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
$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 $USER@login.xsede.org
- Log in to comet. It will automatically detect your username.
gsissh comet
show_accounts
csd524
in the list.
Navigate to your working directory
Once logged into comet, go to your directory for the course:
cd /oasis/projects/nsf/csd524/$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
.
~/.bash_profile
:
/oasis/projects/nsf/csd524/mgymrek/utils/load_modules.sh
Data
Data files used for the course can be found in the appropriate subdirectory in:
/oasis/projects/nsf/csd524/mgymrek/data/
/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 commandsbatch
. 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.