Setting up Scientific Software
From Debian Clusters
Software needs vary widely amongst clusters depending on who is using the cluster and for what purpose. My experience is limited to the scientific research done on my campus, but I'll cover how to install two commonly used molecular dynamics packages - gromacs and NAMD - and mpiBLAST, a parallel implementation of BLAST for searching large databases of nucleotides or proteins.
Some packages may not be available through an apt repository. (In other words, you may not have the option to apt-get them.) For others, the source may be better because the apt version used might be out-of-date, or a more customized installation is needed. For these reasons and more, it's often better to install scientific software packages from source, using the Source Installation Paradigm.
The three software packages I'll show the installation for all require an implementation MPI, a parallel programming standard, in order to run. My MPI implementation of choice is MPICH. MPICH or a similar MPI implementation will need to be installed before installing gromacs, NAMD, or mpiBLAST.
Where to Start
If you're unfamiliar with installing software from source, check out the Source Installation Paradigm page. Then, make sure you have MPICH installed and running. Finally, pick a software package you're interested in installing:
