Hello Paolo, > On 5 Jul 2020, at 1:15 PM, Paolo Lampitella <paololampite...@hotmail.com> > wrote: > > Dear all, > > I just want to update you on my journey to PETSc compilation in Windows under > MSYS2+MINGW64 > > Unfortunately, I haven’t been able to compile petsc-slepc trough Freefem but, > as my final goal required also Fortran bindings (but I only needed blas, > lapack, metis and hypre), I decided to follow my own route using the useful > information from Pierre. > > I started by installing MPI from > https://www.microsoft.com/en-us/download/details.aspx?id=100593 > <https://www.microsoft.com/en-us/download/details.aspx?id=100593>. I don’t > think the SDK is actually needed in my specific workflow, but I installed it > as well together with mpisetup. > Then I installed MSYS2 just following the wizard. Opened the MSYS2 terminal > and updated with pacman -Syuu, closed if asked, reopened it and used again > pacman -Syuu several times until no more updates were available. Closed it > and opened it back. > Under the MSYS2 terminal installed just the following packages: > > pacman -S base-devel git gcc gcc-fortran > pacman -S mingw-w64-x86_64-toolchain > pacman -S mingw-w64-x86_64-cmake > pacman -S mingw-w64-x86_64-msmpi > > Closed the MSYS2 terminal and opened the MINGW64 one, went to > /mingw64/include and compiled my mpi module following > https://www.scivision.dev/windows-mpi-msys2/ > <https://www.scivision.dev/windows-mpi-msys2/>: > > gfortran -c mpi.f90 -fno-range-check -fallow-invalid-boz > > However, I will keep an eye on the MS-MPI GitHub repository because the > fortran side seems to be far from perfect. > > Then I downloaded the 3.13.3 version of petsc and configured it, still under > the MINGW64 terminal, with the following command: > > /usr/bin/python ./configure --prefix=/home/paolo/petsc --with-ar=/usr/bin/ar > --with-shared-libraries=0 --with-debugging=0 --with-windows-graphics=0 > --with-x=0 > COPTFLAGS="-O3 -mtune=native" > CXXOPTFLAGS="-O3 -mtune=native" > FOPTFLAGS="-O3 -mtune=native" > FFLAGS=-fallow-invalid-boz > --with-mpiexec="/C/Program\ Files/Microsoft\ MPI/Bin/mpiexec" > --download-fblaslapack --download-metis --download-hypre > --download-metis-cmake-arguments='-G "MSYS Makefiles"' > --download-hypre-configure-arguments="--build=x86_64-linux-gnu > --host=x86_64-linux-gnu" > > Note that I just bypassed uninstalling python in mingw64 (which doesn’t work) > by using /usr/bin/python and that, as opposed to Pierre, I needed to also use > the MSYS2 archiver (/usr/bin/ar) as opposed to the mingw64 one > (/mingw64/bin/ar that shows up in the Pierre configure) as also mentioned > here > http://hillyuan.blogspot.com/2017/11/build-petsc-in-windows-under-mingw64.html > > <http://hillyuan.blogspot.com/2017/11/build-petsc-in-windows-under-mingw64.html>, > probably because of this issue > https://stackoverflow.com/questions/37504625/ar-on-msys2-shell-receives-truncated-paths-when-called-from-makefile > > <https://stackoverflow.com/questions/37504625/ar-on-msys2-shell-receives-truncated-paths-when-called-from-makefile>.
You are right that you can avoid deinstalling mingw-w64-x86_64-python if you can supply the proper Python yourself (we don’t have that luxury in our Makefile). If you want to avoid using that AR, and stick to /mingw64/bin/ar (not sure what the pros and cons are), you can either: - use another PETSC_ARCH (very short, like pw, for petsc-windows); - use --with-single-library=0. See this post on GitLab https://gitlab.com/petsc/petsc/-/issues/647#note_373507681 <https://gitlab.com/petsc/petsc/-/issues/647#note_373507681> The OS I’m referring to is indeed my Windows + MSYS2 box. Thanks, Pierre > Then make all, make