Using this repository on HPC resources

Links to documentation

• Summit
• Bridges

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Setting up python

The supercomputing resource you are using may have a python distribution already installed. Sometimes this is sufficient for everything in this repository. But usually not. Here is how to use the installed python modules, but bear in mind that you'll probably need to install your own version of anaconda.

Check to see what versions of python are already available:

Summit: First you must ssh onto a compile node: ssh scompile. Next type module spider python or module avail python and you will be presented with a list of available modules. Load the module with module load python/x.x.x.

Bridges: module avail python will list all available versions. Bridges has a lot of python modules and many (most) of them don't have numpy or are compiled wrong. Your best hope is to use python/3.6.4_gcc5_np1.14.5.

There are a few modules that you will need to download in order to be fully compatible with the scripts in this repository. On your local workstation, you can just run sudo pip install module_name, but that doesn't work on a community resource such as Bridges or Summit since the root directory does not belong to any individual users. Each system has their own way of installing python packages:

Summit: See these instructions.

Bridges: Just run pip install --user package_name

For full compatibility with this repository, you'll need to download the following modules: \

• mdtraj
• tqdm
• pymbar

Chances are, something will go wrong with the pre-installed python modules. For example, mdtraj does not install properly on Summit. Research computing advised me to install anaconda myself. In order to install anaconda, download the linux version of the package from their website.