
>
>
> function copydep() { ldd $1 | grep "=> /$2" | awk '{print $3}' | xargs -I
> '{}' cp -v '{}' .; }
>
>
>
> which can be used, with the MINGW64 terminal, by navigating to the folder
> where the final executable, say, my.exe, resides (even if under a Windows
> path) and executing:
>
>
>
> copydep my.exe mingw64
>
>
>
> This, of course, must be done before actually trying to execute the .exe
> in the windows cmd prompt.
>
>
>
> Hopefully, I should now be able to follow Pierre’s instructions for PETSc
> (but first I wanna give a try to the system python before removing it)
>
>
>
> Looks like the hard part is over. It’s usually easier to deal with
> ./configure issues.
>
> If you have weird errors like “incomplete Cygwin install” or whatever,
> this is the kind of issues I was referring to earlier.
>
> In that case, what I’d suggest is just, as before:
>
> pacman -R mingw-w64-x86_64-python mingw-w64-x86_64-gdb
>
> pacman -S python
>
>
>
> Thanks,
>
> Pierre
>
>
>
> Thanks
>
>
>
> Paolo
>
>
>
>
>
--
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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