Difference between revisions of "Modules"

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[[Category:Software]][[Category:Infrastructure]]
 
[[Category:Software]][[Category:Infrastructure]]
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==Introduction==
 
==Introduction==
Creating and maintaining a computing environment for a data analysis pipeline that consists of a large number of heterogenous tools, needs to be run by many users as must provide consistent data analysis results over a long time while frequent software upgrades and underlying operating system environment changes happen is not easy. Fortunately, the major points of this problem can be addressed by the use of an environmental modules system that abstracts the computing environment from the immediate data analysis steps. At the UF HPC we have chosen to implement this system using [http://www.tacc.utexas.edu/tacc-projects/mclay/lmod Lmod] software written by Robert McLay at the Texas Advanced Computing Center [http://www.tacc.utexas.edu/home (TACC)].
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Setting and maintaining your environment while running a large number of diverse software applications with different requirements can be a daunting task.  The Research Computing is adopting the ''modules'' system developed by Robert McLay at the Texas Advanced Computing Center [http://www.tacc.utexas.edu/home (TACC)] in order to ease the complexity of this process and relieve users of this burden.
==Upstream Documentation==
 
Those who would like to learn as much as possible about lmod can use the [http://www.tacc.utexas.edu/tacc-projects/mclay/lmod documentation written by the Lmod author].
 
  
 
==Basic usage==
 
==Basic usage==
See [[Modules Basic Usage]] for a practical introduction to using environment modules at HPC
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See '''[[Modules Basic Usage]]''' for a short practical introduction to using ''modules''.
  
==Transition from mpi-selector==
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==Module Command==
With the introduction of modules, the ''mpi-selector'' has been deprecated. If you have been using ''mpi-selector'' to set up your MPI environment, please see [[From mpi-selector to environment modules]] for more information.
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There is no executable called 'module' in Lmod. The 'module' command or its 'ml' alias, which you can use interactively are enabled when you <code>source /etc/profile.d/modules.sh</code> shell script inside another script or shell environment. It's done automatically for interactive sessions, but if you need access to 'module load' in a script running in a scheduled job source the above script first. Support for other shells and programming languages like python or R is also available (“sh”, “csh”, “perl”, “python”, “lisp”, “fish”, “cmake”, or “r”). See documentation for details.
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==Personal modules==
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You can write and use your own modulefiles. The procedure for making them available is very simple. For example, if you'd like to create version 1.0 of the module 'mymod' pick any directory you own, say ~/modules:
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* Create a personal module directory
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mkdir ~/modules
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* Add a 'mymod' module directory
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mkdir ~/modules/mymod
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* Add a modulefile
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touch ~/modules/mymod/1.0.lua
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Note that you can copy any modulefile we have in /apps/lmod/modulefiles to serve as a starting point for your 'mymod/1.0.lua' modulefile. To test/use the new module:
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* Run the following command or add it to your ~/.bashrc file
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module use ~/modules
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The ''"myapp/1.0"'' module should be available for your use.
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==Loading modules with Python==
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If you need to load an environment module from python set the sys.path to the Lmod installation on HPG. E.g.
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<pre>
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import os, sys
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sys.path.insert(0,"/apps/lmod/lmod/init/")
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from env_modules_python import module
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module("load","somemodule/version")
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</pre>
  
 
==Support==
 
==Support==
To request help with using modules or installation of new module enabled application please file a [http://support.hpc.ufl.edu support request] or if necessary please send us an [mailto:om@hpc.ufl.edu email].
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To request help with using modules or installation of new module enabled application please file a [https://support.rc.ufl.edu support request].
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==Upstream Documentation==
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Those who would like to learn as much as possible about lmod can use this [http://lmod.readthedocs.io/en/latest/ documentation].
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There is a well-written article on Lmod in the [http://www.admin-magazine.com/HPC/Articles/Lmod-Alternative-Environment-Modules?utm_source=ADMIN+Newsletter&utm_campaign=HPC_Update_31_Lmod_Alternative_to_Environment_Modules_2013-01-30 HPC Admin Magazine].

Latest revision as of 02:10, 2 October 2021


Introduction

Setting and maintaining your environment while running a large number of diverse software applications with different requirements can be a daunting task. The Research Computing is adopting the modules system developed by Robert McLay at the Texas Advanced Computing Center (TACC) in order to ease the complexity of this process and relieve users of this burden.

Basic usage

See Modules Basic Usage for a short practical introduction to using modules.

Module Command

There is no executable called 'module' in Lmod. The 'module' command or its 'ml' alias, which you can use interactively are enabled when you source /etc/profile.d/modules.sh shell script inside another script or shell environment. It's done automatically for interactive sessions, but if you need access to 'module load' in a script running in a scheduled job source the above script first. Support for other shells and programming languages like python or R is also available (“sh”, “csh”, “perl”, “python”, “lisp”, “fish”, “cmake”, or “r”). See documentation for details.

Personal modules

You can write and use your own modulefiles. The procedure for making them available is very simple. For example, if you'd like to create version 1.0 of the module 'mymod' pick any directory you own, say ~/modules:

  • Create a personal module directory
mkdir ~/modules
  • Add a 'mymod' module directory
mkdir ~/modules/mymod
  • Add a modulefile
touch ~/modules/mymod/1.0.lua

Note that you can copy any modulefile we have in /apps/lmod/modulefiles to serve as a starting point for your 'mymod/1.0.lua' modulefile. To test/use the new module:

  • Run the following command or add it to your ~/.bashrc file
module use ~/modules

The "myapp/1.0" module should be available for your use.

Loading modules with Python

If you need to load an environment module from python set the sys.path to the Lmod installation on HPG. E.g.

import os, sys
sys.path.insert(0,"/apps/lmod/lmod/init/")
from env_modules_python import module
module("load","somemodule/version")

Support

To request help with using modules or installation of new module enabled application please file a support request.

Upstream Documentation

Those who would like to learn as much as possible about lmod can use this documentation.

There is a well-written article on Lmod in the HPC Admin Magazine.