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Installing and managing LAMMPS on Caviness/DARWIN
IT-RCI does its best to maintain a variety of software packages for all cluster users. Most of these packages tend to be software libraries and tools that can be extended by users. Software having optional features or targeted optimizations would be impossible for IT-RCI to maintain to meet the specifications of every user over the lifetime of a cluster.
The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is one such program. It can be thought of as a driver for molecular dynamics simulations, with the simulation details — interatomic potentials, computed macroscopic properties, time step displacements — implemented by a variety of optional official or user-provided packages. Some of those packages are situated on top of additional libraries that may present their own optional configurational parameters, compounding the issue.
The clusters may have a few versions of a lammps package available but users are cautioned: they contain only the default functionality with which the program ships. Any additional functionalities realized by enabling packages require end users (or workgroups) to build their own copies of LAMMPS. Fortunately, the IT-RCI versions can act as a guide through this process.
Where to install
For the individual
For users who will be building and managing copies of LAMMPS solely for their own personal use, you can put the source code and compiled executables and libraries in several locations:
| Path | Cluster | Discussion |
|---|---|---|
$HOME | Both | Home directories have a quota limit of 20 GiB, so be aware of how much space each LAMMPS is consuming |
$WORKDIR | Caviness | Most workgroups manage their own directory hierarchy, including a spot for each user |
$WORKDIR_USER | DARWIN | Workgroup members have personal workgroup storage at this path |
In all three cases, IT-RCI best-practices would have the user create a directory named `sw` under the path in question, e.g.
[PROMPT]$ mkdir -p "${HOME}/sw"
to hold all managed software.
For the individual user, VALET package definitions should be created in the ~/.valet directory.
For the workgroup
If LAMMPS is meant to be shared by all members of the workgroup, it should be installed in a location visible to all members: the $WORKDIR_SW environment variable holds one such path for the workgroup in which the user is working:
[«workgroup»:PROMPT]$ echo $WORKDIR_SW /work/«workgroup»/sw
For workgroup software, VALET package definitions should be created in the ${WORKDIR_SW}/valet directory.