On Thu, Aug 3, 2023 at 10:10 AM Meyer, Olivia (meyerok) <meyerok.mail.uc.edu>
wrote:
> But if I type python3 --version into Ubuntu, it returns version 3.10.12,
> and I removed the binary version of AmberTools from my computer, so there
> should be no other Python version it is finding... Is that correct?
>
no it's not. AmberTools will install the latest python version for you.
/mnt/c/Users/LivMeyer/Desktop/amber22_src/build/CMakeFiles/miniconda/bin
You can check the manual to find a flag to specify your Python (3.10)
version.
Hai
>
> -Olivia
> ------------------------------
> *From:* Hai Nguyen via AMBER <amber.ambermd.org>
> *Sent:* Thursday, August 3, 2023 8:52 AM
> *To:* AMBER Mailing List <amber.ambermd.org>; Meyer, Olivia (meyerok) <
> meyerok.mail.uc.edu>
> *Subject:* Re: [AMBER] Parallel AmberTools Build Error: mpi4py.MPI fails
> to build
>
> External Email: Use Caution
>
>
> Hi
>
> In your log file, cpython-311 was used.
>
> Hai
>
> On Wed, Aug 2, 2023 at 1:58 PM Meyer, Olivia (meyerok) via AMBER <
> amber.ambermd.org> wrote:
>
> > Hi!
> >
> > I saw that someone posted something similar to the problem I am having
> > with the AmberTools23 install regarding the mpi4py.MPI build failure, but
> > the solution provided, which indicated that the
> > PythonInterpreterConfig.cmake file should be changed at line 60 to
> version
> > 3.10, and I already have Python 3.10.12 installed. Does anyone have any
> > other suggestions? I am very new to building AmberTools and MD
> simulations
> > in general, so if someone could give as detailed instructions to fix as
> > possible that would be appreciated.
> >
> > The following code is related to the errors at the end of the output from
> > the 'make install' command. I have also looked for the longintrepr.h
> file,
> > and it is in the following path:
> >
> \Users\LivMeyer\Desktop\amber22_src\build\CMakeFiles\miniconda\install\pkgs\cython-0.29.36-py311h5eee18b_0\lib\python3.11\site-packages\Cython\Includes\cpython\longintrepr.pxd
> >
> > building 'mpi4py.MPI' extension
> > /usr/bin/gcc -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem
> >
> /mnt/c/Users/LivMeyer/Desktop/amber22_src/build/CMakeFiles/miniconda/install/include
> > -fPIC -O2 -isystem
> >
> /mnt/c/Users/LivMeyer/Desktop/amber22_src/build/CMakeFiles/miniconda/install/include
> > -fPIC -DPyMPI_MISSING_MPI_LB=1 -DPyMPI_MISSING_MPI_UB=1 -DHAVE_DLFCN_H=1
> > -DHAVE_DLOPEN=1
> >
> -I/mnt/c/Users/LivMeyer/Desktop/amber22_src/build/CMakeFiles/miniconda/install/include/python3.11
> > -I/usr/lib/x86_64-linux-gnu/openmpi/include
> > -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -c src/MPI.c -o
> >
> /mnt/c/Users/LivMeyer/Desktop/amber22_src/build/AmberTools/src/mpi4py-3.1.3/CMakeFiles/mpi4py-build/temp.linux-x86_64-cpython-311/src/MPI.o
> > In file included from src/MPI.c:4:
> > src/mpi4py.MPI.c:198:12: fatal error: longintrepr.h: No such file or
> > directory
> > 198 | #include "longintrepr.h"
> > | ^~~~~~~~~~~~~~~
> > compilation terminated.
> > error: command '/usr/bin/gcc' failed with exit code 1
> > make[2]: ***
> > [AmberTools/src/mpi4py-3.1.3/CMakeFiles/mpi4py.dir/build.make:203:
> > AmberTools/src/mpi4py-3.1.3/CMakeFiles/mpi4py-build/mpi4py-build.stamp]
> > Error 1
> > make[1]: *** [CMakeFiles/Makefile2:4539:
> > AmberTools/src/mpi4py-3.1.3/CMakeFiles/mpi4py.dir/all] Error 2
> > make: *** [Makefile:156: all] Error 2
> >
> > If anyone has any suggestions to get around this, please let me know, as
> I
> > cannot continue the remaining steps of the parallel build --> export
> > DO_PARALLEL="mpirun -np 2", because a majority of my tests fail. To be
> > honest, I do not know if these errors are related, but I am assuming they
> > are.
> >
> > -Olivia
> >
> > Olivia K. Meyer
> > Graduate Student, Kumari Lab
> > University of Cincinnati
> > James L. Winkle College of Pharmacy
> > Department of Pharmaceutical Sciences
> > 231 Albert Sabin Way, Cincinnati, OH USA 45229
> >
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
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Received on Thu Aug 03 2023 - 07:30:02 PDT
