From: Peter Freddolino (petefred_at_umich.edu)
Date: Fri Aug 21 2015 - 17:09:40 CDT
> On Aug 21, 2015, at 6:03 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Fri, Aug 21, 2015 at 5:44 PM, Peter Freddolino <petefred_at_umich.edu> wrote:
> Dear Daniel,
> Have you looked into namd’s use of restart files? With appropriate configuration they regularly produce files that can be used for clean restarts.
> Why would you have an ‘exit’ file and not just send a termination signal to the namd process?
> hi peter,
> FYI, restart files in plane-wave DFT calculations can be huge compared to classical MD, and thus writing them frequently has much more impact on performance. also, due to the high algorithmic load of such calculations, you usually run with many more CPU cores. thus the loss of computer time when a job crashes without a usable last restart can be significant. for very large calculations across a some 1000s of CPU cores, it can quickly take of the order of 30 minutes to write a restart. that leads to a different "restart culture"... ;-)
Thanks for the lesson — good to know that the technical issues at play are different.
So especially in light of that, Daniel, I should say that writing restart files for classical MD is typically *not* performance intensive as long as you don’t do it too often — I usually see every 1000-10000 steps; sometimes even more frequent. You can set this with the restartfreq parameter (and related entries) in NAMD.
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