install and make check all went smooth. Also, I don’t > know exactly what with-x=0 and with-windows-graphics=0 do, but I think it is > stuff that I don’t need (yet configure worked with windows-graphics as well). > > Finally I launched make test. As some tests failed, I replicated the same > install procedure on all the systems I have available on this same Windows > machine (Ubuntu 20.04 and Centos 8 under a VirtualBox 6.0.22 VM, Ubuntu 20.04 > under WSL1 and the MSYS2-MINGW64 toolchain). I am attaching a file with the > results printed to screen (not sure about which file should be used for a > comparison/check). Note, however, that the tests in MSYS2 started with some > cyclic reference issues for some .mod files, but this doesn’t show up in any > file I could check. > > I am still left with some doubts about the archiver, the cyclic reference > errors and the differences in the test results, but I am able to link my code > with petsc. Unfortunately, as this Windows porting is part of a large code > restructuring, I can’t do much more with it, now, from my code. But if you > can suggest some specific tutorial to use as test also for the parallel, I > would be glad to dig deeper into the matter. > > Best regards > > Paolo > > Inviato da Posta <https://go.microsoft.com/fwlink/?LinkId=550986> per Windows > 10 > > Da: Pierre Jolivet <mailto:pierre.joli...@enseeiht.fr> > Inviato: martedì 30 giugno 2020 15:22 > A: Paolo Lampitella <mailto:paololampite...@hotmail.com> > Cc: Matthew Knepley <mailto:knep...@gmail.com>; petsc-users > <mailto:petsc-users@mcs.anl.gov> > Oggetto: Re: [petsc-users] PETSc and Windows 10 > > Please use the 3.13.2 tarball, this was fixed by Satish in the previous > commit I already linked > (https://gitlab.com/petsc/petsc/-/commit/2cd8068296b34e127f055bb32f556e3599f17523 > > <https://gitlab.com/petsc/petsc/-/commit/2cd8068296b34e127f055bb32f556e3599f17523>). > (If you want FreeFEM to do the dirty work for you, just switch to the develop > branch, and redo “make petsc-slepc”) > But I think you’ve got everything you need now for a smooth compilation :) > > Thanks, > Pierre > > > On 30 Jun 2020, at 3:09 PM, Paolo Lampitella <paololampite...@hotmail.com > <mailto:paololampite...@hotmail.com>> wrote: > > Dear Pierre, > > thanks for the fast response. Unfortunately it still fails, but now in the > configure of ScaLAPACK > (which means that it went ok for slepc, tetgen, metis, parmetis, ptscotch, > superlu and suitesparse). > > The way I applied the modification is by manually editing the Makefile in the > 3rdparty/ff-petsc folder, adding -fallow-invalid-boz to both CFLAGS and > FFLAGS (this entry added by me). Then executed make petsc-slepc. > > As my project is much less ambitious, I have a good feeling that I will be > able to use your Makefile successfully, but as I am kind of slow I tought > that it would have been useful for you to know. The configure.log is > attached. This time the error is: > > Rank mismatch between actual argument at (1) and actual argument at (2) > (scalar and rank-1) > > in subroutine pclarf.f of ScaLAPACK. > > However, before attampting with my project, I have few questions about your > Makefile, in particular this piece: > > --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" > > I see from MPI.py that I should not use ‘--with-mpi-lib/include’ if I want to > use my now working mpi wrappers. Is this correct? > > Paolo > > Inviato da Posta <https://go.microsoft.com/fwlink/?LinkId=550986> per Windows > 10 > > Da: Pierre Jolivet <mailto:pierre.joli...@enseeiht.fr> > Inviato: lunedì 29 giugno 2020 21:37 > A: Paolo Lampitella <mailto:paololampite...@hotmail.com> > Cc: Matthew Knepley <mailto:knep...