technical:recipes:deepmd

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technical:recipes:deepmd [2024-08-18 10:37] – [OpenMM Python Virtual Environment] bkangtechnical:recipes:deepmd [2024-08-18 11:30] (current) – [Using the Virtual Environment] bkang
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 +====== DeepMD Python Virtual Environment ======
  
 +This page documents the creation of a Python virtual environment (virtualenv) containing the DeepMD software on the Caviness HPC system((The steps should also work on the DARWIN HPC system, though with different package versions.)).  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:
 +
 +<code bash>
 +[user@login01 ~]$ workgroup -g my_workgroup
 +[(my_workgroup:user)@login01 ~]$ mkdir --mode=2775 --parent ${WORKDIR}/sw/deepmd
 +[(my_workgroup:user)@login01 ~]$ mkdir --mode=2775 --parent ${WORKDIR}/sw/valet
 +</code>
 +
 +These commands create any missing directories.  All directories created will have group-write and -inherit permissions.
 +
 +===== Create Virtualenv =====
 +
 +The Python distribution will form the basis for the anaconda virtualenv, so add it to the environment:
 +
 +<code bash>
 +[(my_workgroup:user)@login01 ~]$ 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/deepmd/20240818 --override-channels --channel conda-forge python'=>3.11.9' 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/deepmd/20240818                          
 +#                                                                               
 +# To deactivate an active environment, use                                      
 +#                                                                               
 +#     $ conda deactivate 
 +#
 +</code>
 +
 +
 +Before building and installing DeepMD the environment needs to be activated:
 +
 +<code bash>
 +$ conda activate $WORKDIR/sw/deepmd/20240818
 +(/work/it_css/sw/deepmd/20240818)$ 
 +</code>
 +
 +
 +===== Building DeepMD =====
 +
 +With the new virtual environment activated, we can now build DeepMD.
 +
 +<code base>
 +(/work/it_css/sw/deepmd/20240818)$ conda create -n deepmd deepmd-kit lammps horovod -c conda-forge
 +Solving environment: done
 +    :
 +Proceed ([y]/n)? y
 +    :
 +Preparing transaction: done                                                     
 +Verifying transaction: done                                                     
 +    :
 +
 +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 DeepMD VALET package definition, the following text:
 +
 +<file deepmd.vpkg_yaml>
 +openmm:
 +    prefix: /work/my_workgroup/sw/deepmd
 +    description: deepmd within a conda virtualenv
 +    flags:
 +        - no-standard-paths
 +    actions:
 +        - action: source
 +          script:
 +              sh: anaconda-activate-2020.sh
 +          order: failure-first
 +          success: 0
 +    versions:
 +          "20240818":
 +              description: environment built August 18, 2024
 +              dependencies:
 +                  - anaconda/2024.02
 +</file>
 +
 +would be added to ''${WORKDIR}/sw/valet/deepmd.vpkg_yaml''.
 +
 +===== Using the Virtual Environment =====
 +
 +The versions of the virtual environment declared in the VALET package are listed using the ''vpkg_versions'' command:
 +
 +<code bash>
 +$ vpkg_versions deepmd
 +
 +Available versions in package (* = default version):
 +
 +[/work/it_css/sw/valet/deepmd.vpkg_yaml]
 +deepmd      deepmd within a conda virtualenv
 +* 20240818  environment built August 18, 2024
 +</code>
 +
 +You can import deepmd, activating the virtual environment is accomplished using the ''vpkg_require'' command (in your login shell or inside job scripts):
 +
 +<code bash>
 +$ vpkg_require deepmd/20240818
 +Adding dependency `anaconda/2024.02` to your environment
 +Adding package `deepmd/20240818` 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>