DETECTING HDF5 VERSUS NETCDF GENERATED FILES
REQUEST FOR COMMENTS
AUTHOR: Pedro Vicente
AUDIENCE:
1) HDF, netcdf developers,
Ed Hartnett
Kent Yang
2) HDF, netcdf users, that replied to this thread
Miller, Mark C.
John Shalf
3 ) netcdf tools developers
Mary Haley , NCL
4) HDF, netcdf managers and sponsors
David Pearah , CEO HDF Group
Ward Fisher, UCAR
Marinelli, Daniel J. , Richard Ullmman, Christopher Lynnes, NASA
5)
[CF-metadata] list
After this thread started 2 months ago, there was an annoucement on the [CF-metadata] mail list
about
"a meeting to discuss current and future netCDF-CF efforts and directions.
The meeting will be held on 24-26 May 2016 in Boulder, CO, USA at the UCAR Center Green facility."
This would be a good topic to put on the agenda, maybe?
THE PROBLEM:
Currently it is impossible to detect if an HDF5 file was generated by the HDF5 API or by the netCDF API.
See previous email about the reasons why.
WHY THIS MATTERS:
Software applications that need to handle both netCDF and HDF5 files cannot decide which API to use.
This includes popular visualization tools like IDL, Matlab, NCL, HDF Explorer.
SOLUTIONS PROPOSED: 2
SOLUTION 1: Add a flag to HDF5 source
The hdf5 format specification, listed here
https://www.hdfgroup.org/HDF5/doc/H5.format.html
describes a sequence of bytes in the file layout that have special meaning for the HDF5 API. It is common practice, when designing a data format,
so leave some fields "reserved for future use".
This solution makes use of one of these empty "reserved for future use" spaces to save a byte (for example) that describes an enumerator
of "HDF5 compatible formats".
An "HDF5 compatible format" is a data format that uses the HDF5 API at a lower level (usually hidden from the user of the upper API),
and providing its own API.
This category can still be divide in 2 formats:
1) A "pure HDF5 compatible format". Example, NeXus
http://www.nexusformat.org/
NeXus just writes some metadata (attributes) on top of the HDF5 API, that has some special meaning for the NeXus community
2) A "non pure HDF5 compatible format". Example, netCDF
Here, the format adds some extra feature besides HDF5. In the case of netCDF, these are shared dimensions between variables.
This sub-division between 1) and 2) is irrelevant for the problem and solution in question
The solution consists of writing a different enumerator value on the "reserved for future use" space. For example
Value decimal 0 (current value): This file was generated by the HDF5 API (meaning the HDF5 only API)
Value decimal 1: This file was generated by the netCDF API (using HDF5)
Value decimal 2: This file was generated by <put here another HDF5 based format>
and so on
The advantage of this solution is that this process involves 2 parties: the HDF Group and the other format's organization.
This allows the HDF Group to "keep track" of new HDF5 based formats. It allows to make the other format "HDF5 certified" .
SOLUTION 2: Add some metadata to the other API on top of HDF5
This is what Nexus uses.
A Nexus file on creation writes several attributes on the root group, like "NeXus_version" and other numeric data.
This is done using the public HDF5 API calls.
The solution for netCDF consists of the same approach, just write some specific attributes, and a special netCDF API to write/read them.
This solutions just requires the work of one party (the netCDF group)
END OF RFC
In reply to people that commented in the thread
_at_John Shalf
>>Perhaps NetCDF (and other higher-level APIs that are built on top of HDF5) should include an attribute attached
>>to the root group that identifies the name and version of the API that created the file? (adopt this as a convention)
yes, that's one way to do it, Solution 2 above
_at_Mark Miller
>>>Hmmm. Is there any big reason NOT to try to read a netCDF produced HDF5 file with the native HDF5 library if someone so chooses?
It's possible to read a netCDF file using HDF5, yes.
There are 2 things that you will miss doing this:
1) the ability to inquire about shared netCDF dimensions.
