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

chris.neale at utoronto.ca chris.neale at utoronto.ca
Wed Dec 2 16:19:04 CET 2009

Thanks Berk,

I agree that a single file open action is not going to cause a lot of  
system activity. We're simply trying to cut down wherever possible as  
this is a large shared cluster where the activity of many users  
distributed amongst 30K cores is overwhelming the GPFS. We have been  
instructed to cut as many file operations as possible, and in this  
type of environment it would also be nice to have an option to mdrun  
that reduces the fexist operations (which I had not considered up to  
this point). We have circumvented these issues by running in /dev/shm  
and later moving the desired files to the hard disk.

I don't know exactly how many file operations it takes to cause GPFS  
delay problems, but we actually have two important considerations: a)  
the ability to minimally stress a physical file system in real terms;  
and b) the ability to easily convince system administrators that the  
computational tool is optimized for the given platform.

I don't think that this is likely to be a real problem for many users  
right now, but it will certainly be a concern in the future as the  
number of cores increases and physical filesystems become more and  
more limited by disk operations.


-- original message --


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.


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