I can successfully install amber22 on the system with cray programming environment, but i has a problem with mpi4py when I want to run MMPBSA.py.MPI
My system is AMD EPYC™ 7713 with Nvidia A100, and the network is HPE Slingshot Interconnect. For the compiler, I used gcc/11.2.0, cray-mpich and CUDA 11.7
This the error when i ran MMPBSA.py.MPI:
Traceback (most recent call last):
Traceback (most recent call last):
File "/lustrefs/disk/modules/easybuild/software/Amber/amber22/bin/MMPBSA.py.MPI", line 53, in <module>
Traceback (most recent call last):
File "/lustrefs/disk/modules/easybuild/software/Amber/amber22/bin/MMPBSA.py.MPI", line 53, in <module>
from mpi4py import MPI
ImportError: /usr/lib64/libssh.so.4: undefined symbol: EVP_KDF_CTX_new_id, version OPENSSL_1_1_1d
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/lustrefs/disk/modules/easybuild/software/Amber/amber22/bin/MMPBSA.py.MPI", line 55, in <module>
from mpi4py import MPI
ImportError: /usr/lib64/libssh.so.4: undefined symbol: EVP_KDF_CTX_new_id, version OPENSSL_1_1_1d
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/lustrefs/disk/modules/easybuild/software/Amber/amber22/bin/MMPBSA.py.MPI", line 55, in <module>
Traceback (most recent call last):
File "/lustrefs/disk/modules/easybuild/software/Amber/amber22/bin/MMPBSA.py.MPI", line 53, in <module>
Traceback (most recent call last):
File "/lustrefs/disk/modules/easybuild/software/Amber/amber22/bin/MMPBSA.py.MPI", line 53, 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.
Traceback (most recent call last):
Normally, I can use these approach to install mpi4py on cray system before
source <path_to_amber.sh>
export CC=cc
export MPICC=cc
amber.python setup.py install
but this time i get the error message:
siwakorn.x3002c0s11b0n0: amber.python setup.py install
running install
/home/siwakorn/AMBER/amber22/miniconda/lib/python3.10/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
running build
running build_src
running build_py
running build_clib
error: section/s 'mpi-linux-x86_64,mpi-linux-64bit,mpi-linux,mpi-posix-x86_64,mpi-posix-64bit,mpi-posix,mpi-x86_64,mpi-64bit,mpi' not found in file/s 'mpi.cfg'
running build_ext
error: section/s 'mpi-linux-x86_64,mpi-linux-64bit,mpi-linux,mpi-posix-x86_64,mpi-posix-64bit,mpi-posix,mpi-x86_64,mpi-64bit,mpi' not found in file/s 'mpi.cfg'
running install_lib
running install_egg_info
running egg_info
writing src/mpi4py.egg-info/PKG-INFO
writing dependency_links to src/mpi4py.egg-info/dependency_links.txt
writing top-level names to src/mpi4py.egg-info/top_level.txt
reading manifest file 'src/mpi4py.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE.rst'
writing manifest file 'src/mpi4py.egg-info/SOURCES.txt'
removing '/home/siwakorn/AMBER/amber22/miniconda/lib/python3.10/site-packages/mpi4py-3.1.3-py3.10.egg-info' (and everything under it)
Copying src/mpi4py.egg-info to /home/siwakorn/AMBER/amber22/miniconda/lib/python3.10/site-packages/mpi4py-3.1.3-py3.10.egg-info
running install_scripts
siwakorn.x3002c0s11b0n0: ls
Any suggestion?
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Received on Mon May 15 2023 - 00:00:02 PDT