2) the ability to read remotely with openDAP.
Reading with HDF5 also exposes metadata that is supposed to be private to netCDF. See below
>>>> And, attempting to read an HDF5 file produced by Silo using just the HDF5 library (e.g. w/o Silo) is a major pain.
This I don't understand. Why not read the Silo file with the Silo API?
That's the all purpose of this issue, each higher level API on top of HDF5 should be able to detect "itself".
I am not familiar with Silo, but if Silo cannot do this, then you have the same design flaw that netCDF has.
>>> In a cursory look over the libsrc4 sources in netCDF distro, I see a few things that might give a hint a file was created with netCDF. . .
>>>> First, in NC_CLASSIC_MODEL, an attribute gets attached to the root group named "_nc3_strict". So, the existence of an attribute on the root group by that name would suggest the HDF5 file was generated by netCDF.
I think this is done only by the "old" netCDF3 format.
>>>>> Also, I tested a simple case of nc_open, nc_def_dim, etc. nc_close to see what it produced.
>>>> It appears to produce datasets for each 'dimension' defined with two attributes named "CLASS" and "NAME".
This is because netCDF uses the HDF5 Dimension Scales API internally to keep track of shared dimensions. These are internal attributes
of Dimension Scales. This approach would not work because an HDF5 only file with Dimension Scales would have the same attributes.
>>>> I like John's suggestion here.
>>>>>But, any code you add to any applications now will work *only* for files that were produced post-adoption of this convention.
yes. there are 2 actions to take here.
1) fix the issue for the future
2) try to retroactively have some workaround that makes possible now to differentiate a HDF5/netCDF files made before the adopted convention
see below
>>>> In VisIt, we support >140 format readers. Over 20 of those are different variants of HDF5 files (H5part, Xdmf, Pixie, Silo, Samrai, netCDF, Flash, Enzo, Chombo, etc., etc.)
>>>>When opening a file, how does VisIt figure out which plugin to use? In particular, how do we avoid one poorly written reader plugin (which may be the wrong one for a given file) from preventing the correct one from being found. Its kinda a hard problem.
Yes, that's the problem we are trying to solve. I have to say, that is quick a list of HDF5 based formats there.
>>>> Some of our discussion is captured here. . .
http://www.visitusers.org/index.php?title=Database_Format_Detection
I"ll check it out, thank you for the suggestions
_at_Ed Hartnett
>>>I must admit that when putting netCDF-4 together I never considered that someone might want to tell the difference between a "native" HDF5 file and a netCDF-4/HDF5 file.
>>>>>Well, you can't think of everything.
This is a major design flaw.
If you are in the business of designing data file formats, one of the things you have to do is how to make it possible to identify it from the other formats.
>>> I agree that it is not possible to canonically tell the difference. The netCDF-4 API does use some special attributes to track named dimensions,
>>>>and to tell whether classic mode should be enforced. But it can easily produce files without any named dimensions, etc.
>>>So I don't think there is any easy way to tell.
I remember you wrote that code together with Kent Yang from the HDF Group.
At the time I was with the HDF Group but unfortunately I did follow closely what you were doing.
I don't remember any design document being circulated that explains the internals of the "how to" make the netCDF (classic) model of shared dimensions
use the hierarchical group model of HDF5.
I know this was done using the HDF5 Dimension Scales (that I wrote), but is there any design document that explains it?
Maybe just some internal email exchange between you and Kent Yang?
Kent, how are you?
Do you remember having any design document that explains this?
Maybe something like a unique private attribute that is written somewhere in the netCDF file?
_at_Mary Haley, NCL
NCL is a widely used tool that handles both netCDF and HDF5
Mary, how are you?
How does NCL deal with the case of reading both pure HDF5 files and netCDF files that use HDF5?
Would you be interested in joining a community based effort to deal with this, in case this is an issue for you?
_at_David Pearah , CEO HDF Group
I volunteer to participate in the effort of this RFC together with the HDF Group (and netCDF Group).
