how h5dump works with a VOL plugin

Hdf-forum archives
1

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

2

Unfortunately the HDF5 tools will only work on a file created with the native HDF5 file format.
We have not modified the tools to support non-native VOL plugins, but it’s something we can/should consider for the future once we put this into production.

Thanks,
Mohamad

···

From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] On Behalf Of Dimos Stamatakis
Sent: Sunday, November 01, 2015 11:43 PM
To: hdf-forum@lists.hdfgroup.org
Subject: [Hdf-forum] how h5dump works with a VOL plugin

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

3

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 <dimstamat@gmail.com> 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.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

4

Thanks for your response!

So this mean that the h5dump has to look within the structure representing
the HDF5 container so that to display the contents, right?

Also I noticed that the h5dump first calls native_file_open, then returns
and then calls native_group_open for each group. Does this mean that it
opens the file in the native_file_open, gets the structure with information
about the file, closes the file and then calls native_group_open without
re-opening the file, but only with that structure?

Thanks,

Dimos

···

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Today's Topics:

   1. Building HDF5DotNet - C++/CLI Wrapper of the HDF5 Library
      with current version of HDF5 library (Alex Bogdanov)
   2. Re: HDF 1.8.16-pre2 release candidate is available for
      testing (Sean McBride)

----------------------------------------------------------------------

Message: 1
Date: Mon, 02 Nov 2015 09:04:28 +0300
From: Alex Bogdanov <agb1@mail.ru>
To: HDF Users Discussion List (hdf-forum@lists.hdfgroup.org)
        <hdf-forum@lists.hdfgroup.org>
Subject: [Hdf-forum] Building HDF5DotNet - C++/CLI Wrapper of the HDF5
        Library with current version of HDF5 library
Message-ID: <1446444268.102703165@f61.i.mail.ru>
Content-Type: text/plain; charset="utf-8"

??? 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
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Message: 2
Date: Mon, 2 Nov 2015 12:02:15 -0400
From: "Sean McBride" <sean@rogue-research.com>
To: "HDF Users Discussion List" <hdf-forum@lists.hdfgroup.org>, "Larry
        Knox" <lrknox@hdfgroup.org>
Subject: Re: [Hdf-forum] HDF 1.8.16-pre2 release candidate is
        available for testing
Message-ID: <20151102160215.850320908@mail.rogue-research.com>
Content-Type: text/plain; charset="iso-8859-1"

On Fri, 30 Oct 2015 20:12:51 +0000, Larry Knox said:

>The Mac errors seem to involve flags that we don't test. A Jira issue
>will be created specifying the flags with which the tests fail or
>produce errors to be addressed as possible. Any patches to be
>considered will be welcomed.

Did you also take a look at the dashboard warnings? Many of them are
trivial to fix. If you're not interested in some of the warning flags, I
can turn them off. It would be nice to get the dashboard into a green
state so that it can serve as a tool to catch _new_ problems at least. I
find having a dashboard like that is only useful if you keep it green.

Attached is a patch that fixes several warnings from the Rogue14 bot.

Cheers,

--
____________________________________________________________
Sean McBride, B. Eng sean@rogue-research.com
Rogue Research www.rogue-research.com
Mac Software Developer Montr?al, Qu?bec, Canada
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Hdf-forum@lists.hdfgroup.org
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****************************************

5

Not really.. h5dump only makes HDF5 API calls (or at least should). We would only need to find a way to pass the plugin information to h5dump (maybe using an environment variable or command line options) so it can set the appropriate plugin on the fapl before opening the file. Other than that, the API calls that the tools make should call into the plugin, and as long as all the HDF5 API calls that h5dump makes are handled by the plugin, then h5dump will work normally.

Thanks,
Mohamad

···

From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] On Behalf Of Dimos Stamatakis
Sent: Monday, November 02, 2015 3:47 PM
To: hdf-forum@lists.hdfgroup.org
Subject: Re: [Hdf-forum] Hdf-forum Digest, Vol 77, Issue 2 - how h5dump works with a VOL plugin

Thanks for your response!

