Re: netcdf4 parallel IO owner-netcdf-hdf@xxxxxxxxxxxxxxxx Thu Apr 26 10:07:00 2007

Hi David,

NetCDF4 is using parallel HDF5 underneath to do parallel IO. As far as I know, I don't think HDF5 is doing anything like blocking in its layer. Other experts, please correct me if I am wrong.

If seems that your application fits to what we called irregular selection of data. Parallel HDF5 does support irregular selection of data via collective IO. However, the current netcdf-4 API may not support this yet. One workaround solution is see whether you can combine your cells into several regular selections and then use NF90_PUT_VAR. From your example, you can put (1 2) of cell 1 and (3 4) of cell 2 into one regular selection and call NF90_PUT_VAR.


Kent Yang

The HDF Group

At 10:39 AM 4/26/2007, David Stuebe wrote:


Hi NETCDF folks

I work on an unstructured finite volume coastal ocean model, FVCOM, which is parallel (using MPICH2). The Read Write is a major slow down for our large cases. On our cluster, we have one large storage device, an emc raid array. The network is infini-band - the network is much faster than the raid array.

For our model we need to read large initial condition data sets, and single frames of forcing data while running. We also need to write single frames of data for output (frequently), and large restart files (less frequently).

I am considering two options for recoding the IO from the model. One is based around the future F90 netcdf 4 parallel interface which would allow a symmetric code- every processor does the same thing. The other option is to use netcdf 3, let the master processor read/write the data and distribute it to each node, -an asymmetric coding.

What I need to know-  are netcdf 4 parallel IO operations blocking?

The problem - the order of cells and nodes in our data set does not allow for a simple start, count read format. A data array might have dimensions (time,layers,cells). As an example, in a 2 processor case with 8 cells, proc1 has cells(1 2 5 7) while proc2 has cells (3 4 6 8) - write operations would have to be in a do loop to write each cell individually from the processor that owns it.

For a model with 300,000 cells on 30 processors, this would be 10,000 calls to NF90_PUT_VAR on each processor. Even if the calls are non-blocking this seems dangerous.

Any thoughts?

David




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