[gmx-users] Error in BlueGene

[Cintia C. Vequi-Suplicy]

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