So this mean that the h5dump has to look within the structure representing the HDF5 container so that to display the contents, right?

Also I noticed that the h5dump first calls native_file_open, then returns and then calls native_group_open for each group. Does this mean that it opens the file in the native_file_open, gets the structure with information about the file, closes the file and then calls native_group_open without re-opening the file, but only with that structure?

Thanks,

Dimos

On Mon, Nov 2, 2015 at 11:03 AM, <hdf-forum-request@lists.hdfgroup.org<mailto:hdf-forum-request@lists.hdfgroup.org>> wrote:
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Today's Topics:

   1. Building HDF5DotNet - C++/CLI Wrapper of the HDF5 Library
      with current version of HDF5 library (Alex Bogdanov)
   2. Re: HDF 1.8.16-pre2 release candidate is available for
      testing (Sean McBride)

----------------------------------------------------------------------

Message: 1
Date: Mon, 02 Nov 2015 09:04:28 +0300
From: Alex Bogdanov <agb1@mail.ru<mailto:agb1@mail.ru>>
To: HDF Users Discussion List (hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>)
        <hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>>
Subject: [Hdf-forum] Building HDF5DotNet - C++/CLI Wrapper of the HDF5
        Library with current version of HDF5 library
Message-ID: <1446444268.102703165@f61.i.mail.ru<mailto:1446444268.102703165@f61.i.mail.ru>>
Content-Type: text/plain; charset="utf-8"

??? 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
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Message: 2
Date: Mon, 2 Nov 2015 12:02:15 -0400
From: "Sean McBride" <sean@rogue-research.com<mailto:sean@rogue-research.com>>
To: "HDF Users Discussion List" <hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>>, "Larry
        Knox" <lrknox@hdfgroup.org<mailto:lrknox@hdfgroup.org>>
Subject: Re: [Hdf-forum] HDF 1.8.16-pre2 release candidate is
        available for testing
Message-ID: <20151102160215.850320908@mail.rogue-research.com<mailto:20151102160215.850320908@mail.rogue-research.com>>
Content-Type: text/plain; charset="iso-8859-1"

On Fri, 30 Oct 2015 20:12:51 +0000, Larry Knox said:

The Mac errors seem to involve flags that we don't test. A Jira issue
will be created specifying the flags with which the tests fail or
produce errors to be addressed as possible. Any patches to be
considered will be welcomed.

Did you also take a look at the dashboard warnings? Many of them are trivial to fix. If you're not interested in some of the warning flags, I can turn them off. It would be nice to get the dashboard into a green state so that it can serve as a tool to catch _new_ problems at least. I find having a dashboard like that is only useful if you keep it green.

Attached is a patch that fixes several warnings from the Rogue14 bot.

Cheers,

--
____________________________________________________________
Sean McBride, B. Eng sean@rogue-research.com<mailto:sean@rogue-research.com>
Rogue Research www.rogue-research.com<http://www.rogue-research.com>
Mac Software Developer Montr?al, Qu?bec, Canada
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6

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, <hdf-forum-request@lists.hdfgroup.org> wrote:

