Hi,<br><br>I'm running a number of energy minimizations on a clathrate supercell and I get quite significantly different values for the total energy depending on the number of mpi processes / number of threads I use. More specifically, some numbers I get are:<br>
<br>#cores energy<br>1 -2.41936409202696e+04<br>2 -2.43726425776809e+04<br>3 -2.45516442350804e+04<br>4 -2.47003944216983e+04 <br><br>#threads energy<br>1 -2.41936409202696e+04<br>
2 -2.43726425776792e+04<br>3 -2.45516442350804e+04<br>4 -2.47306458924815e+04<br><br><br>I'd expect some numerical noise, but these differences seem to0 large for that. Before submitting a bug report, I'd like to check:<br>
a) if someone has seen something similar;<br>b) should I just trust the serial version?<br>c) have I simply done something stupid (grompp.mdp appended below);<br><br>Any help greatly appreciated.<br><br>Steve<br><br>NB I am using a flexible methane and settles for TIP4P/2005. I have reproduced the above trend with ubuntu repository versions of gromacs/openmpi and my own compiled versions of gromacs/mpich2.<br>
<br>; run control<br>integrator = steep<br>dt = 0.001<br>nsteps = -1<br>comm_mode = linear<br>nstcomm = 1<br><br>; energy minimization<br>emtol = 0.01<br>emstep = 0.01<br><br>; output control<br>nstxout = 1000<br>
nstvout = 1000<br>nstfout = 1000<br>nstlog = 1000<br>nstcalcenergy = 1<br>nstenergy = 1000<br><br>; neighbour searching<br>nstlist = 1 <br>ns_type = grid<br>pbc = xyz<br>
periodic_molecules = no<br>rlist = 0.9<br><br>; electrostatics<br>coulombtype = pme<br>rcoulomb = 0.9<br><br>; vdw<br>vdwtype = cut-off<br>rvdw = 0.9<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 = 0.5<br>ref_t = 300.0<br>tc_grps = system<br>
<br>constraints<br>constraint_algorithm = lincs<br>shake_tol = 0.0001<br>lincs_order = 8<br>lincs_iter = 2<br><br>