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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>
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Received on Thu Aug 03 2023 - 06:00:02 PDT
