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?
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.
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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