Hi
Rather to put in background your job, try "screen". With screen you detach your script from the shell so even if you close the shell the job keep running.
HTH
and
-----Original Message-----
From: Michael Shokhen [mailto:michael.shokhen.biu.ac.il]
Sent: 30 January 2017 17:57
To: AMBER Mailing List
Subject: Re: [AMBER] script to run background job?
Dear Elvis,
Many thanks for you advice.
It works now in background.
Michael
*****************************
Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
Israel
email: shokhen.mail.biu.ac.il<https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il>
________________________________
From: Elvis Martis <elvis.martis.bcp.edu.in>
Sent: Monday, January 30, 2017 6:35:26 PM
To: AMBER Mailing List
Subject: Re: [AMBER] script to run background job?
Can you try submitting
"./script &"
Best Regards
Elvis Martis
Ph.D. Student (Computational Chemistry)
at Bombay College of Pharmacy
A Kalina, Santacruz [E], Mumbai 400098, INDIA W www.elvismartis.in<
http://www.elvismartis.in>
Skype. adrian_elvis12
-----Original Message-----
From: Michael Shokhen [mailto:michael.shokhen.biu.ac.il]
Sent: Monday, January 30, 2017 10:02 PM
To: AMBER.ambermd.org
Subject: [AMBER] script to run background job?
Dear Amber experts,
The following script well works for running sequential jobs in foreground.
& in the end of the command is not allowed in the script.
What changes and corrections should be added to the script to run job in the background?
Thank you,
Michael
set MDINPUT=0
echo -n "Starting Script at: "
date
echo ""
while ( $MDCURRENTJOB <= $MDENDJOB )
echo -n "Job $MDCURRENTJOB started at: "
date
. MDINPUT = $MDCURRENTJOB - 1
nohup mpirun -np 2 $AMBERHOME/bin/pmemd.cuda.MPI -O -i prod.in \
-o test_md$MDCURRENTJOB.out \
-p ../ras-raf_solvated.prmtop \
-c test_md$MDINPUT.rst \
-r test_md$MDCURRENTJOB.rst \
-x test_md$MDCURRENTJOB.mdcrd
#gzip -9 -v a-dna_md$MDCURRENTJOB.mdcrd
echo -n "Job $MDCURRENTJOB finished at: "
date
. MDCURRENTJOB = $MDCURRENTJOB + 1
end
echo "ALL DONE"
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Received on Tue Jan 31 2017 - 00:30:03 PST
