[gmx-users] fatal errors in parallel but not on single processor

[Patricia Francis-Lyon]

Hi, I'm new to gromacs and I can't figure out what I'm doing wrong with parallel runs. I'm running gromacs 3.3.2 on a 215 residue protein: 1rz4.pdb. The 2 missing residues were added with modloop followed by energy minimization. The protein was put in a dodecahedron box and solvated with a layer of water at least 1.2 nm from the protein and 14 Na+ ions were added to bring the total charge of the system to zero. Energy minimization was done to remove close contacts.
 
When I run on a single processor my MD runs seem fine (heatup position restrained MD, constant temperature position restrained MD, and now the production MD run is almost 86% complete).  But when I run on a cluster some I get strange fatal errors, maybe tripped by boolean checks during writing of energy info to file. During position restrained MD I got:fatal error in function do_enx (line 343 of enxio.c) during the call:gmx_fatal(FARGS,"could not write energies")The fatal error happened after printing Coulomb1-4 energy in the log file, the next line of headings was NOT printed.
 
During production run of MD I got:Source code file: stat.c, line: 283Fatal error: XTC error
happening after writing these lines in the log:
           Step           Time         Lambda         257600      515.20001        0.00000
 
These errors do not appear when I run equilibriation and production MD on a single processor on my own machine, but I’d like to take advantage of the cluster to do runs faster and free up my own machine.
 
Here’s my .mdp file for the production run:integrator     = mdnsteps         = 500000dt             = 0.002nstlist        = 10rlist          = 1.2coulombtype    = pmercoulomb       = 1.2vdw-type       = cut-offrvdw           = 1.2tcoupl         = Berendsentc-grps        = protein  non-proteintau-t          = 0.1  0.1ref-t          = 300  300pcoupl         = Berendsentau-p          = 1.0compressibility = 5e-5ref-p          = 1.0nstxout        = 1000nstvout        = 1000nstxtcout      = 100nstenergy      = 100constraints    = allbonds; Generate velocites is on at 300 K.gen_vel        = yes
 
The same .top, .gro, .mdp and .tpr files are used on both single processor and parallel runs, with the GROMOS96 53a6 force field.  Any help you can offer is much appreciated!
 
Thanks,Patricia Francis-Lyon
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