Dear users,<br><br>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. <br>
<br>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!<br>
<br>I'm using GROMACS 4.5.5 with an intel compiler (I followed the instructions online, with static linking) and using the command:<br><br>#!/bin/bash -f<br># ---------------------------<br>#$ -V<br>#$ -N test<br>#$ -S /bin/bash<br>
#$ -cwd<br>#$ -l vf=2G<br>#$ -pe ib-ompi 32<br>#$ -q infiniband.q<br><br>mpirun mdrun_mpi -cpnum -cpt 60 -npme 16 -dd 4 2 2<br><br>Below is my grompp.mdp.<br><br>Thanks,<br>Steve<br><br>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. <br>
<br>; run control<br>integrator = md<br>dt = 0.002<br>nsteps = -1<br>comm_mode = linear<br>nstcomm = 10<br><br>; energy minimization<br>emtol = 0.01<br>emstep = 0.01<br><br>; output control<br>nstxout = 0<br>
nstvout = 0<br>nstfout = 0<br>nstlog = 0<br>nstcalcenergy = 2500<br>nstenergy = 2500<br>nstxtcout = 2500<br><br>; neighbour searching<br>nstlist = 1 <br>ns_type = grid<br>pbc = xyz<br>
periodic_molecules = no<br>rlist = 0.90<br><br>; electrostatics<br>coulombtype = pme<br>rcoulomb = 0.90<br><br>; vdw<br>vdwtype = cut-off<br>rvdw = 0.90<br>dispcorr = ener<br><br>; ewald<br>fourierspacing = 0.1<br>
pme_order = 4<br>ewald_geometry = 3d<br>optimize_fft = yes<br><br>; temperature coupling<br>tcoupl = nose-hoover<br>nh-chain-length = 10<br>tau_t = 2.0<br>ref_t = 255.0<br>tc_grps = system<br>
<br>; pressure coupling<br>pcoupl = parrinello-rahman<br>pcoupltype = isotropic<br>ref_p = 400.0<br>tau_p = 2.0<br>compressibility = 6.5e-5<br><br>; constraints<br>constraint_algorithm = shake<br>
shake_tol = 0.0001<br>lincs_order = 8<br>lincs_iter = 2<br><br>; velocity generation<br>gen_vel = yes<br>gen_temp = 255.0<br>gen_seed = -1<br><br>