@gmail.com>; petsc-users > <mailto:petsc-users@mcs.anl.gov> > Oggetto: Re: [petsc-users] PETSc and Windows 10 > > I do not give up easily on Windows problems: > 1) that’s around 50% of our (FreeFEM) user-base (and I want them to use PETSc > and SLEPc, ofc…) > 2) most people I work with from corporations just have Windows > laptops/desktops and I always recommend MSYS because it’s very lightweight > and you can pass .exe around > 3) I’ve bothered enough Satish, Jed, and Matt on GitLab to take (at least > partially) the blame now when it doesn’t work on MSYS > > That being said, the magic keyword is the added flag > FFLAGS="-fallow-invalid-boz" (see, I told you ./configure issues were easier > to deal with than the others). > Here you’ll see that everything goes through just fine (sorry, it took me a > long time to post this because everything is slow on my VM): > 1) http://jolivet.perso.enseeiht.fr/win10/configure.log > <http://jolivet.perso.enseeiht.fr/win10/configure.log> > 2) http://jolivet.perso.enseeiht.fr/win10/make.log > <http://jolivet.perso.enseeiht.fr/win10/make.log> (both steps #1 and #2 in > MSYS terminal, gcc/gfortran 10, MS-MPI see screenshot) > 3) http://jolivet.perso.enseeiht.fr/win10/ex2.txt > <http://jolivet.perso.enseeiht.fr/win10/ex2.txt> (Command Prompt, 4 processes > + MUMPS, I can send you the .exe if you want to try on your machine) > I just realize that I didn’t generate the Fortran bindings, but you can see I > compiled MUMPS and ScaLAPACK, so that shouldn’t be a problem. > Or if there is a problem, we will need to fix this in PETSc. > > I’ll push this added flag to the FreeFEM repo, thanks for reminding me of the > brokenness of gcc/gfortran 10 + MS-MPI. > Here is to hoping this won’t affect PETSc ./configure with previous > gcc/gfortran version (unlikely, this option is apparently 13-year old > https://gcc.gnu.org/bugzilla/show_bug.cgi?id=29471 > <https://gcc.gnu.org/bugzilla/show_bug.cgi?id=29471>) > > Let me know of the next hiccup, if any. > Thanks, > Pierre > > > > On 29 Jun 2020, at 8:09 PM, Paolo Lampitella <paololampite...@hotmail.com > <mailto:paololampite...@hotmail.com>> wrote: > > 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.joli...@enseeiht.fr> > Inviato: lunedì 29 giugno 2020 20:01 > A: Matthew Knepley <mailto:knep...@gmail.com> > Cc: Paolo Lampitella <mailto:paololampite...@hotmail.com>; petsc-users > <mailto:petsc-users@mcs.anl.gov> > Oggetto: Re: [petsc-users] PETSc and Windows 10 > > > > > > > On 29 Jun 2020, at 7:47 PM, Matthew Knepley <knep...@gmail.com > <mailto:knep...@gmail.com>> wrote: > > On Mon, Jun 29, 2020 at 1:35 PM Paolo Lampitella <paololampite...@hotmail.com > <mailto:paololampite...@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 > <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.joli...@enseeiht.fr> > Inviato: lunedì 29 giugno 2020 18:34 > A: Paolo Lampitella <mailto:paololampite...@hotmail.com> > Cc: Satish Balay <mailto:ba...@mcs.anl.gov>; petsc-users > <mailto:petsc-users@mcs.anl.gov> > Oggetto: Re: [petsc-users] PETSc and Windows 10 > > > > On 29 Jun 2020, at 6:27 PM, Paolo Lampitella <paololampite...@hotmail.com > <mailto:paololampite...@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 > <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 > > <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/ > <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 > <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/ <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/ > <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 > <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/> > > > <configure.log> > > > <petsc_test.txt>
