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
module load legacy Access software compiled before CRC transition of cluster.

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/6.3   2) python/3.6   3) anaconda/4.3   4) openmpi/2.0   5) StdEnv

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/17
module load octave/4.0.3

or

module load compiler/intel/17 octave/4.0.3 (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/2018 None
abundantotu/0.93b None
abyss/1.5.2 None
anaconda/4.3 None
annovar/2017Jun01 None
augustus/3.3 compiler/gcc/4.9 compiler/gcc/5.4 compiler/gcc/6.3
bamtools/2.4.1 compiler/gcc/4.9 compiler/gcc/5.4 compiler/gcc/6.3 compiler/intel/17
bcftools/1.4.1 None
beagle/3.0.0 None
blasr/5.3.0 None
blast+/2.6.0 None
blast/2.2.26 None
boost/1.63.0 compiler/gcc/4.9 compiler/gcc/5.4 compiler/gcc/6.3 compiler/intel/17
bowtie/1.1.2 None
bowtie2/2.3.4.1 None
breakdancer/1.4.5 None
bwa/0.7.15 None
canu/1.5 None
cloudforest/20140912 None
cmake/3.8.2 compiler/gcc/4.9 compiler/gcc/5.4 compiler/gcc/6.3 compiler/intel/17 compiler/intel/17.4
compiler/gcc/4.9 None
compiler/gcc/5.4 None
compiler/gcc/6.3 None
compiler/intel/17 None
compiler/intel/17.4 None
compiler/pgi/14 None
compiler/pgi/15 None
cp2k/4.1/popt None
cp2k/4.1/sopt None
cp2k/6.0/popt None
cuda/8.0 None
cuda/9.0 None
dmtcp/2.5.1 None
exonerate/2.2.0 None
fastqc/0.11.5 None
ffindex/0.9.9 None
fftw3/3.3.6 compiler/gcc/4.9 compiler/gcc/5.4 compiler/gcc/6.3
fftw3/3.3.7 compiler/intel/17 compiler/intel/17.4
gatk/3.7-0 None
git/2.13.2 None
grace/5.1.25 None
gromacs/5.1.4 None
hdf5/1.8.19 compiler/gcc/4.9 compiler/gcc/5.4 compiler/gcc/6.3 compiler/intel/17 compiler/intel/17.4
hdf5/1.10.1 compiler/gcc/4.9 compiler/gcc/5.4 compiler/gcc/6.3 compiler/intel/17 compiler/intel/17.4
hhsuite/3.0-beta2 None
hmmer/3.1b2 None
htslib/1.7 compiler/gcc/4.9
intel-mpi/17 compiler/intel/17 compiler/intel/17.4
jags/4.3.0 compiler/gcc/4.9 compiler/gcc/5.4 compiler/gcc/6.3
java/1.8.0_131 None
lammps/11Aug17-gpu None
lammps/11Aug17 None
lammps/16Mar18-gpu None
lammps/16Mar18 None
lapack/3.7.1 compiler/gcc/4.9 compiler/gcc/5.4 compiler/gcc/6.3
legacy None
maker/2.31.9 None
matlab/2016b None
matlab/2017b None
mirdeep2/2.0.0.8 None
molden/5.7 None
mplus/7.3_combo None
mrbayes/3.2.6 None
muscle/3.8.31 None
namd/2.12_ibverbs None
namd/2.12_multicore None
namd/20171121_multicore compiler/intel/17
netcdf/4.1.1 None
netcdf/4.5.0-rc1 None
octave/4.0.3 compiler/intel/17
openmpi/1.10 compiler/gcc/4.9 compiler/gcc/5.4 compiler/gcc/6.3 compiler/intel/17 compiler/intel/17.4 compiler/pgi/14 compiler/pgi/15
openmpi/2.0 compiler/gcc/4.9 compiler/gcc/5.4 compiler/gcc/6.3 compiler/intel/17 compiler/intel/17.4 compiler/pgi/14 compiler/pgi/15
orca/4.0.0.2 None
pear/0.9.10 None
perl/5.22 None
picard/2.9.2 None
pypy3/5.9.0 None
python/2.7 None
python/3.4 None
python/3.5 None
python/3.6 None
qiime/1.9.1 None
qiime2/2017.12 None
qt/4.8.6 None
qt/5.9.0 None
R/3.3 None
R/3.4 None
raxml/8.2.11 None
repeatmasker/4.0.6 None
rosetta/3.8 None
rsem/1.3.0 None
rstudio/1.0.153 None
samtools/1.4.1 None
scalapack/2.0.2 None
singularity/2.5.2 None
snap/20131129 None
stampy/1.0.32 None
StdEnv None
usearch/5.2.236 None
usearch/6.1.544 None
vasp/5.4.1 None
viennarna/2.4.6 None
vmd/1.9.3 None
vsearch/2.4.3 None

Singularity Software Containers

Name Version
stacks 2.1
tensorflow 1.9.0
tensorflow gpu 1.9.0

CRC Help

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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