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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 <matthieu.brucher@gmail.com>
To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org>
Subject: Re: [Hdf-forum] Valgrind errors
Message-ID:
        <
CAHCaCk+0nD-84VFvNivT3XjDTsDDxih5jfAZtLN-N1w67A63mg@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 <epourmal@hdfgroup.org>:
> 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 < > matthieu.brucher@gmail.com> > > 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.
> Hdf-forum@lists.hdfgroup.org
> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
> Twitter: https://twitter.com/hdf5
>
>
>
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> Hdf-forum@lists.hdfgroup.org
> 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 <epourmal@hdfgroup.org>:
> 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 < > matthieu.brucher@gmail.com> > > 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.
> Hdf-forum@lists.hdfgroup.org
> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
> Twitter: https://twitter.com/hdf5
>
>
>
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> Hdf-forum@lists.hdfgroup.org
> 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 <acheng@hdfgroup.org>
To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org>
Subject: Re: [Hdf-forum] how h5dump works with a VOL plugin
Message-ID: <31B5931E-B1DE-413F-A35A-9FE602D8519A@hdfgroup.org>
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 <dimstamat@gmail.com> 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.
> Hdf-forum@lists.hdfgroup.org
> 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 <gheber@hdfgroup.org>
To: Alex Bogdanov <agb1@mail.ru>, HDF Users Discussion List
        <hdf-forum@lists.hdfgroup.org>
Subject: Re: [Hdf-forum] Building HDF5DotNet - C++/CLI Wrapper of the
        HDF5 Library with current version of HDF5 library
Message-ID:
        <
BLUPR0701MB1971114120F36769162FAE5AA42B0@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:hdf-forum-bounces@lists.hdfgroup.org] On Behalf
Of Alex Bogdanov
Sent: Monday, November 2, 2015 12:04 AM
To: HDF Users Discussion List (hdf-forum@lists.hdfgroup.org)
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
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------------------------------

End of Hdf-forum Digest, Vol 77, Issue 7
****************************************

7

A link in a group connects to one of its members. A member can be
an HDF5 objects such as datasets, groups, or named datatypes.
A link can be hard (points at a real object), soft (to be dereference
when used), external (an object resides outside of the file).

···

On Nov 3, 2015, at 12:33 PM, Dimos Stamatakis <dimstamat@gmail.com> wrote:

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

8

Thanks for your response!

So this mean that the h5dump has to look within the structure representing
the HDF5 container so that to display the contents, right?

Also I noticed that the h5dump first calls native_file_open, then returns
and then calls native_group_open for each group. Does this mean that it
opens the file in the native_file_open, gets the structure with information
about the file, closes the file and then calls native_group_open without
re-opening the file, but only with that structure?

Thanks,

Dimos

···

On Mon, Nov 2, 2015 at 1:00 PM, <hdf-forum-request@lists.hdfgroup.org> wrote:

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Today's Topics:

   1. Re: HDF 1.8.16-pre2 release candidate is available for
      testing (Elena Pourmal)
   2. Re: how h5dump works with a VOL plugin (Mohamad Chaarawi)
   3. Re: HDF 1.8.16-pre2 release candidate is available for
      testing (Marco Atzeri)

----------------------------------------------------------------------

Message: 1
Date: Mon, 2 Nov 2015 16:34:47 +0000
From: Elena Pourmal <epourmal@hdfgroup.org>
To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org>
Subject: Re: [Hdf-forum] HDF 1.8.16-pre2 release candidate is
        available for testing
Message-ID: <C2314DB0-AC47-465B-9BFE-FFCE1DF44673@hdfgroup.org>
Content-Type: text/plain; charset="iso-8859-1"

Sean,

Thank you for the patch. We will do our best to include it into the
release; it does look straightforward. We will also review the flags and
will get back to you.

Thanks again for your contribution to release testing!

Elena

Sent from my iPhone

> On Nov 2, 2015, at 10:03 AM, Sean McBride <sean@rogue-research.com> > wrote:
>
> On Fri, 30 Oct 2015 20:12:51 +0000, Larry Knox said:
>
>> The Mac errors seem to involve flags that we don't test. A Jira issue
>> will be created specifying the flags with which the tests fail or
>> produce errors to be addressed as possible. Any patches to be
>> considered will be welcomed.
>
> Did you also take a look at the dashboard warnings? Many of them are
trivial to fix. If you're not interested in some of the warning flags, I
can turn them off. It would be nice to get the dashboard into a green
state so that it can serve as a tool to catch _new_ problems at least. I
find having a dashboard like that is only useful if you keep it green.
>
> Attached is a patch that fixes several warnings from the Rogue14 bot.
>
> Cheers,
>
> --
> ____________________________________________________________
> Sean McBride, B. Eng sean@rogue-research.com
> Rogue Research www.rogue-research.com
> Mac Software Developer Montr?al, Qu?bec, Canada
> <hdf-warnings.patch>
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> Hdf-forum@lists.hdfgroup.org
> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
> Twitter: https://twitter.com/hdf5

