[gmx-developers] Re: flushing files

Erik Lindahl lindahl at cbr.su.se
Wed Oct 13 08:20:24 CEST 2010


On Oct 13, 2010, at 7:53 AM, Roland Schulz wrote:

> On Wed, Oct 13, 2010 at 1:02 AM, Erik Lindahl <lindahl at cbr.su.se> wrote:
> Hi,
> File flushing has been a huge issue to get working properly on AFS and other systems that have an extra layer of network disk cache. We also want to make sure the files are available e.g. on the frontend node of a cluster while the simulation is still running.
> Do we want to guarantee that it is available sooner than at each checkpoint (thus by default 15min)?

It's not only a matter of "being available", but making sure you don't lose all that data in the disk cache layer of the node crashes and you (for some reason) disabled checkpointing.

Basically, when a frame has been "written", it is reasonable for the user to expect that it is actually on disk. The default behavior should be safe, IMHO.

> I think the proper solution is rather to have a separate IO thread so the disk operation can take all the latency in the world without delaying the run.
> This won't solve it for all cases. Depending on the write frequency (e.g. every 10 frames) the flushing time can take longer than computing the frames while the actually writing time (measured as the writing time with only infrequent flush) is fast enough to not cause significant overhead. In those situations the simulation would still wait on the IO thread. 
> Also this adds additional complexity. Not all systems like oversubscribing threads as far as I know. I know that older versions of Cray had problems and I heard their are also problems with BlueGene. Thus we would need to make the IO thread functionality optional which would add yet another duplication of code (both with and without IO thread).

The difference is that an IO thread would virtually never run though; it would instantly block waiting for the filesystem, and in the mean time the real threads would get control back?



Erik Lindahl <lindahl at cbr.su.se>
Professor, Computational Structural Biology
Center for Biomembrane Research & Swedish e-Science Research Center
Department of Biochemistry & Biophysics, Stockholm University
Tel: +468164675 Cell: +46703844534

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