Software Collection Upgrade

During the December 10-12, 2018 Milgram scheduled maintenance, we will be switching the default module collection. This upgrade will make the cluster more consistent with our other clusters' software environments and allow us to resolve software installation requests more quickly. The old software collection will be available for the time being (see below), but all new software installations will go into the new collection.

Key Differences

Module Names

The new module collection is built using a tool called "EasyBuild", which uses a system of "toolchains" to more transparently constrain software dependencies and compatibility. See this page for more information on EasyBuild and toolchains. As such, modules will no longer be prefixed with a category such as "Apps" or "Langs", but instead will have a suffix describing its toolchain (if applicable).

# old:
module load Apps/Octave/4.2.1
# new: 
module load Octave/4.2.1-foss-2016b

You will need to update your scripts to load modules using their new names.

Python and R

With the growth of users on our clusters, installing and maintaining central versions of Python and R with all the requested packages has become extremely complicated and unsustainable. As such, our recommendation is now to install a personal Python environment using conda and required R packages using the built-in "install.packages()" which will install the packages of your choosing into your home directory. If you run into any difficulty with these environments, we are happy to help--just email us at hpc@yale.edu.

To Try and/or Switch to the New Collection

To try the new collection and see if all the software you require is available (email us if anything is missing!), run the following command:

source /apps/bin/try_new_modules.sh

This will switch your module collection (visible via "module avail") to the new one for that session. To revert, simply log out and log back in. To switch permanently, run "module save" after running the above command.

To Use Old Software

To use any of the old software, run the following commands on the Milgram login node:

module use /gpfs/milgram/apps/hpc/Modules
module save

Then you should see all the old software if you run "module avail". To then remove the old software collection from your list, run:

module unuse /gpfs/milgram/apps/hpc/Modules
module save

We will be deprecating the old software at a TBD date, so we encourage you to contact us if anything is missing or not working for you in the new collection.