Sysadmin:Software Modules
We offer many different pieces of software, and each machine may have similar or different modules depending on it's specs. These range from different versions of Anaconda Python and GCC, to OpenMPI and Amber (a Molecular Dynamics package). They are all pieces of software that are installed from source and are folded into the Environment Modules software, which in a nutshell, provides a lot of flexibility when working with different versions of software.
There is a specific pattern that is followed where software is installed on both the CS side and Cluster side. For each head node of a cluster, there is a directory /mounts/<machine-name>/software/. For the CS side, software is installed on the tools server, in the directory /mnt/lovelace/software. In each of those directories, there are subdirectories for each piece of software installed, and within those directories, there are subdirectories for each version installed.
So, for example, if we have gcc versions 5.1.0, 4.7.1, and 4.9.0 installed on layout, it would look like this:
$ ls -1 /mounts/layout/software/gcc
5.1.0
4.7.1
4.9.0
/mounts/<machine-name>/software is exported via NFS to every compute node in the cluster. Similarly, /mnt/lovelace/software is exported to each Lovelace machine via NFS. This makes it so the software need only be installed once, but seen on every machine.
Software per each system
Before you install any piece of software, visit the Wiki page about the software and should it require to be installed as a module, read Environment Modules about proper installation.
tools.cs.earlham.edu
- Anaconda Python -
- GCC -
- Prolog -
- Scheme
hopper.cluster.earlham.edu
layout.cluster.earlham.edu
- Anaconda Python -
- GCC -
- Amber -
- Atlas -
- Boost -
- Caffe -
- Cgal -
- CHARMM -
- CUDA -
- Eigen -
- ffmpeg -
- fftw -
- Gromacs -
- hdf5 -
- OpenBabel -
- openBLAS -
- OpenCV -
- OpenMPI -
- Perl
- PGI Community Edition
al-salam.cluster.earlham.edu
- Anaconda Python -
- GCC -
- Amber -
- ATLAS -
- Boost -
- Cgal -
- CUDA -
- Filebench -
- fftw -
- Forrest -
- Gromacs -
- Goto -
- Hadoop -
- Maven -
- MPIBlast -
- Mpich2 -
- OpenMPI -
- Protobuff -
- rrdtool -
- scalablast
pollock.cluster.earlham.edu
- Anaconda Python -
- Boost -
- GCC -
- OpenMPI -
- Mothur
bronte.cluster.earlham.edu
- Anaconda Python -
- Boost -
- Bowtie -
- GCC -
- OpenMPI -
- Samtools -
- SRAToolkit -
- Tophat -
- Blast+