[course homepage] [Slides on using comet]

Getting started with comet

Set up an account on XSEDE

Go to https://portal.xsede.org and create an account. Send your username to me (mgymrek AT ucsd DOT edu) to be added to the class list.

Log into comet

From the command line on your computer, type:

ssh $USER@comet.sdsc.xsede.org

where $USER is your username. Note, if your XSEDE portal username is different than your comet username, you might have to use these steps:

• Sign up for DUO (top right corner when you go to https://portal.xsede.org/group/xup/profile#/
• SSH in to the log in cluster for XSEDE (using your portal username):

  ssh $USER@login.xsede.org

• Log in to comet. It will automatically detect your username.

  gsissh comet

Make sure you're added to the class allocation by typing:

show_accounts

and ensuring that you see csd524 in the list.

Navigate to your working directory

Once logged into comet, go to your directory for the course:

cd /oasis/projects/nsf/csd524/$USER

Loading tools

Many commonly used tools are preinstalled on comet. You can see available modules using the command module avail. To load a specific module, e.g. bedtools, do module load bedtools/2.25.0.

Most of the commands you'll need to load tools for this course are already pre-compiled. To automatically execute these commands upon logging into comet, add the following line to the file ~/.bash_profile:

/oasis/projects/nsf/csd524/mgymrek/utils/load_modules.sh

To load once, simply execute that script.

Data

Data files used for the course can be found in the appropriate subdirectory in:

/oasis/projects/nsf/csd524/mgymrek/data/

e.g. data for problem set 1 can be found in:

/oasis/projects/nsf/csd524/mgymrek/data/ps1

Running jobs

For compute intensive tasks, you'll need to submit jobs to the cluster. On comet this can be done using the command sbatch. This tool is documented extensively on the XSEDE page for comet and there will be example scripts available when relevant. To charge jobs to the class allocation, be sure to add the flag -A csd524 to sbatch commands.