[gmx-users] Unexplained crashes with Gromacs-4.0
Justin A. Lemkul
jalemkul at vt.edu
Tue Oct 14 13:44:07 CEST 2008
David van der Spoel wrote:
> Justin A. Lemkul wrote:
>>
>>
>> Berk Hess wrote:
>>> Hi,
>>>
>>> I don't really know what could be the problem here.
>>>
>>> 0..180 is (confusingly) not including the end, so 180 is out of range.
>>>
>>> The only thing I can think of (except for unknown bugs of coarse),
>>> is that I corrected the coupling time of the Parrinello-Rahman barostat
>>> when going from 4.0 RC4 to the official 4.0 release.
>>> I guess all your old simulations were with older Gromacs releases.
>>> So to get the same coupling as before, so would need to multiply
>>> tau_t by 16.6.
>>> I don't know if this would help.
>>
>> I did see this same error under RC2, but noticed that you fixed this
>> bug shortly after I saw it, and that's what I assumed it was. But now
>> I have seen it under the official 4.0 release.
>>
>>>
>>> You did not get pressure coupling warnings before the crash?
>>>
>>
>> There are no messages printed before this error pops up. What's
>> really confusing is that if I simply try the same .tpr file again, it
>> runs without a problem. I know that's not terribly scientific, but it
>> seemed odd to me that my systems running for 40+ ns suddenly had a
>> problem.
>>
>> Is there any diagnostic information I can provide? This problem seems
>> like it would be elusive, since even I can't fully reproduce it.
>
> That sounds like hardware problems, unless you use dynamic load
> balancing which depends on timings and hence may make runs irreproducible.
>
That might be it then. I use -dlb auto, and in the mdrun output to the logfile,
it reports that it is turning on dynamic load balancing. Is there any way to
diagnose this, i.e. -dlb no? Or is this a problem I'm stuck with based on my
hardware?
-Justin
>>
>> -Justin
>>
>>> Berk
>>>
>>>
>>> ------------------------------------------------------------------------
>>> > Date: Mon, 13 Oct 2008 16:55:20 -0400
>>> > From: jalemkul at vt.edu
>>> > To: gmx-users at gromacs.org
>>> > Subject: [gmx-users] Unexplained crashes with Gromacs-4.0
>>> >
>>> >
>>> > Hi,
>>> >
>>> > I've gotten the following error with two of my simulation systems.
>>> Usually this
>>> > weird "variable ci" error means the system is unstable, and I've
>>> seen it before
>>> > when I've done a poor job of equilibrating. But now I'm seeing it
>>> a long time
>>> > into my simulations (after 48 ns in one case, 60 ns in the other).
>>> If I simply
>>> > re-submit the job, it runs fine. The error shown is as follows:
>>> >
>>> > -------------------------------------------------------
>>> > Program mdrun_4.0_mpi, VERSION 4.0
>>> > Source code file: nsgrid.c, line: 357
>>> >
>>> > Range checking error:
>>> > Explanation: During neighborsearching, we assign each particle to
>>> a grid
>>> > based on its coordinates. If your system contains collisions or
>>> parameter
>>> > errors that give particles very high velocities you might end up
>>> with some
>>> > coordinates being +-Infinity or NaN (not-a-number). Obviously, we
>>> cannot
>>> > put these on a grid, so this is usually where we detect those errors.
>>> > Make sure your system is properly energy-minimized and that the
>>> potential
>>> > energy seems reasonable before trying again.
>>> >
>>> > Variable ci has value 180. It should have been within [ 0 .. 180 ]
>>> >
>>> > -------------------------------------------------------
>>> >
>>> > It seems to me that this "ci" variable is still within the range
>>> of 0->180, if
>>> > those values are inclusive.
>>> >
>>> > My .mdp file is as follows:
>>> >
>>> > title = NPT simulation for a membrane protein
>>> > ; Run parameters
>>> > integrator = md
>>> > dt = 0.002
>>> > nsteps = 5000000 ; 10000 ps (10 ns)
>>> > tinit = 40000
>>> > nstcomm = 1
>>> > ; Output parameters
>>> > nstxout = 50000 ; every 100 ps
>>> > nstvout = 50000
>>> > nstfout = 50000
>>> > nstlog = 5000 ; every 10 ps
>>> > nstenergy = 5000
>>> > nstxtcout = 5000
>>> > ; Bond parameters
>>> > constraint_algorithm = lincs
>>> > constraints = all-bonds
>>> > continuation = yes
>>> > ; Cut-off's and neighborsearching
>>> > nstlist = 5
>>> > ns_type = grid
>>> > rlist = 1.2
>>> > rcoulomb = 1.2
>>> > rvdw = 1.2
>>> > ; PME electrostatics parameters
>>> > coulombtype = PME
>>> > fourierspacing = 0.18
>>> > ;fourier_nx = 0
>>> > ;fourier_ny = 0
>>> > ;fourier_nz = 0
>>> > pme_order = 4
>>> > ewald_rtol = 1e-5
>>> > optimize_fft = yes
>>> > ; Berendsen temperature coupling is on in three groups
>>> > Tcoupl = Nose-Hoover
>>> > tc_grps = Protein POPC SOL_NA+_CL-
>>> > tau_t = 0.1 0.1 0.1
>>> > ref_t = 310 310 310
>>> > ; Pressure coupling is not on
>>> > Pcoupl = Parrinello-Rahman
>>> > pcoupltype = semiisotropic
>>> > tau_p = 2.0
>>> > compressibility = 4.5e-5 4.5e-5
>>> > ref_p = 1.0 1.0
>>> > ; Generate velocities is off
>>> > gen_vel = no
>>> > gen_temp = 310
>>> > gen_seed = 7041776
>>> > ; Periodic boundary conditions are on in all directions
>>> > pbc = xyz
>>> > ; Long-range dispersion correction
>>> > DispCorr = EnerPres
>>> >
>>> > Any ideas what's going on?
>>> >
>>> > Thanks,
>>> > Justin
>>> >
>>> > --
>>> > ========================================
>>> >
>>> > Justin A. Lemkul
>>> > Graduate Research Assistant
>>> > Department of Biochemistry
>>> > Virginia Tech
>>> > Blacksburg, VA
>>> > jalemkul[at]vt.edu | (540) 231-9080
>>> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>> >
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>>
>
>
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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