AMBER Archive (2009)

Subject: Re: [AMBER] Different simulation times for similar systems

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Dec 14 2009 - 12:11:56 CST

it doesn't look like the jobs are taking a significantly different amount of
time per step. maybe one of the nodes has a problem?

On Mon, Dec 14, 2009 at 7:31 AM, Oliver Kuhn <oak.amber_at_web.de> wrote:

> Hi amber users,
>
> I am simulating two HIV protease - inhibitor complex simulations (wildtype
> and l76v mutant).
>
> I am running the two systems (with equal setups) on our cluster for similar
> times:
>
> 1580 knecht nmwWT_si kuhn R 5-22:44:00 1 node08
> 1582 knecht nmw76_si kuhn R 5-22:42:00 1 node12
>
> The wt system has already gone to the 5. ns (each production phase is 0.5
> ns) while the l76v system is still simulating the second ns.
>
> Preliminary results (timings):
>
> ### WT ###
> ==> wt/min.out <==
> | Total time 296.05 (100.0% of ALL )
> | Job began at 14:09:47.361 on 12/08/2009
> | Setup done at 14:09:49.789 on 12/08/2009
> | Run done at 14:14:43.414 on 12/08/2009
>
> ==> wt/heat.out <==
> | Total time 26210.07 (100.0% of ALL )
> | Job began at 14:14:47.666 on 12/08/2009
> | Setup done at 14:14:49.719 on 12/08/2009
> | Run done at 21:31:37.741 on 12/08/2009
>
> ==> wt/prod01.out <==
> | Master Total wall time: 53294 seconds 14.80 hours
>
> ==> wt/prod02.out <==
> | Master Total wall time: 52230 seconds 14.51 hours
>
> ==> wt/prod03.out <==
> | Master Total wall time: 54318 seconds 15.09 hours
>
> ==> wt/prod04.out <==
> | Master Total wall time: 49513 seconds 13.75 hours
>
> ==> wt/prod05.out <==
> | Master Total wall time: 49742 seconds 13.82 hours
>
> ==> wt/prod06.out <==
> | Master Total wall time: 49788 seconds 13.83 hours
>
> ==> wt/prod07.out <==
> | Master Total wall time: 49550 seconds 13.76 hours
>
> ==> wt/prod08.out <==
> | Master Total wall time: 49106 seconds 13.64 hours
>
> ==> wt/prod09.out <==
> | Master Total wall time: 49093 seconds 13.64 hours
>
> ==> wt/prod10.out <==
> NSTEP = 156500 TIME(PS) = 4863.000 TEMP(K) = 299.42 PRESS =
> -52.4
> ...
>
>
>
> ### L76V ###
> ==> l76v/min.out <==
> | Total time 214.39 (100.0% of ALL )
> | Job began at 14:11:47.965 on 12/08/2009
> | Setup done at 14:11:59.925 on 12/08/2009
> | Run done at 14:15:22.358 on 12/08/2009
>
> ==> l76v/heat.out <==
> | Total time 26542.96 (100.0% of ALL )
> | Job began at 14:15:29.835 on 12/08/2009
> | Setup done at 14:15:31.889 on 12/08/2009
> | Run done at 21:37:52.800 on 12/08/2009
>
> ==> l76v/prod01.out <==
> | Master Total wall time: 54707 seconds 15.20 hours
>
> ==> l76v/prod02.out <==
> | Master Total wall time: 52301 seconds 14.53 hours
>
> ==> l76v/prod03.out <==
> | Master Total wall time: 54294 seconds 15.08 hours
>
> ==> l76v/prod04.out <==
> NSTEP = 198000 TIME(PS) = 1946.000 TEMP(K) = 298.48 PRESS =
> 36.5
> ...
>
>
>
> How can I check what is causing the slowdown of the l76v simulation and
> what might be the reason for it!?
>
> Any hint and help is greatly appreciated.
>
> Best regards,
> Oliver Kuhn
>
>
>
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