Issue 60 in casacore: Build of casacore-1.5.0 with HDF5 support failed in Debian Wheezy and Ubuntu 12.04 LTS

[casa...@googlecode.com]

Status: New
Owner: ----
Labels: Type-Defect Priority-Medium Milestone-Release1.4

New issue 60 by nudomari...@gmail.com: Build of casacore-1.5.0 with HDF5
support failed in Debian Wheezy and Ubuntu 12.04 LTS
http://code.google.com/p/casacore/issues/detail?id=60

I could not build casacore-1.5.0 neither in Debian Wheezy nor in Ubuntu
12.04 LTS with HDF5 support.
I started in both cases from a clean installation of the OS and installed
the dependencies needed.
I have tried with several of the available versions of libhdf5-dev
(libhdf5-lam-dev, libhdf5-openmpi-dev, libhdf5-serial-dev and
libhdf5-mpich-dev).

I run:
cmake .. -DUSE_HDF5=ON -DUSE_FFTW3=ON
-DHDF5_INCLUDE_DIRS=/usr/lib/openmpi/include
make

Note.- The option "-DHDF5_INCLUDE_DIRS=/usr/lib/openmpi/include" is needed
for the mpi versions of libhdf5-dev

This is the error I got:
[ 3%] Building CXX object
casa/CMakeFiles/casa_casa.dir/HDF5/HDF5Record.cc.o
/home/vagrant/casacore-1.5.0/casa/HDF5/HDF5Record.cc: In static member
function 'static void casa::HDF5Record::writeScalar(hid_t, const
casa::String&, const void*, const casa::HDF5DataType&)':
/home/vagrant/casacore-1.5.0/casa/HDF5/HDF5Record.cc:420:38: error: too
many arguments to function 'hid_t H5Acreate1(hid_t, const char*, hid_t,
hid_t, hid_t)'
/usr/include/H5Apublic.h:105:16: note: declared here
/home/vagrant/casacore-1.5.0/casa/HDF5/HDF5Record.cc: In static member
function 'static void casa::HDF5Record::writeScaString(hid_t, const
casa::String&, const casa::String&)':
/home/vagrant/casacore-1.5.0/casa/HDF5/HDF5Record.cc:439:38: error: too
many arguments to function 'hid_t H5Acreate1(hid_t, const char*, hid_t,
hid_t, hid_t)'
/usr/include/H5Apublic.h:105:16: note: declared here
/home/vagrant/casacore-1.5.0/casa/HDF5/HDF5Record.cc: In static member
function 'static void casa::HDF5Record::writeArray(hid_t, const
casa::String&, const void*, const casa::IPosition&, const
casa::HDF5DataType&)':
/home/vagrant/casacore-1.5.0/casa/HDF5/HDF5Record.cc:460:38: error: too
many arguments to function 'hid_t H5Acreate1(hid_t, const char*, hid_t,
hid_t, hid_t)'
/usr/include/H5Apublic.h:105:16: note: declared here
/home/vagrant/casacore-1.5.0/casa/HDF5/HDF5Record.cc: In static member
function 'static void casa::HDF5Record::writeArrString(hid_t, const
casa::String&, const casa::Array<casa::String>&)':
/home/vagrant/casacore-1.5.0/casa/HDF5/HDF5Record.cc:500:38: error: too
many arguments to function 'hid_t H5Acreate1(hid_t, const char*, hid_t,
hid_t, hid_t)'
/usr/include/H5Apublic.h:105:16: note: declared here
make[2]: *** [casa/CMakeFiles/casa_casa.dir/HDF5/HDF5Record.cc.o] Error 1
make[1]: *** [casa/CMakeFiles/casa_casa.dir/all] Error 2
make: *** [all] Error 2



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[casa...@googlecode.com]

Comment #1 on issue 60 by nudomari...@gmail.com: Build of casacore-1.5.0

with HDF5 support failed in Debian Wheezy and Ubuntu 12.04 LTS
http://code.google.com/p/casacore/issues/detail?id=60

A correction: when I said Debian Wheezy I meant Debian Squeeze.

Apparently the problem comes from the version of the HDF5 libraries that
are bundled in each OS version. Debian Squeeze and Ubuntu 12.04 LTS contain
the version 1.8.4 of the libraries. If I use Debian Wheezy (version 1.8.8
of HDF5) or I install from the source, casacore compiles without raising
this error.

Some questions related to that:
- Does casacore require HDF5 to be compiled with parallel support?
- Is the "thread-safe" option of HDF5 required?
- Taking into account that Ubuntu 12.04 LTS will have support for about 4
more years. Is there any way to allow casacore to be built using an older
version of the HDF5 library (~ 1.8.4)?

[casa...@googlecode.com]

Comment #2 on issue 60 by jdswinb...@gmail.com: Build of casacore-1.5.0

with HDF5 support failed in Debian Wheezy and Ubuntu 12.04 LTS
http://code.google.com/p/casacore/issues/detail?id=60

This is likely due to Debian bug #537414, wherein despite shipping libhdf5
1.8.4, it was configured to provide the HDF5 1.6 API. This has now been
resolved in Debian (as of March 2011), but it looks like Ubuntu hasn't
picked up those changes yet.

This is fundamentally an Ubuntu bug, but obviously a workaround on the
casacore side would make life easier for our Ubuntu-using colleagues!

(See http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=537414 for back-story
and workarounds)

[casa...@googlecode.com]

Updates:
Status: Fixed
Owner: gervandi...@gmail.com
Cc: Malte.Marquarding

Comment #3 on issue 60 by gervandi...@gmail.com: Build of casacore-1.5.0

with HDF5 support failed in Debian Wheezy and Ubuntu 12.04 LTS
http://code.google.com/p/casacore/issues/detail?id=60

This has been fixed in the trunk version which will be released aoon.
Ger