CIS Computing & Information Services

Software

Many scientific and HPC software packages are already installed on Oscar, and additional packages can be requested by submitting a ticket to support@ccv.brown.edu. If you want a particular version of the software, do mention it in the email along with a link to the web page from where it can be downloaded.

CCV cannot, however, supply funding for the purchase of commercial software. This is normally attributed as a direct cost of research, and should be purchased with research funding. CCV can help in identifying other potential users of the software to potentially share the cost of purchase and maintenance. Several commercial software products that are licensed campus-wide at Brown are available on Oscar, however.

For software that requires a Graphical User Interface (GUI) we recommend using CCV's VNC client rather than X-Forwarding.

All programs are installed under /gpfs/runtime/opt/<software-name>/<version>. Example files and other files can be copied to your home, scratch or data directory if needed.


Software modules

CCV uses the PyModules package for managing the software environment on OSCAR. The advantage of the modules approach is that it allows multiple versions of the same software to be installed at the same time. With the modules approach, you can "load'' and "unload'' modules to dynamically control your environment.

Module commands

module list Lists all modules that are currently loaded in your software environment.
module avail Lists all available modules on the system. Note that a module can have multiple versions.
module help name Prints additional information about the given software.
module load name Adds a module to your current environment. If you load using just the name of a module, you will get the default version. To load a specific version, load the module using its full name with the version: "module load gcc/6.2"
module unload name Removes a module from your current environment.

Notes

Looking for available modules and versions

Note that the module avail command allows searching modules based on partial names. For example:

 $ module avail bo

will list all available modules whose name starts with "bo".

Output:

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ name: bo*/* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
boost/1.49.0        boost/1.63.0        bowtie2/2.3.0
boost/1.62.0-intel  bowtie/1.2.0

This feature can be used for finding what versions of a module are available.

Auto-completion using tab key

Moreover, the module load command supports auto-completion of the module name using the "tab" key. For example, writing "module load bo" on the shell prompt and hitting "tab" key a couple of times will show results similar to that shown above. Similarly, the module unload command also auto completes using the names of modules which are loaded.

Modules loaded at startup

You can also customize the default environment that is loaded when you login. Simply put the appropriate module commands in the .modules file in your home directory. For instance, if you edited your .modules file to contain

module load matlab

then the default module for Matlab will be available every time you log in.

What modules actually do...

They simply set the relevant environment variables like PATH, LD_LIBRARY_PATH and CPATH. For example, PATH contains all the directory paths (colon separated) where executable programs are searched for. So, by setting PATH through a module, now you can execute a program from anywhere in the file-system. Otherwise, you would have to mention the full path to the executable program file to run it which is very inconvenient. Similarly, LD_LIBRARY_PATH has all the directory paths where the run time linker searches for libraries while running a program, and so on. To see the values in an environment variable, use the echo command. For instance, to see what's in PATH:

$ echo $PATH
/gpfs/runtime/opt/perl/5.18.2/bin:/gpfs/runtime/opt/python/2.7.3/bin:/gpfs/runtime/opt/java/7u5/bin:
/gpfs/runtime/opt/intel/2013.1.106/bin:/gpfs/runtime/opt/centos-updates/6.3/bin:/usr/lib64/qt-3.3/bin:
/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/ibutils/bin:/gpfs/runtime/bin