Molecular chemistry cluster

The molecular chemistry cluster is comprised of cn100-103 and cn142 (see Molecular software). Access to the cluster needs to be requested as detailed in Requesting access.

Logging in on cn142

Once you have access to lilo and are part of the molmech group, you can access cn142. The first step is logging into lilo with 'ssh user@lilo8.science.ru.nl' (described in https://cncz.science.ru.nl/nl/howto/ssh/). Afterwards you can log into cn142 by 'ssh cn142'.

In order for the molecular modelling software to boot correctly, a set of environment variables etc. need to be set. This is achieved by 'source /opt/molmech/login_molmech.sh'. Afterwards programmes on cn142 (apart from Gaussian) should function as intended. Most programs also have their special set of settings which were compiled into modules. To see which modules are available use 'module avail'. Use 'module load X' to load module X and use 'module unload X' to unload it again. Additional options can be viewed with 'module --help'.

Cn142 directory structure

Cn142 (like many Linux systems) has the following relevant directories which you should be aware of:

• /opt stores all optional software for the node. Most modelling software is actually found at /opt/molmech with soft-link executables in /opt/molmech/bin.
• /scratch is meant for temporary data storage. When submitting computational jobs, this is where the system will most often save your working files. Keep in mind /scratch is for temporary storage and hence data can be purged without warning to the users .
• /vol which is unlike the others not a local dr

On cn142 we use SLURM for managing computational resources among so-called jobs: computational tasks. With a SLURM submission script for instance you can specify the amount of memory & CPU needed for your job and SLURM will then schedule your job and those of other users. For this we have the partition molmech. Should you wish to run larger jobs (for instance large-scale dockings with DOCK 3.8), you may need to submit the job to a different partition (other

The general intended workflow of using cn142 is:

• Do a small-scale test run with the software you intend to use. This step should be using minimal computing resources
• Submit the computational task as a SLURM-s