[gmx-users] running in background?

[Mario Orsi]

Hi gmx users,
How is it possible to put a simulation running in the
"background" so that the job continues running
after closin' the command shell/loggin' off?
-mario

"Alone, alone, all all alone
Alone on the wide wide Sea;
And Christ would take no pity on
My soul in agony." -Coleridge






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[Peter Zoon]

just add & at the end of your commandline.

eg. mdrun -deffnm output &

cheers

Post by Mario Orsi
Hi gmx users,
How is it possible to put a simulation running in the
"background" so that the job continues running
after closin' the command shell/loggin' off?
-mario
"Alone, alone, all all alone
Alone on the wide wide Sea;
And Christ would take no pity on
My soul in agony." -Coleridge
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[Oliver Beckstein]

Post by Mario Orsi
How is it possible to put a simulation running in the
"background" so that the job continues running
after closin' the command shell/loggin' off?

Under Linux I use 'nohup' which lets a command ignore hangup signals
(which are emitted by the shell on logout), and redirect all terminal
output into a file (which I delete after the job has completed).

(b)ash:

nohup mdrun [options] >output.log 2>&1 &

(t)csh:

nohup mdrun [options] >& output.log &

Oliver

[Karsten Suhre]

Post by Oliver Beckstein

Post by Mario Orsi
How is it possible to put a simulation running in the
"background" so that the job continues running
after closin' the command shell/loggin' off?

Under Linux I use 'nohup' which lets a command ignore hangup signals
(which are emitted by the shell on logout), and redirect all terminal
output into a file (which I delete after the job has completed).
nohup mdrun [options] >output.log 2>&1 &
nohup mdrun [options] >& output.log &

If you start you nohup via ssh this may hang your shell. In such cases you may
try the following:

prompt> at now -f script.sh

and put a command like

mdrun [options] >output.log 2>&1

into the file script.sh

Kind regards,

Karsten.

[Michael Brunsteiner]

Post by Mario Orsi
Hi gmx users,
How is it possible to put a simulation running in the
"background" so that the job continues running
after closin' the command shell/loggin' off?

In a terminal on any unix machine you say, e.g,:
"mdrun -s topol.tpr >& out &"
(the 2nd apersand makes the job go into the background)
Then you can close the window and log off.
The output that you normally see on the screen goes
into the file "out". (be careful, any error-messages also
go there, check the file bedore you log off)
If the job's already running you can put it in the background by
1) press Ctrl-Z
2) enter the command "bg"
then you will lose whatever goes to stdout and stderr
but that doesn't matter in most cases.

Post by Mario Orsi
-mario
"Alone, alone, all all alone
Alone on the wide wide Sea;
And Christ would take no pity on
My soul in agony." -Coleridge
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http://companion.yahoo.it
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gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
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