technical:recipes:openmm

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technical:recipes:openmm [2024-07-29 14:44] – bkangtechnical:recipes:openmm [2024-07-29 14:50] (current) – [VALET Package Definition] bkang
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 would be added to ''${WORKDIR}/sw/valet/openmm.vpkg_yaml''. would be added to ''${WORKDIR}/sw/valet/openmm.vpkg_yaml''.
  
-=== Using the Virtual Environment ===+===== Using the Virtual Environment =====
  
 The versions of the virtual environment declared in the VALET package are listed using the ''vpkg_versions'' command: The versions of the virtual environment declared in the VALET package are listed using the ''vpkg_versions'' command:
  
 <code bash> <code bash>
-$ vpkg_versions my-sci-app+$ vpkg_versions openmm
  
 Available versions in package (* = default version): Available versions in package (* = default version):
  
-[/home/1001/.valet/my-sci-app.vpkg_yaml] +[/work/it_css/sw/valet/openmm.vpkg_yaml] 
-my-sci-app  Some scientific app project in Python +openmm      openmm within a conda virtualenv 
-* 20201102  environment built Nov 2, 2020+* 20240726  environment built July 26, 2024
 </code> </code>
  
-Activating the virtual environment is accomplished using the ''vpkg_require'' command (in your login shell or inside job scripts):+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> <code bash>
-$ vpkg_require my-sci-app/20201102 +$ vpkg_require openmm/20240726 
-Adding dependency `libfabric/1.9.0` to your environment +Adding dependency `anaconda/2024.02` to your environment 
-Adding dependency `openmpi/4.0.2` to your environment +Adding package `openmm/20240726` to your environment 
-Adding dependency `intel-python/2020u2:python3` to your environment +(/work/it_css/sw/openmm/20240726)$ python
-Adding package `my-sci-app/20201102` to your environment +
-(/home/1001/conda-envs/my-sci-app/20201102)$ which python3+
 ~/conda-envs/my-sci-app/20201102/bin/python3 ~/conda-envs/my-sci-app/20201102/bin/python3
-(/home/1001/conda-envs/my-sci-app/20201102)$ pip list | grep mpi4py +Python 3.12.4 | packaged by conda-forge | (main, Jun 17 2024, 10:23:07) [GCC 12.3.0] on linux 
-mpi4py      3.0.3 +Type "help", "copyright", "credits" or "license" for more information. 
-$ which mpirun +>>> import openmm as mm 
-/opt/shared/openmpi/4.0.2/bin/mpirun+>>>
 </code> </code>
  • technical/recipes/openmm.1722278671.txt.gz
  • Last modified: 2024-07-29 14:44
  • by bkang