Maybe we could make a "task force" between HDF Group, netCDF Group and any volunteer (such as tools developers that happen to be in these mail lists)?
The "task force" would have 2 tasks:
1) make a HDF5 based convention for the future and
2) try to retroactively salvage the current design issue of netCDF
My phone is 217-898-9356, you are welcome to call in anytime.
----------------------
Pedro Vicente
pedro.vicente at space-research.org
https://twitter.com/_pedro__vicente
http://www.space-research.org/
----- Original Message -----
From: Miller, Mark C.
To: HDF Users Discussion List
Cc: netcdfgroup at unidata.ucar.edu ; Ward Fisher
Sent: Wednesday, March 02, 2016 7:07 PM
Subject: Re: [Hdf-forum] Detecting netCDF versus HDF5
I like John's suggestion here.
But, any code you add to any applications now will work *only* for files that were produced post-adoption of this convention.
There are probably a bazillion files out there at this point that don't follow that convention and you probably still want your applications to be able to read them.
In VisIt, we support >140 format readers. Over 20 of those are different variants of HDF5 files (H5part, Xdmf, Pixie, Silo, Samrai, netCDF, Flash, Enzo, Chombo, etc., etc.) When opening a file, how does VisIt figure out which plugin to use? In particular, how do we avoid one poorly written reader plugin (which may be the wrong one for a given file) from preventing the correct one from being found. Its kinda a hard problem.
Some of our discussion is captured here. . .
http://www.visitusers.org/index.php?title=Database_Format_Detection
Mark
From: Hdf-forum <hdf-forum-bounces at lists.hdfgroup.org> on behalf of John Shalf <jshalf at lbl.gov>
Reply-To: HDF Users Discussion List <hdf-forum at lists.hdfgroup.org>
Date: Wednesday, March 2, 2016 1:02 PM
To: HDF Users Discussion List <hdf-forum at lists.hdfgroup.org>
Cc: "netcdfgroup at unidata.ucar.edu" <netcdfgroup at unidata.ucar.edu>, Ward Fisher <wfisher at ucar.edu>
Subject: Re: [Hdf-forum] Detecting netCDF versus HDF5
Perhaps NetCDF (and other higher-level APIs that are built on top of HDF5) should include an attribute attached to the root group that identifies the name and version of the API that created the file? (adopt this as a convention)
-john
On Mar 2, 2016, at 12:55 PM, Pedro Vicente <pedro.vicente at space-research.org> wrote:
Hi Ward
As you know, Data Explorer is going to be a general purpose data reader for many formats, including HDF5 and netCDF.
Here
http://www.space-research.org/
Regarding the handling of both HDF5 and netCDF, it seems there is a potential issue, which is, how to tell if any HDF5 file was saved by the HDF5 API or by the netCDF API?
It seems to me that this is not possible. Is this correct?
netCDF uses an internal function NC_check_file_type to examine the first few bytes of a file, and for example for any HDF5 file the test is
/* Look at the magic number */
/* Ignore the first byte for HDF */
if(magic[1] == 'H' && magic[2] == 'D' && magic[3] == 'F') {
*filetype = FT_HDF;
*version = 5;
The problem is that this test works for any HDF5 file and for any netCDF file, which makes it impossible to tell which is which.
Which makes it impossible for any general purpose data reader to decide to use the netCDF API or the HDF5 API.
I have a possible solution for this , but before going any further, I would just like to confirm that
1) Is indeed not possible
2) See if you have a solid workaround for this, excluding the dumb ones, for example deciding on a extension .nc or .h5, or traversing the HDF5 file to see if it's non netCDF conforming one. Yes, to further complicate things, it is possible that the above test says OK for a HDF5 file, but then the read by the netCDF API fails because the file is a HDF5 non netCDF conformant
Thanks
----------------------
Pedro Vicente
pedro.vicente at space-research.org
http://www.space-research.org/
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