[gmx-users] strange lincs warning with version 4.6
Roland Schulz
roland at utk.edu
Tue Dec 4 18:21:20 CET 2012
On Tue, Dec 4, 2012 at 11:30 AM, sebastian <
sebastian.waltz at physik.uni-freiburg.de> wrote:
> On 12/04/2012 05:09 PM, Mark Abraham wrote:
> > 2fs is normally considered too large a time step for stable integration
> > with only bonds to hydrogen constrained, so your observation of
> > non-reproducible LINCS warnings is not indicative of some other problem.
> >
>
> Sorry, but why is this whole setup running on my local desktop with
> GPUs? As far as I know this is a rather typical set of parameters.
>
I agree with you that normally a well equilibrated system should not crash
because of that. But the integration error is relative large with that so
you might want to change it for accuracy. Also you don't want to use a
system like that for bug hunting because as Mark said, the stability can
depend on slight numerical differences. And for bug hunting you want a
system which only crashes if something is wrong and not also sometimes if
everything is OK.
> The only difference what I can think of is that gromacs was compiled
> with intel and mkl libs on the cluster there as it was compiled with gcc
> and fftw3 libs on the local desktop.
>
Did you run the regressiontests as suggested by Szilard? Can you narrow it
down to one compontent? E.g. by compiling a version on the cluster with
gcc+fftw (to make sure it is not any other cluster componennt e.g. the MPI
library) and a version with icc+fftw (to see whether it correlates with
either icc or mkl?).
Roland
>
> Sebastian
>
> > Also, if you ran your CPU-only calculations with nstlist=25 then AFAIK
> this
> > works fine, but is inefficient.
> >
> > Mark
> >
> > On Tue, Dec 4, 2012 at 3:41 PM, sebastian<
> > sebastian.waltz at physik.uni-freiburg.de> wrote:
> >
> >
> >> On 11/23/2012 08:29 PM, Szilárd Páll wrote:
> >>
> >>
> >>> Hi,
> >>>
> >>> On Fri, Nov 23, 2012 at 9:40 AM, sebastian<
> >>> sebastian.waltz at physik.uni-**freiburg.de<
> sebastian.waltz at physik.uni-freiburg.de>>
> >>> wrote:
> >>>
> >>>
> >>>
> >>>
> >>>> Dear GROMCS user,
> >>>>
> >>>> I installed the git gromacs VERSION 4.6-dev-20121117-7a330e6-dirty on
> my
> >>>> local desktop
> >>>>
> >>>>
> >>>>
> >>> Watch out, the dirty version suffix means you have changed something in
> >>> the
> >>> source.
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>> (2*GTX 670 + i7) and everything works as smooth as possible. The
> outcomes
> >>>> are very reasonable and match the outcome of the 4.5.5 version without
> >>>> GPU
> >>>> acceleration. On our
> >>>>
> >>>>
> >>>>
> >>> What does "outcome" mean? If that means performance, than something is
> >>> wrong, you should see a considerable performance increase (PME,
> >>> non-bonded,
> >>> bondeds have all gotten a lot faster).
> >>>
> >>>
> >>>
> >>>
> >> With outcome I mean the trajectory not the performance.
> >>
> >>
> >>
> >>
> >>>
> >>>> cluster (M2090+2*Xeon X5650) I installed the VERSION
> >>>> 4.6-dev-20121120-0290409. Using the same .tpr file used for runs with
> my
> >>>> desktop I get lincs warnings that the watermolecules can't be settled.
> >>>>
> >>>>
> >>>>
> >>>>
> >>> The group kernels have not "stabilized" yet and there have been some
> fixes
> >>> lately. Could you please the latest version and check again.
> >>>
> >>>
> >>>
> >> I installed the beta1 release and still the water can not be settled.
> >>
> >> Additionally, you could try running our regression tests suite (
> >>
> >>> git.gromacs.org/**regressiontests<
> http://git.gromacs.org/regressiontests>)
> >>> to see if at least the tests pass with the
> >>> binaries you compiled
> >>> Cheers,
> >>> --
> >>> Szilárd
> >>>
> >>>
> >>>
> >>>
> >>>
> >> Cheers,
> >>
> >> Sebastian
> >>
> >>
> >> My .mdp file looks like:
> >>
> >>>> ;
> >>>> title = ttt
> >>>> cpp = /lib/cpp
> >>>> include = -I../top
> >>>> constraints = hbonds
> >>>> integrator = md
> >>>> cutoff-scheme = verlet
> >>>>
> >>>> ;define = -DPOSRES ; for possition restraints
> >>>>
> >>>> dt = 0.002 ; ps !
> >>>> nsteps = 100000000 \
> >>>> 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 = 10000 ; 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;yes
> >>>> gen_temp = 300
> >>>> gen_seed = -1
> >>>>
> >>>>
> >>>> Thanks a lot
> >>>>
> >>>> Sebastian
> >>>> --
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