High Performance Computing

After installing an application, variables such as PATH and LD_LIBRARY_PATH must be set in order to call the application from any directory. The preferred method of setting the environment is to use the module load command. Typing module avail shows the modules installed by staff that are available system wide.

Users may also create their own custom modules.

Creating a custom module

Here is the general procedure to create a module for user maintained software.

Make a directory for the module files:

mkdir /usr/local/usrapps/$GROUP/modulefiles

In the modulefiles directory, make a directory for each software, e.g.,
```
mkdir /usr/local/usrapps/$GROUP/modulefiles/appname
```
In the directory appname, create a text file appropriately named to indicate version number and, if applicable, the compiler version. The staff naming convention for modules is generally
appname/[app version number]-[name and version of compiler]
Module files start with the line
```
#%Module
```
followed by definitions for the environment variables. To see examples of how to define the environment variables, see the contents of various staff created modules here: /usr/local/apps/modulefiles. For an example of a more complex module file, see one of the Intel modules, e.g., /opt/intel/modulefiles/intel/2017.1.132.
The default module can be set by creating a text file called .version in the directory /usr/local/usrapps/$GROUP/modulefiles/appname/ containing
```
#%Module
set ModulesVersion [app version number]-[name and version of compiler]
```

Loading a custom module

To load the module, the whole path may be specified

module load /usr/local/usrapps/$GROUP/modulefiles/appname/[app version number]-[name and version of compiler]

Alternatively, the path to the modulefiles can be added by doing the following. (Do not add a slash '/' after modulefiles.)

module use --append /usr/local/usrapps/$GROUP/modulefiles

After doing module use --append, the custom modules should be visible when typing module avail, and then modules may be loaded as usual:

module load appname

Example

Here is a full example of creating a module. This was done to install and create a module for SPAdes in the software group bioinfo. (Only members of bioinfo can access this module.)

Install the application

The following was done to install SPAdes:

mkdir /usr/local/usrapps/bioinfo/spades
cd /usr/local/usrapps/bioinfo/spades
wget http://cab.spbu.ru/files/release3.14.0/SPAdes-3.14.0-Linux.tar.gz
tar -xzf SPAdes-3.14.0-Linux.tar.gz
rm SPAdes-3.14.0-Linux.tar.gz

This results in a directory called SPAdes-3.14.0-Linux, containing the directories

bin     #contains the executables
share   #often contains documentation

Create the module

To create the module, first create the modulefiles and appname directories:

mkdir /usr/local/usrapps/bioinfo/modulefiles
cd /usr/local/usrapps/bioinfo/modulefiles
mkdir spades
cd spades

SPAdes was downloaded as a binary executable rather than being compiled; therefore, the naming convention is appname/[app version number]. The version number was 3.14.0.

From the directory /usr/local/usrapps/bioinfo/modulefiles/spades, create a text file called 3.14.0 containing

#%Module
prepend-path PATH {/usr/local/usrapps/bioinfo/spades/SPAdes-3.14.0-Linux/bin};

Set the default module

In case there are or will be other versions of SPAdes installed, set 3.14.0 as default by creating a file /usr/local/usrapps/bioinfo/modulefiles/spades/.version containing

#%Module
set ModulesVersion 3.14.0

Call the module

The module for SPAdes may be called from the command line or from an LSF batch script by doing

module load /usr/local/usrapps/bioinfo/modulefiles/spades/3.14.0

or by doing

module use --append /usr/local/usrapps/bioinfo/modulefiles
module load spades

Set the modules path to be available on login

To make the modules available upon logging in, without having to specify the full path or doing module use, add the following to the ~/.tcsh or ~/.bashrc file:

#User defined modules
module use --append /usr/local/usrapps/bioinfo/modulefiles

Usually modifications to the login files (.tcsh, .bashrc., .login) are discouraged, but this an appropriate use case for modifying those files.

Custom Modules