Parallel IO with Dedalus?

[Martin Lellep]

Dear all,

I plan to run larger scale simulations on a cluster and noticed that each processor writes its own HDF5 file.

When talking of 1000's of cores, this might be problematic for the cluster file system.

Is parallel IO supported in Dedalus? With that, I mean that each processor writes its data into its part of a single file. NetCDF is a format that supports this feature.

I was not able to find anything online on that topic, but might have simply missed it.

Best wishes and thanks,

Martin

[Daniel Michael Lecoanet]

Hi Martin,

hdf5 does support parallel IO, and in principle this feature is supported in Dedalus as well. However, our tests of this from ~8-9 years ago indicated that the parallel IO was significantly slower than serial IO, which is why that is the default in Dedalus. It could be things have changed, or it is possible to change certain configuration options to speed things up.

You can change to parallel IO by adding the parallel=True flag when you initialize a FileHandler. Or you can modify the dedalus.cfg configuration file to change the default.

Personally, I normally run simulations on up to 4096 cores on the Pleiades computer, and the serial IO is an insignificant cost. Note that the Pleiades file system is very slow, so I would expect this conclusion to also follow for other computers.

Daniel

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