That totally makes sense! But I have the feeling that creating a link is something internal and specific in each VOL plugin, right? I mean each plugin is responsible to create the links of the HDF5 objects in its own way, while creating the objects.
So the question is how does h5dump determine those links if it only uses VOL API callbacks? I traced the function calls of h5dump and it does not call the link_get callback at anytime. It only calls file_open to get file contents, then group_open and group_get for each contained group and I guess these have information about the created links. I am mostly confused with the concepts, since you also have link callbacks for the VOL plugins. Maybe a specialized person in the VOL plugins would know details about that. Thanks a lot, Dimos On Tue, Nov 3, 2015 at 1:33 PM, <[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. how h5dump works with a VOL plugin (Dimos Stamatakis) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 3 Nov 2015 13:33:09 -0500 > From: Dimos Stamatakis <[email protected]> > To: [email protected] > Subject: [Hdf-forum] how h5dump works with a VOL plugin > Message-ID: > <CAB8CW0FJq-7GWZZw-0n574k_SfajVtrud2bKJ68h8UU28oTq= > [email protected]> > Content-Type: text/plain; charset="utf-8" > > Thanks Albert, it is more clear now. > > By 'link' you mean a HDF5 link (soft, hard, or UD link), or just a > connection to the child group? So creating a group involves creating a HDF5 > link to its parent? (using the link function callbacks), or you just mean a > connection? > > Thanks, > > Dimos > > > On Tue, Nov 3, 2015 at 8:26 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: Valgrind errors (Matthieu Brucher) > > 2. Re: how h5dump works with a VOL plugin (Albert Cheng) > > 3. Re: Building HDF5DotNet - C++/CLI Wrapper of the HDF5 Library > > with current version of HDF5 library (Gerd Heber) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Mon, 2 Nov 2015 22:43:38 +0000 > > From: Matthieu Brucher <[email protected]> > > To: HDF Users Discussion List <[email protected]> > > Subject: Re: [Hdf-forum] Valgrind errors > > Message-ID: > > < > > cahcack+0nd-84vfvnivt3xjdtsddxih5jfaztln-n1w67a6...@mail.gmail.com> > > Content-Type: text/plain; charset=UTF-8 > > > > Hi Elena, > > > > Actually, it's not that simple... We decided to go for this release > > and are not planning on upgrading, but I'll have a go at the newest, > > once it's out. > > I guess no one reported this kind of issue? > > > > Cheers, > > > > 2015-11-02 2:39 GMT+01:00 Elena Pourmal <[email protected]>: > > > Hi Matthieu, > > > > > > Could you please try the latest (1.8.16-pre2) and check if the errors > are > > > still there? > > > > > > Thank you! > > > > > > Elena > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > Elena Pourmal The HDF Group http://hdfgroup.org > > > 1800 So. Oak St., Suite 203, Champaign IL 61820 > > > 217.531.6112 > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > > > > > > > > > > > > On Oct 30, 2015, at 4:17 AM, Matthieu Brucher < > > [email protected]> > > > wrote: > > > > > > Hi all, > > > > > > I've noticed some valgrind errors coming from HDF5 calls (HDF5 1.8.12): > > > > > > Invalid read of size 4 > > > (see: http://valgrind.org/docs/manual/mc-manual.html#mc-manual.badrw) > > > at 0x172FBCF6: H5_build_extpath > > > by 0x17347C5A: H5F_open > > > by 0x173490F5: H5Fopen > > > > > > Is this something that may occur when reading from different ranks the > > > same file, or is there a valgrind suppression file for HDF5? > > > > > > Cheers, > > > > > > Matthieu Brucher > > > -- > > > Information System Engineer, Ph.D. > > > Blog: http://matt.eifelle.com > > > LinkedIn: http://www.linkedin.com/in/matthieubrucher > > > > > > _______________________________________________ > > > 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 > > > > > > > > > > > > _______________________________________________ > > > 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 > > > > > > > > -- > > Information System Engineer, Ph.D. > > Blog: http://matt.eifelle.com > > LinkedIn: http://www.linkedin.com/in/matthieubrucher > > > > 2015-11-02 1:39 GMT+00:00 Elena Pourmal <[email protected]>: > > > Hi Matthieu, > > > > > > Could you please try the latest (1.8.16-pre2) and check if the errors > are > > > still there? > > > > > > Thank you! > > > > > > Elena > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > Elena Pourmal The HDF Group http://hdfgroup.org > > > 1800 So. Oak St., Suite 203, Champaign IL 61820 > > > 217.531.6112 > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > > > > > > > > > > > > On Oct 30, 2015, at 4:17 AM, Matthieu Brucher < > > [email protected]> > > > wrote: > > > > > > Hi all, > > > > > > I've noticed some valgrind errors coming from HDF5 calls (HDF5 1.8.12): > > > > > > Invalid read of size 4 > > > (see: http://valgrind.org/docs/manual/mc-manual.html#mc-manual.badrw) > > > at 0x172FBCF6: H5_build_extpath > > > by 0x17347C5A: H5F_open > > > by 0x173490F5: H5Fopen > > > > > > Is this something that may occur when reading from different ranks the > > > same file, or is there a valgrind suppression file for HDF5? > > > > > > Cheers, > > > > > > Matthieu Brucher > > > -- > > > Information System Engineer, Ph.D. > > > Blog: http://matt.eifelle.com > > > LinkedIn: http://www.linkedin.com/in/matthieubrucher > > > > > > _______________________________________________ > > > 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 > > > > > > > > > > > > _______________________________________________ > > > 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 > > > > > > > > -- > > Information System Engineer, Ph.D. > > Blog: http://matt.eifelle.com > > LinkedIn: http://www.linkedin.com/in/matthieubrucher > > > > > > > > ------------------------------ > > > > Message: 2 > > Date: Tue, 3 Nov 2015 08:50:10 +0000 > > From: Albert Cheng <[email protected]> > > To: HDF Users Discussion List <[email protected]> > > Subject: Re: [Hdf-forum] how h5dump works with a VOL plugin > > Message-ID: <[email protected]> > > Content-Type: text/plain; charset="Windows-1252" > > > > Hi Dimos, > > > > h5dump, starting at the root group (?