<div dir="ltr"><div dir="ltr">On Mon, Jun 29, 2020 at 1:35 PM Paolo Lampitella <<a href="mailto:paololampitella@hotmail.com">paololampitella@hotmail.com</a>> wrote:<br></div><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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<p class="MsoNormal">Dear Pierre, sorry to bother you, but I already have some issues. What I did:</p>
<p class="MsoNormal"><u></u> <u></u></p>
<ul type="disc">
<li class="gmail-m_2888408931258405589MsoListParagraph">pacman -R mingw-w64-x86_64-python mingw-w64-x86_64-gdb (is gdb also troublesome?)</li><li class="gmail-m_2888408931258405589MsoListParagraph">Followed points 6 and 7 at
<a href="https://doc.freefem.org/introduction/installation.html#compilation-on-windows" target="_blank">
https://doc.freefem.org/introduction/installation.html#compilation-on-windows</a></li></ul>
<p class="MsoNormal">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:</p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">tar xzf ../pkg/petsc-lite-3.13.0.tar.gz</p>
<p class="MsoNormal">patch -p1 < petsc-suitesparse.patch</p>
<p class="MsoNormal">patching file petsc-3.13.0/config/BuildSystem/config/packages/SuiteSparse.py</p>
<p class="MsoNormal">touch petsc-3.13.0/tag-tar</p>
<p class="MsoNormal">cd petsc-3.13.0 && ./configure MAKEFLAGS='' \</p>
<p class="MsoNormal"> --prefix=/home/paolo/freefem/ff-petsc//r \</p>
<p class="MsoNormal"> --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</p>
<p class="MsoNormal">===============================================================================</p>
<p class="MsoNormal"> Configuring PETSc to compile on your system</p>
<p class="MsoNormal">===============================================================================</p>
<p class="MsoNormal">TESTING: FortranMPICheck from config.packages.MPI(config/BuildSystem/config/pack*******************************************************************************</p>
<p class="MsoNormal"> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):</p>
<p class="MsoNormal">-------------------------------------------------------------------------------</p>
<p class="MsoNormal">Fortran error! mpi_init() could not be located!</p>
<p class="MsoNormal">*******************************************************************************</p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">make: *** [Makefile:210: petsc-3.13.0/tag-conf-real] Errore 1</p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Note that I didn’t add anything to any PATH variable, because this is not mentioned in your documentation.</p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">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.</p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">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</p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">But I’m not sure why this is happening</p></div></div></blockquote><div><br></div><div>Pierre,</div><div><br></div><div>Could this be due to gcc 10?</div><div><br></div><div>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 <br>Possible ERROR while running compiler: exit code 1<br>stderr:<br>C:/msys64/home/paolo/FreeFem-sources/3rdparty/include/msmpi/mpif.h:227:36:<br><br> 227 | PARAMETER (MPI_DATATYPE_NULL=z'0c000000')<br> | 1<br>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']<br>C:/msys64/home/paolo/FreeFem-sources/3rdparty/include/msmpi/mpif.h:303:27:<br><br> 303 | PARAMETER (MPI_CHAR=z'4c000101')<br> | 1<br>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']<br>C:/msys64/home/paolo/FreeFem-sources/3rdparty/include/msmpi/mpif.h:305:36:<br><br> 305 | PARAMETER (MPI_UNSIGNED_CHAR=z'4c000102')<br> | 1<br></div><div><br></div><div> Thanks,</div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div lang="IT"><div class="gmail-m_2888408931258405589WordSection1">
<p class="MsoNormal">Thanks</p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Paolo</p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Inviato da <a href="https://go.microsoft.com/fwlink/?LinkId=550986" target="_blank">
Posta</a> per Windows 10</p>
<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal" style="border:none;padding:0cm"><b>Da: </b><a href="mailto:pierre.jolivet@enseeiht.fr" target="_blank">Pierre Jolivet</a><br>
<b>Inviato: </b>lunedì 29 giugno 2020 18:34<br>
<b>A: </b><a href="mailto:paololampitella@hotmail.com" target="_blank">Paolo Lampitella</a><br>
<b>Cc: </b><a href="mailto:balay@mcs.anl.gov" target="_blank">Satish Balay</a>; <a href="mailto:petsc-users@mcs.anl.gov" target="_blank">
petsc-users</a><br>
<b>Oggetto: </b>Re: [petsc-users] PETSc and Windows 10</p>
