Cluster Grid

How to submit and view the output of jobs from a Makefile

Usually this little bit of code should be handy. You can submit a job, say hello_world from the makefile,and you can also track the job and see its output.

This code is available on fep.grid.pub.ro in /srv/ncitCluster/examples/BasicMPI_Makefile.

Output example:

[heri@fep mpi]$ make run_fep
mpicc -o hello_sun hello_world.c
Running job: 52526
Job queued: .............................................
Running. Job started: Tue Dec 30 18:33:24 EET 2008
Job ended: Tue Dec 30 18:34:11 EET 2008
==> hello_sun.10514.e <==
 
==> hello_sun.10514.o <==
Hello world from process 4 of 12
Hello world from process 3 of 12
Hello world from process 1 of 12
Hello world from process 5 of 12
Hello world from process 6 of 12
Hello world from process 11 of 12
Hello world from process 9 of 12
Hello world from process 8 of 12
Hello world from process 10 of 12
Hello world from process 7 of 12
 

The makefile looks like this:

#Author: Heri
#Date: 30dec08
 
PROG_NAME := hello_sun
NPROCS := 12
TMPFILE := ${PROG_NAME}.${shell echo $$RANDOM}
JID := ${shell set `qsub -q ibm-quad -pe ibm-quad ${NPROCS} -cwd -N
${PROG_NAME} \
-e ${TMPFILE}.e -o ${TMPFILE}.o -b y \
"/opt/openmpi/default/bin/mpirun -np ${NPROCS} ./${PROG_NAME}"` ;
echo $$3}
 
all:
@echo "Usage: make run_fep"
compile:
mpicc -o ${PROG_NAME} hello_world.c
run_fep: compile
@echo "Running job: ${JID}"
@sleep 2
@echo -ne "Job queued: "
@JSTATUS=`qstat | grep ${JID}` ; while [ `echo $$JSTATUS | wc -l`
-gt 0 ] ; do set $$JSTATUS ; \
case $$5 in \
*q*) echo -ne "." ; sleep 1 ;; \
E*) echo "Sheduling error" ; exit 2 ;; \
r|t) echo "" ; echo "Running. Job started: `date`" ; break ;; esac
; \
JSTATUS=`qstat | grep ${JID}` ; done
@while [ `qstat | grep ${JID} | wc -l` -gt 0 ] ; do sleep 1 ;
done
@echo "Job ended: `date`"
@tail --retry ${TMPFILE}.e ${TMPFILE}.o 2>/dev/null
@rm ${TMPFILE}.e ${TMPFILE}.o
clean:
rm ${PROG_NAME}