Using pre-installed software packages

To view all of the software modules available by default, use one of the versions of this command:

• module available
• module avail
• module av

Once you find the software module you would like to use, you will need to load the package. For example:

• module load gnu7
• module load openmpi
• module load scalapack

In addition to the primary packages provided by the OpenHPC software stack, these are some of the additional software packages available in /hb/software/apps directory (note – this list is not exhaustive; please always check to see if your package might be available even if it isn’t listed here):

• bamtools-2.4.1 – analyzing and managing BAM files
• beagle-2.1
• beast 1 and 2
• bedtools-2.26.0
• bfctools-1.5
• bowtie1-2.1.1
• bowtie2-2.3.2
• cadence
• Clustal-omega v 1.2.4
• cp2k-4.1
• ffmpeg-4.0
• gatk-3.8-0
• Gaussian 09 (need to ask for access contact us)
• gsl 2.4
• Gromacs-5.1.4 and 2016.3
• hisat2-2.1.0
• hmmer-3.1b2
• java-8
• lftp-4.8.3
• MATLAB 2017b, 2018b, 2021b
• mercurial-3.7.3-1
• migrate-3.6.11
• namd-2.12
• nwchem v 6.6
• Quantum Espresso v 6.1
• R –  3.3.2, 3.4.1, and 3.5.0
• samtools-1.5
• singularity-2.4.2 and 2.3.1
• SPAdes-3.11.1
• sratoolkit-2.8.2-1
• star2-2.5.3a
• stata-15.0.0
• trinity-2.4.0.

Additional toolkits are also available. These include:

• CUDA and CUDANN
• Multiple version of Python 2 and Python 3
• The Anaconda/miniconda software distribution system
• PGI (2018) compiler toolchain (loaded via “module load hb-pgi”)

Don’t See the software you want?

Installing via Conda

Many software distributions (particularly those built on Python and R) can be installed via the conda build system. If you feel up to the task of doing this installation yourself, then please visit our guides on how to install packages on Hummingbird using the conda system. While these guides are not exhaustive, they should hopefully provide enough of a baseline for being able to do the installations yourself. If you do run into any problems however, please feel free to contact us for help.

Compiling your own software

A large selection of software is already pre-installed on the cluster, though users are also welcome to download and compile programs in their own home folder. Frequently software packages come precompiled for most linux flavors, so users are encouraged to use those versions first, if possible.

If you are planning to compile your own software, please make sure you that you set your environment variables correctly when you use the configure and/or build commands.  For almost all standard software projects, this is done by setting the --prefix= variable during the configuration step. (By default, many packages set this to /usr/local which is inaccessible to users, thus you would want to set this as --prefix=$HOME instead).

Make a request

If you would like to see a package software package added to the module system for use by yourself and others, please send in a request including the name of the software package, the version you would like installed, and a link to the software download page.