To request software for the KU Community Cluster, fill out the Software Request form
Modules
The Modules environment is used to manage your software environment. Unlike a traditional computer, software needs to be loaded in your environment before it is ready to use. This simplifies the management of environment variables associated with various software packages.
Some common Modules commands include:
| Command | Action |
|---|---|
module avail |
List all software packages available on the system |
module spider package |
Search and list all versions of package available on the system; for example:
module spider python |
module list |
List all packages currently added to your user environment |
module load package |
Add the default version of the package to your user environment; for example:
module load R |
module load package/version |
Add the specified version of the package to your user environment; for example:
module load R/3.4 |
module unload package |
Remove the specified package from your user environment |
module purge |
Removes all previously loaded modules from your user environment |
The KU Community Cluster uses the Lmod module environment.
Standard Environment
When you log on to the cluster and when running a job, a default stack of software will be loaded automatically.
1) compiler/gcc/8.3 2) openmpi/4.0
If you don't wish to use the standard enviornment, the command module purge will remove all modules loaded, then you can load the modules you wish
Available Software
Some modules will load the necessary dependencies automatically when loaded. Other modules with prerequisites will need the prerequisites loaded before or along with that module.
For example, the module octave/4.0.3 requires compiler/intel/17. To load the octave module, doing either
module load compiler/intel/19 module load boost/1.70.0 or module load compiler/intel/19 boost/1.70.0 (Note the prerequisite module must be first.)
Multiple Versions: Some packages list multiple compilers for prerequisites. This means that the package has been built with each version of the compilers listed.
| Module Name | Prerequisites | Description |
|---|---|---|
| abaqus/2017 | None | |
| abundantotu/0.95b | None | Requires at least compiler/gcc/6.5 |
| abyss/2.1.5 | None | Requires at least compiler/gcc/6.5 |
| allpathslg/52488 | None | |
| anaconda/4.7 | None | |
| ant/1.10.1 | None | |
| augustus/3.3.2 | compiler/gcc/6.5 | |
| bamtools/2.5.1 | compiler/gcc/6.5 compiler/gcc/8.3 | |
| bcftools/1.9 | None | |
| beagle/3.1.2 | None | |
| beast/1.10.4 | None | |
| blasr/5.3.3 | None | |
| blast+/2.9.0 | None | |
| boost/1.63.0 | compiler/gcc/6.5 compiler/gcc/8.3 | |
| boost/1.70.0 | compiler/gcc/6.5 compiler/gcc/8.3 compiler/intel/19 | |
| bowtie/1.2.3 | None | |
| bowtie2/2.3.5.1 | None | Requires at least compiler/gcc/6.5 |
| busco/3.0.2 | None | |
| bwa/0.7.17 | None | |
| caffe/1.0 | None | |
| canu/1.8 | None | |
| cdhit/4.8.1 | None | Requires at least compiler/gcc/6.5 |
| cmake/3.14.5 | compiler/gcc/6.5 compiler/gcc/8.3 compiler/intel/18 compiler/intel/19 | |
| compiler/gcc/6.5 | None | |
| compiler/gcc/8.3 | None | |
| compiler/intel/18 | None | |
| compiler/intel/19 | None | |
| compiler/pgi/19 | None | |
| cp2k/6.1/popt | None | |
| cuda/10.1 | None | |
| cuda/9.2 | None | |
| cutadapt/2.3 | None | |
| dmtcp/2.5.2 | compiler/gcc/6.5 compiler/gcc/8.3 compiler/intel/19 | |
| edirect/1.0 | None | |
| emacs/26.2 | None | |
| exabayes/1.5 | None | |
| exonerate/2.2.0 | None | Requires at least compiler/gcc/6.5 |
| fastqc/0.11.8 | None | |
| fastx_toolkit/0.0.14 | None | |
