Mahnam wrote:
In God We Trust
Hello GMX users
I am trying to run one gromacs simulation in parallel. I have
successfully compiled gromacs 4 with mpi support on a cluster with
x86_64 architecture with 4 cpus (intel core 2 Quad 6600).
when I run mdrun with single-processor ,it works fine and everything
is ok, but when I run the same simulation with 4 cpu,
it finishs again normally and I don't get any error messages , but my
protein breaks and box of sol becomes deformed.
Which (specific) version are you using? Prior to 4.0.2 (I think), the final
output was fragmented as a consequence of domain decomposition. It can be
"fixed" (i.e., molecules can be made whole again) with trjconv.
"Deformed" is a matter of perspective, and is typically an artifact of
visualization. You will have to describe your system in much greater detail to
get any useful advice.
These are first few lines of my output (on screen)
These lines just indicate the run is being split between nodes; they are not
indicative of a problem.
-Justin
NNODES=4, MYRANK=3, HOSTNAME=localhost.localdomain
NODEID=3 argc=16
NNODES=4, MYRANK=0, HOSTNAME=localhost.localdomain
NNODES=4, MYRANK=2, HOSTNAME=localhost.localdomain
NNODES=4, MYRANK=3, HOSTNAME=localhost.localdomain
NODEID=2 argc=15
NNODES=4, MYRANK=1, HOSTNAME=localhost.localdomain
NODEID=1 argc=15
NODEID=3 argc=15
NODEID=0 argc=15
here is my commands and mdp file :
commands:
grompp -f sp.mdp -c fprmd.gro -r fprmd.gro -p n.top -o sp.tpr -n n.ndx
-maxwarn 1000
mpirun -np 4 mdrun -s sp.tpr -o sp.trr -c fsp.gro -g sp.log -e sp.edr -n
n.ndx -N 4
mdf file:
title = n.pdb
restraining
warnings = 10
cpp = /lib/cpp
define = -DFLEXIBLE
constraints = none
integrator = steep
nsteps = 10000
nstcomm = 1
comm_mode = Linear
comm_grps = protein
nstxout = 250
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 1.2
coulombtype = PME
rcoulomb = 1.2
rvdw = 1.4
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
emtol = 10.0
emstep = 0.01
whould you please help me to overcome this problem.
Many thanks in advance for your help and your reply.
Yours truly
Karim Mahnam
Institute of Biochemistry and Biophysics (IBB)
Tehran University
P.O.box 13145-1384
Tehran
Iran
http://www.ibb.ut.ac.ir/
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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