Hi,
I'm no expert for this stuff, but could it be that you generate about 40
of the #my_mol.log.$n# files (probably only 39)?
It could be that the 'mpirun' starts 40 'mdrun'-jobs and each generates
its own out put.
For GROMACS 4.6.x I always used
mdrun -nt X ...
to start a parallel run (where X would be 40 in your case). I think
GROMACS 4.6.x has the MPI stuff build into it and therefore doesn't need
an external 'mpirun' (but i could be wrong - I only know how to use the
stuff, but don't completly understand it...)
Hope this helps a little
Greetings
Thomas
Am 13.02.2014 18:13, schrieb
gromacs.org_gmx-users-requ...@maillist.sys.kth.se:
Dear GROMACS users,
I am facing a strange situation by running Gromacs (v - 4.6.3) in our local
cpu-cluster using MPI/OpenMP parallelization process. I am trying to simulate a
big heterogeneous aquas-polymer system in octahedron box.
I use the following command to run my simulations and use sge queuing system to
submit the job in the cluster.
mpirun -nolocal -np 40 mdrun -ntomp 1
Immediately after launching the job a huge number of backup files are getting
generated in the same directory. Generally naming conventions of these backup
files are #my_mol.log.$n# OR #my_mol.edr.$n# etc, i.e. more than one backup log,
.edr, .gro, etc files are generated, I suppose due to the parallelization. But,
after running some steps the log file and the sge-error file starts complaining
about the disk space although there is no disk space scarcity. Lowering the
frequency of writing to the output did not help neither increasing -cpt from 15
-> 50 helped.
The stranger part is here when I see the backup files are getting updated
regularly individually at the same directory (although the main .log file
stopped updating itself) and run for the entire steps (e.g. 10000 steps)
individually as if $n number of individual simulations are running.
My .mdp file is :
title = MD test run of 2 ns
; using Verlet scheme
cutoff-scheme = Verlet
; Run parameters
integrator = md
nsteps = 1000000
dt = 0.002
; Output control
nstxout = 10000
nstvout = 5000
nstxtcout = 1000
nstenergy = 1000
nstlog = 1000
; Bond parameters
continuation = yes
constraint_algorithm = lincs
constraints = all-bonds
lincs_iter = 1
lincs_order = 4
; Neighborsearching
ns_type = grid
nstlist = 10
rlist = 1.0
rcoulomb = 1.0
vdw-type = cut-off
rvdw = 1.0
; Electrostatics
coulombtype = PME
pme_order = 4
fourierspacing = 0.16
; Temperature coupling is on
tcoupl = V-rescale
tc-grps = polymer SOL_Ion
tau_t = 0.1 0.1
ref_t = 300 300
; Pressure coupling is on
pcoupl = Parrinello-Rahman
pcoupltype = isotropic
tau_p = 2.0
ref_p = 1.0
compressibility = 4.5e-5
; Periodic boundary conditions
pbc = xyz
; Dispersion correction
DispCorr = EnerPres
; Velocity generation
gen_vel = no
The commands I used to run:
J = i-1
### When I changing in .mdp file
grompp -f md.mdp -c test_$j.tpr -o test_$i.tpr -t test_$j.cpt -p test_solv.top -n
my_index.ndx >& log.grompp
mpirun -nolocal -np 40 $GMX_HOME/bin/mdrun -ntomp 1 -s test_$i.tpr -deffnm
test_$i -cpt 30
### When I try to extend the simulations
tpbconv -s test_${j}.tpr -o test_${i}.tpr -extend 1000 >& log_${i}.tpbconv
mpirun -nolocal -np 40 $GMX_HOME/bin/mdrun -s test_${i}.tpr -deffnm test_${i}
-cpi test_${j}.cpt -cpt 30
As this is my first attempt with the Gromacs and no one has ever used
MD/Gromacs in my surrounding I could not verify this strange behavior. I have
tried to search for the error in the web as well as in the community forum but
not found any reference to this issue. I may not have searched with proper
terminology however. I am also in touch with my sys admin who are also little
bit lost in this. If anyone could help me to get out of this situation I would
be highly obliged. Please let me know if I am not very explicit in describing
the issue.
Looking forward to hear from you.
Thanks in advance,
Mousumi
Ontario Institute for Cancer Research
MaRS Centre
Toronto, Ontario
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