Dear users, I'm trying to run an isotropic NPT simulation on a cubic cell containing TIP4P/ice water and methane. I'm using the Parrinello-Rahman barostat. I've been playing around with the different decomposition flags of mdrun to get better performance and scaling and have found that the standard -npme (half number of cores) works pretty well. I've also tried using the -dd flags, and I appear to get decent performance and scaling. However, after a few nanoseconds (corresponding to about 3 hours run time), the program just stalls; no output and no error messages. I realise NPT may cause domain decompositon some issues if the cell vectors vary wildly, but this isn't happening in my system.
Has anybody else experienced issues with domain decomposition and NPT simulations? If so, are there any workarounds? For the moment, I've had to resort to using -pd, which is giving relatively poor performance and scaling, but at least it isn't dying! I'm using GROMACS 4.5.5 with an intel compiler (I followed the instructions online, with static linking) and using the command: #!/bin/bash -f # --------------------------- #$ -V #$ -N test #$ -S /bin/bash #$ -cwd #$ -l vf=2G #$ -pe ib-ompi 32 #$ -q infiniband.q mpirun mdrun_mpi -cpnum -cpt 60 -npme 16 -dd 4 2 2 Below is my grompp.mdp. Thanks, Steve P.S. I think that there may be an issue with memory leak that occurs for domain decomposition with NPT. I seem to remember seeing this happening on my desktop and my local cluster. I don't see this with NVT simulations. This would be consistent with the lack of error message: I've just run a short test run and the memory usage was climbing streadily. ; run control integrator = md dt = 0.002 nsteps = -1 comm_mode = linear nstcomm = 10 ; energy minimization emtol = 0.01 emstep = 0.01 ; output control nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 0 nstcalcenergy = 2500 nstenergy = 2500 nstxtcout = 2500 ; neighbour searching nstlist = 1 ns_type = grid pbc = xyz periodic_molecules = no rlist = 0.90 ; electrostatics coulombtype = pme rcoulomb = 0.90 ; vdw vdwtype = cut-off rvdw = 0.90 dispcorr = ener ; ewald fourierspacing = 0.1 pme_order = 4 ewald_geometry = 3d optimize_fft = yes ; temperature coupling tcoupl = nose-hoover nh-chain-length = 10 tau_t = 2.0 ref_t = 255.0 tc_grps = system ; pressure coupling pcoupl = parrinello-rahman pcoupltype = isotropic ref_p = 400.0 tau_p = 2.0 compressibility = 6.5e-5 ; constraints constraint_algorithm = shake shake_tol = 0.0001 lincs_order = 8 lincs_iter = 2 ; velocity generation gen_vel = yes gen_temp = 255.0 gen_seed = -1
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