Thanks Mohamad, I managed to do that two weeks ago and it worked perfectly! I serialized the data structure of the datatype and dataspace and now there are no issues. Thanks for the help!
Dimos --- Dimokritos Stamatakis PhD student, Brandeis University > On Jun 14, 2016, at 10:27 AM, [email protected] wrote: > > Send Hdf-forum mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org > > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Hdf-forum digest..." > > > Today's Topics: > > 1. Re: group/dataset sequence (?????? ?????????) > 2. Re: Parallel HDF5 file locking error (Mohamad Chaarawi) > 3. Re: implementing the attribute callbakcs in a VOL plugin > (Mohamad Chaarawi) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 14 Jun 2016 16:02:26 +0300 > From: ?????? ????????? <[email protected]> > To: [email protected] > Subject: Re: [Hdf-forum] group/dataset sequence > Message-ID: <[email protected]> > Content-Type: text/plain; charset=UTF-8; format=flowed > > 14.06.2016 4:02, ??? ?????: >> I am a newer to HDF5. I have a question, and didn't find the solution on >> internet. Could you help me? Thanks. >> >> I create three group named "fileHead" "auxiliaryInfo" "observationData" >> in sequence. But the HDFView show is "auxiliaryInfo" "fileHead" >> "observationData" by alphabet. I want to show by the creation sequence. >> So what should I do when I create these groups? >> The dataset is also has this phenomenon. > > Hello ???! > > This documentation page should be of help for you: > https://www.hdfgroup.org/HDF5/doc/RM/RM_H5P.html#Property-SetLinkCreationOrder > > Best wishes, > Andrey Paramonov > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > > > > ------------------------------ > > Message: 2 > Date: Tue, 14 Jun 2016 14:25:09 +0000 > From: Mohamad Chaarawi <[email protected]> > To: HDF Users Discussion List <[email protected]> > Subject: Re: [Hdf-forum] Parallel HDF5 file locking error > Message-ID: <[email protected]> > Content-Type: text/plain; charset="utf-8" > > Hi Andrew, > > Since it?s going to be hard to replicate this, could you provide more > information by attaching a debugger and show the trace of where the hang is? > > Thanks, > Mohamad > > From: Hdf-forum <[email protected]> on behalf of Andrew Ho > <[email protected]> > Reply-To: hdf-forum <[email protected]> > Date: Friday, June 10, 2016 at 10:06 PM > To: hdf-forum <[email protected]> > Subject: [Hdf-forum] Parallel HDF5 file locking error > > I'm having some issues with file locking on a parallel filesystem which I > believe is related the problem here: > https://lists.hdfgroup.org/pipermail/hdf-forum_lists.hdfgroup.org/2011-February/004254.html > > I tried the suggestion of disabling romio_ds_read and romio_ds_write, but > this doesn't fix the problem. I've also tried setting H5Pset_seive_buf_size > to 0 to disable data striding in HDF5 itself, but that doesn't work, either. > > Here's a short snippet of the relevant code: > > hid_t fapl_id = H5Pcreate(H5P_FILE_ACCESS); > MPI_Info info; > MPI_Info_create(&info); > MPI_Info_set(info, "romio_ds_read", "disable"); > MPI_Info_set(info, "romio_ds_write", "disable"); > H5Pset_sieve_buf_size(fapl_id, 0); > H5Pset_fapl_mpio(fapl_id, comm, info); > > hid_t f_id = H5Fcreate("test_file.h5", H5F_ACC_TRUNC, H5P_DEFAULT, fapl_id); > > It's on this last line that the program hangs, and eventually MPI_ABORT gets > called. Note that I get the same problem regardless of if I try to create a > new file, or if I try to open an existing file: > > hid_t f_id = H5Fopen("test_file.h5", H5F_ACC_RDWR, fapl_id); > > Other relevant information: > > 1. Filesystem is NFS v3 with noac off (can't change) > 2. Tested with HDF 5.8.13 and 5.8.14 > 3. Tested with OpenMPI 1.6.5 and 1.10.2 > > What am I missing? I saw that there's an option to disable filesystem > atomicity, but this requires that the file already be opened, and I can't > even get that far. > > I also know that my code does work on different computers with different > filesystems and/or mount options. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > <http://lists.hdfgroup.org/pipermail/hdf-forum_lists.hdfgroup.org/attachments/20160614/a81fc4c2/attachment-0001.html> > > ------------------------------ > > Message: 3 > Date: Tue, 14 Jun 2016 14:27:12 +0000 > From: Mohamad Chaarawi <[email protected]> > To: HDF Users Discussion List <[email protected]> > Subject: Re: [Hdf-forum] implementing the attribute callbakcs in a VOL > plugin > Message-ID: <[email protected]> > Content-Type: text/plain; charset="utf-8" > > Usually in custom VOL plugin, the easiest way to store the datatype and > dataspace for an attribute or dataset is to serialize them and store them as > a blob. > Look into the function H5Tencode/decode() and H5Sencode/decode(). > > Thanks, > Mohamad > > From: Hdf-forum <[email protected]> on behalf of Dimos > Stamatakis <[email protected]> > Reply-To: hdf-forum <[email protected]> > Date: Friday, May 27, 2016 at 1:20 AM > To: hdf-forum <[email protected]> > Subject: [Hdf-forum] implementing the attribute callbakcs in a VOL plugin > > Hi all, > > Regarding my previous question about an extra call of H5Fclose, there was > indeed an extra open handle. Now everything works perfectly! > Now I have a question about the attribute callbacks of a VOL plugin and the > datatype. I am guessing on attribute create we have to store the specified > datatype and dataspace using the custom VOL plugin. The question is how will > we restore them, since for example the datatype has to be in the HDF5 format > (H5T_t type), it is not something custom like the VOL objects. I saw that > calling H5I_register() on a datatype generates a location ID, but it is not > working properly. > What is the correct procedure of implementing attribute callbacks for a VOL > plugin? Also I saw that the datatype callbacks are not invoked in the native > HDF5 when creating and accessing string attributes. > For example, when creating a string attribute, closing it, then opening it > again and getting its datatype it should return a location ID of its > datatype. This is quite confusing, since how will the VOL plugin create these > HDF5 specific objects? > > Thanks, > > Dimos > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > <http://lists.hdfgroup.org/pipermail/hdf-forum_lists.hdfgroup.org/attachments/20160614/493b516a/attachment.html> > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Hdf-forum is for HDF software users discussion. > [email protected] > http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org > > > ------------------------------ > > End of Hdf-forum Digest, Vol 84, Issue 10 > *****************************************
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