[gmx-users] Problem with the mdrun_openmpi on cluster

[James Starlight]

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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