OpenMM Python Virtual Environment
This page documents the creation of a Python virtual environment (virtualenv) containing the OpenMM software on the Caviness HPC system1). It assumes that the user is adding the software to the workgroup storage.
Prepare Workgroup Directory
Prepare to add software in the standard sub-directories of the workgroup storage:
[user@login01 ~]$ workgroup -g my_workgroup [(my_workgroup:user)@login01 ~]$ mkdir --mode=2775 --parent ${WORKDIR}/sw/openmm [(my_workgroup:user)@login01 ~]$ mkdir --mode=2775 --parent ${WORKDIR}/sw/valet
These commands create any missing directories. All directories created will have group-write and -inherit permissions.
Create Virtualenv
The Python distribution will form the basis for the anaconda virtualenv, so add it to the environment:
[(my_workgroup:user)@login01 ~]$ vpkg_require anaconda/2024.02 Adding package `anaconda/2024.02` to your environment
The virtual environment is first populated with all packages that do not require OpenMM. Any packages requiring OpenMM must be installed after we build and install our local copy of OpenMM in the virtual environment. In this example, neither Numpy nor Scipy require OpenMM.
The two channel options are present to ensure only the default Anaconda channels are consulted – otherwise the command could still pick packages from the Intel channel, for example, which would still have the binary compatibility issues!
$ conda create --prefix=$WORKDIR/sw/openmm/20240726 --override-channels --channel conda-forge python'=>3.7' numpy scipy Solving environment: done : Proceed ([y]/n)? y : Preparing transaction: done Verifying transaction: done Executing transaction: done # # To activate this environment, use # # $ conda activate /work/it_css/sw/openmm/20240726 # # To deactivate an active environment, use # # $ conda deactivate #
Before building and installing OpenMM the environment needs to be activated:
$ conda activate $WORKDIR/sw/openmm/20240726 (/work/it_css/sw/openmm/20240726)$
Building OpenMM
With the new virtual environment activated, we can now build OpenMM.
(/work/it_css/sw/openmm/20240726)$ conda install -c conda-forge openmm
Solving environment: done
:
Proceed ([y]/n)? y
:
Preparing transaction: done
Verifying transaction: done
Executing transaction: \ By downloading and using the CUDA Toolkit conda packages, you accept the terms and conditions of the CUDA End User License Agreement (EULA): https://docs.nvidia.com/cuda/eula/index.html
done
VALET Package Definition
The new virtual environment can easily be added to your login shell and job runtime environments using VALET. Assuming the workgroup does not already have a OpenMM VALET package definition, the following text:
openmm:
prefix: /work/my_workgroup/sw/openmm
description: openmm within a conda virtualenv
flags:
- no-standard-paths
actions:
- action: source
script:
sh: anaconda-activate-2020.sh
order: failure-first
success: 0
versions:
"20240726":
description: environment built July 26, 2024
dependencies:
- anaconda/2024.02
would be added to ${WORKDIR}/sw/valet/openmm.vpkg_yaml.
Using the Virtual Environment
The versions of the virtual environment declared in the VALET package are listed using the vpkg_versions command:
$ vpkg_versions openmm Available versions in package (* = default version): [/work/it_css/sw/valet/openmm.vpkg_yaml] openmm openmm within a conda virtualenv * 20240726 environment built July 26, 2024
You can import openmm, activating the virtual environment is accomplished using the vpkg_require command (in your login shell or inside job scripts):
$ vpkg_require openmm/20240726 Adding dependency `anaconda/2024.02` to your environment Adding package `openmm/20240726` to your environment (/work/it_css/sw/openmm/20240726)$ python ~/conda-envs/my-sci-app/20201102/bin/python3 Python 3.12.4 | packaged by conda-forge | (main, Jun 17 2024, 10:23:07) [GCC 12.3.0] on linux Type "help", "copyright", "credits" or "license" for more information. >>> import openmm as mm >>>