Collective H5Dopen

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5

Hi Barbara and Mark,

thanks for getting back to me.

As we tried to implement direct MPI I/O we discovered that HDF5 does not
directly allocate created datasets so we could not get the offsets to do
the direct writing. Doing

auto plist = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_layout(plist, H5D_CONTIGUOUS);
H5Pset_alloc_time(plist, H5D_ALLOC_TIME_EARLY);

before calling H5Dcreate(); and passing plist does allocate the data -
then the offsets works.

Turns out that closing the serially written file, reopening it in
parallel and writing independently with H5DOpen() and H5Dwrite() then
works fine. So I guess the modification of the dataset does then not
count as a modification and it does not have to be collective. The files
close cleanly and the output is correct.

Hope it helps someone who runs into the same issue!

It would also be very helpful to document what exactly counts as a
modification the collective/independent call page.

Cheers!

Lion

···

On 20/03/2017 18:13, Barbara Jones wrote:

Hi Lion,

I checked with the developers…

H5DOwrite_chunk() does not work with parallel HDF5.

-Barbara

help@hdfgroup.org

*From:*Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] *On
Behalf Of *Lion Krischer
*Sent:* Tuesday, March 14, 2017 3:43 PM
*To:* hdf-forum@lists.hdfgroup.org
*Subject:* Re: [Hdf-forum] Collective H5Dopen

Thanks a lot for your input!

We'll try to directly use MPI I/O to write to the file after getting
the offsets from the initially created file. Thanks for the
suggestion! As we use none of the advanced features a straight mmap or
its equivalent with MPI I/O should work.

Our code guarantees that each data set is only written to from a
single rank so that should work and metadata synchronization issues do
not really exist. It would be great if something like this could be
supported directly via the hdf5 library. Maybe a H5DOwrite_directly()
that does some very basic checks and then writes straight to the
uncompressed, unchunked, .. dataset without even touching the metadata
so it should work fine with parallel I/O?

Does H5DOwrite_chunk() work for parallel code? I cannot really tell
from the documentation and it also appears to solve the way more
complicated problem of efficiently writing chunked data.

We'd still be happy to hear additional suggestions :slight_smile:

Cheers!

Lion

Hmm. Interesting question. I would think *any* operation that changes
data (either

metadata or raw data) is a *modification*. But, I think I kinda see
where you are

going here...If you've created a (non-extendible) dataset with no
checksum or compression

filters etc., all you wanna do is change the raw data but not perterb
any of the HDF5 file's

metadata. I don't think the HDF5 library would treat that as a
non-modification though. I think a write

operation (even on the raw data) can wind up changing how the library
caches dataset and file

metadata in memory thereby creating a situation where two different
tasks have a different idea

of the file's cached metadata. When it comes time to close the file,
which tasks' view of the metadata

is correct?

Its concievable you could manually do it by obtaining the dataset's
offset in the file, calling

any necessary H5Tconvert method on your buffer just prior to writing
in and then writing the

buffer yourself to the file via pwrite or something. That would
essentially skirt HDF5 though

and probably be too complex to be worth it.

It might be worth looking at, H5DOwrite_chunk() though,
https://support.hdfgroup.org/HDF5/doc/HL/RM_HDF5Optimized.html

to ask how that works and if it achieves or gets close to behavior you
want.

Mark

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_______________________________________________
Hdf-forum is for HDF software users discussion.
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http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: x.com