[gmx-developers] Re: flushing files

Roland Schulz roland at utk.edu
Wed Oct 13 07:53:00 CEST 2010

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)?

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).

You are more then welcome to play with it (but not in the release branch!) -
No this is only going into the CollectiveIO branch and from their into the
master branch.

>  you might already have anaccount on the AFS-equipped clusters here, or we
> can arrange it!
> Alternatively, sync with Sander and he might be able to test new code on
> AFS.

Yes if I could get an account or Sander could test the CollectiveIO branch
that would be great. I'll write Sander directly tomorrow.


> On Oct 12, 2010, at 23:26, Roland Schulz <roland at utk.edu> wrote:
> Erik, Berk,
> you added flushing of trn, xtc and ern before the checkpointing
> functionality had been added. The additional flush can add quite a bit
> of unnecessary time especially with parallel file systems and/or MPI-IO. Am
> I right that with checkpointing it is not necessary anymore?  The
> checkpointing is flushing the file before writing the checkpoint.
> Also gmx_fio_check_file_position is flushing the file before checking
> whether the file is too large for gmx_off_t
> Roland
> --
> ORNL/UT Center for Molecular Biophysics <http://cmb.ornl.gov>cmb.ornl.gov
> 865-241-1537, ORNL PO BOX 2008 MS6309

ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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