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 > **************************************** >
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