I've a few more comments. First of all, please upload to redmine the full
mdrun.debug output!
It looks like the detection of the number of cores in your machine does not
work with cygwin because when you only set "-ntmp 1" N OpenMP threads
should be auto-set (N=#cores), but based on your output it
Hi,
That is a likely cause. I can not comment with full certainty on the use of
MARTINI with the Verlet scheme & without shifts, but I know that it is a
topic that's being investigated and hopefully other can comment on it.
However, the hanging should definitely not happen, but instead an error
s
Hello,
It looks like the problem might be in my mdp settings. I am using the
MARTINI force field which uses shift functions for both electrostatics and
vdw which are only available in the group-based cut-off scheme. OpenMP
doesn't seem to run with the group-based cut-off scheme, just Verlet
Hi Mike
On 25.02.2013 17:25, toma0...@umn.edu wrote:
...
Estimated maximum distance required for P-LINCS: 0.810 nm
...
Domain decomposition grid 4 x 2 x 1, separate PME nodes 0
Do your runs use PME and/or P-LINCS?
Maybe you could point out the problem by disabling
each or both in yout .mdp fi
Hi,
I have run the 3 scenarios that you mentioned. The commands and output
are pasted below.
Thanks,
Mike
***Trial 1***
mdrun -v -deffnm Clp_Test -ntmpi 1 -ntomp 1
Reading file Clp_Test.tpr, VERSION 4.6 (single precision)
Using 1 MPI thread
Can not set thread affinities on the current pl
That's strange, it seems that mdrun gets stuck somewhere. This should not
happen, but as we don't actively test cygwin, we can't be sure what's
happening. It would be great if you could help us figure out what is going
wrong.
Could you try doing the following:
- run with -ntmpi 1 -ntomp 1 (i.e sin
Hello,
Thanks for the help. After setting the library path properly, I seem
to be able to get gromacs up and running. However, I have run into another
problem with mdrun and actually running any jobs. When I execute
mdrun -v -deffnm Clp_Test -nt
The output is: Reading file Clp_Test.tpr, V
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