[petsc-users] R: PETSc and Windows 10

Mon Jun 29 12:34:31 CDT 2020

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

Thanks

Paolo

Inviato da Posta<https://go.microsoft.com/fwlink/?LinkId=550986> per Windows 10

Da: Pierre Jolivet<mailto:pierre.jolivet at enseeiht.fr>
Inviato: lunedì 29 giugno 2020 18:34
A: Paolo Lampitella<mailto:paololampitella at hotmail.com>
Cc: Satish Balay<mailto:balay at mcs.anl.gov>; petsc-users<mailto: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<mailto: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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20200629/db5951c7/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: configure.log
Type: application/octet-stream
Size: 662202 bytes
Desc: configure.log
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20200629/db5951c7/attachment-0001.obj>