HI,
On Oct 5, 2007, at 10:04 PM, David van der Spoel wrote:
vijaya subramanian wrote:
Hi
I have been running GROMACS jobs on a Cray XT3 MPP machine. I
get limited time, 12 hr, for any given run and find that the
.edr file and .log files do not get written to continuously. This
is ok if the run
finishes but I lose data everytime the runtime exceeds the 12 hr
limit. The following is the info I got from the sys admn about
the issue: The problem with GROMACS looks like it is caused by the
way GROMACS
buffers its IO, which would not be easy for us to fix. Is there a
GROMACS
keyword that you can use to change this?
Does anyone know of a workaround this problem?
Of course, you can make the runs so short that they finish in 11:30
h. Do also try the -v option to mdrun.
This has actually been circumvented in the CVS / 3.99 version; we
still buffer IO while it happens (for performance reasons), but once
a frame is written we flush the file to make sure everything is
written out.
In addition, Gromacs will clean up and finish nicely if it receives a
SIGHUP signal, and finish at the next neighborsearching step if it
received SIGUSR1.
Cheers,
Erik
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