[gmx-users] Storage of large output files

[Erik Marklund]

This is an interesting topic and has been discussed before:
http://www.gromacs.org/component/option,com_wrapper/Itemid,165/

We use a tape-drive for backups.

/Erik

9 aug 2007 kl. 11.56 skrev Alan Dodd:

> I've always used HDDs for the main backup/working copies, and DVDs  
> for longer-term backup.  You can get hold of 100x spindles of DVDs  
> quite cheaply these days...  I wouldn't call it convenient, though.
>
> ----- Original Message ----
> From: Monika Sharma <mon_sharma at research.iiit.ac.in>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Thursday, August 9, 2007 10:48:52 AM
> Subject: Re: [gmx-users] Storage of large output files
>
>
> 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.
> Regards,
> Monika
>
> 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.
>>
>> Mark
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_______________________________________________
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,	75124 Uppsala, Sweden
phone:	+46 18 471 4537		fax: +46 18 511 755
erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys