Hey GROMACS users,
using mdrun (version 4.6-beta3) on a GPU node (1 nvidia K10 with cuda
drivers and runtime 4.2 + 2 times intel 6 core E5 with hyper threading
and SSE4.1) I get allways after a few or few 100 ns the following segfault:
line 15: 28957 Segmentation fault mdrun -deffnm pdz_trans_NVT_equi_4
-maxh 95
I can restart the system using the cpt file and run the it for the next
few or few 100 ns and when I get the same segfault again.
The same system runs on a different cluster (mdrun version 4.6-beta3 on
a GPU node (1 nvidia M2090 with cuda drivers and runtime 4.2 + 2 times
intel 6 core X5 and SSE4.1) fine for 1μs without any complains.
My system consists of a 95 residue protein solvated in approx 6000 spc
water molecules.
.mdp parameters:
;
title = ttt
cpp = /lib/cpp
include = -I../top
constraints = hbonds
integrator = md
cutoff-scheme = verlet
dt = 0.002 ; ps !
nsteps = 500000000 ; total 5 ns
nstcomm = 25 ; frequency for center of mass motion removal
nstcalcenergy = 25
nstxout = 100000 ; frequency for writting the trajectory
nstvout = 100000 ; frequency for writting the velocity
nstfout = 100000 ; frequency to write forces to output trajectory
nstlog = 1000000 ; frequency to write the log file
nstenergy = 10000 ; frequency to write energies to energy file
nstxtcout = 10000
xtc_grps = System
nstlist = 25 ; Frequency to update the neighbor list
ns_type = grid ; Make a grid in the box and only check atoms in
neighboring grid cells when constructing a new neighbor
rlist = 1.4 ; cut-off distance for the short-range neighbor list
coulombtype = PME ; Fast Particle-Mesh Ewald electrostatics
rcoulomb = 1.4 ; cut-off distance for the coulomb field
vdwtype = cut-off
rvdw = 1.4 ; cut-off distance for the vdw field
fourierspacing = 0.12 ; The maximum grid spacing for the FFT grid
pme_order = 6 ; Interpolation order for PME
optimize_fft = yes
pbc = xyz
Tcoupl = v-rescale
tc-grps = System
tau_t = 0.1
ref_t = 300
energygrps = Protein Non-Protein
Pcoupl = no;berendsen
tau_p = 0.1
compressibility = 4.5e-5
ref_p = 1.0
nstpcouple = 5
refcoord_scaling = all
Pcoupltype = isotropic
gen_vel = no
gen_temp = 300
gen_seed = -1
Since I have no clue on which paramter should be tuned any guess would
be very welcomed.
Thanks
Sebastian
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