[gmx-users] Problem with the mdrun_openmpi on cluster

[James Starlight]

forgot to add that I tried to decrease number of CPUs to 16 and error
was the same

2016-03-14 17:26 GMT+01:00 James Starlight <jmsstarlight at gmail.com>:
> the error is likely when I try to run not very big system on large
> number of CPUs in parallel
>
>
> my system is receptor embedded within the membrane consisted of 120 lipids
> that was produced by grompp
>
> Initializing Domain Decomposition on 64 nodes
> Dynamic load balancing: no
> Will sort the charge groups at every domain (re)decomposition
> Initial maximum inter charge-group distances:
>     two-body bonded interactions: 1.174 nm, Bond, atoms 3610 3611
>   multi-body bonded interactions: 1.174 nm, Improper Dih., atoms 3604 3610
> Minimum cell size due to bonded interactions: 1.200 nm
> Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 2.626 nm
> Estimated maximum distance required for P-LINCS: 2.626 nm
> This distance will limit the DD cell size, you can override this with -rcon
> Guess for relative PME load: 0.87
> Using 0 separate PME nodes, as guessed by mdrun
> Optimizing the DD grid for 64 cells with a minimum initial size of 2.626 nm
> The maximum allowed number of cells is: X 3 Y 3 Z 3
>
>
> are there sollutions for this kind of system probably altering some cutoffs etc/
>
> 2016-03-14 17:22 GMT+01:00 Smith, Micholas D. <smithmd at ornl.gov>:
>> What is your box size (x, y, z)?
>>
>> What happens if you use half that number of nodes?
>>
>> ===================
>> Micholas Dean Smith, PhD.
>> Post-doctoral Research Associate
>> University of Tennessee/Oak Ridge National Laboratory
>> Center for Molecular Biophysics
>>
>> ________________________________________
>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of James Starlight <jmsstarlight at gmail.com>
>> Sent: Monday, March 14, 2016 12:19 PM
>> To: Discussion list for GROMACS users
>> Subject: [gmx-users] Problem with the mdrun_openmpi on cluster
>>
>> Hello,
>>
>> I am trying to submit job on 64 nodes on mu local cluster using below
>> combination of software
>>
>>
>> DO="mpiexec -np 64"
>> PROG="g_mdrun_openmpi"
>>
>>
>> $DO $PROG -deffnm sim
>>
>>
>> obtaining error
>>
>>
>>
>> Program g_mdrun_openmpi, VERSION 4.5.7
>> Source code file:
>> /builddir/build/BUILD/gromacs-4.5.7/src/mdlib/domdec.c, line: 6436
>>
>> Fatal error:
>> There is no domain decomposition for 64 nodes that is compatible with
>> the given box and a minimum cell size of 2.6255 nm
>> Change the number of nodes or mdrun option -rcon or your LINCS settings
>>
>> Could someone provide me trivial sollution/
>>
>> Thanks!
>>
>> J.
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