Hi Håkon,
Actually, given this behavior, it’s reasonably possible that you have
found a bug in the MPI implementation that you have, so I wouldn’t rule that
out. What implementation and version of MPI are you using?
Quincey
> On May 19, 2017, at 4:14 AM, Håkon Strandenes <[email protected]> wrote:
>
> Hi,
>
> I have an MPI application where each process sample some data. Each
> process can have an arbitrary number of sampling points (or no points at
> all). During the simulation each process buffer the sample values in
> local memory until the buffer is full. At that point each process send
> its data to designated IO processes, and the IO processes open a HDF5
> file, extend a dataset and write the data into the file.
>
> The filespace can be quite compicated, constructed with numerous calls
> to "h5sselect_hyperslab_f". The memspace is always a simple contiguous
> block of data. The chunk size is equal to the buffer size, i.e. each
> time the dataset is extended it is extended by exactly one chunk.
>
> The problem is that in some cases, the application hang in h5dwrite_f
> (Fortran application). I cannot see why. It happens on multiple systems
> with different MPI implementations, so I believe that the problem is in
> my application or in the HDF5 library, not in the MPI implementation or
> on the system level.
>
> The problem disappear if I turn off collective IO.
>
> I have tried to compile HDF5 with as much error checking as possible
> (--enable-debug=all --disable-production) and I do not get any errors or
> warnings from the HDF5 library.
>
> I ran the code through TotalView, and got the attached backtrace for the
> 20 processes that participate in the IO communicator.
>
> Does anyone have any idea on how to continue debugging this problem?
>
> I currently use HDF5 version 1.8.17.
>
> Best regards,
> Håkon Strandenes
> <Backtrace HDF5 err.png>_______________________________________________
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