[Date Prev][Date Next] [Thread Prev][Thread Next] [Date Index] [Thread Index]

Re: netcdf Transition

On 28-07-15 18:20, Sebastiaan Couwenberg wrote:
> To followup on the rebuilds done by Ross, I've also started a round of
> rebuilds.

I sent the above a bit earlier than I had planned, so here's the
followup with additional results.

There are a couple of easy to solve FTBFS that cannot find the hdf5
library that will need a patch add the HDF5 variant specific library
path. For those issues bugs haven't been filed yet, for all other bugs
related to the netcdf transition see:


ncview (2.1.5+ds1-1) FTBFS because the mpicc that was used to compile
netcdf is missing:

 checking for nc-config... yes
 Netcdf library version: netCDF 4.4.0-rc2
 Netcdf library has version 4 interface present: yes
 Netcdf library was compiled with C compiler: /usr/bin/mpicc
 checking for /usr/bin/mpicc... no
 configure: error: in `/tmp/buildd/ncview-2.1.5+ds1':
 configure: error: no acceptable C compiler found in $PATH

Because netcdf is built with the openmpi HDF5 variant, it needs to pull
in libopenmpi-dev for its mpicc. I've changed the (build) dependencies
to libhdf5-mpi-dev in netcdf (1:4.4.0~rc2-1~exp3). libhdf5-mpi-dev
depends on libhdf5-openmpi-dev & mpi-default-dev, the latter is required
for its dependency on libopenmpi-dev whose mpicc was used to build
netcdf. Unfortunately despite having /usr/bin/mpicc available, ncview
still refuses to accept it. I've filed the issue in #793902.

netcdf4-python (1.1.8-2) FTBFS because it needs to be adapted for the
HDF5 openmpi variant. I've uploaded a fixed version (1.1.8-3~exp1) to
experimental, but it unfortunately FTBFS on most architectures due to a
missing version constraint on the libnetcdf-dev version. That's fix in
netcdf4-python (1.1.8-3~exp2).

oasis3 (3.mct+dfsg.121022-3 / 3.mct+dfsg.121022-4) both FTBFS because
they're missing the build dependency on libnetcdff-dev. The -4 revision
in experimental is missing it too. I've forwarded the patch in #793920.

octave-octcdf (1.1.8-1) FTBFS just like gnudatalanguage:

 g++ -shared -Wl,-Bsymbolic  -o netcdf.oct  ov-netcdf.o ov-ncfile.o \
   ov-ncvar.o ov-ncatt.o ov-ncdim.o   -Wl,-z,relro -Wl,--as-needed \
   -L/usr/lib -lnetcdf -lhdf5_hl -lhdf5 -lz -ldl -lm -lcurl \
   -L/usr/lib/x86_64-linux-gnu/octave/4.0.0 \
   -L/usr/lib/x86_64-linux-gnu -loctinterp -loctave -Wl,-z,relro \
 /usr/bin/ld: cannot find -lhdf5_hl
 /usr/bin/ld: cannot find -lhdf5
 collect2: error: ld returned 1 exit status

It looks like these are easily fixed by adding the HDF5 openmpi library
path with -L/usr/lib/$(DEB_HOST_MULTIARCH)/hdf5/openmpi.

r-cran-ncdf4 (1.13-1) FTBFS just like gnudatalanguage &

 gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o ncdf4.so \
   ncdf.o ncdf2.o ncdf3.o src_ncdf4.o -L/usr/lib -lnetcdf -lhdf5_hl \
   -lhdf5 -lz -ldl -lm -lcurl -L/usr/lib/R/lib -lR
 /usr/bin/ld: cannot find -lhdf5_hl
 /usr/bin/ld: cannot find -lhdf5
 collect2: error: ld returned 1 exit status
 /usr/share/R/share/make/shlib.mk:6: recipe for target 'ncdf4.so' failed

We could probably avoid these if we'd stuck to the HDF5 serial variant
which supports pkgconfig unlike the mpi variants. I'm starting to doubt
if it's wise to only provide NetCDF built with HDF5 MPI. Most if not all
our packages use only the HDF5 serial variant.

ruby-netcdf (0.6.6-2) FTBFS because it cannot find main() in -lnetcdf.
This may be related to the HDF5 MPI variant. I've filed the issue in
#793976. ruby-netcdf ( was quickly uploaded in response, but
that still fails to build due to the common hdf5 linking problem.

