Hello Amber Developers,
We have a problem with building the MMPBSA.py.MPI on HPC following the
recommended installation by Amber manual. We have also tested the
suggestion by Prof. Case on copying the .py to .py.MPI and it didn't work.
The summary of the problem is provided as follows and any suggestions to
solve this problem is very much appreciated.
Best,
Amir
Executive summary:
==================
In a "standard" cmake MPI install
ll /apps/intel/2019.1.144/openmpi/4.0.1/amber/20/bin/MM*
ls: cannot access /apps/intel/2019.1.144/openmpi/4.0.1/amber/20/bin/MM*: No
such file or directory
using miniconda, which is supposed to do the python part, the resulting /bin
has no
MMPBSA.py and MMPBSA.py.MPI
and is non-python-fuctional.
In a cmake non-MPI install, e.g.
ll /apps/gcc/7.3.0/amber/20/bin/MM*
-rwxrwxr-x 1 dimi amber 4129 Jun 4 2020
/apps/gcc/7.3.0/amber/20/bin/MMPBSA.py
python is OK, MMPBSA.py is there and works, no hacking involved.
The idea to just cp MMPBSA.py to MMPBSA.py.MPI fails, not surprisingly for a
serial install, on the lines
if sys.argv[0].endswith('MPI'):
try:
from mpi4py import MPI
MMPBSA.py.MPI
Traceback (most recent call last):
File "./MMPBSA.py.MPI", line 53, in <module>
from mpi4py import MPI
ModuleNotFoundError: No module named 'mpi4py'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "./MMPBSA.py.MPI", line 55, in <module>
raise MMPBSA_Error('Could not import mpi4py package! Use serial version
'
MMPBSA_mods.exceptions.MMPBSA_Error: Could not import mpi4py package! Use
serial version or install mpi4py.
Summary: cmake serial and OMP installs work for python, but not MPI
installs.
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Received on Sun Sep 18 2022 - 12:00:06 PDT
