[gmx-users] Segmentation fault - Implicit solvent

Thu Mar 1 22:59:38 CET 2012

On Thu, Mar 1, 2012 at 5:43 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Steven Neumann wrote:
>
>>
>>
>> On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann <s.neumann08 at gmail.com<mailto:
>> s.neumann08 at gmail.com>**> wrote:
>>
>>
>>
>>    On Thu, Mar 1, 2012 at 3:32 PM, Steven Neumann
>>    <s.neumann08 at gmail.com <mailto:s.neumann08 at gmail.com>**> wrote:
>>
>>
>>
>>        On Thu, Mar 1, 2012 at 2:55 PM, Justin A. Lemkul
>>        <jalemkul at vt.edu <mailto:jalemkul at vt.edu>> wrote:
>>
>>
>>
>>            Steven Neumann wrote:
>>
>>                Dear Gmx Users,
>>                 I am trying to run nvt simulation (equilibration) of
>>                the protein in implicit solvent. My mdp:
>>                                 integrator = md ; leap-frog integrator
>>
>>                nsteps = 1000000 ; 0.0005 * 1000000 = 0.5 ns
>>
>>                dt = 0.0005 ; 0.5 fs
>>
>>                ; Output control
>>
>>                nstxout = 10000
>>
>>                nstxtcout = 10000 ; xtc compressed trajectory output
>>                every 2 ps
>>
>>                nstenergy = 10000 ; save energies every 2 ps
>>
>>                nstlog = 10000 ; update log file every 2 ps
>>
>>                ; Bond parameters
>>
>>                continuation = no
>>
>>                constraints = none
>>
>>                ; Neighborsearching
>>
>>                ns_type = simple ; search neighboring grid cells
>>
>>                nstlist = 0 ; 10 fs
>>
>>                rlist = 0 ; short-range neighborlist cutoff (in nm)
>>
>>                ; Infinite box with no cutoffs
>>
>>                pbc = no
>>
>>                rcoulomb = 0 ; short-range electrostatic cutoff (in nm)
>>
>>                coulombtype = cut-off
>>
>>                vdwtype = cut-off
>>
>>                rvdw = 0 ; short-range van der Waals cutoff (in nm)
>>
>>                epsilon_rf = 0
>>
>>                comm_mode = angular ; remove angular and com motions
>>
>>                ; implicit solvent
>>
>>                implicit_solvent = GBSA
>>
>>                gb_algorithm = OBC
>>
>>                gb_epsilon_solvent = 80.0
>>
>>                sa_surface_tension = 2.25936
>>
>>                rgbradii = 0
>>
>>                sa_algorithm = Ace-approximation
>>
>>                nstgbradii = 1
>>
>>                ; Temperature coupling is on
>>
>>                Tcoupl = v-rescale
>>
>>                tau_t = 0.1
>>
>>                tc_grps = system
>>
>>                ref_t = 298
>>
>>                ; Velocity generation
>>
>>                gen_vel = yes ; Velocity generation is on
>>
>>                gen_temp = 298.0
>>
>>                gen_seed = -1
>>
>>                Then after grompp I am trying to run the simulation on
>>                the cluster:
>>
>>                mdrun -pd -deffnm nvt500ps
>>
>>                My log file:
>>
>>                Back Off! I just backed up nvt500ps.log to
>>                ./#nvt500ps.log.1#
>>
>>                Reading file nvt500ps.tpr, VERSION 4.5.4 (single precision)
>>
>>                Starting 8 threads
>>
>>                Back Off! I just backed up nvt500ps.trr to
>>                ./#nvt500ps.trr.1#
>>
>>                Back Off! I just backed up nvt500ps.xtc to
>>                ./#nvt500ps.xtc.1#
>>
>>                Back Off! I just backed up nvt500ps.edr to
>>                ./#nvt500ps.edr.1#
>>
>>                starting mdrun 'Protein'
>>
>>                1000000 steps, 500.0 ps.
>>
>>                Segmentation fault
>>
>>                                 Do you have any clue what is happening?
>>
>>
>>            Try running in serial or with a maximum of 2 threads.  Your
>>            problem could be related to
>>            http://redmine.gromacs.org/__**issues/777<http://redmine.gromacs.org/__issues/777>
>>            <http://redmine.gromacs.org/**issues/777<http://redmine.gromacs.org/issues/777>>.
>>  You will need to
>>
>>            upgrade to 4.5.5 (serial should work on 4.5.4).
>>
>>            -Justin
>>
>>                 Thank you. What do you mean by running in serial? Well...
>> with 2
>>        threads it does not make sense to use implicit solvent. Will
>>        4.5.5 resolve this problem?
>>
>>         Indeed, it works in serial. Will version 4.5.5 resolve it run it
>> on
>>    e.g. 12 nodes?
>>
>>  Sorry, the same problem :
>>
>>
>
> I think, as stated in the redmine issue cited before, the limit is 2
> threads/processors.
>
> -Justin
>

I tried on one thread and on two threads and the error is still the same.
Without particle decomposition the problem remains. Any suggestions?

Steven

>
>> Initial temperature: 298.398 K
>>
>> Started mdrun on node 0 Thu Mar 1 15:56:04 2012
>>
>> Step Time Lambda
>>
>> 0 0.00000 0.00000
>>
>> Energies (kJ/mol)
>>
>> Bond U-B Proper Dih. Improper Dih. CMAP Dih.
>>
>> 2.27391e+02 4.27461e+02 1.27733e+03 2.73432e+01 -6.95645e+02
>>
>> GB Polarization Nonpolar Sol. LJ-14 Coulomb-14 LJ (SR)
>>
>> inf 3.59121e+02 6.85627e+02 3.68572e+04 -7.57140e+02
>>
>> Coulomb (SR) Potential Kinetic En. Total Energy Conserved En.
>>
>> -3.30643e+04 inf nan nan nan
>>
>> Temperature Pressure (bar)
>>
>> nan 0.00000e+00
>>
>>
>>    -
>>    ==============================**__==========
>>
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    MILES-IGERT Trainee
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
>>    <tel:%28540%29%20231-9080>
>>    http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>    <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> >
>>
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> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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