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<p class="MsoNormal">On 29 Jun 2020, at 6:27 PM, Paolo Lampitella <<a href="mailto:paololampitella@hotmail.com" target="_blank">paololampitella@hotmail.com</a>> wrote:<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">I think I made the first step of having mingw64 from msys2 working with ms-mpi.<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">I found that the issue I was having was related to:<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<div>
<p class="MsoNormal"><a href="https://gcc.gnu.org/bugzilla/show_bug.cgi?id=91556" target="_blank">https://gcc.gnu.org/bugzilla/show_bug.cgi?id=91556</a><u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">and, probably (but impossible to check now), I was using an msys2 and/or mingw mpi package before this fix:<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<div>
<p class="MsoNormal"><a href="https://github.com/msys2/MINGW-packages/commit/11b4cff3d2ec7411037b692b0ad5a9f3e9b9978d#diff-eac59989e3096be97d940c8f47b50fba" target="_blank">https://github.com/msys2/MINGW-packages/commit/11b4cff3d2ec7411037b692b0ad5a9f3e9b9978d#diff-eac59989e3096be97d940c8f47b50fba</a><u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">Admittedly, I never used gcc 10 before on any machine. Still, I feel that reporting that sort of error in that way is,<u></u><u></u></p>
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<p class="MsoNormal">at least, misleading (I would have preferred the initial implementation as mentioned in the gcc bug track).<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">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:<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal"><a href="https://www.scivision.dev/windows-mpi-msys2/" target="_blank">https://www.scivision.dev/windows-mpi-msys2/</a><u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">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:<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<div>
<p class="MsoNormal"><a href="https://github.com/microsoft/Microsoft-MPI/issues/33" target="_blank">https://github.com/microsoft/Microsoft-MPI/issues/33</a><u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">which, to me, are both signs of lack of attention on the fortran side by those that maintain this thing.<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">In summary, this is the procedure I followed so far (on a 64 bit machine with Windows 10):<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<ul style="margin-top:0cm" type="disc">
<li class="gmail-m_2888408931258405589MsoListParagraph" style="margin-top:0cm;margin-bottom:0.0001pt">
Install MSYS2 from<span class="gmail-m_2888408931258405589apple-converted-space"> </span><a href="https://www.msys2.org/" target="_blank">https://www.msys2.org/</a><span class="gmail-m_2888408931258405589apple-converted-space"> </span>and just follow the install wizard<u></u><u></u></li><li class="gmail-m_2888408931258405589MsoListParagraph" style="margin-top:0cm;margin-bottom:0.0001pt">
Open the MSYS2 terminal and execute: pacman -Syuu<u></u><u></u></li><li class="gmail-m_2888408931258405589MsoListParagraph" style="margin-top:0cm;margin-bottom:0.0001pt">
Close the terminal when asked and reopen it<u></u><u></u></li><li class="gmail-m_2888408931258405589MsoListParagraph" style="margin-top:0cm;margin-bottom:0.0001pt">
Keep executing ‘pacman -Syuu’ until nothing else needs to be updated<u></u><u></u></li><li class="gmail-m_2888408931258405589MsoListParagraph" style="margin-top:0cm;margin-bottom:0.0001pt">
Close the MSYS2 terminal and reopen it (I guess because was in paranoid mode), then install packages with:<u></u><u></u></li></ul>
<div style="margin-left:36pt">
<p class="MsoNormal"> <u></u><u></u></p>
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<div style="margin-left:70.8pt">
<p class="MsoNormal">pacman -S base-devel git gcc gcc-fortran bsdcpio lndir pax-git unzip<u></u><u></u></p>
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<div style="margin-left:70.8pt">
<p class="MsoNormal">pacman -S mingw-w64-x86_64-toolchain<u></u><u></u></p>
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<div style="margin-left:70.8pt">
<p class="MsoNormal">pacman -S mingw-w64-x86_64-msmpi<u></u><u></u></p>
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<div style="margin-left:70.8pt">
<p class="MsoNormal">pacman -S mingw-w64-x86_64-cmake<u></u><u></u></p>
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<div style="margin-left:70.8pt">
<p class="MsoNormal">pacman -S mingw-w64-x86_64-freeglut<u></u><u></u></p>
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<div style="margin-left:70.8pt">
<p class="MsoNormal">pacman -S mingw-w64-x86_64-gsl<u></u><u></u></p>
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<div style="margin-left:70.8pt">
<p class="MsoNormal">pacman -S mingw-w64-x86_64-libmicroutils<u></u><u></u></p>
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<p class="MsoNormal">pacman -S mingw-w64-x86_64-hdf5<u></u><u></u></p>
