[Debian-med-packaging] source code for JHDF5?

[Tim Booth]

Dear Bernd and colleagues,

Just to let you know that the JHDF5 libraries are now an official part
of Debian:

https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=796390

and soon to be tracked at:

https://tracker.debian.org/pkg/libsis-jhdf5-java

Many thanks again for creating this software and for your earlier
assistance in getting the package built.

Cheers,

TIM

On Thu, 2015-08-13 at 22:57 +0200, Bernd Rinn wrote:
> Hi Andreas,
> 
> Sure. I'll focus on the compilation of the C libraries. Antti (on the
> CC) who will come back from vacation beginning of next week will help
> you with the Java (gradle) build.
> 
> For the compilation of the two base C libraries, you'll need libc6-dev
> and the jdk1.6.0 package installed on the build machine (not sure how
> that is called on Debian). It would be easy to change it to use
> jdk1.7.0, but you need to change that in the compile scripts yourself.
> 
> 1. Checkout
>   http://svncisd.ethz.ch/repos/cisd/base/tags/release/14.12.x/14.12.0/base
> or whatever is the release you want to build.
> 
> 2. Go to subdirectory source/c and run './compile_linux_amd64.sh',
> './compile_linux_i386.sh' or './compile_linux_arm.sh'. This will create
> the two libraries libunix.so and libnativedata.so. Copy them to
> libs/native/nativedata/<platform> and libs/native/unix/<platform>, or
> where ever you need them for packaging.
> 
> For the compilation of the JHDF5 C library, you'll need the same headers
> as for the base libraries, plus a recent version of HDF5. If you want to
> use the compile_scripts we are using, the static HDF5 library needs to
> be available (for AMD64, HDF5 needs to have been compiled with compiler
> option '-fPIC'). The compile scripts for the JHDF5 native library
> assumes that HDF5 is installed in /opt/hdf5-<VERSION> and that gcc
> supports Graphite, i.e. compiler options '-floop-interchange
> -floop-strip-mine -floop-block -fgraphite-identity' are understood by gcc.
> 
> 1. Checkout
>   svn co
> http://svncisd.ethz.ch/repos/cisd/jhdf5/tags/release/14.12.x/14.12.1/jhdf5
> or whatever is the release you want to build.
> 
> 2. Go to subdirectory source/c, adapt the version number of HDF5 in
> 'version.sh' (at the time of this writing, it is 1.8.14), check the
> compiler flags in compile_linux_amd64.sh, compile_linux_i386.sh or
> compile_linux_arm.sh to see that they are supported by your version of
> gcc. The compile script for ARM is kind of the basic version and if you
> don't care about optimizations, you should be fine using those flags.
> 
> 3. Run './compile_linux<xxx>.sh' where xxx is amd64, i386 or arm. If
> everything works out, you will find 'libjhdf5.so' which you can copy to
> libs/native/jhdf5/<platform>, or  where ever you need them for packaging.
> 
> Next week, Antti will show you how to use Gradle for doing the Java builds.
> 
> Hope that helps,
> 
> Bernd
> 
> 
> On 2015-08-13 12:57, Andreas Tille wrote:
> > Hi Bernd,
> > 
> > thanks for your quick reply (and thanks for Axel for the contact).
> > 
> > Just to answer your question:  For Debian packaging we need to build all
> > components from source and thus we need the source also for the small
> > JNI libraries.  I'm not directly involved in the packaging (but Olivier
> > and Tim in CC).  They were seeking the source repository of the basic
> > components.  It would be great if you could provide these.
> > 
> > Kind regards
> > 
> >       Andreas.
> > 
> > On Thu, Aug 13, 2015 at 12:39:57PM +0200, Bernd Rinn wrote:
> >> Hello Alex,
> >>
> >> At this point, I am really the only contact for JHDF5, so feel free to
> >> ask me. When you are packaging it, you first need to decide on whether
> >> you want to use the native libraries I've built for HDF5 and two other,
> >> small JNI libraries (nativedata and unix) which are available in the
> >> repository below libs/native/jhdf5, or whether you want to build the
> >> native libraries yourself. The native libraries for Linux x64 and x86
> >> have been built on CentOS 5. They are working well on Ubuntu and should
> >> work on any Linux system with a glibc >= 2.5. The libraries for Linux
> >> arm have been built on Raspbian (not sure which version,
> >> '/etc/debian_version' reads '7.5').
> >>
> >> What are you looking for?
> >>
> >> Best,
> >>
> >> Bernd
> >>
> >> On 2015-08-13 11:47, Axel Beckert wrote:
> >>> Hallo Bernd,
> >>>
> >>> [Olivier, Tim: Andreas and me are trying to find the right contact for
> >>>  you at ETH Zurich]
> >>>
> >>> Steven Armstrong schrieb am Thu, Aug 13, 2015 at 09:08:28AM +0200:
> >>>> Axel Beckert [1] (im cc) von der ISG D-PHYS
> >>>
> >>> Ja, allerdings in meiner Funktion als Debian-Entwickler, nicht als
> >>> ISG'ler. Deswegen Antworten bitte vorzugsweise an meine
> >>> @debian.org-Adresse -- auch weil ich im Urlaub bin und die ISG-Mail
> >>> zur Zeit nicht lese. :-)
> >>>
> >>>> hat mich via irc folgendes gefragt:
> >>>>
> >>>> 23:36 < XTaran> sar: Weisst Du, wer bei Euch (SIS) jetzt für
> >>>> https://wiki-bsse.ethz.ch/pages/viewpage.action?pageId=26609113
> >>>> zuständig ist? Da scheint's Aktivitäten zu geben, das für Debian zu
> >>>> paketieren, aber irgendwie scheint der verfügbare Quellcode
> >>>> unvollständig zu sein und wir suchen einen Ansprechpartner dafür.
> >>>
> >>> Jupp, im Anhang die Mail, die ich dazu bekommen habe.
> >>>
> >>> Hier auf der Debian Conference (DebConf) ist Andreas Tille
> >>> <tille at debian.org> (im Cc) auf mich zugekommen, da ich an der ETH
> >>> arbeite. Antwort bitte auch an ihn und seine Kollegen.
> >>>
> >>> Seine Kollegen sprechen kein Deutsch, Antwort deswegen bitte auf
> >>> Englisch wenn möglich.
> >>>
> >>> 		Mit freundlichem Gruss, Axel Beckert
> >>
> >> -- 
> >> Dr. Bernd Rinn
> >> Scientific IT Services
> >> ETH Zurich IT Services
> >> SIB Swiss Institute of Bioinformatics
> >> Weinbergstr. 11 (WEC D 19), 8092 Zürich, Switzerland, +41 44 632 0608
> >> Mattenstr. 26 (1078 1.01), 4058 Basel, Switzerland, +41 61 387 3130
> >>
> > 
> 

-- 
Hanlon's Razor: Never attribute to malice that which can be adequately
explained by stupidity... but don't rule out malice.