Getting started with comet
Set up an account on XSEDEGo 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 cometFrom the command line on your computer, type:
$USERis 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):
- Log in to comet. It will automatically detect your username.
csd524in the list.
Navigate to your working directoryOnce logged into comet, go to your directory for the course:
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.
DataData files used for the course can be found in the appropriate subdirectory in:
Running jobsFor 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 csd524to sbatch commands.