[gmx-users] MPI error in gromacs 4.6, more Errors
Mark Abraham
mark.j.abraham at gmail.com
Mon Mar 24 14:23:09 CET 2014
The segmentation fault is highly unusual, and suggests that the
installation of gromacs used a shared library that has now
migrated/changed/whatever. I suggest you discuss that with your system
admins and ask them to re-install, or re-run the GROMACS regression tests,
to check things are OK.
Mark
On Mon, Mar 24, 2014 at 2:13 PM, Ankita Naithani
<ankitanaithani at gmail.com>wrote:
> Hi Justin,
>
> Thank you very much for your reply. I shall try to work my way around and
> see.
>
>
> Kind regards,
>
> Ankita
>
>
> On Mon, Mar 24, 2014 at 12:12 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 3/24/14, 7:57 AM, Ankita Naithani wrote:
> >
> >> Hi, so I modified my mdp file which now looks like the following:
> >>
> >> title = production MD
> >> ; Run parameters
> >> integrator = md ; leap-frog algorithm
> >> ;nsteps = 20000000 ; 0.005 * 20000000 = 100000 ps or 100 ns
> >> ;nsteps = 200000 ; 0.005 * 200000 = 1 ns
> >> ;dt = 0.005 ; 5 fs
> >> nsteps = 33333333 ; 0.003 * 33333333 = 100000 ps or 100 n
> >> dt = 0.003 ; 3 fs
> >> ; Output control
> >> nstxout = 0 ; save coordinates every 2 ps
> >> nstvout = 0 ; save velocities every 2 ps
> >> nstxtcout = 1000 ; xtc compressed trajectory output every 5 ps
> >> nstenergy = 1000 ; save energies every 5 ps
> >> nstlog = 1000 ; update log file every 5 ps
> >> ; Bond parameters
> >> constraint_algorithm = lincs ; holonomic constraints
> >> constraints = all-bonds ; all bonds (even heavy atom-H bonds)
> >> constrained
> >> lincs_iter = 1 ; accuracy of LINCS
> >> lincs_order = 4 ; also related to accuracy
> >> ; Neighborsearching
> >> ns_type = grid ; search neighboring grid cells
> >> nstlist = 5 ; 25 fs
> >> rlist = 1.0 ; short-range neighborlist cutoff (in nm)
> >> rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
> >> rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
> >> rlistlong = 1.0 ; long-range neighborlist cutoff (in nm)
> >> cutoff-scheme = Verlet
> >> ; Electrostatics
> >> coulombtype = PME ; Particle Mesh Ewald for long-range
> >> electrostatics
> >> pme_order = 4 ; cubic interpolation
> >> fourierspacing = 0.16 ; grid spacing for FFT
> >> nstcomm = 10 ; remove com every 10 steps
> >> ; Temperature coupling is on
> >> tcoupl = V-rescale ; modified Berendsen thermostat
> >> tc-grps = Protein Non-Protein ; two coupling groups - more
> >> accurate
> >> tau_t = 0.1 0.1 ; time constant, in ps
> >> ref_t = 318 318 ; reference temperature, one for each
> group,
> >> in K
> >> ; Pressure coupling is off
> >> pcoupl = berendsen ; Berendsen thermostat
> >> pcoupltype = isotropic ; uniform scaling of box vectors
> >> tau_p = 1.0 ; time constant, in ps
> >> ref_p = 1.0 ; reference pressure, in bar
> >> compressibility = 4.5e-5 ; isothermal compressibility of water,
> bar^-1
> >> ; Periodic boundary conditions
> >> pbc = xyz ; 3-D PBC
> >> ; Dispersion correction
> >> DispCorr = EnerPres ; account for cut-off vdW scheme
> >> ; Velocity generation
> >> gen_vel = yes ; Velocity generation is on
> >> gen_temp = 318 ; reference temperature, for protein in K
> >> --------------------------------------------------
> >>
> >>
> >> But, when I try to generate the tpr file on the cluster itself using
> >> gromacs 4.6.3, I get the following error:
> >>
> >>
> >> NOTE 1 [file md3.mdp]:
> >> With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
> >> that with the Verlet scheme, nstlist has no effect on the accuracy of
> >> your simulation.
> >>
> >>
> >> NOTE 2 [file md3.mdp]:
> >> nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
> >> nstcomm to nstcalcenergy
> >>
> >> Generated 3403 of the 3403 non-bonded parameter combinations
> >> Generating 1-4 interactions: fudge = 0.5
> >> Generated 3403 of the 3403 1-4 parameter combinations
> >> Segmentation fault
> >>
> >> Can anyone please suggest further?
> >>
> >>
> > Do as the notes suggest. They're not fatal errors, they're just
> > cautionary. You should probably educate yourself a bit further on what
> all
> > of these algorithms are by taking a look at http://www.gromacs.org/
> > Documentation/Cut-off_schemes. The Verlet scheme is not mandatory, but
> > it is required by the type of parallelization you requested.
> >
> > Reviewers may question the changes in version and cutoff methods when
> > critiquing your work, so be aware of that. Also, the instability you are
> > seeing is probably a result of the large time step, unless you are using
> > virtual sites.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 601
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> >
> > --
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>
>
> --
> Ankita Naithani
> --
> Gromacs Users mailing list
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