/?), loops through every link of the > > group > > and follows it to its target. If the target is a dataset, it dumps its > > information. If it > > is another group, its recursively go to the target group and repeats the > > process. > > > > Another way to describe the process is: > > You may consider an HDF5 file as a single-root-directed-graph where > groups > > are the nodes, > > datasets are the leaves. h5dump initially traverses the whole graph to > > collect all the nodes. > > (This is needed so that h5dump can detect any circles.) > > Then h5dump, starting at the root group, walks down every node (group), > > loops through all its > > links. If a link leads to another node (group), it move to it and > > recursively loops through > > all its links. (That is, it is depth first traverse). If it encounters a > > leaf (e.g., a dataset), > > it dump its information. > > > > Hope this answers your question about the structure. > > > > -Albert Cheng > > THG staff > > > > On Nov 1, 2015, at 11:43 PM, Dimos Stamatakis <[email protected]> > wrote: > > > > > Hello, > > > > > > sorry for the double post, but for some reason this question went under > > another thread. > > > > > > I am working on creating a custom VOL plugin, and I have trouble > > understanding how the h5dump determines the contents of the file. > > > > > > Say for example that we have a file with two groups, like: > > /group1/group2. > > > > > > I noticed that initially it calls native_file_get to get the structure > > containing information about accessing the file and then it calls > > native_group_open and native_group_get for each group in the file, so it > > would call: > > > > > > 1) native_file_open > > > 2) native_group_open and native_group_get for ?/? > > > 3) native_group_open and native_group_get for ?group1? > > > 4) native_group_open and native_group_get for group2? > > > > > > > > > > > > I understand that the VOL plugin developer is responsible for > > representing the contents of the file, but how does the h5dump tool know > > that the file contains these groups, and calls native_group_open and > > native_group_get for each of them? > > > > > > Many thanks in advance, > > > > > > Dimos > > > _______________________________________________ > > > 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 > > > > > > > > > > ------------------------------ > > > > Message: 3 > > Date: Tue, 3 Nov 2015 13:26:04 +0000 > > From: Gerd Heber <[email protected]> > > To: Alex Bogdanov <[email protected]>, HDF Users Discussion List > > <[email protected]> > > Subject: Re: [Hdf-forum] Building HDF5DotNet - C++/CLI Wrapper of the > > HDF5 Library with current version of HDF5 library > > Message-ID: > > < > > > blupr0701mb1971114120f36769162fae5aa4...@blupr0701mb1971.namprd07.prod.outlook.com > > > > > > > Content-Type: text/plain; charset="utf-8" > > > > Alexey, how are you? Have you tried casting the last argument (buffer > > size) to unsigned int? > > > > Best, G. > > > > From: Hdf-forum [mailto:[email protected]] On Behalf > > Of Alex Bogdanov > > Sent: Monday, November 2, 2015 12:04 AM > > To: HDF Users Discussion List ([email protected]) > > Subject: [Hdf-forum] Building HDF5DotNet - C++/CLI Wrapper of the HDF5 > > Library with current version of HDF5 library > > > > Hello, > > I would like to query if anyone was successful in building of HDF5DotNet > - > > C++/CLI wrapper > > of the HDF5 library with current version of HDF5 library - i.e. > > HDF5-1.8.15 Patch 1 ? > > I was trying to get it compiled using Visual Studio 2013 and as well > > Visual Studio 2015 - but > > compilation failed in both cases with following error messages: > > > > 1. in ObjectReference.cpp: > > error C2668: > > 'System::Array::Copy' : ambiguous call to overloaded function > > > > D:\DATA\src\HDF5DotNet\trunc\src\ObjectReference.cpp 30 1 > > HDF5DotNet Code: > Array::Copy(a, > > m_or, H5R_OBJ_REF_BUF_SIZE); > > > > 2. in RegionReference.cpp: > > error C2668: > > 'System::Array::Copy' : ambiguous call to overloaded function > > > > D:\DATA\src\HDF5DotNet\trunc\src\RegionReference.cpp 30 1 > > HDF5DotNet Code: > > Array::Copy(a, m_rr, H5R_DSET_REG_REF_BUF_SIZE); > > > > 3. in RegionReference.cpp: > > 4 IntelliSense: more than one > > instance of overloaded function "System::Array::Copy" matches the > argument > > list: function > > "System::Array::Copy(System::Array ^sourceArray, System::Array > > ^destinationArray, int length)" function > > > > "System::Array::Copy(System::Array ^sourceArray, System::Array > > ^destinationArray, long long length)" > > argument types are: (cli::array > > ^, cli::array ^, unsigned int) > > > > D:\DATA\src\HDF5DotNet\trunc\src\RegionReference.cpp 30 9 HDF5DotNet > > > > Could you please advice ? > > > > Thank you beforehand, > > Regards, > > Alexey > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: < > > > http://lists.hdfgroup.org/pipermail/hdf-forum_lists.hdfgroup.org/attachments/20151103/b22fce03/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 77, Issue 7 > > **************************************** > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.hdfgroup.org/pipermail/hdf-forum_lists.hdfgroup.org/attachments/20151103/5067cc99/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 77, Issue 8 > **************************************** >
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