Hi,
One extra comment: By default, checkpointing will result in separate
output files to avoid filling up your disk, or just in case something
horrible happens just when we are about to resume the simulation.
There are also some old strange versions of the GPFS file system where
append operations are not allowed (no idea what happens if we were to
try it anyway).
However... it IS possible to have Gromacs 4 automatically checkpoint
and just append to the previous output files if you (think you) know
what you're doing. We haven't experienced any bugs with this yet, but
this is one of the things we'd like you to test!
So, to enable all this stuff, simply execute mdrun e.g. as:
mdrun -v -deffnm test -cpi test -append
* The -cpi option will tell mdrun to look for the checkpoint file (the
first time when we don't have it, you'll just get a normal run)
* The -append option will tell mdrun to append to the previous output
files.
Thus: the command line should preferrably be identical in all runs.
This far we've only tested it when we're nice and don't move files,
but feel free to stress-test it and report bugs to us. Don't complain
if your trajectories are eaten after you've moved them in the middle
of a simulation, though ;-)
Cheers,
Erik
On Sep 22, 2008, at 8:46 AM, Erik Lindahl wrote:
Stockholm, September 22 2008
In a bold move today, the Gromacs developers finally decided not to
wait for Duke Nukem Forever before releasing Gromacs 4.0, and just
put out release candidate 1 together with a new manual at
ftp://ftp.gromacs.org:/pub/beta/
"We realize it could be a big disappointment to many users not
having g_dukenukemforever built-in, but sometimes you have to make
hard decisions. Had we waited further, we might even have had to
release Gromacs 5 before Gromacs 4", an anonymous developer said.
If you haven't already been playing around with CVS for the last
year we think you'll be pretty impressed with the scalability of the
new code, in addition to full checkpointing support, REMD, and
various optimizations.
Having said that, since the code has changed a lot we decided to
have a fairly short cycle of "release candidates" before putting out
the real version. Please download the code above, try to compile and
run with it (see manual and html pages in the distro for
documentation of new stuff), and submit any bugs you find to
bugzilla ("If it's not in bugzilla, it's not a bug").
Have fun!
Erik, Berk, and David.
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Erik Lindahl <[EMAIL PROTECTED]> Backup: <[EMAIL PROTECTED]>
Associate Professor, Computational Structural Biology
Center for Biomembrane Research, Dept. Biochemistry & Biophysics
Stockholm University, SE-106 91 Stockholm, Sweden
Tel: +46(0)8164675 Mobile: +46(0)703844534 Fax: mail a PDF instead
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