Hello Sir,
The job runs for 8 processes given 1 , 2 or 8 nodes but not for more than
that.
16 proceses : Segmentation fault and
For 32 processes it gives :
Fatal error : 467 particles communicated to PME node 4 are more than 2/3
times
the cut off out of the domain decomposition cell of their
One cannot run an arbitrary simulation on an arbitrary number of
processors. The particles in the simulation have to get mapped to
processors that handle them. This is done in small parcels called domains.
The atoms move between domains, and so the responsibility moves too. If the
velocities are
They're just MPI error messages and don't provide any useful GROMACS
diagnostics. Look in the end of the .log file, stderr and stdout for clues.
One possibility is that your user's system is too small to scale
effectively. Below about 1000 atoms/core you're wasting your time unless
you've
Sir,
Thanks for your reply
But the same script runs on some other cluster with apprx same
configuration but not on cluster on which I am doing set up.
Also job hangs after some 16000 steps but not come out immediately.
It might be problem with configuration or what?
Thanks...
Chaitali
On
It could be anything. But until we see some GROMACS diagnostic messages,
nobody can tell.
Mark
On Tue, Mar 12, 2013 at 10:08 AM, Chaitali Chandratre chaitujo...@gmail.com
wrote:
Sir,
Thanks for your reply
But the same script runs on some other cluster with apprx same
configuration but
Hello Sir,
Actually I have been given work to setup gromacs-4.5.4 in our cluster which
is being used
by users.I am not gromacs user and not aware of its internal details.
I have got only .tpr file from user and I need to test my installation
using that .tpr file.
It works fine for 2 nodes 8
Dear Sir ,
I am new to this installation and setup area. I need some information for
-stepout option for
mdrun_mpi and also probable causes for segmentation fault in gromacs-4.5.4.
(my node having 64 GB mem running with 16 processes, nsteps = 2000)
Thanks in advance.
--
With Regards,
On 3/6/13 4:20 AM, Chaitali Chandratre wrote:
Dear Sir ,
I am new to this installation and setup area. I need some information for
-stepout option for
What more information do you need?
mdrun_mpi and also probable causes for segmentation fault in gromacs-4.5.4.
(my node having 64 GB mem
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