[gmx-users] Regarding REMD using gromacs4.5.5

[Daniel Burns]

Hi Amit,

I’m not the best resource for solutions but I’ve been having this issue
with gromacs 2018.  It seems to be related to the process manager or our
open mpi module we are using. The job would hang on some open mpi
communication step.

I found it would work if each replica was assigned its own entire node but
that becomes prohibitively resource expensive with more than a few
replicas.

I was finally able to get it to work on our least used cluster where things
must have been installed correctly.

You might have your IT look at what’s happening with the process manager
and open mpi or whatever dependencies you have loaded. You might try a
small job where you can assign each replica to its own node and see if you
get the full output. Our IT dept has been working for two weeks and still
haven’t gotten it to work on the other clusters.


Dan


On Tuesday, March 3, 2020, Amit Kumar <amitkumar879792 at gmail.com> wrote:

> Dear Gromacs users,
>
> I am trying to run a REMD simulation in gromacs 4.5.5 in implicit solvent
> but I am unable to get any output file containing significant data (logfile
> is obtained with only developers' details) or any error file.
> I am unable to understand why this is happening and how can I tackle the
> situation?
> Kindly, help me out of this situation.
>
> ThankYou
> Amit Kumar
>