[gmx-users] Error in BlueGene

[David van der Spoel]

On 2013-01-30 23:48, Ricardo Soares wrote:
> Hello,
>
> before submitting to Bluegene, I always test the system in my local 8 core
> cpu, and if it works, it will also work in Bluegene, as long as I balance the
> domain decomposition for the larger number of cores. If your system insists in
> exploding, even after energy minimization, you could try to decrease the
> integration timestep (dt) to something lower than 2 fs, maybe to 1fs or, in
> some cases even 0.5 fs. Did you tried that?

And check the energies.
Which term causes the crash?

> Cheers,
>
> Ricardo.
>
>
>
> On Wed, 30 Jan 2013 15:44:53 -0200, Cintia C. Vequi-Suplicy wrote
>> Mark,
>>
>> Thank you for your answer.
>>
>> I did an energy minimization with the file em.mdp (below) and then I
>> did a  40 ns simulation with the same md.mdp I send before. These
>> two steps were done in my local cluster. After that I took the
>> configuration for the simulation in the bluegene and I got these
>> error. I notice that the step that the error occurs depends on the
>> number of nodes I use. I am also including the end of the min.out file.
>>
>> I also tried others integrators for the energy minimization but I
>> always get the same error.
>>
>> Thank you again,
>> Cíntia
>>
>> -------------------------------------------------------
>> em.mdp
>>
>> integrator               = steep
>> tinit                    = 0.0
>> dt                       = 0.002
>> nsteps                   = 5000000
>> nstcomm                  = 1
>> comm-grps                = Other SOL
>>
>> nstxout                  = 100
>> nstvout                  = 100
>> nstfout                  = 0
>> nstlog                   = 100
>> nstenergy                = 100
>> nstxtcout                = 100
>> xtc_precision            = 100
>> xtc-grps                 =
>> energygrps               = Other SOL
>>
>> nstlist                  = 5
>> ns_type                  = grid
>> pbc                      = xyz
>> rlist                    = 1.4
>>
>> coulombtype              = reaction-field
>> rcoulomb                 = 1.4
>> epsilon_rf               = 66
>>
>> vdw_type                 = cut-off
>> rvdw                     = 1.4
>> DispCorr                 = No
>>
>> constraints              = none
>> -------------------------------------------------------
>> min.out
>> ...
>> Step= 5192, Dmax= 1.9e-11 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
>> atom= 22015
>> Step= 5193, Dmax= 9.5e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
>> atom= 22015
>> Step= 5194, Dmax= 4.7e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
>> atom= 22015
>> Step= 5195, Dmax= 2.4e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
>> atom= 22015
>> Step= 5196, Dmax= 2.8e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
>> atom= 22015
>> Step= 5197, Dmax= 1.4e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
>> atom= 22015
>> Step= 5198, Dmax= 1.7e-12 nm, Epot= -1.79302e+06 Fmax= 6.65023e+02,
>> atom= 22015
>> Stepsize too small, or no change in energy.
>> Converged to machine precision,
>> but not to the requested precision Fmax < 10
>> You might need to increase your constraint accuracy, or turn
>> off constraints alltogether (set constraints = none in mdp file)
>>
>> writing lowest energy coordinates.
>>
>> Steepest Descents converged to machine precision in 5199 steps,
>> but did not reach the requested Fmax < 10.
>> Potential Energy  = -1.79302464181879e+06
>> Maximum force     =  6.65022934447791e+02 on atom 22015
>> Norm of force     =  4.90065871184878e+00
>>
>> gcq#0: Thanx for Using GROMACS - Have a Nice Day
>> -------------------------------------------------------
>>
>>>
>>>
>>>      -------------------------------------------------------
>>>      md.mdp file
>>>
>>>
>>>      integrator               = md
>>>      tinit                    = 0.0
>>>      dt                       = 0.002
>>>      nsteps                   = 5000000
>>>      nstcomm                  = 5
>>>      comm-grps                = Other SOL
>>>
>>>      nstxout                  = 1000
>>>      nstvout                  = 1000
>>>      nstfout                  = 0
>>>      nstlog                   = 1000
>>>      nstenergy                = 1000
>>>      nstxtcout                = 1000
>>>      xtc_precision            = 1000
>>>      xtc-grps                 =
>>>      energygrps               = Other SOL
>>>
>>>      nstlist                  = 5
>>>      ns_type                  = grid
>>>      pbc                      = xyz
>>>      rlist                    = 1.4
>>>
>>>      coulombtype              = reaction-field
>>>      rcoulomb                 = 1.4
>>>      epsilon_rf               = 66
>>>
>>>      vdw_type                 = cut-off
>>>      rvdw                     = 1.4
>>>      DispCorr                 = No
>>>
>>>      tcoupl                   = v-rescale
>>>      tc-grps                  = Other SOL
>>>      tau_t                    = 0.4 0.4
>>>      ref_t                    = 296 296
>>>
>>>      Pcoupl                   = berendsen
>>>      Pcoupltype               = semiisotropic
>>>      tau_p                    = 0.2 0.2
>>>      compressibility          = 4.51e-5 4.51e-5
>>>      ref_p                    = 1.0 1.0
>>>
>>>      constraints              = hbonds
>>>      constraint_algorithm     = lincs
>>>
>>
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-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se