Software - Alphabetical List
Software Guide
There are many software that are already installed on the cluster. They can be searched and then loaded using the module system.
If the software or the specific version you want to use is not available on the cluster, you can try to install it on your own.
Please follow the guideline on this page: Software Installation InstructionTo build the application yourself, you can also use any of the programming languages available on the cluster.
If the Software available in HPC is the licensed one (see Software Guide), you need to explicitly request for it via email. To maintain the licensed software for you, you would need to contact the vendor and find out about the software and its feasibility on the HPC (license model and control). We would ask that your PI would get the HPC membership (see HPC access policy).
Software-related Tips
To get the listing of all the software installed in HPC, use the command "module spider". To see software modules available to load for the current hierarchy, use "module avail" command. Visit HPC Guide to Modules for details.
Software modules are only available to load for the hierarchy active in the shell. By default, that will be the Intel-17/OpenMPI-2.0.1 hierarchy. Switch hierarchies to use "module avail" to view available software under that hierarchy.
To check the dependency modules such as cmake, boost etc, load the depends module first "module load depends"
The path of the executable and libraries of the <software> can be obtained using the command "module display <software>"
The default binaries/executable (compiler or software) are available at /usr/bin and /usr/local/bin
The default libraries are available at /usr/lib, /usr/lib64, /usr/local/lib, /usr/local/lib64
Note that he name of the executable may have been changed in the latest version of Software. You can check the path /usr/local/<software>/bin. For e.g. for GROMACS:
ls /usr/local/gromacs/bin/
grompp_mpi pdb2gmx_mpi ....
If you are using large data-file for your jobs, please avoid copying it to the compute nodes for each job that you run. Otherwise this will increase the network traffic in the cluster. To know more about this, please contact the admin about how to run jobs with large data. Also, if your job uses large amount of resources (processors and/or memory), kindly refer to HPC FAQ and contact us.
License is needed to run the applications that have * (Asterisk) behind them. Please verify by clicking on the link to each specific application.
Applications displayed in italics are 'Not fully-supported Software'. The software has been installed on the cluster and seems to work in the small sample tests that we conducted, but has not been confirmed to fully work for wide variety of tests on the cluster.