[gmx-users] How to get log written to file ...

[Dallas B. Warren]

Is there something that can do to force the files to be written to the disk?

I am trying to work out why a simulation on a SC is not doing what it should.  Problem is, only the very start of the files are present, since they are not large enough to be written, and the job reaches it's walltime (longer walltime does not good) and is killed.

Might as well put here what the issue is too, someone might have an idea.  I have contacted the SC people, but they are yet to get back to me.

Have a simulation that runs fine on my own computer that is completed within 1.25 hr.  Using all the exactly fines and execution files (except they are within a script on the SC), put it on SC, run the job, and it is killed with a 10 hr walltime.  Something is majorly wrong, just trying to work out how I can look into what is going on, since only have initial output to look at.  Last thing in the log file is:

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak
Molecular dynamics with coupling to an external bath
J. Chem. Phys. 81 (1984) pp. 3684-3690

Catch ya,

Dr Dallas Warren
Pharmacy and Pharmaceutical Sciences
Monash University

A polar bear is a Cartesian bear that has undergone a polar transformation
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