[gmx-users] Problem with gromacs in Cluster

[Mark Abraham]

This works well until you use a system that permits job suspension. Then
-maxh gets double-crossed... :-)

Mark
On Apr 25, 2013 3:41 PM, "Richard Broadbent" <
richard.broadbent09 at imperial.ac.uk> wrote:

> I generally build a tpr for the whole simulation then submit one job using
> a command such as:
>
> mpirun -n ${NUM_PROCESSORS} mdrun -deffnm ${NAME} -maxh
> ${WALL_TIME_IN_HOURS}
>
> copy all the files back at the end of the script if necessary then:
>
> then resubmit it (sending out all the files again if necessary) this time
> using the command
>
> mpirun -n ${NUM_PROCESSORS} mdrun -deffnm ${NAME} -maxh
> ${WALL_TIME_IN_HOURS} -cpi
>
> you can then keep resubmitting with that line till the job is finished.
>
> In my case I have a maximum wall clock of 24hrs on some machines so this
> gets used a lot
>
> I also think that 1.6ns/day which is what you seem to be getting is very
> low performance and you might want to consider using more processors. Check
> the log file as the profiling information at the end will indicate whether
> this might be beneficial.
>
> Richard
>
>
> On 25/04/13 13:58, Francesco wrote:
>
>> You can split the simulation in different part (for example 5 ns each),
>> every time you'll finish one you will extend it adding more time.
>> http://www.gromacs.org/**Documentation/How-tos/**Extending_Simulations?**
>> highlight=extend<http://www.gromacs.org/Documentation/How-tos/Extending_Simulations?highlight=extend>
>>
>> My cluster uses a different "script system" than yours so I can't help
>> with it, but basically you have to submit more than 1 job with different
>> command to execute:
>>
>> 1) first production
>> mpirun -n 8 mdrun -s md_test.tpr -deffnm md_test -np 8
>> 2) modify the tpr file
>> tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
>> 3) next X ns
>> mpirun -n 8 mdrun -s next.tpr -cpi previous.cpt
>> 4) modify the tpr file
>> 5) production md
>> and so on
>>
>> with qsub you can submit a depending job (-hold_jid) that will run only
>> when the previous step will finish, in your case there should be a
>> similar way to do it.
>>
>> cheers
>>
>> Fra
>>
>> On Thu, 25 Apr 2013, at 12:28 PM, Sainitin Donakonda wrote:
>>
>>> Hey all,
>>>
>>> I recently ran 20ns simulation of protein ligand complex on cluster i
>>> used
>>> following script to run simulation
>>>
>>> grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o
>>> md_test.tpr
>>>
>>> mpirun -n 8 mdrun -s md_test.tpr -deffnm md_test -np 8
>>>
>>> *I saved this as MD.sh And then submited to cluster using following
>>> script*
>>>
>>> #!/bin/bash
>>> #BSUB -J testgromacs             # the job's name/array job
>>> #BSUB -W 120:00                       # max. wall clock time in hh:mm
>>> #BSUB -n 8,8                          # number of processors Min,Max
>>> #BSUB -o test/output_%J.log             # output file
>>> #BSUB -e test/errors_%J.log             # error file
>>> #BSUB -M 8192     #Memory limit in MB
>>>
>>> echo "Started at `date`"
>>> echo
>>>
>>> cd test
>>>
>>> echo "Running gromacs test in `pwd`"
>>>
>>> ./MD.sh
>>>
>>> echo "Finished at `date`"
>>>
>>>
>>> It gave result but when checked files .xtc and created RMSD plots in that
>>> x-axis of this plot i see only 8ns ...but in MD.MDP file i specified
>>> 20ns..
>>>
>>> Cluster Output says that "TERM_RUNLIMIT: job killed after reaching LSF
>>> run
>>> time limit.
>>> Exited with exit code 140". i gave maximum cluster time 120 hours..still
>>> it
>>> is not sufficient ..
>>>
>>> Can any body tell me  how do it split script i such  that i will get all
>>> 20ns simulation
>>>
>>>
>>> Thanks in advance ,
>>>
>>> Sainitin
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>> * Please search the archive at
>>> http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>>> * Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>>
>>
>>
>>  --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>