[petsc-users] R: PETSc and Windows 10

[Paolo Lampitella]

Dear Pierre,

thanks again for your time

I guess there is no way for me to use the toolchain you are using (I don’t remember having any choice on which version of MSYS or GCC I could install)

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 20:01
A: Matthew Knepley<mailto:knepley at gmail.com>
Cc: Paolo Lampitella<mailto:paololampitella at hotmail.com>; petsc-users<mailto:petsc-users at mcs.anl.gov>
Oggetto: Re: [petsc-users] PETSc and Windows 10




On 29 Jun 2020, at 7:47 PM, Matthew Knepley <knepley at gmail.com<mailto:knepley at gmail.com>> wrote:

On Mon, Jun 29, 2020 at 1:35 PM Paolo Lampitella <paololampitella at hotmail.com<mailto: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?

Sorry, I’m slow. You are right. Our workers use gcc 9, everything is fine, but I see on my VM which I updated that I use gcc 10 and had to disable Fortran, I guess the MUMPS run I showcased was with a prior PETSc build.
I’ll try to resolve this and will keep you posted.
They really caught a lot of people off guard with gfortran 10…

Thanks,
Pierre


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<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




--
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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