Bug#686926: [Pkg-octave-devel] Bug#686926: liboctave-dev: creates broken .oct files when the OpenMPI flavor of HDF5 (libhdf5-openmpi-dev) is installed
On Mon, Apr 08, 2013 at 09:17:48AM -0400, Jordi Gutiérrez Hermoso wrote: On 4 April 2013 19:54, Bradley M. Froehle brad.froe...@gmail.com wrote: If only there was a way for the different variants of HDF5 to be simultaneously installable… I think this is the real problem,and it goes way up to HDF5 upstream. They basically ship two completely different libraries with the same soname and the same symbols. *That* is the real bug. This is well stated since the very initial opening of this bug, and also well-known upstream. HDF5 staff still saw this problem as secondary at the time (i.e. they have not a dedicated budget for solving this issue). This is because HDF5 is still seen as an ad-hoc tool for specific applications, not as a general commodity library. If you had to build everything from scratch for your own purposes, those aspects are non-issues, of course. Unfortunately, that is not the case of a binary distribution, as in Debian case. The only practical thing to do is patching for splitting MPI and serial library names and proposing those patches to upstream. Of course, it would break compatibility for tons of other packages and third-parties products, but I see no other possibilities. -- Francesco P. Lovergine -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#686926: [Pkg-octave-devel] Bug#686926: liboctave-dev: creates broken .oct files when the OpenMPI flavor of HDF5 (libhdf5-openmpi-dev) is installed
On 4 April 2013 19:54, Bradley M. Froehle brad.froe...@gmail.com wrote: If only there was a way for the different variants of HDF5 to be simultaneously installable… I think this is the real problem,and it goes way up to HDF5 upstream. They basically ship two completely different libraries with the same soname and the same symbols. *That* is the real bug. - Jordi G. H. -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#686926: [Pkg-octave-devel] Bug#686926: liboctave-dev: creates broken .oct files when the OpenMPI flavor of HDF5 (libhdf5-openmpi-dev) is installed
Add HDF5 upstream contact address. On 08/04/2013 15:17, Jordi Gutiérrez Hermoso wrote: On 4 April 2013 19:54, Bradley M. Froehle brad.froe...@gmail.com wrote: If only there was a way for the different variants of HDF5 to be simultaneously installable… I think this is the real problem,and it goes way up to HDF5 upstream. They basically ship two completely different libraries with the same soname and the same symbols. *That* is the real bug. I do agree with Jordi. I reported the issue upstream on this subject a while ago (feb 2012) and the anwser was: There are no current plans to change the parallel HDF5 library name to another name. However, this has been a source of confusion over the years, so I entered a bug report for it. (I don't know of any ramifications to renaming the parallel library, but I think the best solution would be for us to provide it with a different name.) For your reference, the bug report is HDFFV-7925. (Our bug system is not open but feel free to ask about it if you want to know the status.) Sylvestre -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#686926: [Pkg-octave-devel] Bug#686926: liboctave-dev: creates broken .oct files when the OpenMPI flavor of HDF5 (libhdf5-openmpi-dev) is installed
Hello All, You should not have to install multiple HDF5 libraries. You can use the same library for parallel or serial use, which is why it works the way it does. Can you give us more information on why you would like to have the parallel library renamed? Thanks, -Barbara Barbara Jones The HDF Helpdesk The HDF Group h...@hdfgroup.org On Mon, 8 Apr 2013, Sylvestre Ledru wrote: Add HDF5 upstream contact address. On 08/04/2013 15:17, Jordi Gutiérrez Hermoso wrote: On 4 April 2013 19:54, Bradley M. Froehle brad.froe...@gmail.com wrote: If only there was a way for the different variants of HDF5 to be simultaneously installable… I think this is the real problem,and it goes way up to HDF5 upstream. They basically ship two completely different libraries with the same soname and the same symbols. *That* is the real bug. I do agree with Jordi. I reported the issue upstream on this subject a while ago (feb 2012) and the anwser was: There are no current plans to change the parallel HDF5 library name to another name. However, this has been a source of confusion over the years, so I entered a bug report for it. (I don't know of any ramifications to renaming the parallel library, but I think the best solution would be for us to provide it with a different name.) For your reference, the bug report is HDFFV-7925. (Our bug system is not open but feel free to ask about it if you want to know the status.) Sylvestre --
Bug#686926: [Pkg-octave-devel] Bug#686926: liboctave-dev: creates broken .oct files when the OpenMPI flavor of HDF5 (libhdf5-openmpi-dev) is installed
On Fri, Sep 7, 2012 at 4:50 AM, Sébastien Villemot wrote: Note that this problem is only present with libhdf5-openmpi-dev: it is not present with libhdf5-dev (serial version, the default) or libhdf5-mpich2-dev. Hm, are you sure? I see the same error with either libhdf5-mpich2-dev or libhdf5-openmpi-dev installed. -- mike -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#686926: [Pkg-octave-devel] Bug#686926: liboctave-dev: creates broken .oct files when the OpenMPI flavor of HDF5 (libhdf5-openmpi-dev) is installed
Mike Miller mtmil...@ieee.org writes: On Fri, Sep 7, 2012 at 4:50 AM, Sébastien Villemot wrote: Note that this problem is only present with libhdf5-openmpi-dev: it is not present with libhdf5-dev (serial version, the default) or libhdf5-mpich2-dev. Hm, are you sure? I see the same error with either libhdf5-mpich2-dev or libhdf5-openmpi-dev installed. When testing against libhdf5-mpich2-dev, you should make sure that all OpenMPI libraries are removed (in particular libopenmpi-dev). Otherwise they take precedence over MPICH2 because of the alternatives priority. -- .''`.Sébastien Villemot : :' :Debian Maintainer `. `' http://www.dynare.org/sebastien `- GPG Key: 4096R/381A7594 pgp2PMZG7FJYE.pgp Description: PGP signature
Bug#686926: [Pkg-octave-devel] Bug#686926: liboctave-dev: creates broken .oct files when the OpenMPI flavor of HDF5 (libhdf5-openmpi-dev) is installed
On Fri, Sep 7, 2012 at 8:51 AM, Sébastien Villemot wrote: Mike Miller mtmil...@ieee.org writes: On Fri, Sep 7, 2012 at 4:50 AM, Sébastien Villemot wrote: Note that this problem is only present with libhdf5-openmpi-dev: it is not present with libhdf5-dev (serial version, the default) or libhdf5-mpich2-dev. Hm, are you sure? I see the same error with either libhdf5-mpich2-dev or libhdf5-openmpi-dev installed. When testing against libhdf5-mpich2-dev, you should make sure that all OpenMPI libraries are removed (in particular libopenmpi-dev). Otherwise they take precedence over MPICH2 because of the alternatives priority. Yep, just found that out myself. Thanks. So here's a workaround that works for me with either set of libraries installed. Each has their own symbol to avoid including the C++ API, which is where the trouble lies. mkoctfile -DMPICH_SKIP_MPICXX=1 -DOMPI_SKIP_MPICXX=1 helloworld.cc I don't know enough about HDF5, but if it doesn't make use of the MPI C++ bindings at all, I'd argue this should be reassigned to hdf5 upstream so H5public.h would now contain: #ifdef H5_HAVE_PARALLEL # define MPICH_SKIP_MPICXX 1 # define OMPI_SKIP_MPICXX 1 # include mpi.h #endif -- mike -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
