Dear All,
I've been having some issues with energies with gromacs running on
various core counts for a 7469 polymer in solvent system, constraining
all bonds and running with a 2fs time step. I used PME-shift (1.05nm,
1.10nm), and a shift with the same parameters for the VdW, I am using
the OPLS-AA force field with fourierspacing = 0.10. and the md-vv
integrator.
I am running gromacs 4.5.5 compiled from the tarball on gromacs.org
To try and track it down I ran a 100ps NVE simulation outputting
coordinates and velocities every 1ps. I then used the trr trajectory
file and ran:
$ mdrun_d -s nve_short.tpr -rerun reference.trr -deffnm 8_cores -reprod
-nt 8
$ mdrun_d -s nve_short.tpr -rerun reference.trr -deffnm 4_cores -reprod
-nt 4
$ mdrun_d -s nve_short.tpr -rerun reference.trr -deffnm 1_cores -reprod
-nt 1
then:
$ g_energy_d -f 8_cores.edr -o 8_cores.xvg << EOF
10
11
12
13
14
15
EOF
etc.
Where nve_short.tpr is the input file used for the original simulation
and reference.trr is the trajectory it produced (I did not output forces
into this which was an oversight).
These were run on my machine a quad core hyper-threaded intel xeon. I
also used performed the rerun on our local cluster on 12, 24, and 36
cores (dual 6 core intel xeon nodes with infiniband interconnects)
The resulting energy files are significantly different energies for these
snapshots summarised in this table:
number of cores, Potential Energy, Standard Deviation
------------------------------------------------------------------------------------
reference 7912.74479607 180.525445863
1_cores 9635.92644669 180.525445891
4_cores 1061.8467459 244.14154375
8_cores 776.470114871 208.368028756
12_cores 374.243502525 204.012539953
24_cores 667.44876102 502.041766722
36_cores 616.93105205 476.190500738
(reference is the energy extracted from the original simulation run on a
12 core node)
The large variation in standard deviation means that these energies are
not simply shifted but behaving differently which is apparent from a
plot of the potential energies.
has anyone else noticed any sort of inconsistency? Does anyone have any
advice about what might cause this? Am I doing anything stupid?
Thanks,
Richard
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