Interactive jobs via scheduler

You can use node n6 (ssh n6), for simple interactive prototyping, low-load installations etc., but if you need to run large interactive jobs, please let the scheduler allocate the resources that you need.

Request interactive shell

Using option -I (upper case i) will tell qsub that you want an interactive job shell, e.g.

{cclc01}$ qsub -I
qsub: waiting for job 693822.cclc01.som.ucsf.edu to start
qsub: job 693822.cclc01.som.ucsf.edu ready
{n3}$: echo $PBS_NUM_PPN  ## Maximum number of parallel tasks
1
{n3}$: 

This will give a single-core slot on any machine that the scheduler finds suitable (here it happened to be n3). From here on you can use the terminal as a regular terminal. Your job is listed by qstat -u $USER just like any other jobs. As soon as you log out, the job will be freed.

Request interactive shell for high-memory multi-core processing

To run multi-core processes interactively, you can request more cores. Likewise, you can specify memory needs and other resources. For instance, if you need four cores and 10 GiB of RAM, use:

$ qsub -I -l nodes=1:ppn=4 -l vmem=10gb
qsub: waiting for job 693829.cclc01.som.ucsf.edu to start
qsub: job 693829.cclc01.som.ucsf.edu ready
{n2}$: echo $PBS_NUM_PPN  ## Maximum number of parallel tasks
4
{n2}$: