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
Line 9: Line 9:
 <code bash> <code bash>
 [user@login01 ~]$ workgroup -g my_workgroup [user@login01 ~]$ workgroup -g my_workgroup
-[(my_workgroup:user)@login01 ~]$ mkdir --mode=2775 --parent ${WORKDIR}/sw/openmm+[(my_workgroup:user)@login01 ~]$ mkdir --mode=2775 --parent ${WORKDIR}/sw/deepmd
 [(my_workgroup:user)@login01 ~]$ mkdir --mode=2775 --parent ${WORKDIR}/sw/valet [(my_workgroup:user)@login01 ~]$ mkdir --mode=2775 --parent ${WORKDIR}/sw/valet
 </code> </code>
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 <code bash> <code bash>
-$ conda create --prefix=$WORKDIR/sw/openmm/20240726 --override-channels --channel conda-forge python'=>3.7' numpy scipy+$ conda create --prefix=$WORKDIR/sw/deepmd/20240818 --override-channels --channel conda-forge python'=>3.11.9' numpy scipy
 Solving environment: done Solving environment: done
     :     :
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 # To activate this environment, use                                              # To activate this environment, use                                             
 #                                                                                #                                                                               
-#     $ conda activate /work/it_css/sw/openmm/20240726                          +#     $ conda activate /work/it_css/sw/deepmd/20240818                          
 #                                                                                #                                                                               
 # To deactivate an active environment, use                                       # To deactivate an active environment, use                                      
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-Before building and installing OpenMM the environment needs to be activated:+Before building and installing DeepMD the environment needs to be activated:
  
 <code bash> <code bash>
-$ conda activate $WORKDIR/sw/openmm/20240726 +$ conda activate $WORKDIR/sw/deepmd/20240818 
-(/work/it_css/sw/openmm/20240726)$ +(/work/it_css/sw/deepmd/20240818)$ 
 </code> </code>
  
  
-===== Building OpenMM =====+===== Building DeepMD =====
  
-With the new virtual environment activated, we can now build OpenMM.+With the new virtual environment activated, we can now build DeepMD.
  
 <code base> <code base>
-(/work/it_css/sw/openmm/20240726)$ conda install -c conda-forge openmm+(/work/it_css/sw/deepmd/20240818)$ conda create -n deepmd deepmd-kit lammps horovod -c conda-forge
 Solving environment: done Solving environment: done
     :     :
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 Preparing transaction: done                                                      Preparing transaction: done                                                     
 Verifying 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 done
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 The new virtual environment can easily be added to your login shell and job runtime environments using VALET. 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:+Assuming the workgroup does //not// already have a DeepMD VALET package definition, the following text:
  
-<file openmm.vpkg_yaml>+<file deepmd.vpkg_yaml>
 openmm: openmm:
-    prefix: /work/my_workgroup/sw/openmm +    prefix: /work/my_workgroup/sw/deepmd 
-    description: openmm within a conda virtualenv+    description: deepmd within a conda virtualenv
     flags:     flags:
         - no-standard-paths         - no-standard-paths
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           success: 0           success: 0
     versions:     versions:
-          "20240726": +          "20240818": 
-              description: environment built July 26, 2024+              description: environment built August 18, 2024
               dependencies:               dependencies:
                   - anaconda/2024.02                   - anaconda/2024.02
 </file> </file>
  
-would be added to ''${WORKDIR}/sw/valet/openmm.vpkg_yaml''.+would be added to ''${WORKDIR}/sw/valet/deepmd.vpkg_yaml''.
  
 ===== Using the Virtual Environment ===== ===== Using the Virtual Environment =====
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 <code bash> <code bash>
-$ vpkg_versions openmm+$ vpkg_versions deepmd
  
 Available versions in package (* = default version): Available versions in package (* = default version):
  
-[/work/it_css/sw/valet/openmm.vpkg_yaml] +[/work/it_css/sw/valet/deepmd.vpkg_yaml] 
-openmm      openmm within a conda virtualenv +deepmd      deepmd within a conda virtualenv 
-* 20240726  environment built July 26, 2024+* 20240818  environment built August 18, 2024
 </code> </code>
  
-You can import openmm, activating the virtual environment is accomplished using the ''vpkg_require'' command (in your login shell or inside job scripts):+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> <code bash>
-$ vpkg_require openmm/20240726+$ vpkg_require deepmd/20240818
 Adding dependency `anaconda/2024.02` to your environment Adding dependency `anaconda/2024.02` to your environment
-Adding package `openmm/20240726` to your environment+Adding package `deepmd/20240818` to your environment
 (/work/it_css/sw/openmm/20240726)$ python (/work/it_css/sw/openmm/20240726)$ python
 ~/conda-envs/my-sci-app/20201102/bin/python3 ~/conda-envs/my-sci-app/20201102/bin/python3
  • technical/recipes/deepmd.1723991821.txt.gz
  • Last modified: 2024-08-18 10:37
  • by bkang