Cluster Commands and Tricks 06/09/11

Every node has 8 cores 16GB of RAM

Useful Commands for the cluster:

List Queues and times of execution

scontrol show partitions

List Jobs


Cancel Job (jobid)

scancel -v 179

List nodes status


Submit a process

srun -p long|medium|shot| -w veredas17 -o output_file COMMAND
Example of a command:
srun -p medium -o piccard java -jar ../../bin/picard-tools-1.52/SamFormatConverter.jar INPUT=../alignment/aln.sam OUTPUT=exome.bam VALIDATION_STRINGENCY=LENIENT TMP_DIR=/tmp