technical:recipes:openmm

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technical:recipes:openmm [2024-07-29 14:27] – bkangtechnical:recipes:openmm [2024-07-29 14:50] (current) – [VALET Package Definition] bkang
Line 59: Line 59:
  
  
-==== Building OpenMM ====+===== Building OpenMM =====
  
 With the new virtual environment activated, we can now build OpenMM. With the new virtual environment activated, we can now build OpenMM.
Line 78: Line 78:
 ===== VALET Package Definition ===== ===== VALET Package Definition =====
  
-Assuming the workgroup does //not// already have a TensorFlow VALET package definition, the following text:+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 tensorflow.vpkg_yaml> +<file openmm.vpkg_yaml> 
-tensorflow: +openmm: 
-    prefix: /work/my_workgroup/sw/tensorflow +    prefix: /work/my_workgroup/sw/openmm 
-    description: TensorFlow Python environments+    description: openmm within a conda virtualenv
     flags:     flags:
         - no-standard-paths         - no-standard-paths
Line 89: Line 90:
         - action: source         - action: source
           script:           script:
-              sh: anaconda-activate.sh+              sh: anaconda-activate-2020.sh
           order: failure-first           order: failure-first
           success: 0           success: 0
     versions:     versions:
-        "2.2.0:gpu": +          "20240726": 
-            description: 2.2.0 with GPU support +              description: environment built July 26, 2024 
-            dependencies: +              dependencies: 
-                - intel-python/2020u2:python3 +                  - anaconda/2024.02
-        "2.3.0:intel,python3.8": +
-            description: 2.3.0 with Python 3.8, Intel optimizations +
-            dependencies: +
-                - intel-python/2020u2:python3+
 </file> </file>
  
-would be added to ''${WORKDIR}/sw/valet/tensorflow.vpkg_yaml''.  If that file already exists, add your new version at the same level as others:+would be added to ''${WORKDIR}/sw/valet/openmm.vpkg_yaml''.
  
-<file tensorflow.vpkg_yaml> +===== Using the Virtual Environment =====
-tensorflow: +
-    prefix: /work/my_workgroup/sw/tensorflow +
-    description: TensorFlow Python environments +
-    flags: +
-        - no-standard-paths +
-    actions: +
-        - action: source +
-          script: +
-              sh: anaconda-activate.sh +
-          order: failure-first +
-          success: 0 +
-    versions: +
-        "2.2.0:gpu": +
-            description: 2.2.0 with GPU support +
-            dependencies: +
-                - intel-python/2020u2:python3 +
-        "2.3.0:intel,python3.8": +
-            description: 2.3.0 with Python 3.8, Intel optimizations +
-            dependencies: +
-                - intel-python/2020u2:python3 +
-        "1.8.0": +
-            description: 1.8.0 from pkgs/main +
-            dependencies: +
-                - intel-python/2018u3:python3 +
-</file>+
  
-<note warning>Make sure you modify ''prefix: /work/my_workgroup/sw/tensorflow'' for your workgroup (e.g. If my workgroup is ''it_nss'', then use I would use ''prefix: /work/it_nss/sw/tensorflow'').</note> +The versions of the virtual environment declared in the VALET package are listed using the ''vpkg_versions'' command:
- +
-<note tip>On Caviness after a user has used the ''workgroup'' command, VALET searches for package definitions in ''${WORKDIR}/sw/valet'' by default.  VALET also searches a ''~/.valet'' directory (in your home directory) if it exists, so that's the best location for personal package definitions -- for software you've installed in your home directory, for example.</note> +
- +
-With a properly-constructed package definition file, you can now check for your versions of TensorFlow:+
  
 <code bash> <code bash>
-[(it_nss:frey)@login00 ~]$ vpkg_versions tensorflow+$ vpkg_versions openmm
  
 Available versions in package (* = default version): Available versions in package (* = default version):
  
-[/work/my_workgroup/sw/valet/tensorflow.vpkg_yaml] +[/work/it_css/sw/valet/openmm.vpkg_yaml] 
-tensorflow               TensorFlow Python environments +openmm      openmm within a conda virtualenv 
-* 2.2.0:gpu              2.2.0 with GPU support +* 20240726  environment built July 26, 2024 
-  2.3.0:intel,python3.8  2.3.0 with Python 3.8, Intel optimizations +</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> </code>
  • technical/recipes/openmm.1722277664.txt.gz
  • Last modified: 2024-07-29 14:27
  • by bkang