Users may need to run jobs interactively sometimes. Such jobs should not be run on the SCC login node.
Instead allocate an interactive node as described below, and run the interactive job there.
[user@scc] $ srun -p debug -N 1 --ntasks-per-node=2 --mem 1024 --pty bash [user@node02]$ cd /genome/scratch/group/user/myruns [user@node02]$ module load BEDTOOLS2 [user@node02]$ cd /genome/scratch/group/user/myruns/run1 [user@node02]$ bamToBed -i input.bam > output.bed [user@node02]$ ........... [user@node02] exit [user@scc]$
The srun command above will allocate a node with at least 1 GB of memory. If you need more than that, you can specify the memory requirement on the srun command line, will allocate a node with 10 GB of memory.
[user@scc]$ srun -p debug -N 1 --ntasks-per-node=2 --mem 10240 --pty bash
Interactive are only allowed in debug and gpu partition on Scc Cluter. The maximum walltime allowed is 2 hours.