[gmx-users] Re: High frequency output slow down the simulation?

Mark Abraham Mark.Abraham at anu.edu.au
Sun Nov 9 08:43:47 CET 2008

Yang Ye wrote:
> Writing on local or remote certainly makes a difference. How about the 
> speed with no output at all?

Absolutely. Depending on the cluster setup, the best option is often 
along the lines of

1) Write to disk physically associated with the CPUs (IIRC for GROMACS, 
preferably the disk associated with MPI node 0, where applicable).
2) Write minimally often for your needs - using XTC rather than TRR 
output wherever high precision is not required.
3) Arrange for the file to be returned to more convenient or permanent 
file space at the end of the job.

This last step might be as simple as adding some cp commands to your 
batch script, or perhaps issuing some "stage file out" instructions to 
your batch system.

Your first port of call should be the cluster administrator / 
documentation for how best you should be doing these steps. We can't 
help much there.


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