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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Received on Wed Aug 02 2023 - 11:00:02 PDT