------------------------------

Message: 2
Date: Mon, 2 Nov 2015 16:44:49 +0000
From: Mohamad Chaarawi <chaarawi@hdfgroup.org>
To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org>
Subject: Re: [Hdf-forum] how h5dump works with a VOL plugin
Message-ID:
        <
BY2PR0701MB19574CBEE467597C150716EDBD2C0@BY2PR0701MB1957.namprd07.prod.outlook.com
>

Content-Type: text/plain; charset="utf-8"

Unfortunately the HDF5 tools will only work on a file created with the
native HDF5 file format.
We have not modified the tools to support non-native VOL plugins, but it?s
something we can/should consider for the future once we put this into
production.

Thanks,
Mohamad

From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] On Behalf
Of Dimos Stamatakis
Sent: Sunday, November 01, 2015 11:43 PM
To: hdf-forum@lists.hdfgroup.org
Subject: [Hdf-forum] how h5dump works with a VOL plugin

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
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------------------------------

Message: 3
Date: Mon, 2 Nov 2015 18:11:23 +0100
From: Marco Atzeri <marco.atzeri@gmail.com>
To: hdf-forum@lists.hdfgroup.org
Subject: Re: [Hdf-forum] HDF 1.8.16-pre2 release candidate is
        available for testing
Message-ID: <5637993B.3020400@gmail.com>
Content-Type: text/plain; charset=windows-1252; format=flowed

On 30/10/2015 21:12, Larry Knox wrote:
> Hello everyone,
>
> A second pre-release candidate version of HDF5 1.8.16 is available for
> testing and can be downloaded at the following link:
>
> https://gamma.hdfgroup.org/ftp/pub/outgoing/hdf5/hdf5-1.8.16-pre2/
[cut]
>
> The effect on the numbers from HDF5-1.8.15-patch1 to HDF5-1.8.16 was to
> increase libhdf5.so.10.0.1 to libhdf5.so.10.1.0, libhdf5_cpp.so.10.0.1
> to libhdf5_cpp.so.11.0.0, and all other wrapper library files from
> libhdf5*.so.10.0.1 to libhdf5*.so.10.0.2.

Question:
- is it really needed to implement a new API bump for C++ interface ?

The continuous API bump forces to maintain several legacy version
of the library and/or to recompile every time the software depending
on the library.
Library API should be as stable as possible.

Only ImageMagick is worst than HDF5 for the packages that I am
managing for cygwin.

> Larry

Regards
Marco

------------------------------

Subject: Digest Footer

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

------------------------------

End of Hdf-forum Digest, Vol 77, Issue 3
****************************************

9

So I still don’t understand how the h5dump determines the contents of the file if it only makes API calls. How can it access the struct, since it is void* and it does not know the contents? Only with file_get and group_get, etc, but how does it know how many times to call them (how many groups are within the file) ?

Thanks,

Dimos

···

On Nov 2, 2015, at 5:09 PM, hdf-forum-request@lists.hdfgroup.org wrote:

Send Hdf-forum mailing list submissions to
  hdf-forum@lists.hdfgroup.org

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When replying, please edit your Subject line so it is more specific
than "Re: Contents of Hdf-forum digest..."

