dorsal team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

I assume you mean

  -DHDF5_ENABLE_PARALLEL=1

When I enable it, the build fails:

  /usr/bin/ld: unrecognized option '--export-dynamic;'
  /usr/bin/ld: use the --help option for usage information

--export-dynamic is a valid flag for ld so from what I can tell the
semicolon at the end is the problem.

Can you build HDF5 with the same options as in the Dorsal package file
or are you using other options?

 cmake ${CONFOPTS} -DCMAKE_INSTALL_PREFIX=${INSTALL_PATH} -DHDF5_ENABLE_PARALLEL=0 ..
 make ${MAKEOPTS} -j ${PROCS}

Both CONFOPTS and MAKEOPTS are empty.

--
Anders


On Sun, Oct 21, 2012 at 04:59:40PM +0100, Garth N. Wells wrote:
> 'parallel' should be enabled for HDF5.
>
> Garth
>
>
> ---------- Forwarded message ----------
> From:  <noreply@xxxxxxxxxxxxx>
> Date: Sun, Oct 21, 2012 at 4:45 PM
> Subject: [Branch ~dorsal-core/dorsal/main] Rev 749: Add package for HDF5
> To: Garth Wells <gnw20@xxxxxxxxx>
>
>
> ------------------------------------------------------------
> revno: 749
> committer: Anders Logg <logg@glaurung>
> branch nick: dorsal
> timestamp: Sun 2012-10-21 08:44:12 -0700
> message:
>   Add package for HDF5
> added:
>   FEniCS/packages/hdf5.package
> modified:
>   FEniCS/packages/mpfr.package
>   FEniCS/platforms/contributed/precise-hpc.platform
>   dorsal.sh
>
>

> === added file 'FEniCS/packages/hdf5.package'
> --- FEniCS/packages/hdf5.package	1970-01-01 00:00:00 +0000
> +++ FEniCS/packages/hdf5.package	2012-10-21 15:44:12 +0000
> @@ -0,0 +1,22 @@
> +NAME=hdf5-1.8.9
> +SOURCE=http://www.hdfgroup.org/ftp/HDF5/current/src/
> +PACKING=.tar.bz2
> +BUILDCHAIN=custom
> +
> +package_specific_build () {
> +
> +    # Download and apply patch
> +    if [ ! -e cmake_patch.txt ]
> +    then
> +        wget http://www.hdfgroup.org/ftp/HDF5/current/src/cmake_patch.txt
> +        patch -N -Z -p0 < cmake_patch.txt
> +    fi
> +
> +    # Configure and build
> +    mkdir -p dorsal_build_dir
> +    cd dorsal_build_dir
> +    cmake ${CONFOPTS} -DCMAKE_INSTALL_PREFIX=${INSTALL_PATH} ..
> +    make ${MAKEOPTS} -j ${PROCS}
> +    make install
> +
> +}
>
> === modified file 'FEniCS/packages/mpfr.package'
> --- FEniCS/packages/mpfr.package	2012-05-29 08:10:52 +0000
> +++ FEniCS/packages/mpfr.package	2012-10-21 15:44:12 +0000
> @@ -8,7 +8,7 @@
>      if [ ! -e patches ]
>      then
>  	wget http://www.mpfr.org/mpfr-2.2.0/patches
> -    fi
> +    fi
>      patch -N -Z -p1 < patches
>      ./configure --prefix=${INSTALL_PATH} --enable-shared=yes
>      make -j ${PROCS}
>
> === modified file 'FEniCS/platforms/contributed/precise-hpc.platform'
> --- FEniCS/platforms/contributed/precise-hpc.platform	2012-10-21 15:19:41 +0000
> +++ FEniCS/platforms/contributed/precise-hpc.platform	2012-10-21 15:44:12 +0000
> @@ -69,25 +69,28 @@
>  echo
>  read -p "Press any key to continue"
>
> -#- Most important is ATLAS for BLAS (if MKL is not available)
> -#   CHECK: added atlas.package
> -#- Build LAPACK to use ATLAS BLAS
> -#   CHECK: handled as part of ATLAS build
> -#- Build latest OpenMPI with support for threads turned on. MPICH2
> -#  works fine too
> -#   CHECK: using existing openmpi.package
> -#- Build Boost so that Boost.MPI uses the manually installed MPI
> -#   CHECK: using existing boost.package, did it detect MPI???
> -#- Install CGAL to use the manually installed Boost
> -#   CHECK: using existing cgal.package
> -#- Build latest METIS and ParMETIS (Ubuntu ParMETIS is broken, and it
> -#  pull in MPI)
> -#   CHECK: using existing vtk.package
> -#- Build VTK (so that the Ubuntu version doesn't pull in MPI)
> -#- Build HDF5 with parallel suppport  (so that the Ubuntu version
> -#  doesn't pull in MPI)
> -#- Build SCOTCH and PaStiX with support for 64 bit integers
> -#- Build PETSc, SLEPc and Trilinos, linking to the above libraries.
> +#(x) Most important is ATLAS for BLAS (if MKL is not available)
> +#    CHECK: added atlas.package
> +#(x) Build LAPACK to use ATLAS BLAS
> +#    CHECK: handled as part of ATLAS build
> +#(x) Build latest OpenMPI with support for threads turned on. MPICH2
> +#    works fine too
> +#    CHECK: using existing openmpi.package
> +#(x) Build Boost so that Boost.MPI uses the manually installed MPI
> +#    CHECK: using existing boost.package, did it detect MPI???
> +#(x) Install CGAL to use the manually installed Boost
> +#    CHECK: using existing cgal.package
> +#(x) Build latest METIS and ParMETIS (Ubuntu ParMETIS is broken, and it
> +#    pull in MPI)
> +#    CHECK: using existing parmetis.package
> +#(x) Build VTK (so that the Ubuntu version doesn't pull in MPI)
> +#    CHECK: using existing vtk.package
> +#(!) Build HDF5 with parallel suppport  (so that the Ubuntu version
> +#    doesn't pull in MPI)
> +#(x) CHECK: added hdf5.package
> +#(!) Build SCOTCH with support for 64 bit integers
> +#(!) Build PaStiX with support for 64 bit integers
> +#(!) Build PETSc, SLEPc and Trilinos, linking to the above libraries.
>
>  # Platform specific variables
>  default PETSC_ARCH=linux-gnu-cxx-opt
>
> === modified file 'dorsal.sh'
> --- dorsal.sh	2012-10-21 15:17:00 +0000
> +++ dorsal.sh	2012-10-21 15:44:12 +0000
> @@ -548,7 +548,7 @@
>
>      # Store timing
>      TOC="$(($(date +%s%N)-TIC))"
> -    TIMINGS="$TIMINGS"$"\n""$PACKAGE: "$"\t\t""$((TOC/1000000000)) s"
> +    TIMINGS="$TIMINGS"$"\n""$PACKAGE: ""$((TOC/1000000000)) s"
>
>  done
>
>

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