Hdf5 1.8.15 Patch 1

Basic information

Tested on (Requirements)

  • OS base: CentOS (x86_64) \(\boldsymbol{\ge}\) 6.6 (Rocks 6.2)
  • Dependencies:
    • mpich2 v3.2.1
    • Zlib v1.2.11
    • Szip v2.1.1

Installation

  1. Load required modules.

    module purge
module load gcc/5.5.0
module load mpich2/3.2.1_gcc-5.5.0
module load szip/2.1.1_gcc-5.5.0
module load zlib/1.2.11_gcc-5.5.0

  2. Configure the following environment variables that specify the compilers to use:

    $ export CC=mpicc
$ export CXX=mpic++
$ export FC=mpif90
$ export F90=mpif90

  3. Download the desired version of the software (Source code - tar.gz)

    cd /home/mgomezzul/apps/hdf5/src/
wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.15-patch1/src/hdf5-1.8.15-patch1.tar.gz
tar -xvf hdf5-1.8.15-patch1.tar.gz

  4. After unpacking HDF5, continue with the following steps for configuration and compilation:

    cd hdf5-1.8.15-patch1

./configure --prefix=/share/apps/hdf5/1.8.15-patch1/gcc-5.5.0_mpich2-3.2.1 --build=x86_64-redhat-linux --enable-fortran --enable-parallel --with-zlib=/share/apps/zlib/1.2.11/gcc-5.5.0 --with-szlib=/share/apps/szip/2.1.1/gcc-5.5.0

make -j 10 2>&1 | tee hdf5-make.log
make check 2>&1 | tee hdf5-make-check.log
sudo mkdir -p /share/apps/hdf5/1.8.15-patch1/gcc-5.5.0_mpich2-3.2.1
sudo chown -R mgomezzul.apolo /share/apps/hdf5/1.8.15-patch1/gcc-5.5.0_mpich2-3.2.1
make install 2>&1 | tee hdf5-make-install.log
sudo chown -R root.root /share/apps/hdf5/1.8.15-patch1/gcc-5.5.0_mpich2-3.2.1

Module

#%Module1.0####################################################################
##
## module load hdf5/1.8.15-patch1_gcc-5.5.0_mpich2-3.2.1
##
## /share/apps/modules/hdf5/1.8.15-patch1_gcc-5.5.0_mpich2-3.2.1
## Written by Mateo Gómez-Zuluaga
##

proc ModulesHelp {} {
    global version modroot
    puts stderr "Sets the environment for using HDF5-1.8.15-patch1\
                \nin the shared directory /share/apps/hdf5/1.8.15-patch1/gcc-5.5.0_mpich2-3.2.1\
                \nbuilded with gcc-5.5.0, mpich2-3.2.1, zlib-1.2.1, szip-2.1.1."
}

module-whatis "(Name________) hdf5"
module-whatis "(Version_____) 1.8.15-patch1"
module-whatis "(Compilers___) gcc-5.5.0_mpich2-3.2.1"
module-whatis "(System______) x86_64-redhat-linux"
module-whatis "(Libraries___) szip-2.1.1, zlib-1.2.11"

# for Tcl script use only
set         topdir        /share/apps/hdf5/1.8.15-patch1/gcc-5.5.0_mpich2-3.2.1
set         version       1.8.15-patch1
set         sys           x86_64-redhat-linux

conflict hdf5
module load mpich2/3.2.1_gcc-5.5.0
module load szip/2.1.1_gcc-5.5.0
module load zlib/1.2.11_gcc-5.5.0

setenv          HDF5                    $topdir

prepend-path    PATH                    $topdir/bin

prepend-path    LD_LIBRARY_PATH         $topdir/lib
prepend-path    LIBRARY_PATH            $topdir/lib
prepend-path    LD_RUN_PATH             $topdir/lib

prepend-path    C_INCLUDE_PATH          $topdir/include
prepend-path    CXX_INCLUDE_PATH        $topdir/include
prepend-path    CPLUS_INCLUDE_PATH      $topdir/include

Use

module load hdf5/1.8.15-patch1_gcc-5.5.0_mpich2-3.2.1

Author

  • Andrés Felipe Zapata Palacio