I've NMU'd libint2 to fix the FTBFS with mpqc3, below. However it takes
~6 hours to compile on my decent laptop, and has been failing to build
on build systems, typically terminating with memory exhaustion.
What, if anything, can be done to fix this?
mpi4py was also failing to build with openmpi-2.0.1 due to hangs in the
test suite; I've just uploaded 2.0.1-5 which includes a fix for this.
mpi4py will need to be rebuilt (there is an older RC bug due to FTBFS on
1.10.3, which is now obsolete).
I've uploaded a fixed aces3 to DELAYED/5 , and mathgl.
Working on tachyon and abyss now.
Regards
Alastair
On 08/09/2016 12:07, Sebastiaan Couwenberg wrote:
> I've done a round of rebuilds to assess the impact of this transition.
> The results are summarized below. Several package suffer from
> uninstallable build dependencies by having libopenmpi1.10 pulled in by
> dependencies that failed to rebuild.
>
> fftw (2.1.5-4) FTBFS due to . being removed from @INC in recent perl.
>
> The gmsh (2.13.2+dfsg1-1) dependencies could initially not be installed
> because hdf5 was still pulling in libopenmpi1.10 which conflicts with
> libopenmpi2. The ben dependency levels did not reflect that. With the
> rebuilt hdf5 the gmsh rebuild succeeded.
>
> The molds (0.3.1-1) had a similar issue due to boost pulling in the old
> libopenmpi1.10. With the rebuilt boost the molds rebuild succeeded too.
>
> p4est (1.1-2) FTBFS due to test failures.
>
> tachyon (0.99~b6+dsx-5) FTBFS due to: undefined reference to symbol
> 'XNextEvent'
>
> abyss (1.9.0-1) FTBFS due to: db-csv.cc:23:9: error: cannot convert
> 'std::ifstream {aka std::basic_ifstream<char>}' to 'bool' in return
>
> gromacs (2016-2) FTBFS due to test failures.
>
> scalapack (1.8.0-12.3) FTBFS due to undefined references to MPI symbols.
>
> Bugreports for the above will be filed soon.
>
>
> Transition: openmpi
>
> libopenmpi1.10 (1.10.3-3) -> libopenmpi2 (2.0.1-3)
>
> The status of the most recent rebuilds is as follows.
>
> aces3 (sid only) (3.0.8-5) FTBFS (#831164)
> arpack (3.4.0-1) OK
> blacs-mpi (1.1-37) OK
> boost1.58 (1.58.0+dfsg-5.1) FTBFS (#811651)
> boost1.61 (1.61.0+dfsg-2.1) OK
> cctools (sid only) (4.0-1) OK
> dune-grid (2.4.1-1) OK
> fftw (2.1.5-4) FTBFS
> fftw3 (3.3.4-2) OK
> gerris (20131206+dfsg-9) OK
> gmsh (2.13.2+dfsg1-1) OK
> gpaw (1.1.0-1) OK
> hdf5 (1.8.16+docs-8) OK
> hpcc (1.4.3-1) OK
> hyphy (2.2.6+dfsg-5) OK
> hypre (2.8.0b-3) OK
> molds (0.3.1-1) OK
> mpi4py (2.0.0-2) OK
> mpqc (sid only) (2.3.1-16.1) FTBFS (#812036)
> mpqc3 (0.0~git20160216-3) OK
> mrbayes (3.2.6+dfsg-1) OK
> mrmpi (1.0~20140404-1) OK
> octave-mpi (1.2.0-2) OK
> open-coarrays (1.7.0-1) OK
> otf (1.12.5+dfsg-2) OK
> p4est (1.1-2) FTBFS
> palabos (1.5~r1+repack1-2) OK
> parmetis (4.0.3-4) OK
> pnetcdf (1.7.0-1) OK
> ray (2.3.1-4) OK
> regina-normal (4.96-4) OK
> rmpi (0.6-6-1) OK
> ruby-mpi (0.3.0-1) OK
> scotch (5.1.12b.dfsg-2) OK
> spooles (2.2-12) OK
> tachyon (0.99~b6+dsx-5) FTBFS
> valgrind (1:3.12.0~svn20160714-1) OK
>
> abyss (1.9.0-1) FTBFS
> adios (1.9.0-12) BD-UNINST
> ampliconnoise (1.29-5) OK
> code-saturne (4.2.1+repack-1) OK
> elkcode (sid only) (2.3.22-1) FTBFS (#825934)
> ffindex (0.9.9.7-1) OK
> gfsview (20121130+dfsg-2) OK
> gromacs (2016-2) FTBFS
> lammps (0~20151117.gite3c4db7-3) OK
> libghemical (sid only) (3.0.0-4.1) BD-UNINST
> libgpiv (0.6.1-4.3) OK
> mathgl (2.3.4-1) FTBFS (#835680)
> meep-mpi-default (1.3-3) OK
> meep-openmpi (1.3-3) OK
> mpb (1.5-2) OK
> murasaki (1.68.6-6) OK
> music (sid only) (1.0.7-1.2) FTBFS (#811907)
> netpipe (3.7.2-7.4) OK
> ns3 (3.25+dfsg2-3) OK
> openmx (3.7.6-1) OK
> paraview (5.1.2+dfsg1-1) BD-UNINST
> phyml (3:3.2.0+dfsg-2) OK
> prime-phylo (1.0.11-4) OK
> python-escript (4.2.0.1-4) OK
> relion (1.4+dfsg-2) OK
> scalapack (1.8.0-12.3) FTBFS
> silo-llnl (4.10.2-6) OK
> starpu (1.1.4+dfsg-6) OK
> starpu-contrib (1.1.4+dfsg-6) OK
> tessa (sid only) (0.3.1-6.1) FTBFS (#817690)
> tree-puzzle (5.2-8) OK
> vtk6 (6.3.0+dfsg1-1) BD-UNINST
> yorick (2.2.04+dfsg1-6) OK
> zalign (0.9.1-2) OK
>
> elpa (2016.05.001-1) BD-UNINST
> esys-particle (2.3.4+dfsg1-2) BD-UNINST
> eztrace (1.1-3-1) OK
> freefoam (0.1.0+dfsg+1-4) BD-UNINST
> gyoto (1.0.2-3) OK
> ifrit (4.1.2-5) BD-UNINST
> liggghts (3.4.0+repack1-2) BD-UNINST
> mumps (4.10.0.dfsg-4) BD-UNINST
> nwchem (sid only) (6.6+r27746-2) BD-UNINST
>
> cp2k (3.0.0-1) BD-UNINST
> espresso (5.4.0+dfsg-1) BD-UNINST
> freefem++ (sid only) (3.47+dfsg1-1) BD-UNINST
> petsc (3.7.3.dfsg1-2) BD-UNINST
> rheolef (6.7-1) BD-UNINST
> trilinos (12.6.4-1) BD-UNINST
>
> aster (11.5.0+dfsg2-4) BD-UNINST
> petsc4py (3.7.0-2) BD-UNINST
> slepc (3.7.2+dfsg1-2) BD-UNINST
>
> deal.ii (8.4.2-1) BD-UNINST
> getdp (2.9.2+dfsg1-1) BD-UNINST
> slepc4py (3.7.0-2) BD-UNINST
>
> dolfin (2016.1.0-2) BD-UNINST
>
>
> Kind Regards,
>
> Bas
>
--
Alastair McKinstry, <alastair@sceal.ie>, <mckinstry@debian.org>, https://diaspora.sceal.ie/u/amckinstry
Misentropy: doubting that the Universe is becoming more disordered.
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