Manik Mayur wrote:
On Fri, Jun 12, 2009 at 8:46 AM, Mark Abraham <[email protected]
<mailto:[email protected]>> wrote:
Manik Mayur wrote:
Hi,
The last mail supposedly bounced from the server due to
attachments. So please excuse in case you find this as a repetition.
I am trying to simulate a system where I want to exclude all nb
interactions between frozen groups. So I followed the manual and
defined them in energygrp_excl. But upon doing that it throws
the following warning.
WARNING 1 [file topol.top, line 1583]:
Can not exclude the lattice Coulomb energy between energy groups
What is the reason of the warning and should I be worried about
it or safely ignore it.
So, what algorithm are you using for your long-ranged electrostatic
interactions? Do you know roughly how it works? Does it then make
sense to try to exclude some of the long-range interactions?
I am using PME. I honestly do not have much idea about its
implementation details but I will definitely look into it. Here I was
trying to remove all interactions between the frozen group so that I can
speedup my simulation a little bit. Also since the atoms in the frozen
group are uncharged, my basic concern was to remove even the LJ
interaction calculation.
OK. The description in the GROMACS manual is OK on the maths and
implementation details, but doesn't describe the underlying strategy.
See http://en.wikipedia.org/wiki/Particle_mesh_Ewald for starters. The
long-ranged component cannot be decomposed group-wise, so cannot be
excluded group-wise. There are many posts in the archive on this topic.
Till now I have ignored the warning. So is it ok?
Yes, but you're only saving time in your short-ranged electrostatic
calculations.
Next, I am facing a strange problem with mdrun_mpi. If I run it
on 4 nodes then it throws up the following error. Which I traced
to md.log where I saw:
There are: 15923 Atoms
Charge group distribution at step 0: 0 3264 3185 0 (why these
zeroes?)
You have atoms that are not part of a charge group (or, probably,
are part of one of size one and charge zero.
In my topology file, All the atoms that I have defined within a molecule
do belong to a charge group. Could you please elaborate on the second
part of your statement?
I'm not sure how the accounting works - GROMACS might not be counting
charge groups that have only excluded interactions, or not counting
charge groups that have no non-zero charges (and thus never participate
in an electrostatic interaction). Whatever is going on, the workload
looks like it might be unbalanced over the four processors.
Mark
Grid: 3 x 4 x 5 cells
However with 2 nodes it has and runs fine:
There are: 15923 Atoms
Charge group distribution at step 0: 3226 3223
Grid: 4 x 5 x 25 cells
The error-
No, that's the dump from MPI after the error. You need to consult
both the stdout and the .log file.
Mark
Making 1D domain decomposition 1 x 1 x 4
starting mdrun 'TransverseElectrode'
100000 steps, 200.0 ps.
step 0
NOTE: Turning on dynamic load balancing
[md-comp1:32374] *** Process received signal ***
[md-comp1:32377] *** Process received signal ***
[md-comp1:32377] Signal: Segmentation fault (11)
[md-comp1:32377] Signal code: Address not mapped (1)
[md-comp1:32377] Failing at address: (nil)
[md-comp1:32374] Signal: Segmentation fault (11)
[md-comp1:32374] Signal code: Address not mapped (1)
[md-comp1:32374] Failing at address: (nil)
[md-comp1:32377] [ 0] [0xb7fd8440]
[md-comp1:32374] [ 0] [0xb7ef0440]
[md-comp1:32374] *** End of error message ***
[md-comp1:32377] *** End of error message ***
I would be extremely thankful, if somebody points me to the
source of the error and the workaround.
Thanks,
Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA
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Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA
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