Hi Carlos,
I've tried previous runs where I've allowed the minimization to run for 10 hours and it still gave me the same error.
Thank you,
Aanshi Gandhi (she/her)
M.ASc Candidate, Garton Lab
Email <mailto:aanshi.gandhi@mail.utoronto.ca> | LinkedIn <
https://www.linkedin.com/in/aanshigandhi/>
On 2020-12-18, 3:46 PM, "Carlos Simmerling" <carlos.simmerling.gmail.com> wrote:
EXTERNAL EMAIL:
the slurm time limit is set by your system administrator, not inside Amber.
it looks like it ran for about 3.5 hours before being killed. you might
want to check to see if there is a different queue where you can run longer
jobs. You can reduce the number of minimization steps to get this to work,
but it will be hard to get your later MD jobs finished in that amount of
time.
On Fri, Dec 18, 2020 at 3:40 PM Aanshi Gandhi <
aanshi.gandhi.mail.utoronto.ca> wrote:
> Hello!
>
> I am trying to run a minimization on a protein using sander on a Compute
> Canada cluster (beluga to be specific). I have attached my two minimization
> input files (one for water & ions restrained [HC1_minwat.in] and one for
> the entire protein [HC1_minall.in] and my submission script
> (submit_min.sh). When running this minimization, I get the following error:
> “Starting MD Minimization at: Fri Dec 18 13:26:34 EST 2020
> slurmstepd: error: *** JOB 14510696 ON blg5805 CANCELLED AT
> 2020-12-18T18:56:06 DUE TO TIME LIMIT ***”. I have tried changing various
> parameters in all my files based on previous email forums and the Amber
> 2020 manual to no avail. If anyone has any ideas or suggestions, I would
> greatly appreciate it.
>
> Thank you,
> Aanshi Gandhi (she/her)
> M.ASc Candidate, Garton Lab
> Email<mailto:aanshi.gandhi.mail.utoronto.ca> | LinkedIn<
> https://www.linkedin.com/in/aanshigandhi/>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Dec 18 2020 - 13:00:03 PST