vtk (5.8.0-17.5) FTBFS because it's missing a build dependency on

 [ 24%] Building CXX object IO/CMakeFiles/vtkIO.dir/vtkMPASReader.cxx.o
 In file included from /tmp/buildd/vtk-5.8.0/IO/vtkMPASReader.cxx:89:0:
 /tmp/buildd/vtk-5.8.0/Utilities/vtk_netcdfcpp.h:21:23: fatal error:
netcdfcpp.h: No such file or directory
  #include <netcdfcpp.h>
 compilation terminated.
 IO/CMakeFiles/vtkIO.dir/build.make:1526: recipe for target
'IO/CMakeFiles/vtkIO.dir/vtkMPASReader.cxx.o' failed
 make[3]: *** [IO/CMakeFiles/vtkIO.dir/vtkMPASReader.cxx.o] Error 1

Adding the build dependency is suffient to allow both versions to build
successfully. I've forwarded them in #794010.

gmt (5.1.2+dfsg1-1) FTBFS because it couldn't find the HDF5 libraries
either, but that was easily solved in gmt (5.1.2+dfsg1-2~exp1).

metview (4.5.6-3 & 4.5.6-4exp1) FTBFS because they're missing a build
dependency on libnetcdf-cxx-legacy-dev, with those build dependencies
added the builds succeed. The patches are forwarded in #794027.

vtk6 (6.2.0+dfsg1-1) is pretty much the same story as for vtk
(5.8.0-17.5 / 5.10.1+dfsg-1). Patch forwarded in #794040.

Transition: netcdf

 libnetcdfc7   (1:4.1.3-7.2) -> libnetcdf7       (1:4.4.0~rc2-1~exp3)
 libnetcdfc++4 (1:4.1.3-7.2) -> libnetcdf-c++4-1 (4.2.1-1~exp3) [cxx4]
 libnetcdfc++4 (1:4.1.3-7.2) -> libnetcdf-c++4   (4.2-1~exp3)   [legacy]
 libnetcdff5   (1:4.1.3-7.2) -> libnetcdff6      (4.4.2-1~exp4)

The status of the most recent rebuilds is as follows.

 adios              (1.8.0-2 / 1.8.0-3)                  OK / OK
 cdftools           (3.0-1 / 3.0-2~exp1)                 FTBFS / OK
 cmor               (2.9.1-5 / 2.9.1-6)                  OK / OK
 dx                 (1:4.4.4-7)                          OK
 etsf-io            (1.0.3-4 / 1.0.4-1~exp1)             OK / OK [+]
 exodusii           (6.02.dfsg.1-5 / 6.02.dfsg.1-6)      OK / OK
 ferret-vis         (6.9.3-1 / 6.9.3-2~exp1)             FTBFS / OK
 gdal               (1.10.1+dfsg-9 / 1.11.2+dfsg-1~exp4) OK / OK
 gnudatalanguage    (0.9.5-2)                            FTBFS
 grace              (1:5.1.25-1)                         OK
 grads              (2:2.0.2-5 / 2:2.0.2-6)              OK / OK
 gri                (2.12.23-8)                          FTBFS
 kst                (2.0.3-4)                            OK
 libpdl-netcdf-perl (4.20-1)                             OK [+]
 magics++           (2.24.7-3)                           OK [+]
 minc               (2.2.00-6)                           OK [+]
 nco                (4.5.1-1)                            FTBFS
 ncview             (2.1.5+ds1-1)                        FTBFS
 netcdf4-python     (1.1.8-2 / 1.1.8-3~exp2)             FTBFS / OK
 oasis3      (3.mct+dfsg.121022-3 / 3.mct+dfsg.121022-4) OK / OK [+]
 octave-octcdf      (1.1.8-1)                            FTBFS
 ovito              (2.3.3+dfsg1-1)                      OK
 python-scientific  (2.9.4-3)                            OK
 r-cran-ncdf4       (1.13-1)                             FTBFS
 r-cran-rnetcdf     (1.6.3-1-1)                          OK
 ruby-netcdf        (                          FTBFS
 v-sim              (3.7.2-1)                            OK
 vtk                (5.8.0-17.5 / 5.10.1+dfsg-1)         OK / OK [+]

 cdo                (1.6.6+dfsg.1-3 / 1.6.6+dfsg.1-4)    OK / OK
 gmt                (5.1.2+dfsg1-1 / 5.1.2+dfsg1-2~exp1) FTBFS / OK
 metview            (4.5.6-3 / 4.5.6-4exp1)              OK / OK [+]
 ncl                (6.3.0-3~exp1 / 6.3.0-3)             OK / OK
 vtk6               (6.2.0+dfsg1-1)                      OK [+]

Kind Regards,


 GPG Key ID: 4096R/6750F10AE88D4AF1
Fingerprint: 8182 DE41 7056 408D 6146  50D1 6750 F10A E88D 4AF1

Reply to: