Lonestar

From Henkelman Group

Example submit script:

bsub < vasp.bsub

[edit] Commands

bjobs: see status of the jobs current user is running
showq: see the list of all jobs on the lonestar2 nodes
showq -u:see the list of the current user's jobs on lonestar2 nodes
quota: see how much space you've used

[edit] Setting up an account

When using Lonestar2 make sure to keep all work in your work directory and not your home directory. There is a strict quota on the disk usage in your home directory. If this quota is exceeded, for example by running a job in your home, the job will simply die.

For those with a muskoka account:

First, copy over the .cshrc, .tcshrc, and .alias from your muskoka account to your home directory on the TACC machines to have the environment set up as on muskoka. BUT, the .cshrc should be renamed .cshrc_user to work with the systems at TACC. Do not overwrite your .cshrc file on lonestar.

The files can be moved using the scp command:

scp username@muskoka.cm.utexas.edu:file target

where path is the path to the files you are copying. For example, on lonestar use:

scp muskoka.cm.utexas.edu:.cshrc ~/.cshrc_user
scp muskoka.cm.utexas.edu:.tcshrc ~/.tcshrc
scp muskoka.cm.utexas.edu:.alias ~/.alias 

Create a bin/ directory in your home directory and grab the required scripts from CVS. This should make all the muskoka commands work on the TACC machines as well as the other scripts in the directories:

mkdir ~/bin
cd bin
cvs checkout vtstscripts
cvs checkout bader

Lastly, you can prevent lonestar from automatically deleting your files every two weeks by adding a crontab. To do so, type "crontab -e". The editor is vi. To insert text, press "i" and type:

10 0 * * 1 find /work/utexas/ch/username -exec touch {} \;
10 0 * * * find /work/utexas/ch/username -exec chmod g+rX {}\;

where username is your username. Save and quit by pressing the Esc key, and then typing :wq.

[edit] Possible Errors

Run outputs nothing

Check to make sure the id_rsa and authorized_keys files in your .ssh directory have only read/write permission by the owner (you). You can do this with the commands

chmod go-rwx ~/.ssh/id_rsa
chmod go-rwx ~/.ssh/authorized_keys

ll_err file cannot link to child process

Check to see if your submit files are in order. Sometimes typos mess things up.