UMass Boston

A workflow is normally implemented as a script which submits a series of jobs, setting up dependencies between them. Can be used on GHPCC

Alternative #1        go to #2

Download all scripts

job-a.sh

#!/bin/bash
# Usage:
#BSUB -J "Job-a"
#BSUB -R rusage[mem=4096]
#BSUB -q short
#BSUB -W 4:00

#BSUB -e job-a.err

echo "Job-a is starting" >> workflow.log

date  >> workflow.log

sleep 60
echo "Job-a finished"  >> workflow.log
date  >> workflow.log
bsub < job-b.sh

job-b.sh

#!/bin/bash
# Usage:
#BSUB -J "Job-b"
#BSUB -R rusage[mem=4096]
#BSUB -q short
#BSUB -W 4:00

#BSUB -e job-b.err

echo "Job-b is starting"  >> workflow.log

date  >> workflow.log

sleep 60

echo "Job-b finished"  >> workflow.log
date >> workflow.log
bsub < job-c.sh

job-c.sh

#!/bin/bash
# Usage:
#BSUB -J "Job-c"
#BSUB -R rusage[mem=4096]
#BSUB -q short
#BSUB -W 4:00

#BSUB -e job-c.err

echo "Job-c is starting"  >> workflow.log

date  >> workflow.log

sleep 60
echo "Job-c finished"  >> workflow.log
date  >> workflow.log

To implement workflow using command below

bsub < job-a.sh

Check the status of the job

bjobs

Alternative #2

Download all scripts                                go top

job-a.sh

#!/bin/bash
# Usage:
#BSUB -J "Job-a"
#BSUB -R rusage[mem=4096]
#BSUB -q short
#BSUB -W 4:00

#BSUB -e job-a.err

echo "Job-a is starting" >> workflow.log

date  >> workflow.log

sleep 60
echo "Job-a finished"  >> workflow.log
date  >> workflow.log

job-b.sh

#!/bin/bash
# Usage:
#BSUB -J "Job-b"
#BSUB -R rusage[mem=4096]
#BSUB -q short
#BSUB -W 4:00

#BSUB -e job-b.err

echo "Job-b is starting"  >> workflow.log

date  >> workflow.log

sleep 60

echo "Job-b finished"  >> workflow.log
date >> workflow.log

job-c.sh

#!/bin/bash
# Usage:
#BSUB -J "Job-c"
#BSUB -R rusage[mem=4096]
#BSUB -q short
#BSUB -W 4:00

#BSUB -e job-c.err

echo "Job-c is starting"  >> workflow.log

date  >> workflow.log

sleep 60
echo "Job-c finished"  >> workflow.log
date  >> workflow.log

To implement workflow using command below

bsub < job-a.sh

bsub < job-b.sh -w Job-a

bsub < job-c.sh -w Job-b

Check the status of the job

bjobs

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