-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Hi,
This is a plea to revisit the parallel vs serial hdf5 / netcdf issue for jessie. Firstly, references to previous work: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=657949 https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=591346 In summary: HDF5 has two modes, parallel and serial. The design bug (*) is that they share the same API/ABI but are incompatible. In particular, * The parallel version can do parallel read /writes via MPI but * The parallel version cannot use compression plugins, variable length records, etc. * Parallel version has no C++ support, is not threadsafe. So they conflict. This then means that packages like netcdf4, which can be either serial or parallel, cannot be built against both: it must be one or the other. Currently netcdf in Debian is serial, and cannot do parallel writes. This cannot be fixed (e.g. by providing both serial and parallel netcdf packages) because libhdf5-dev (serial) conflicts with libhdf5-mpi-dev. (parallel). This goes on, with packages choosing one version or the other, until you end up with a package that can't be built in Debian (e.g visit, which i'm working on), because it depends on both conflicting stacks. The best solution I can think of is: (1) make the packages install into /usr/lib/$MPIV/... with $MPIV equalling either mpiversion (openmpi, mpich2, ...) or 'serial', or 'any'. (2) Use alternatives to set a default. (3) Mangle the libnames as follows: /usr/lib/openmpi/lib/libhdf5.so --> /usr/lib/$(DEB_HOST_MULTIARCH)/libhdf5_openmpi.so.7.1.1 ie. adding _$(MPIV) to the libname. This results in a library that uses it being hard-coded to use that particular version, but (4) the version in /usr/lib/any/ does _not_ mangle the libname, but points to a version with libhdf5.so.7.1.1 with SONAME 'libhdf5.so.7', which is just a shell for linking against, but which itself is linked against a version (any, default serial) of the HDF5 libs. Hence any application which does not care of the given features (threadsafe, compression, parallelism) can use this version. Binaries built with it will resolve /usr/lib/*/libhdf5.so.7.1.1 pointing to the default version on the system. This will enable the building of a libnetcdf-$mpi version, for parallel writes, and other libraries. Any comments? best regards Alastair - -- Alastair McKinstry, <[email protected]>, <[email protected]>, https://diaspora.sceal.ie/u/amckinstry A decent provision for the poor is the true test of civilization. ~Samuel Johnson, Boswell: Life of Johnson -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iQIcBAEBCAAGBQJTfKzHAAoJEN9LdrZRJ3QsPtMQAJXPDHUbyBkgxhd6tDq5NzM6 w18DyCNpzWz9nnNXmkENIUxN6kRER23f3NmeHvuSS+bJqMbi3rUwNWxKEc5IsgqB V5Up/kBtVzD1+ThMNAKhzCfSLSzyvNwRr07hMvdwbEbMG9ed/B3+nbkzJuhCpLPN TXZ+VaIePqtn2X8gqlR2ZHUTV+BH4j5A+I7N3Bcek1gky7fpmsKU3ZGk1o+DF+4o LeyQMOEv0L2ZFm1fzcSJGZPNUEo2m5doGAvlD1lI5a7HZB6cT10jd7RcBlVqqmsI +dd/yXtQdnrpUjABf7mjUcdb9e1xNiJseeNiiBBgiToDKSYvm3SysQlM6oWRm7cp hGFmhsMFmu22wDLFpFMTPZPHUO9QzsT/iPY/CgfslkMb86+FIbrXKjhnm0IS4msc Xn0Q5V70pWvQClxHCsrvZpg5CLjhdkQhIiUU2/m762M9hgvrUEv1bLRCWoW8dub9 p+pyU/d5hfVsEfBjV+v9JgX6+PjkrFjp7bPNhGfFH5/G9m3I7ZzMt6vtW1zxcnrm AGltobIerdjM19N9UQN4MIXSklS7wBP+GT7t6ByQacjvpEfwWpQ+GLd/VN+bJFzd AVerj9PwSxjk5Rdl2fubZCpI9ZnBZPBEzLjTJciRIREU3BImu03YV9bVlyotUNcM KFp+n7VoZe6jmwAcBVO1 =K/xZ -----END PGP SIGNATURE----- -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected] Archive: https://lists.debian.org/[email protected]
