[gmx-users] Domain Decomposision and Frozen Groups

Reza Salari resal81 at yahoo.com
Thu Jan 22 21:37:24 CET 2009

Hi everyone;

I am trying to do some simulation using frozen groups on an 8 core computer. I have tow boxes: 

1) Box 1 has two proteins and both of them are kept frozen (I used [exclusions] directive in topology file to exclude the interactions in each frozen group, NVT). 

2) Box 2 has those two proteins but without being frozen (no use of [exclusions] and freeze options).

Here is the mdp file:
integrator     =     sd
dt     =      0.002
nsteps     =     50000
comm_mode = None
ns_type                  = grid
pbc                      = xyz
nstlist    = 10
rlist     =     1
coulombtype     =     PME
rcoulomb     =     1
fourierspacing     =     0.12
pme_order     =     6
ewald_rtol     =     1e-6
vdwtype     =     Switch
rvdw_switch     =     0.8
rvdw     =     0.9
DispCorr     =     EnerPres
nstxout     =     500
nstvout     =     500
nstlog     =     500
nstenergy     =     500
nstxtcout                = 5000
xtc-precision            = 1000
tc_grps                  = system
tau_t                    = 1
ref_t                    = 310
energygrps    = chainC chainF SOL  ; these three lines were commented out for the box 2 simulation
freezegrps    = chainC chainF
freezedim    = Y Y Y Y Y Y

I used this command to run the simulations:
mpiexec -n 8 mdrunmpi -s eqvspc.tpr -c eqvspc.gro -o eqvspc.trr -x eqvspc.xtc -g eqvspc.log -e eqvspc.edr

It works for the box two (no freeze), but for box 1 gives me this error:
Back Off! I just backed up eqvspc.log to ./#eqvspc.log.11#
Reading file eqvspc.tpr, VERSION 4.0.3 (single precision)
Program mdrunmpi, VERSION 4.0.3
Source code file: domdec.c, line: 5858

Fatal error:
There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 6.25692 nm
Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
Error on node 0, will try to stop all the nodes
Halting parallel program mdrunmpi on CPU 0 out of 8

The serial version of mdrun works with box 1.
I searched the user mailing list and found that some people had similar problem with restraints in the past. I tried to use some -rdd and -dds values, but without any success. Can you please point out where is the source of this error and how I can get domain decomposition and frozen (or restraint) groups to work.

Any help or hint is highly appreciated!

Reza Salari

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