Hi Lion, I checked with the developers... H5DOwrite_chunk() does not work with parallel HDF5.
-Barbara [email protected] From: Hdf-forum [mailto:[email protected]] On Behalf Of Lion Krischer Sent: Tuesday, March 14, 2017 3:43 PM To: [email protected] 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 :) 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 _______________________________________________ Hdf-forum is for HDF software users discussion. [email protected]<mailto:[email protected]> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org Twitter: https://twitter.com/hdf5 _______________________________________________ Hdf-forum is for HDF software users discussion. [email protected]<mailto:[email protected]> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org Twitter: https://twitter.com/hdf5
_______________________________________________ Hdf-forum is for HDF software users discussion. [email protected] http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org Twitter: https://twitter.com/hdf5
