Package of hdf-1.8.3, first try

[Heiko Klein]

Hi,

I'm eager to build a debian/ubuntu package of netcdf4 which requires
hdf-1.8.3. I've seen that it is on the todo list of this group, but
without explicit roadmap, so I gave it a try to build a hdf5-package:

http://pastebin.met.no/pastebin/cgi-bin/file?id=afbf25c4b95a64a3ecf0e97ca4b713731f08f589/hdf5_1.8.3.orig.tar.gz
http://pastebin.met.no/pastebin/cgi-bin/file?id=4e69a51659c8fa467ed66534b0e5105d2209a1d9/hdf5_1.8.3-1.diff.gz

It was generated from the 1.6.5 debian package with uscan, and some
smaller changes to get hdf5 to build. The biggest change I introduce is
to name the library to the ABI version rather than the hdf package
version. hdf5 tries uses libtool and tries to be ABI compatible
(currently at library version 6) so I don't see a reason why the hdf5
packages should still force the correct version number.

I have tested the package under hardy and debian 5.0.1. lintian gives
some complaints about man-page and the ABI-VERSION conflicts, but
otherwise it seems to work.

I include the orig.tar.gz since the official hdf5_1.8.3.tar.gz contains
a file twice (detype_files.txt), which conflicts with debuild 'tar -xkf'.

Best regards,

Heiko

Format: 1.7
Date: Tue, 09 Jun 2009 12:00:36 +0200
Source: hdf5
Binary: libhdf5-serial-1.8.3-0 libhdf5-serial-dev libhdf5-lam-1.8.3-0 libhdf5-lam-dev libhdf5-mpich-1.8.3-0 libhdf5-mpich-dev libhdf5-doc hdf5-tools
Architecture: source
Version: 1.8.3-1
Distribution: hardy
Urgency: low
Maintainer: Debian GIS Project <[hidden email]>
Changed-By: Heiko Klein <[hidden email]>
Description:
 hdf5-tools - Hierarchical Data Format 5 (HDF5) - Runtime tools
 libhdf5-doc - Hierarchical Data Format 5 (HDF5) - Documentation
 libhdf5-lam-1.8.3-0 - Hierarchical Data Format 5 (HDF5) - runtime files - LAM version
 libhdf5-lam-dev - Hierarchical Data Format 5 (HDF5) - development files - LAM versi
 libhdf5-mpich-1.8.3-0 - Hierarchical Data Format 5 (HDF5) - runtime files - MPICH version
 libhdf5-mpich-dev - Hierarchical Data Format 5 (HDF5) - development files - MPICH ver
 libhdf5-serial-1.8.3-0 - Hierarchical Data Format 5 (HDF5) - runtime files - serial versio
 libhdf5-serial-dev - Hierarchical Data Format 5 (HDF5) - development files - serial ve
Changes:
 hdf5 (1.8.3-1) hardy; urgency=low
 .
   * New upstream release
   * adding --disable-threadsafe to --enable-parallel and --enable-cxx,
     as forced by configure
   * Adding html-documentation as link to online-documentation
   * Correcting release-docs/HISTORY* files
   * changing from library-names like [hidden email] to libhdf5.so.@ABI@
     in shlibs.in since hdf5-1.8 sets soname version explicitly
Files:
 b42e9eaab74d29713c72d4161a323b53 620 science optional hdf5_1.8.3-1.dsc
 3754feb7f2c6787e658f2813b9933434 7537219 science optional hdf5_1.8.3.orig.tar.gz
 47921c7ff83a2ff00f469b9bd6308c2e 31990 science optional hdf5_1.8.3-1.diff.gz

Format: 1.0
Source: hdf5
Binary: libhdf5-serial-1.8.3-0, libhdf5-serial-dev, libhdf5-lam-1.8.3-0, libhdf5-lam-dev, libhdf5-mpich-1.8.3-0, libhdf5-mpich-dev, libhdf5-doc, hdf5-tools
Architecture: any
Version: 1.8.3-1
Maintainer: Debian GIS Project <[hidden email]>
Uploaders: Francesco Paolo Lovergine <[hidden email]>
Standards-Version: 3.7.2
Build-Depends: debhelper (>> 5), lam4-dev (>= 7.1.1-3.2), libjpeg62-dev, libmpich1.0-dev (>= 1.2.7-1), zlib1g-dev
Files:
 3754feb7f2c6787e658f2813b9933434 7537219 hdf5_1.8.3.orig.tar.gz
 47921c7ff83a2ff00f469b9bd6308c2e 31990 hdf5_1.8.3-1.diff.gz

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[Francesco P. Lovergine]

On Thu, Jun 18, 2009 at 10:44:58AM +0200, Heiko Klein wrote:

> Hi,
>
> I'm eager to build a debian/ubuntu package of netcdf4 which requires  
> hdf-1.8.3. I've seen that it is on the todo list of this group, but  
> without explicit roadmap, so I gave it a try to build a hdf5-package:
>
> http://pastebin.met.no/pastebin/cgi-bin/file?id=afbf25c4b95a64a3ecf0e97ca4b713731f08f589/hdf5_1.8.3.orig.tar.gz
> http://pastebin.met.no/pastebin/cgi-bin/file?id=4e69a51659c8fa467ed66534b0e5105d2209a1d9/hdf5_1.8.3-1.diff.gz
>
> It was generated from the 1.6.5 debian package with uscan, and some  
> smaller changes to get hdf5 to build. The biggest change I introduce is  
> to name the library to the ABI version rather than the hdf package  
> version. hdf5 tries uses libtool and tries to be ABI compatible  
> (currently at library version 6) so I don't see a reason why the hdf5  
> packages should still force the correct version number.
>
> I have tested the package under hardy and debian 5.0.1. lintian gives  
> some complaints about man-page and the ABI-VERSION conflicts, but  
> otherwise it seems to work.
>
> I include the orig.tar.gz since the official hdf5_1.8.3.tar.gz contains  
> a file twice (detype_files.txt), which conflicts with debuild 'tar -xkf'.
>

Nice try. We have an ongoing discussion about 1.8.3 specifically about
the thread-safety and C++/Fortran. The reason for having a different
name is the following: the existance of the soname for the library is
a recent discovery of HDF group. Unfortunately they use the same
soname for all libraries (C/C++/Fotran) so I think it's much more
safe embedding the library version into the package name. Note that
they often in the past changed API and ABI at every new release
and I suspect that would be done again if the C interface only was
left stable.

A good improvement would be dropping the unused (unuseful?) additional
ABI version in the package, which is what I did for 1.8.2.

But for that it is now time to issue a svn branch for the available
stuff in order to have a common reference for all available parties.


--
Francesco P. Lovergine

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[Francesco P. Lovergine]

On Thu, Jun 18, 2009 at 01:18:24PM +0200, Francesco P. Lovergine wrote:

> On Thu, Jun 18, 2009 at 10:44:58AM +0200, Heiko Klein wrote:
> > Hi,
> >
> > I'm eager to build a debian/ubuntu package of netcdf4 which requires  
> > hdf-1.8.3. I've seen that it is on the todo list of this group, but  
> > without explicit roadmap, so I gave it a try to build a hdf5-package:
> >
> > http://pastebin.met.no/pastebin/cgi-bin/file?id=afbf25c4b95a64a3ecf0e97ca4b713731f08f589/hdf5_1.8.3.orig.tar.gz
> > http://pastebin.met.no/pastebin/cgi-bin/file?id=4e69a51659c8fa467ed66534b0e5105d2209a1d9/hdf5_1.8.3-1.diff.gz
> >
> > It was generated from the 1.6.5 debian package with uscan, and some  
> > smaller changes to get hdf5 to build. The biggest change I introduce is  
> > to name the library to the ABI version rather than the hdf package  
> > version. hdf5 tries uses libtool and tries to be ABI compatible  
> > (currently at library version 6) so I don't see a reason why the hdf5  
> > packages should still force the correct version number.
> >
> > I have tested the package under hardy and debian 5.0.1. lintian gives  
> > some complaints about man-page and the ABI-VERSION conflicts, but  
> > otherwise it seems to work.
> >
> > I include the orig.tar.gz since the official hdf5_1.8.3.tar.gz contains  
> > a file twice (detype_files.txt), which conflicts with debuild 'tar -xkf'.
> >
>
> Nice try. We have an ongoing discussion about 1.8.3 specifically about
> the thread-safety and C++/Fortran. The reason for having a different
> name is the following: the existance of the soname for the library is
> a recent discovery of HDF group. Unfortunately they use the same
> soname for all libraries (C/C++/Fotran) so I think it's much more
> safe embedding the library version into the package name. Note that
> they often in the past changed API and ABI at every new release
> and I suspect that would be done again if the C interface only was
> left stable.
>
> A good improvement would be dropping the unused (unuseful?) additional
> ABI version in the package, which is what I did for 1.8.2.
>
> But for that it is now time to issue a svn branch for the available
> stuff in order to have a common reference for all available parties.
>
>