Today's Topics:

  1. Re: Hdf-forum Digest, Vol 77, Issue 2 - how h5dump works with
     a VOL plugin (Mohamad Chaarawi)

----------------------------------------------------------------------

Message: 1
Date: Mon, 2 Nov 2015 22:08:38 +0000
From: Mohamad Chaarawi <chaarawi@hdfgroup.org>
To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org>
Subject: Re: [Hdf-forum] Hdf-forum Digest, Vol 77, Issue 2 - how
  h5dump works with a VOL plugin
Message-ID:
  <BY2PR0701MB1957B711FF6119DB57D0567ABD2C0@BY2PR0701MB1957.namprd07.prod.outlook.com>
  
Content-Type: text/plain; charset="utf-8"

Not really.. h5dump only makes HDF5 API calls (or at least should). We would only need to find a way to pass the plugin information to h5dump (maybe using an environment variable or command line options) so it can set the appropriate plugin on the fapl before opening the file. Other than that, the API calls that the tools make should call into the plugin, and as long as all the HDF5 API calls that h5dump makes are handled by the plugin, then h5dump will work normally.

Thanks,
Mohamad

From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] On Behalf Of Dimos Stamatakis
Sent: Monday, November 02, 2015 3:47 PM
To: hdf-forum@lists.hdfgroup.org
Subject: Re: [Hdf-forum] Hdf-forum Digest, Vol 77, Issue 2 - how h5dump works with a VOL plugin

Thanks for your response!

So this mean that the h5dump has to look within the structure representing the HDF5 container so that to display the contents, right?

Also I noticed that the h5dump first calls native_file_open, then returns and then calls native_group_open for each group. Does this mean that it opens the file in the native_file_open, gets the structure with information about the file, closes the file and then calls native_group_open without re-opening the file, but only with that structure?

Thanks,

Dimos

On Mon, Nov 2, 2015 at 11:03 AM, <hdf-forum-request@lists.hdfgroup.org<mailto:hdf-forum-request@lists.hdfgroup.org>> wrote:
Send Hdf-forum mailing list submissions to
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When replying, please edit your Subject line so it is more specific
than "Re: Contents of Hdf-forum digest..."

Today's Topics:

  1. Building HDF5DotNet - C++/CLI Wrapper of the HDF5 Library
     with current version of HDF5 library (Alex Bogdanov)
  2. Re: HDF 1.8.16-pre2 release candidate is available for
     testing (Sean McBride)

----------------------------------------------------------------------

Message: 1
Date: Mon, 02 Nov 2015 09:04:28 +0300
From: Alex Bogdanov <agb1@mail.ru<mailto:agb1@mail.ru>>
To: HDF Users Discussion List (hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>)
       <hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>>
Subject: [Hdf-forum] Building HDF5DotNet - C++/CLI Wrapper of the HDF5
       Library with current version of HDF5 library
Message-ID: <1446444268.102703165@f61.i.mail.ru<mailto:1446444268.102703165@f61.i.mail.ru>>
Content-Type: text/plain; charset="utf-8"

??? 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
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Message: 2
Date: Mon, 2 Nov 2015 12:02:15 -0400
From: "Sean McBride" <sean@rogue-research.com<mailto:sean@rogue-research.com>>
To: "HDF Users Discussion List" <hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>>, "Larry
       Knox" <lrknox@hdfgroup.org<mailto:lrknox@hdfgroup.org>>
Subject: Re: [Hdf-forum] HDF 1.8.16-pre2 release candidate is
       available for testing
Message-ID: <20151102160215.850320908@mail.rogue-research.com<mailto:20151102160215.850320908@mail.rogue-research.com>>
Content-Type: text/plain; charset="iso-8859-1"

On Fri, 30 Oct 2015 20:12:51 +0000, Larry Knox said:

The Mac errors seem to involve flags that we don't test. A Jira issue
will be created specifying the flags with which the tests fail or
produce errors to be addressed as possible. Any patches to be
considered will be welcomed.

Did you also take a look at the dashboard warnings? Many of them are trivial to fix. If you're not interested in some of the warning flags, I can turn them off. It would be nice to get the dashboard into a green state so that it can serve as a tool to catch _new_ problems at least. I find having a dashboard like that is only useful if you keep it green.

Attached is a patch that fixes several warnings from the Rogue14 bot.

