Re: netcdf4 parallel IO

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We probably confused you with our answers :-) Let me reiterate what 
Quincey said in his email.

Bottom line is that HDF5 uses MPI_File_read(write)_*  and does not 
use MPI_File_iread(iwrite)_* functions.

I/O for HDF5 metadata is always a collective call; raw data can be 
read/written using noncollective calls (also called "independent" in 
our docs)  or collective calls.

HDF5 parallel performance  depends on many factors and we will be 
happy to work with you, Ed and LLNL's Visit team to get the best from 
the parallel NetCDF-4.


At 1:48 PM -0400 4/27/07, David Stuebe wrote:
>Thank you all for the help with Netcdf4. I am really excited about 
>the great response. I have to do some work on my end to look at the 
>state of the F90 interface - I will look at the NETCDF 4 C and F90 
>interface and the HDF5v1.8beta to see what needs to be done and 
>where these tools will be useful in the FVCOM model.
>My questions about blocking during IO operations have to do with my 
>very vague understanding of what exactly happens during a parallel 
>read/write call. The problem I want to solve is that at the moment, 
>using netcdf 3 to write output for a given timestep, we have to 
>collect all the data on the master node, and then all the nodes have 
>to wait for the master to catch up after it finishes writing the 
>data. It seems the best solution might be to have a dedicated node 
>for writing data in compressed netcdf4 format, while using parallel 
>reads for forcing data?
>One area that I have focused on in my work for FVCOM is parallel 
>visualization of our unstructured grid data using LLNL's VisIt. I 
>will have to talk to those folks and see what there plans are for 
>supporting netcdf4/HDF5 parallel IO. It sounds like a great 
>application for parallel reads of compressed data!
>On 4/27/07, Quincey Koziol 
><<mailto:koziol@xxxxxxxxxxxx>koziol@xxxxxxxxxxxx> wrote:
>On Apr 26, 2007, at 12:03 PM, Elena Pourmal wrote:
>>  David,
>>  NetcDF-4 is built on top of HDF5 that uses blocking MPI IO calls.
>>  We are thinking of implementing non-blocking calls for the HDF5
>>  metadata writes.
>         It depends whether David is concerned about blocking during metadata
>operations (which HDF5 does right now), or during dataset I/O (which
>the application can choose whether to use collective or independent
>parallel I/O, neither of which is "blocking" in the same sense)...
>         Quincey
>>  Elena
>>  At 11:39 AM -0400 4/26/07, 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
>>  --
>>  ------------------------------------------------------------
>>  Elena Pourmal
>>  The HDF Group
>>  1901 So First ST.
>>  Suite C-2
>>  Champaign, IL 61820
>>  <mailto:epourmal@xxxxxxxxxxxx> epourmal@xxxxxxxxxxxx
>>  (217)333-0238 (office)
>>  (217)333-9049 (fax)
>>  ------------------------------------------------------------
>>  =====================================================================
>>  ========
>>  To unsubscribe netcdf-hdf, visit:
>>  =====================================================================
>>  ========


Elena Pourmal
The HDF Group
1901 So First ST.
Suite C-2
Champaign, IL 61820

(217)333-0238 (office)
(217)333-9049 (fax)

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