[gmx-users] any chance to write avoid writing out trr but only xtc file ?

[Berk Hess]

Hi,

We should remove the opening of the trr file in Gromacs 4.1 when no output is requested.
But opening one output file on one process should not cause a lot of system activity,
independently of the size of the cluster, right?

More costly are the fexist operations that all processes perform for all in and output files
with multiple possible file names. In git master only the master process calls fexist.

Berk 

> Date: Wed, 2 Dec 2009 09:17:00 -0500
> From: chris.neale at utoronto.ca
> To: gmx-users at gromacs.org
> Subject: [gmx-users] any chance to write avoid writing out trr but only xtc	file ?
> 
> We have the same desire on a large cluster in order to reduce the  
> number of file operations overall. In addition to Xavier's suggestion,  
> you can also write your .trr to memory:
> mdrun -deffnm xx -t /dev/shm/xx.trr
> or to the local disk:
> mdrun -deffnm xx -t ${TMPDIR}/xx.trr
> if those exist and depending on your architecture. Contact your  
> sysadmin for the best option here... just be sure to rm -f your  
> unwanted .trr.
> 
> While I agree that the ability to not create the .trr at all or to  
> write the .trr to /dev/null would be ideal, that appears to be  
> incompatible with the automated file name extension determination and  
> the provided solution will probably be just as fast.
> 
> Chris.
> 
> -- original message --
> 
> you can define the frequency of writing to the trr file in the mdp file.
> 
> using:
> 
> nstxout = 0
> nstvout = 0
> nstfout =0
> 
> should fix your problem.
> 
> On Dec 1, 2009, at 4:30 PM, Jörn-Benjamin Lenz wrote:
> 
> > dear users of gromacs,
> >
> > i updated my gromacs from 4.0.1 to 4.0.5 and now i am facing the   
> > following problem:
> >
> > using the older version of gromacs I submitted REMD jobs to our   
> > cluster (which also was updated from suse 10.3 to suse 11.1) and two  
> >  differently formatted output files were generated: trr files and  
> > xtc  files
> > since we always are short on disk space in our home folders i did   
> > the following:
> > the trr files were written to the a folder in my home directory on   
> > our fileserver whereas the xtc files were written to the local   
> > machine i was using. in order to save disk storage on our fileserver  
> >  (i.e. in /home/joern/...) i deleted the trr files once as soon as   
> > they were produced and the job on our cluster was still happy and   
> > wrote the xtc files to my local machine and i was very happy with   
> > that behaviour.
> >
> > using gromacs 4.0.5, again trr and xtc files are written. however,   
> > as soon as i delete the trr files the mdrun jobs die and the whole   
> > job finishes without keep on writing the xtc files as it did with   
> > the older version.
> >
> > is there  a chance to say gromacs not to write out a trr file at all  
> >  but only a xtc file. without using the mdrun -o command gromacs   
> > still writes out the standard trajX.trr files. or is this becuase of  
> >  the update from suse 10.3 to suse 11.1 ?
> >
> > any help and / or advice is much appreciated !
> > many thanks in advance,
> >
> > joern
> > --
> 
> 
> -- 
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