[gmx-users] Storage of large output files
mon_sharma at research.iiit.ac.in
Thu Aug 9 11:48:52 CEST 2007
Thanks Mark for your reply. Thats a sound advice. I will really take
care of. Actually, through my previous mail, I wanted to know that what
other groups are using as storage devices for the backup of their large
files, that must have figured out that which way is best-" economical
and efficient" way to store their data.
Mark Abraham wrote:
> Monika Sharma wrote:
>> Dear All,
>> We have started our venture into MD recently, for which we are using
>> our in-house resources. Now that MD runs are giving very large output
>> files like for trr files. The files keep piling up and using spaces
>> on the work machines. This is creating problems with the depletion of
>> space with every run. Can anyone please suggest an "economical and
>> efficient" way how to take backup of such a large files of the order
>> of Gb or so, so that we dont end up piling up our work machines with
>> such files. And the data need to be saved for future references..
> First, consider whether you are producing more output than you need.
> Look at the options for output frequency of positions and velocities
> in .trr files, whether you should be using .xtc files, and whether you
> should only be outputting subsets of your data.
> Normally you only want a full frame of positions and velocities in
> your .trr file with frequency with which you might ever want to do an
> exact restart (and make sure your energy output frequency is a
> suitable multiple so you also have energies at this time). This
> frequency is invariably much smaller than the frequency with which you
> want output data. If you only want position data for your solute for
> your later analysis, then outputting only that group to an .xtc file
> with frequency as low as you'd ever need will be a tiny fraction of
> the cost of a .trr file of the whole system with positions and
> velocities at every step. Be aware that analysis types that require
> autocorrelation functions need data sampled much more frequently than
> the characteristic times of the system.
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