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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