Requesting Resources - Reference

If youve read this document up to this point you should be able to submit simple jobs using default resources. For most serious jobs, the default resources are insufficient, and to effectively use the cluster you need to learn how to specifically request resources. In TORQUE, there are two methods you can use to request resources, directives and command line arguments.

In subsequent examples both forms will be demonstrated. Both forms may also be freely mixed, however, the command line arguments take priority over directives. For this most people find it useful to define a complete set of directives with all the defaults necessary for the job, and use command line arguments to adjust certain variables such as walltime or queue according to the specific needs of their input set.

All examples in this section will be using a script similar to that at the end of the preceding section. However, only the first lines of the script will be demonstrated in the directive examples. The practium section will then submit jobs using the two methods and you can compare it against the baseline to see the differences.

blast.sh :

#!/bin/bash

echo âScript begins hereâ
cd $PBS_O_WORKDIR

# setup and copy workdir
LOCAL_WORKDIR=/tmp/$USER/$PBS_JOBID
mkdir -p $LOCAL_WORKDIR
cp -r * $LOCAL_WORKDIR
cd $LOCAL_WORKDIR

/opt/bio/ncbi/bin/blastall -p blastp -i sv.fasta -d /library/yzhang/nr/nr -o blast.out -O blast.seq

# copy back data
cp -r * $PBS_O_WORKDIR
cd $PBS_O_WORKDIR

# cleanup
rm -rf $LOCAL_WORKDIR

Job baseline for blast.sh:

Job Id: 2498949.umms-amino.ccmb.med.umich.edu 
    Job_Name = blast.sh 
    Job_Owner = jdpoisso@umms-amino.ccmb.med.umich.edu 
    job_state = R 
    queue = default
    server = umms-amino.ccmb.med.umich.edu 
    Checkpoint = u 
    ctime = Mon Aug 23 10:20:59 2010 
    Error_Path = umms-amino.ccmb.med.umich.edu:/home/jdpoisso/blast_test/blast 
	.sh.e2498949
    exec_host = compute-4-5/0 
    Hold_Types = n 
    Join_Path = n 
    Keep_Files = n 
    Mail_Points = a 
    mtime = Mon Aug 23 10:21:00 2010 
    Output_Path = umms-amino.ccmb.med.umich.edu:/home/jdpoisso/blast_test/blas 
	t.sh.o2498949
    Priority = 0 
    qtime = Mon Aug 23 10:20:59 2010 
    Rerunable = True 
    Resource_List.nodect = 1 
    Resource_List.nodes = 1 
    Resource_List.walltime = 01:00:00 
    session_id = 11639 
    substate = 42 
    Variable_List = PBS_O_HOME=/home/jdpoisso,PBS_O_LANG=en_US.iso885915, 
	PBS_O_LOGNAME=jdpoisso, 
	PBS_O_PATH=/usr/kerberos/bin:/usr/java/latest/bin:/usr/local/bin:/bin 
	:/usr/bin:/opt/bio/ncbi/bin:/opt/bio/mpiblast/bin/:/opt/bio/hmmer/bin: 
	/opt/bio/EMBOSS/bin:/opt/bio/clustalw/bin:/opt/bio/tcoffee/bin:/opt/bi 
	o/phylip/exe:/opt/bio/mrbayes:/opt/bio/fasta:/opt/bio/glimmer/bin://op 
	t/bio/glimmer/scripts:/opt/bio/gromacs/bin:/opt/bio/gmap/bin:/opt/bio/ 
	tigr/bin:/opt/bio/autodocksuite/bin:/opt/ganglia/bin:/opt/ganglia/sbin 
	:/opt/openmpi/bin/:/opt/maui/bin:/opt/torque/bin:/opt/torque/sbin:/opt 
	/rocks/bin:/opt/rocks/sbin:/opt/sun-ct/bin:/home/jdpoisso/bin, 
	PBS_O_MAIL=/var/spool/mail/jdpoisso,PBS_O_SHELL=/bin/bash, 
	PBS_O_HOST=umms-amino.ccmb.med.umich.edu, 
	PBS_SERVER=umms-amino.ccmb.med.umich.edu, 
	PBS_O_WORKDIR=/home/jdpoisso/blast_test,PBS_O_QUEUE=urgent 
    euser = jdpoisso 
    egroup = jdpoisso 
    hashname = 2498949.umms-amino.ccmb.med.umich.edu 
    queue_rank = 2463766 
    queue_type = E 
    etime = Mon Aug 23 10:20:59 2010 
    submit_args = blast.sh 
    start_time = Mon Aug 23 10:21:00 2010 
    Walltime.Remaining = 359 
    start_count = 1 
    fault_tolerant = False