[gmx-users] Problem with the mdrun_openmpi on cluster

[James Starlight]

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.

BTW how I could quickly check some info about performance of the
simulation7 what logs should I expect7 If somebody has already done it
I will be very thankful for some usefull combination of shell commands
which will extract performance information from sim log.

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
>>>
>>> ==================================================
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a
>>> mail to gmx-users-request at gromacs.org.
>
>
> --
> ==================================================
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
> mail to gmx-users-request at gromacs.org.