technical:recipes:openmm

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technical:recipes:openmm [2024-07-29 13:46] – bkangtechnical:recipes:openmm [2024-07-29 14:50] (current) – [VALET Package Definition] bkang
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 <code bash> <code bash>
 [user@login01 ~]$ workgroup -g my_workgroup [user@login01 ~]$ workgroup -g my_workgroup
-[(my_workgroup:user)@login01 ~]$ mkdir --mode=2775 --parent ${WORKDIR}/sw/tensorflow+[(my_workgroup:user)@login01 ~]$ mkdir --mode=2775 --parent ${WORKDIR}/sw/openmm
 [(my_workgroup:user)@login01 ~]$ mkdir --mode=2775 --parent ${WORKDIR}/sw/valet [(my_workgroup:user)@login01 ~]$ mkdir --mode=2775 --parent ${WORKDIR}/sw/valet
 </code> </code>
  
 These commands create any missing directories.  All directories created will have group-write and -inherit permissions. 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:
 +
 +<code bash>
 +[(my_workgroup:user)@login01 ~]$ vpkg_require anaconda/2024.02
 +Adding package `anaconda/2024.02` to your environment
 +</code>
 +
 +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.
 +
 +<WRAP center round important 60%>
 +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!
 +</WRAP>
 +
 +<code bash>
 +$ 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 
 +#
 +</code>
 +
 +
 +Before building and installing OpenMM the environment needs to be activated:
 +
 +<code bash>
 +$ conda activate $WORKDIR/sw/openmm/20240726
 +(/work/it_css/sw/openmm/20240726)$ 
 +</code>
 +
 +
 +===== Building OpenMM =====
 +
 +With the new virtual environment activated, we can now build OpenMM.
 +
 +<code base>
 +(/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
 +</code>
 +
 +===== 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:
 +
 +<file openmm.vpkg_yaml>
 +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
 +</file>
 +
 +would be added to ''${WORKDIR}/sw/valet/openmm.vpkg_yaml''.
 +
 +===== Using the Virtual Environment =====
 +
 +The versions of the virtual environment declared in the VALET package are listed using the ''vpkg_versions'' command:
 +
 +<code bash>
 +$ 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
 +</code>
 +
 +You can import openmm, activating the virtual environment is accomplished using the ''vpkg_require'' command (in your login shell or inside job scripts):
 +
 +<code bash>
 +$ 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
 +>>>
 +</code>
  • technical/recipes/openmm.1722275182.txt.gz
  • Last modified: 2024-07-29 13:46
  • by bkang