[gmx-users] Error in BlueGene

[Cintia C. Vequi-Suplicy]

Hello,

I am writing just to tell how the problem was solved.

I contact a person that works with the BlueGene cluster and he installed 
the Gromacs 4.6 in the cluster.
And all my problems were solved. I did not get the same error over and 
over again.

Apparently, it was some problem with the 4.5.5 version.

Thank you all for your help, I learned a lot with all the suggestions.

Cíntia


On 05/02/2013 13:10, Cintia C. Vequi-Suplicy wrote:
> Mark,
>
> Thank you for your answer.
>
> I have already tried to run with several numbers of processors from 8 
> to 512 and I always got the same error.
>
> And I transfer the simulation to the BlueGene in two different ways. 
> In both ways, I got the same error.
> They were the following:
>
> 1) only using the .gro file after the simulation on my local cluster 
> with the velocities, generate a new .tpr using the md.mdp I sent 
> before. And the use this .tpr file to run in the bluegene. The 
> commands were these:
>
> grompp -f md.mdp -c min_dppc.gro  -p dppc512.top -o dppc10ns.tpr 
> /*(this was done in my computer)
>
> and then in the bgp, I submitted the following script:
>
> #@ job_name = dppc_001ps
> #@ comment = "bilayer continuacao gauss com cpi"
> #@ error = $(job_name).$(jobid).out
> #@ output = $(job_name).$(jobid).out
> #@ environment = COPY_ALL
> #@ wall_clock_limit = 80:00:00
> #@ notification = error
> #@ job_type = bluegene
> #@ class = compute
> #@ bg_size = 128
> #@ queue
>
> /bgsys/drivers/ppcfloor/bin/mpirun -np 512 -exe 
> /opt/apps/gromacs/4.5.5/bin/mdrun -args " -s dppc10.tpr -v" -mode VN
>
>
> 2) I used the .tpr and the state.cpt from the simulation on my local 
> cluster to restart the simulation on the bluegene with more nodes. And 
> the script I used  was:
>
> #@ job_name = gromacs_dppc
> #@ comment = "bilayer"
> #@ error = $(job_name).$(jobid).out
> #@ output = $(job_name).$(jobid).out
> #@ environment = COPY_ALL
> #@ wall_clock_limit = 80:00:00
> #@ notification = error
> #@ job_type = bluegene
> #@ class = compute
> #@ bg_size = 128
> #@ queue
>
> /bgsys/drivers/ppcfloor/bin/mpirun -np 512 -exe 
> /opt/apps/gromacs/4.5.5/bin/mdrun -args "-cpi state.cpt -s 
> dppc_min.tpr -v " -mode VN
>
>
> In both ways, I got the same error.
>
> Cheers,
> Cíntia
>
>
> md.mdp
>
> 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
>