[gmx-users] Problem with the mdrun_openmpi on cluster

[Justin Lemkul]

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

==================================================