[gmx-users] gromacs 4.6 segfault

[Szilárd Páll]

Hi,

Please try to run the very same simulation that crashes on CPUs only (-nb
cpu). If that also crashes, please file a bug report because we surely have
a software bug.

If that does not crash, we will have to dig a bit deeper into what could be
causing the issue.

 Log files from the two runs would be useful, could you share them?

Cheers,

--
Szilárd


On Tue, Jan 15, 2013 at 12:10 AM, sebastian <
sebastian.waltz at physik.uni-freiburg.de> wrote:

> 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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