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<p class="MsoNormal">pacman -S mingw-w64-x86_64-openblas<u></u><u></u></p>
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<p class="MsoNormal">pacman -S mingw-w64-x86_64-arpack<u></u><u></u></p>
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<p class="MsoNormal">pacman -S mingw-w64-x86_64-jq<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">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.<u></u><u></u></p>
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<ul style="margin-top:0cm" type="disc">
<li class="gmail-m_2888408931258405589MsoListParagraph" style="margin-top:0cm;margin-bottom:0.0001pt">
Open the MINGW64 terminal and create the .mod file out of the mpi.f90 file, as mentioned here<span class="gmail-m_2888408931258405589apple-converted-space"> </span><a href="https://www.scivision.dev/windows-mpi-msys2/" target="_blank"><span class="gmail-m_2888408931258405589apple-converted-space"><span style="color:windowtext;text-decoration:none">https://www.scivision.dev/windows-mpi-msys2/</span></span></a>,
with:<u></u><u></u></li></ul>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">cd /mingw64/include<u></u><u></u></p>
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<p class="MsoNormal">gfortran mpif90 -c -fno-range-check -fallow-invalid-boz<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">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.<u></u><u></u></p>
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<br>
<u></u><u></u></p>
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<p class="MsoNormal">This is needed to ‘USE mpi’ (as opposed to INCLUDE ‘mpif.h’)<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<ul style="margin-top:0cm" type="disc">
<li class="gmail-m_2888408931258405589MsoListParagraph" style="margin-top:0cm;margin-bottom:0.0001pt">
Install the latest MS-MPI (both sdk and setup) from<span class="gmail-m_2888408931258405589apple-converted-space"> </span><a href="https://www.microsoft.com/en-us/download/details.aspx?id=100593" target="_blank"><span class="gmail-m_2888408931258405589apple-converted-space"><span style="color:windowtext;text-decoration:none">https://www.microsoft.com/en-us/download/details.aspx?id=100593</span></span></a><u></u><u></u></li></ul>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">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:<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<div style="margin-left:35.4pt">
<p class="MsoNormal">function copydep() { ldd $1 | grep "=> /$2" | awk '{print $3}' | xargs -I '{}' cp -v '{}' .; }<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">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:<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">copydep my.exe mingw64<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">This, of course, must be done before actually trying to execute the .exe in the windows cmd prompt.<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">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)<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Looks like the hard part is over. It’s usually easier to deal with ./configure issues.<u></u><u></u></p>
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<p class="MsoNormal">If you have weird errors like “incomplete Cygwin install” or whatever, this is the kind of issues I was referring to earlier.<u></u><u></u></p>
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<p class="MsoNormal">In that case, what I’d suggest is just, as before:<u></u><u></u></p>
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<p class="MsoNormal">pacman -R mingw-w64-x86_64-python mingw-w64-x86_64-gdb<u></u><u></u></p>
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<p class="MsoNormal">pacman -S python<u></u><u></u></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal">Thanks,<u></u><u></u></p>
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<p class="MsoNormal">Pierre<u></u><u></u></p>
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<p class="MsoNormal"><br>
<br>
<u></u><u></u></p>
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<p class="MsoNormal">Thanks<u></u><u></u></p>
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<p class="MsoNormal"> <u></u><u></u></p>
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<p class="MsoNormal">Paolo<u></u><u></u></p>
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</blockquote>
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<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
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</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>-- Norbert Wiener</div><div><br></div><div><a href="http://www.cse.buffalo.edu/~knepley/" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br></div></div></div></div></div></div></div></div>