| fftw3/3.3.8 | compiler/gcc/6.5 compiler/gcc/8.3 compiler/pgi/19 | |
| flash/1.2.11 | None | |
| gatk/4.1.2.0 | None | |
| gdal/3.0.0 | None | |
| gdb/8.3 | None | |
| geos/3.7.2 | None | |
| gnuplot/5.2.7 | None | |
| grace/5.1.25 | None | |
| graphicsmagick/1.3.32 | None | |
| graphviz/2.40.1 | None | |
| gromacs/2019.3 | None | |
| gromacs/5.1.5 | None | |
| hdf5/1.10.5 | compiler/gcc/6.5 compiler/gcc/8.3 compiler/intel/19 compiler/pgi/19 | |
| hhsuite/3.2.0 | None | |
| hmmer/3.2.1 | None | |
| htslib/1.9 | None | |
| intel-mpi/18 | compiler/intel/18 | |
| intel-mpi/19 | compiler/intel/19 | |
| ipyrad/0.7.30 | None | |
| jags/4.3.0 | compiler/gcc/6.5 compiler/gcc/8.3 compiler/intel/19 | |
| java/1.8.0_212 | None | |
| jellyfish/2.2.10 | None | Requires at least compiler/gcc/6.5 |
| lammps/12Dec2018 | compiler/intel/18 | |
| lammps/12Dec2018 | None | |
| lapack/3.8.0 | None | |
| libfabric/1.8.0 | compiler/intel/19 | |
| maker/2.31.10 | None | Requires at least compiler/gcc/6.5 |
| matlab/2017b | None | |
| matlab/2019a | None | |
| molden/5.9 | None | |
| mrbayes/3.2.7 | None | |
| muscle/3.8.31 | None | |
| namd/2.13_ibverbs | None | |
| namd/2.13_multicore | None | |
| nbo/6.0 | None | |
| netcdf/4.7.0 | compiler/gcc/6.5 compiler/gcc/8.3 compiler/intel/19 compiler/pgi/19 | |
| nwchem/6.8.1 | None | |
| octave/5.1.0 | None | |
| openbabel/2.4.1 | None | Requires at least compiler/gcc/6.5 |
| openblas/0.3.6 | None | |
| openmpi/2.1 | compiler/gcc/6.5 compiler/gcc/8.3 compiler/intel/19 compiler/pgi/19 | |
| openmpi/3.1 | compiler/gcc/6.5 compiler/gcc/8.3 compiler/intel/19 compiler/pgi/19 | |
| openmpi/4.0 | compiler/gcc/6.5 compiler/gcc/8.3 compiler/intel/19 | |
| orca/4.1.2 | None | |
| pear/0.9.11 | None | |
| perl/5.30 | None | |
| picard/2.20.3 | None | |
| proj/6.0.0 | None | |
| pylammps/12Dec2018 | None | |
| python/2.7 | None | |
| python/3.7 | None | |
| qhull/7.3.2 | None | |
| qiime/1.9.1 | None | |
| qiime2/2019.4 | None | |
| qiime2/2019.7 | None | |
| qt/5.12.1 | None | Requires at least compiler/gcc/6.5 |
| quast/5.0.2 | None | |
| R/3.5 | None | |
| raxml/8.2.12 | None | |
| raxml-ng/0.9.0 | None | |
| repeatmasker/4.0.9 | None | |
| repeatmodeler/1.0.11 | None | |
| rosetta/3.10-gcc | None | |
| rosetta/3.10-intel | None | |
| rsem/1.3.1 | None | Requires at least compiler/gcc/6.5 |
| rstan/2.18.2 | compiler/gcc/6.5 compiler/gcc/8.3 | |
| rstudio/1.2.1335 | None | Requires at least compiler/gcc/6.5 |
| salmon/0.14.1 | None | |
| samtools/1.9 | None | |
| sas/9.4 | None | |
| scalapack/2.0.2 | None | |
| singularity/2.6.1 | None | |
| snap/20131129 | None | |
| sortmerna/3.0.3 | None | Requires at least compiler/gcc/6.5 |
| spades/3.13.1 | None | Requires at least compiler/gcc/6.5 |
| spark/2.4.3 | None | |
| sratoolkit/2.9.6 | None | |
| stacks/2.41 | None | Requires at least compiler/gcc/6.5 |
| stampy/1.0.32 | None | |
| starccm+/13.06 | None | |
| suitesparse/5.4.0 | None | Requires at least compiler/gcc/6.5 |
| sumatra/1.0.34 | None | |
| tbb/2019u8 | compiler/gcc/6.5 | |
| tensorflow/1.14.0 | None | |
| tensorflow-gpu/1.14.0 | None | |
| transabyss/2.0.1 | None | |
| trimmomatic/0.39 | None | |
| trinity/2.8.5 | None | |
| usearch/11.0.667 | None | |
| usearch/5.2.236 | None | |
| usearch/6.1.544 | None | |
| vasp/5.4.4 | None | |
| viennarna/2.4.13 | None | |
| vmd/1.9.3 | None | |
| vsearch/2.13.6 | None | Requires at least compiler/gcc/6.5 |
| zlib/1.2.11 | compiler/gcc/6.5 compiler/gcc/8.3 compiler/intel/19 compiler/pgi/19 |
Singularity Software Containers
| Name | Version |
|---|
