Hello,
I am writing just to tell how the problem was solved.
I contact a person that works with the BlueGene cluster and he installed
the Gromacs 4.6 in the cluster.
And all my problems were solved. I did not get the same error over and
over again.
Apparently, it was some problem with the 4.5.5 version.
Thank you all for your help, I learned a lot with all the suggestions.
Cíntia
On 05/02/2013 13:10, Cintia C. Vequi-Suplicy wrote:
Mark,
Thank you for your answer.
I have already tried to run with several numbers of processors from 8
to 512 and I always got the same error.
And I transfer the simulation to the BlueGene in two different ways.
In both ways, I got the same error.
They were the following:
1) only using the .gro file after the simulation on my local cluster
with the velocities, generate a new .tpr using the md.mdp I sent
before. And the use this .tpr file to run in the bluegene. The
commands were these:
grompp -f md.mdp -c min_dppc.gro -p dppc512.top -o dppc10ns.tpr
/*(this was done in my computer)
and then in the bgp, I submitted the following script:
#@ job_name = dppc_001ps
#@ comment = "bilayer continuacao gauss com cpi"
#@ error = $(job_name).$(jobid).out
#@ output = $(job_name).$(jobid).out
#@ environment = COPY_ALL
#@ wall_clock_limit = 80:00:00
#@ notification = error
#@ job_type = bluegene
#@ class = compute
#@ bg_size = 128
#@ queue
/bgsys/drivers/ppcfloor/bin/mpirun -np 512 -exe
/opt/apps/gromacs/4.5.5/bin/mdrun -args " -s dppc10.tpr -v" -mode VN
2) I used the .tpr and the state.cpt from the simulation on my local
cluster to restart the simulation on the bluegene with more nodes. And
the script I used was:
#@ job_name = gromacs_dppc
#@ comment = "bilayer"
#@ error = $(job_name).$(jobid).out
#@ output = $(job_name).$(jobid).out
#@ environment = COPY_ALL
#@ wall_clock_limit = 80:00:00
#@ notification = error
#@ job_type = bluegene
#@ class = compute
#@ bg_size = 128
#@ queue
/bgsys/drivers/ppcfloor/bin/mpirun -np 512 -exe
/opt/apps/gromacs/4.5.5/bin/mdrun -args "-cpi state.cpt -s
dppc_min.tpr -v " -mode VN
In both ways, I got the same error.
Cheers,
Cíntia
md.mdp
integrator = md
tinit = 0.0
dt = 0.002
nsteps = 5000000
nstcomm = 5
comm-grps = Other SOL
nstxout = 1000
nstvout = 1000
nstfout = 0
nstlog = 1000
nstenergy = 1000
nstxtcout = 1000
xtc_precision = 1000
xtc-grps =
energygrps = Other SOL
nstlist = 5
ns_type = grid
pbc = xyz
rlist = 1.4
coulombtype = reaction-field
rcoulomb = 1.4
epsilon_rf = 66
vdw_type = cut-off
rvdw = 1.4
DispCorr = No
tcoupl = v-rescale
tc-grps = Other SOL
tau_t = 0.4 0.4
ref_t = 296 296
Pcoupl = berendsen
Pcoupltype = semiisotropic
tau_p = 0.2 0.2
compressibility = 4.51e-5 4.51e-5
ref_p = 1.0 1.0
constraints = hbonds
constraint_algorithm = lincs
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