[gmx-users] Problem with the mdrun_openmpi on cluster

Tue Mar 15 14:45:59 CET 2016

Right, thanks so much!

2016-03-15 13:58 GMT+01:00 Mark Abraham <mark.j.abraham at gmail.com>:
> Hi,
>
>
> On Tue, Mar 15, 2016 at 11:57 AM James Starlight <jmsstarlight at gmail.com>
> wrote:
>
>> just performed some benchmarks with full atomic system- short md of
>> the water soluble protein still using mpiexec -np 46 mdrun_openmpi of
>> the GMX 4.5 and there were no such errors with DD so it seems that the
>> problem indeed in MARTINI atoms representation.
>>
>
> Not really. The bonded interactions have a longer physical range in a CG
> model, and that limits the current implementation of domain decomposition.
>
>
>> BTW how I could quickly check some info about performance of the
>> simulation7 what logs should I expect7 If somebody has already done it
>>
>
> Depends on your simulation and hardware, so nobody has anything that is
> obviously comparable.
>
>
>> I will be very thankful for some usefull combination of shell commands
>> which will extract performance information from sim log.
>>
>
> Start with tail -n 50 md.log ;-)
>
> Mark
>
> Thanks in advance!!
>>
>> J.
>>
>> 2016-03-14 18:27 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
>> >
>> >
>> > On 3/14/16 1:26 PM, James Starlight wrote:
>> >>
>> >> For that system I have not defined virtual sites.
>> >
>> >
>> > That disagrees with the error message, which explicitly complains about
>> > vsites.
>> >
>> >> BTW the same simulation on local desctop using 2 cores from core2 duo
>> runs
>> >> OK =)
>> >>
>> >
>> > Because you're not invoking DD there.
>> >
>> >> so one of the solution probably is to try to use more recent gmx 5.0
>> >> to see what will happenes
>> >>
>> >
>> > Good idea.
>> >
>> > -Justin
>> >
>> >
>> >> 2016-03-14 18:22 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
>> >>>
>> >>>
>> >>>
>> >>> On 3/14/16 1:19 PM, James Starlight wrote:
>> >>>>
>> >>>>
>> >>>> I tried to increase size on the system providding much bigger bilayer
>> >>>> in the system
>> >>>>
>> >>>> for this task I obtained another error also relevant to DD
>> >>>>
>> >>>> Program g_mdrun_openmpi, VERSION 4.5.7
>> >>>> Source code file:
>> >>>> /builddir/build/BUILD/gromacs-4.5.7/src/mdlib/domdec_con.c, line: 693
>> >>>>
>> >>>> Fatal error:
>> >>>> DD cell 0 2 1 could only obtain 0 of the 1 atoms that are connected
>> >>>> via vsites from the neighboring cells. This probably means your vsite
>> >>>> lengths are too long compared to the domain decomposition cell size.
>> >>>> Decrease the number of domain decomposition grid cells.
>> >>>> For more information and tips for troubleshooting, please check the
>> >>>> GROMACS
>> >>>> website at http://www.gromacs.org/Documentation/Errors
>> >>>> -------------------------------------------------------
>> >>>>
>> >>>> "It's So Fast It's Slow" (F. Black)
>> >>>>
>> >>>> Error on node 9, will try to stop all the nodes
>> >>>> Halting parallel program g_mdrun_openmpi on CPU 9 out of 64
>> >>>>
>> >>>>
>> >>>> BTW I checked the bottom of the syste,.gro file and found the next
>> >>>> sizes which are seems too small for my syste, consisted for several
>> >>>> hundreds of lipid, arent it7
>> >>>>
>> >>>>     15.00000  15.00000  15.00000   0.00000   0.00000   0.00000
>>  0.00000
>> >>>>     0.00000   0.00000
>> >>>>
>> >>>
>> >>> No, that seems fine.  But if your box is set up wrong, that's your
>> fault
>> >>> from the command below :)
>> >>>
>> >>>>
>> >>>> for my case that gro file was produced automatically using MARTINI
>> >>>> method
>> >>>>
>> >>>> ./insane.py -f test.pdb -o system.gro -p system.top -pbc cubic -box
>> >>>> 15,15,15 -l DPPC:4 -l DOPC:3 -l CHOL:3 -salt 0.15 -center -sol W
>> >>>>
>> >>>>
>> >>>> Will be very thankful for any help!!
>> >>>>
>> >>>
>> >>> So you've got a system that is a CG model, with virtual sites?  That's
>> >>> going
>> >>> to create all kinds of havoc.  Please do try Googling your error,
>> because
>> >>> this difficulty has come up before specifically in the case of CG
>> >>> systems,
>> >>> which have longer-than-normal bonded interactions and requires some
>> mdrun
>> >>> tuning.
>> >>>
>> >>> -Justin
>> >>>
>> >>> --
>> >>> ==================================================
>> >>>
>> >>> Justin A. Lemkul, Ph.D.
>> >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>> >>>
>> >>> Department of Pharmaceutical Sciences
>> >>> School of Pharmacy
>> >>> Health Sciences Facility II, Room 629
>> >>> University of Maryland, Baltimore
>> >>> 20 Penn St.
>> >>> Baltimore, MD 21201
>> >>>
>> >>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> >>> http://mackerell.umaryland.edu/~jalemkul
>> >>>
>> >>> ==================================================
>> >>>
>> >>> --
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>> >
>> >
>> > --
>> > ==================================================
>> >
>> > Justin A. Lemkul, Ph.D.
>> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
>> >
>> > Department of Pharmaceutical Sciences
>> > School of Pharmacy
>> > Health Sciences Facility II, Room 629
>> > University of Maryland, Baltimore
>> > 20 Penn St.
>> > Baltimore, MD 21201
>> >
>> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> > http://mackerell.umaryland.edu/~jalemkul
>> >
>> > ==================================================
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