[needs packaging] please include hdf5-1.8 in jaunty jackalope

Bug #308280 reported by Darren Dale on 2008-12-15
Affects Status Importance Assigned to Milestone
hdf5 (Ubuntu)

Bug Description

hdf5-1.8.2 is the latest release from the hdf5 group. Version 1.8 still provides the ability for programs to be compiled against the 1.6 api, so backwards compatibility should not be a major issue. Programs compiled against the 1.8 can take advantage of a host of new features, which I have been using on my fedora and gentoo systems. I would like to continue development on my kubuntu laptop, but this is not possible with hdf5-1.6.x. Is there any chance version 1.8 could be included in juanty?

I found this page which may be useful: http://soma.mit.edu/svn/software/hdf5-1.8/debian/


Brian Murray (brian-murray) wrote :

*** This is an automated message ***

This bug is tagged needs-packaging which identifies it as a request for a new package in Ubuntu. As a part of the managing needs-packaging bug reports specification, https://wiki.ubuntu.com/QATeam/Specs/NeedsPackagingBugs, all needs-packaging bug reports have Wishlist importance. Subsequently, I'm setting this bug's status to Wishlist.

Changed in hdf5:
importance: Undecided → Wishlist
Darren Dale (dsdale24) wrote :

I dont know anything about packaging for ubuntu (though I am willing to learn if you can point me in the right direction).

This morning I upgraded to jaunty alpha 6 and compiled hdf5-1.8.2 from source. There were two issues, both covered at http://www.hdfgroup.org/HDF5/release/known_problems5.html:

1) edit the ./perform/zip_perf.c file in the source and change line 552 to:

    output = open(filename, O_RDWR | O_CREAT, S_IRWXU);

2) edit ./config/gnu-flags file in the HDF5 source code and setting PROD_CFLAGS from "-O" to "-O0".

Here is the code that needs to be modified:

        # The optimization level is reduced for gcc 3.* and 4.* due to problems
        # with code generation for src/H5Tconv.c with the -O2 & -O3
        # optimization levels (which shows up as failures for various integer
        # types -> long long conversions in the test/dtypes test). Perhaps
        # later versions of gcc will fix this bug... - QAK - 2003/10/20

After making these two changes, I ran:

    ./configure --enable-threadsafe --with-pthreads=/usr --prefix=/usr/local
    make test
    sudo make install

All tests pass

slayton (slayton) wrote :

I'm was the maintainer of http://soma.mit.edu/svn/software/hdf5-1.8/debian/ our server went down and hasn't yet been fully recovered. Until then I've created a tar.gz of the mentioned directory for the OP.

slayton (slayton) wrote :

I've packaged up hdf5-serial-dev-1.8.3, hdf5-serial-1.8.3, and hdf5-tools for Jaunty. You can find them at:

If you need the other version of hdf5 (mpich, lam, etc..) I'd be more then willing to help you get them packaged.

Also packaging for a different distribution shouldn't be too difficult either.

Darren Dale (dsdale24) wrote :

Thank you Slayton. Would you consider packaging for Karmic?

It would really be nice if Ubuntu would include these in the standard repositories.

slayton (slayton) wrote :

It will be very easy to package this up for Karmic.

Getting 1.8.X into the official repositories is going to be a challenge. It is maintained by Debian so Ubuntu won't introduce an Ubuntu specific version. I've been in communication with the Debian maintainer and he is currently fighting with Upstreams about some issues with the newest version...

Basically Debian needs to package this so I can't, sorry, but I will keep updating until it gets introduced into the official repositories.

slayton (slayton) wrote :

The above link is obselete... I am not hosting hdf5-1.8.3 in my ppa. I did however start a launchpad hdf5 that has a ppa. This ppa currently has a build for Jaunty. My attempts to build for Karmic failed but I'm working on getting that fixed.

You can use this link to access the HDF5 ppa

Darren Dale (dsdale24) wrote :

Looks like this has been accepted for inclusion in debian: http://packages.qa.debian.org/h/hdf5.html . Any chance ubuntu can fold them in from debian?

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