On 9/03/2012 9:43 PM, Stephen Cox wrote:
Dear users,
I'm trying to run an isotropic NPT simulation on a cubic cell
containing TIP4P/ice water and methane. I'm using the
Parrinello-Rahman barostat. I've been playing around with the
different decomposition flags of mdrun to get better performance and
scaling and have found that the standard -npme (half number of cores)
works pretty well. I've also tried using the -dd flags, and I appear
to get decent performance and scaling. However, after a few
nanoseconds (corresponding to about 3 hours run time), the program
just stalls; no output and no error messages. I realise NPT may cause
domain decompositon some issues if the cell vectors vary wildly, but
this isn't happening in my system.
Has anybody else experienced issues with domain decomposition and NPT
simulations? If so, are there any workarounds? For the moment, I've
had to resort to using -pd, which is giving relatively poor
performance and scaling, but at least it isn't dying!
I'm using GROMACS 4.5.5 with an intel compiler (I followed the
instructions online, with static linking) and using the command:
#!/bin/bash -f
# ---------------------------
#$ -V
#$ -N test
#$ -S /bin/bash
#$ -cwd
#$ -l vf=2G
#$ -pe ib-ompi 32
#$ -q infiniband.q
mpirun mdrun_mpi -cpnum -cpt 60 -npme 16 -dd 4 2 2
Below is my grompp.mdp.
Thanks,
Steve
P.S. I think that there may be an issue with memory leak that occurs
for domain decomposition with NPT. I seem to remember seeing this
happening on my desktop and my local cluster. I don't see this with
NVT simulations. This would be consistent with the lack of error
message: I've just run a short test run and the memory usage was
climbing streadily.
; run control
integrator = md
dt = 0.002
nsteps = -1
comm_mode = linear
nstcomm = 10
; energy minimization
emtol = 0.01
emstep = 0.01
; output control
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 0
nstcalcenergy = 2500
nstenergy = 2500
nstxtcout = 2500
; neighbour searching
nstlist = 1
ns_type = grid
pbc = xyz
periodic_molecules = no
rlist = 0.90
; electrostatics
coulombtype = pme
rcoulomb = 0.90
; vdw
vdwtype = cut-off
rvdw = 0.90
dispcorr = ener
; ewald
fourierspacing = 0.1
pme_order = 4
ewald_geometry = 3d
optimize_fft = yes
; temperature coupling
tcoupl = nose-hoover
nh-chain-length = 10
tau_t = 2.0
ref_t = 255.0
tc_grps = system
; pressure coupling
pcoupl = parrinello-rahman
pcoupltype = isotropic
ref_p = 400.0
tau_p = 2.0
compressibility = 6.5e-5
; constraints
constraint_algorithm = shake
shake_tol = 0.0001
lincs_order = 8
lincs_iter = 2
; velocity generation
gen_vel = yes
gen_temp = 255.0
gen_seed = -1
You're generating velocities and immediately using a barostat that is
unsuitable for equilibration. You're using an integration step that
requires constraints=all-bonds but I don't see that. You may have better
stability if you equilibrate with Berendsen barostat and then switch.
I've seen no other reports of memory usage growing without bounds, but
if you can observe it happening after choosing a better integration
regime then it suggests a code problem that wants fixing.
Mark
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