[aspect-devel] Writing output in parallel

[Thomas Geenen]

ok
that sounds good to me
i would like to do this io in the background so i will re implement that
and put it in as an option for the poor mans cluster

thomas

On Tue, Feb 28, 2012 at 5:12 PM, Timo Heister <heister at math.tamu.edu> wrote:

> > When you
> > merge it using (synchronous) MPI I/O, you still have at least one node
> > that has to wait till the writing is finished. This will take a long
> > time no matter what you do (writing from each node to the central file
> > system or writing via MPI I/O) and that the only way to avoid this is
> > doing it in the background.
>
> For a cluster with a decent parallel file system (like the gluster in
> our hurr cluster) we can write 500MB/s or more. That means writing 180
> Million DoFs in 3d takes a second or two compared to solving the
> linear system which takes a minute or more. I don't think we need to
> do tricks with background i/o, especially because we don't want to
> output every time step anyway.
>
> > Is there an asynchronous MPI I/O interface where you hand MPI the data
> > and then go off doing something else while MPI decides what to do with
> > the data?
>
> Yes, but the default MPI implementation is not thread-safe (you
> discovered that too). So one can only start a non-blocking
> MPI_file_write* and then complete it at a later point in time. But
> where in the code are we going to complete the call (I don't see a
> clean way to do that)? Additionally, MPI I/O will use the fast
> interconnect and not the slow ethernet in the case Thomas has.
> I think Thomas is best of writing to the local disk only. There is no
> danger in symlinking the output folder to local scratch space or a
> different filesystem (I am doing that all the time).
>
> I think we have two cases:
> 1. big cluster with fast interconnect: use MPI I/O and hope we have a
> fast parallel filesystem (not some NFS)
> 2. slow small cluster or desktop: we just use the method we have right
> now and you have the option to write to local disk space.
>
> --
> Timo Heister
> http://www.math.tamu.edu/~heister/
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>
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