[gmx-users] Re: gromacs 4.6 segfault

[Dr. Vitaly Chaban]

> 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.
>

I think the reason of the issue is outside your MDP file and is rather
in the GPU installation. A primitive advice would be to decrease a
time-step, say twice, and see what happens. Even very well
equilibrated systems and even without GPU support, sometimes crash
after a few millions of steps...


Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark