The "jasmin-sci" software environment

This article describes the "jasmin-sci" software environment on JASMIN. It covers the following topics:

  • Overview of the "jasmin-sci" software environment
  • Activating and deactivating the "jasmin-sci" environment
  • Using the "jasmin-sci" environment with Jaspy

Overview of the "jasmin-sci" software environment

The jasmin-sci software environment is intended as a supplement to Jaspy and contains extra software packages for use with scientific data analysis which, for various reasons, are not provided as part of Jaspy itself.  These packages are generally installed on the same CentOS7 machines where Jaspy is available, so, for example, this will include the new "sci" machines (e.g. and CentOS7 LOTUS nodes, but would not include the login gateway machines.  It is not intended for jasmin-sci in itself to provide a complete suite of analysis software.

The packages included in jasmin-sci are provided via RPMs.  A list of explicitly included packages can be seen using the command "rpm -qR jasmin-sci", although some additional packages may be installed to satisfy dependencies.

The packages fall into two categories:

  • Packages provided by standard RPM repositories (example "gnuplot") - these are installed into ordinary system paths (such as /usr/bin/gnuplot for the gnuplot program) and require no special setup in order to run.  So if you are on a relevant machine, you should just be able to type "gnuplot".
  • Packages which we have built locally for use on JASMIN (although most are third-party software).  To avoid any potential later conflicts with standard packages, they are installed under the path /opt/rh/jasmin-sci/ rather than in system paths.  Also, the RPM package names, as can be seen in the above "rpm -qR jasmin-sci" command, are prefixed with "jasmin-sci-".  So for example, the local build of "nccmp" (a program to compare netCDF files) is a package called jasmin-sci-nccmp, and the executable is at /opt/rh/jasmin-sci/root/usr/bin/nccmp.  Before these packages can be conveniently used, it is necessary to "activate" the environment as described below, so that when you type e.g. "nccmp" the relevant files can be found.

Unlike the Jaspy environments, jasmin-sci can only provide one version of each package at a time, so the versions are subject to change when updates are done.  If we anticipate any important changes, then we will notify JASMIN users by email.

In a few cases, software packages are provided in jasmin-sci which are also provided in Jaspy.  This is only done where other RPM packages depend on it.  For example, the netcdf package is provided in Jaspy, but is also installed as an RPM because the nccmp package requires it.  This means that copies of the netCDF libraries exist both in Jaspy (for the full path, type "nc-config --libs" after activating Jaspy) and also under /usr/lib64 (from the RPM).  When linking code to the netCDF library, it is recommended to use the one in Jaspy because this will be version controlled.  Also, although the jasmin-sci software might provide some software that happens to be implemented in Python, any such Python modules are not intended to be imported into your own code.  For Python development, packages from Jaspy should be used.

The development for jasmin-sci takes place via the extra-sci-packages GitHub repository, and an associated issues page.  The readme file on the repository has some package-specific documentation (including how to build the python bindings for Misr toolkit).

Activating and deactivating the "jasmin-sci" environment

To activate the jasmin-sci environment, use the command:

module load jasmin-sci

and to deactivate it, use the command:

module unload jasmin-sci

("add" and "purge" can also be used).

The "module load" command must be done in each session, or added to your $HOME/.bashrc file.

As mentioned above, this is only required for a subset of packages in jasmin-sci.  The majority of packages do not require it, but for example, those which do include ferret, and the leafpad (notepad-like) editor.

Ferret users should note that it is still necessary to do "source" after activating jasmin-sci, in order for ferret to find all its additional resource files.

Using the "jasmin-sci" environment with Jaspy

To activate both jasmin-sci and Jaspy, it is best to activate them in the following order:

module load jasmin-sci
module load jaspy

This will ensure that in the unlikely event of an executable in Jaspy also existing under /opt/rh/jasmin-sci/, then one in Jaspy will take priority.

The corresponding "module unload" commands can be done in either order.

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