Cheers,

--
____________________________________________________________
Sean McBride, B. Eng sean@rogue-research.com<mailto:sean@rogue-research.com>
Rogue Research www.rogue-research.com<http://www.rogue-research.com>
Mac Software Developer Montr?al, Qu?bec, Canada
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****************************************

10

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, <hdf-forum-request@lists.hdfgroup.org> wrote:

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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 <dimstamat@gmail.com>
To: hdf-forum@lists.hdfgroup.org
Subject: [Hdf-forum] how h5dump works with a VOL plugin
Message-ID:
        <CAB8CW0FJq-7GWZZw-0n574k_SfajVtrud2bKJ68h8UU28oTq=
A@mail.gmail.com>
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, <hdf-forum-request@lists.hdfgroup.org> > wrote:

> Send Hdf-forum mailing list submissions to
> hdf-forum@lists.hdfgroup.org
>
> 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
> hdf-forum-request@lists.hdfgroup.org
>
> You can reach the person managing the list at
> hdf-forum-owner@lists.hdfgroup.org
>
> 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 <matthieu.brucher@gmail.com>
> To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org>
> Subject: Re: [Hdf-forum] Valgrind errors
> Message-ID:
> <
> CAHCaCk+0nD-84VFvNivT3XjDTsDDxih5jfAZtLN-N1w67A63mg@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 <epourmal@hdfgroup.org>:
> > 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 < > > matthieu.brucher@gmail.com> > > > 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.
> > Hdf-forum@lists.hdfgroup.org
> >
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
> > Twitter: https://twitter.com/hdf5
> >
> >
> >
> > _______________________________________________
> > Hdf-forum is for HDF software users discussion.
> > Hdf-forum@lists.hdfgroup.org
> >
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 <epourmal@hdfgroup.org>:
> > 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 < > > matthieu.brucher@gmail.com> > > > 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.
> > Hdf-forum@lists.hdfgroup.org
> >
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
> > Twitter: https://twitter.com/hdf5
> >
> >
> >
> > _______________________________________________
> > Hdf-forum is for HDF software users discussion.
> > Hdf-forum@lists.hdfgroup.org
> >
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 <acheng@hdfgroup.org>
> To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org>
> Subject: Re: [Hdf-forum] how h5dump works with a VOL plugin
> Message-ID: <31B5931E-B1DE-413F-A35A-9FE602D8519A@hdfgroup.org>
> 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 <dimstamat@gmail.com> > 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.
> > Hdf-forum@lists.hdfgroup.org
> >
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 <gheber@hdfgroup.org>
> To: Alex Bogdanov <agb1@mail.ru>, HDF Users Discussion List
> <hdf-forum@lists.hdfgroup.org>
> Subject: Re: [Hdf-forum] Building HDF5DotNet - C++/CLI Wrapper of the
> HDF5 Library with current version of HDF5 library
> Message-ID:
> <
>
BLUPR0701MB1971114120F36769162FAE5AA42B0@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:hdf-forum-bounces@lists.hdfgroup.org] On Behalf
> Of Alex Bogdanov
> Sent: Monday, November 2, 2015 12:04 AM
> To: HDF Users Discussion List (hdf-forum@lists.hdfgroup.org)
> 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
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>
> Subject: Digest Footer
>
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> Hdf-forum@lists.hdfgroup.org
> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
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****************************************

11

h5dump makes HDF5 API calls such as H5Literate and H5Lvisit to traverse the file and get the information for each object that it iterates over. The visit and iterate map to the VOL link_specific class of callbacks, not the link_get class.

The link_get VOL callbacks get information about a specific link in the file such as the link name or value (H5Lget_val(), H5Lget_info(), H5Lget_name_by_idx()), but not about the entire structure of the file.

