Useful sun grid engine commands

[Michael Cianfrocco]

qstat

Lists jobs that are in the queue

qstat -g c

Displays the number of total, avialalbe, and busy CPUs within cluster

 

qstat -f 

Shows a list of cluster nodes along with total number of CPUs and number of CPUs being used 

qsub 

Used to submit jobs to the cluster (e.g. $ qsub submit.csh)

qdel

Delete job from cluster using the job number (e.g. $ qdel 2)

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Sun grid engine options to specify in submission script 

Below is a typical submission script for a relion refinement: 

#!/bin/bash

#$ -cwd                #Run from current working directory

#$ -S /bin/bash        #Shell

#$ -pe orte 64         #Number of CPUs to use

#$ -q all.q            #Queue type. Default = all.q

#$ -V                  #Specify same running environment

#$ -N r3_8xlarge_2     #Name of job

mpirun relion_refine_mpi --o Class3D/run_r3_8xlarge_2 --i particles_sel.star --particle_diameter 350 --angpix 3.54 --ref ref_filt60A_sca.mrc --firstiter_cc --ctf --iter 2 --tau2_fudge 2 --K 4 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 3 --offset_range 5 --offset_step 2 --sym C1 --norm --scale  --j 1 --memory_per_thread 10