[gmx-users] Problem with the mdrun_openmpi on cluster

[James Starlight]

also below my mdp options which might be relevant- I am using here a
MArtini ff of the system for simulating of GPCR embedded within
lidips.

title           = production run for GPCR
dt               =  0.02
nsteps           =  500000000
nstxout          =  0
nstvout          =  0
nstlog           =  5000
nstxtcout        =  5000
xtc-precision    =  5000
nstlist         = 1                 ; Frequency to update the neighbor
list and long range forces
ns_type         = grid          ; Method to determine neighbor list
(simple, grid)
rlist           = 1.2           ; Cut-off for making neighbor list
(short range forces)
coulombtype     = PME           ; Treatment of long range
electrostatic interactions
rcoulomb        = 1.2           ; Short-range electrostatic cut-off
rvdw            = 1.2           ; Short-range Van der Waals cut-off
pbc                 = xyz               ; Periodic Boundary
Conditionscoulomb         =  1.2



what -rcon flag provided with mdrub should do following the advises of
error mesage7

2016-03-14 17:27 GMT+01:00 James Starlight <jmsstarlight at gmail.com>:
> 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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