Just for note, this is the current set of libraries with 1.8.2. This is not
different for 1.8.3:

lrwxrwxrwx 1 frankie 1000      16 Mar 31 12:44 libhdf5.so.6 -> libhdf5.so.6.0.1*
-rwxr-xr-x 1 frankie 1000 3038106 Mar 31 12:43 libhdf5.so.6.0.1*
lrwxrwxrwx 1 frankie 1000      20 Mar 31 12:44 libhdf5_cpp.so.0 -> libhdf5_cpp.so.0.0.0*
-rwxr-xr-x 1 frankie 1000  534867 Mar 31 12:43 libhdf5_cpp.so.0.0.0*
lrwxrwxrwx 1 frankie 1000      24 Mar 31 12:44 libhdf5_fortran.so.0 -> libhdf5_fortran.so.0.0.0*
-rwxr-xr-x 1 frankie 1000  278892 Mar 31 12:43 libhdf5_fortran.so.0.0.0*
lrwxrwxrwx 1 frankie 1000      19 Mar 31 12:44 libhdf5_hl.so.0 -> libhdf5_hl.so.0.0.0*
-rwxr-xr-x 1 frankie 1000  126402 Mar 31 12:43 libhdf5_hl.so.0.0.0*
lrwxrwxrwx 1 frankie 1000      23 Mar 31 12:44 libhdf5_hl_cpp.so.0 -> libhdf5_hl_cpp.so.0.0.0*
-rwxr-xr-x 1 frankie 1000   12177 Mar 31 12:44 libhdf5_hl_cpp.so.0.0.0*
lrwxrwxrwx 1 frankie 1000      26 Mar 31 12:44 libhdf5hl_fortran.so.0 -> libhdf5hl_fortran.so.0.0.0*
-rwxr-xr-x 1 frankie 1000   65326 Mar 31 12:44 libhdf5hl_fortran.so.0.0.0*

If you check in the building scripts, only the C binding uses the explicitly set LT_VERSION.
The resulting non-C binding use always the same versioning.

----
My own conclusion about the thread-safety is enabling both thread-support AND C++/Fortran
interfaces in the same libraries, adding a note in the documentation about possible problems
in using HDF5 non-C functions in multi-thread programs. This is the same choice done
by Fedora folks.



--
Francesco P. Lovergine

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[Francesco P. Lovergine]

On Thu, Jun 18, 2009 at 10:44:58AM +0200, Heiko Klein wrote:
> Hi,
>
> I'm eager to build a debian/ubuntu package of netcdf4 which requires
> hdf-1.8.3. I've seen that it is on the todo list of this group, but
> without explicit roadmap, so I gave it a try to build a
> hdf5-package:
>
> http://pastebin.met.no/pastebin/cgi-bin/file?id=afbf25c4b95a64a3ecf0e97ca4b713731f08f589/hdf5_1.8.3.orig.tar.gz
> http://pastebin.met.no/pastebin/cgi-bin/file?id=4e69a51659c8fa467ed66534b0e5105d2209a1d9/hdf5_1.8.3-1.diff.gz

Interestingly enough the configure.in of 1.8.3 has some bugs and
currently openmpi on i386 has some issues with HDF5...

...
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether to enable maintainer-specific portions of Makefiles...
no
checking build system type... i486-pc-linux-gnu
checking host system type... i486-pc-linux-gnu
checking shell variables initial values... done
checking if basename works... yes
checking if xargs works... yes
checking for cached host... none
checking for config i486-pc-linux-gnu... no
checking for config i486-pc-linux-gnu... no
checking for config pc-linux-gnu... no
checking for config pc-linux-gnu... no
checking for config i486-linux-gnu... no
checking for config i486-linux-gnu... no
checking for config i486-pc... no
checking for config linux-gnu... found
../../config/linux-gnulibc1: line 59: 13019 Segmentation fault      $FC
-V > $tmpfile
checking for config ../../config/site-specific/host-klecker... no
checking for i486-linux-gnu-gcc... mpicc.openmpi
checking for C compiler default output file name...
configure: error: in
`/users/frankie/debian/debian-gis/supported/hdf5/hdf5-1.8.2/debian/build-openmpi':
configure: error: C compiler cannot create executables
See `config.log' for more details.



--
Francesco P. Lovergine

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[Francesco P. Lovergine]

On Fri, Jun 19, 2009 at 08:41:09PM +0200, Francesco P. Lovergine wrote:

> On Thu, Jun 18, 2009 at 10:44:58AM +0200, Heiko Klein wrote:
> > Hi,
> >
> > I'm eager to build a debian/ubuntu package of netcdf4 which requires
> > hdf-1.8.3. I've seen that it is on the todo list of this group, but
> > without explicit roadmap, so I gave it a try to build a
> > hdf5-package:
> >
> > http://pastebin.met.no/pastebin/cgi-bin/file?id=afbf25c4b95a64a3ecf0e97ca4b713731f08f589/hdf5_1.8.3.orig.tar.gz
> > http://pastebin.met.no/pastebin/cgi-bin/file?id=4e69a51659c8fa467ed66534b0e5105d2209a1d9/hdf5_1.8.3-1.diff.gz
>
> Interestingly enough the configure.in of 1.8.3 has some bugs and
> currently openmpi on i386 has some issues with HDF5...
>

Oh well has an issue with fakeroot :)

--
Francesco P. Lovergine

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