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

Cluster Support

If you need any help with the cluster or have general questions related to the cluster, please contact crchelp@ku.edu.

In your email, please include your submission script, any relevant log files, and steps in which you took to produce the problem

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