Thanks.
Mohamad

···

From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] On Behalf Of Dimos Stamatakis
Sent: Tuesday, November 03, 2015 11:18 PM
To: hdf-forum@lists.hdfgroup.org
Subject: [Hdf-forum] how h5dump works with a VOL plugin

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, <hdf-forum-request@lists.hdfgroup.org<mailto:hdf-forum-request@lists.hdfgroup.org>> wrote:
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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 <dimstamat@gmail.com<mailto:dimstamat@gmail.com>>
To: hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>
Subject: [Hdf-forum] how h5dump works with a VOL plugin
Message-ID:
        <CAB8CW0FJq-7GWZZw-0n574k_SfajVtrud2bKJ68h8UU28oTq=A@mail.gmail.com<mailto:A@mail.gmail.com>>
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, <hdf-forum-request@lists.hdfgroup.org<mailto:hdf-forum-request@lists.hdfgroup.org>> wrote:

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When replying, please edit your Subject line so it is more specific
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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 <matthieu.brucher@gmail.com<mailto:matthieu.brucher@gmail.com>>
To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>>
Subject: Re: [Hdf-forum] Valgrind errors
Message-ID:
        <
CAHCaCk+0nD-84VFvNivT3XjDTsDDxih5jfAZtLN-N1w67A63mg@mail.gmail.com<mailto:CAHCaCk%2B0nD-84VFvNivT3XjDTsDDxih5jfAZtLN-N1w67A63mg@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 <epourmal@hdfgroup.org<mailto:epourmal@hdfgroup.org>>:
> 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<tel:217.531.6112>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
>
>
>
> On Oct 30, 2015, at 4:17 AM, Matthieu Brucher < > matthieu.brucher@gmail.com<mailto:matthieu.brucher@gmail.com>> > > 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.
> Hdf-forum@lists.hdfgroup.org<mailto:Hdf-forum@lists.hdfgroup.org>
> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
> Twitter: https://twitter.com/hdf5
>
>
>
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> Hdf-forum@lists.hdfgroup.org<mailto:Hdf-forum@lists.hdfgroup.org>
> 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 <epourmal@hdfgroup.org<mailto:epourmal@hdfgroup.org>>:
> 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<tel:217.531.6112>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
>
>
>
> On Oct 30, 2015, at 4:17 AM, Matthieu Brucher < > matthieu.brucher@gmail.com<mailto:matthieu.brucher@gmail.com>> > > 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.
> Hdf-forum@lists.hdfgroup.org<mailto:Hdf-forum@lists.hdfgroup.org>
> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
> Twitter: https://twitter.com/hdf5
>
>
>
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> Hdf-forum@lists.hdfgroup.org<mailto:Hdf-forum@lists.hdfgroup.org>
> 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 <acheng@hdfgroup.org<mailto:acheng@hdfgroup.org>>
To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>>
Subject: Re: [Hdf-forum] how h5dump works with a VOL plugin
Message-ID: <31B5931E-B1DE-413F-A35A-9FE602D8519A@hdfgroup.org<mailto:31B5931E-B1DE-413F-A35A-9FE602D8519A@hdfgroup.org>>
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 <dimstamat@gmail.com<mailto:dimstamat@gmail.com>> 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.
> Hdf-forum@lists.hdfgroup.org<mailto:Hdf-forum@lists.hdfgroup.org>
> 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 <gheber@hdfgroup.org<mailto:gheber@hdfgroup.org>>
To: Alex Bogdanov <agb1@mail.ru<mailto:agb1@mail.ru>>, HDF Users Discussion List
        <hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>>
Subject: Re: [Hdf-forum] Building HDF5DotNet - C++/CLI Wrapper of the
        HDF5 Library with current version of HDF5 library
Message-ID:
        <
BLUPR0701MB1971114120F36769162FAE5AA42B0@BLUPR0701MB1971.namprd07.prod.outlook.com<mailto:BLUPR0701MB1971114120F36769162FAE5AA42B0@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:hdf-forum-bounces@lists.hdfgroup.org<mailto:hdf-forum-bounces@lists.hdfgroup.org>] On Behalf
Of Alex Bogdanov
Sent: Monday, November 2, 2015 12:04 AM
To: HDF Users Discussion List (hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>)
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
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