Hdf5 1.12.0

Basic information

Tested on (Requirements)

  • OS base: CentOS (x86_64) \(\boldsymbol{\ge}\) 6.6 (Rocks 6.2)
  • Dependencies:
    • Intel Parallel Studio XE Cluster Edition >= 17.0.1
    • zlib >= 1.2.11
    • szip >= 2.1

Installation

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

    cd $HOME/apps/hdf5/intel
wget https://hdf-wordpress-1.s3.amazonaws.com/wp-content/uploads/manual/HDF5/HDF5_1_12_0/source/hdf5-1.12.0.tar.gz
tar -xvf hdf5-1.8.19.tar

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

    cd hdf5-1.8.19
module load intel/intel-19.0.4 zlib/1.2.11_intel-19.0.4 szip/2.1.1_intel-19.0.4
./configure -prefix=/share/apps/hdf5/1.12/intel-19.0.4 --with-zlib=/share/apps/zlib/1.2.11/intel_19.0.4 --with-szlib=/share/apps/szip/2.1.1/intel_19.0.4 --enable-fortran --enable-cxx
make 2>&1 | tee hdf5-make.log
sudo mkdir -p /share/apps/hdf5/1.12/intel-19.0.4
make install 2>&1 | tee hdf5-make-install.log

Troubleshooting

If you have an erro during the configure that says Can not find ifort or another compiler then do the followin:

Please export these variables

export CC=icc
export F9X=ifort
export CXX=icpc

If you continue to have the error, burn the variables in the ./configure command

./configure CC=icc F9X=ifort CXX=icpc ...

If you continue to have an error, burn the path of the icc and ifort commands to the configure command

./configure CC=/path/to/icc F9X=/path/to/ifort CXX=/path/to/icpc ...

Module

#%Module1.0####################################################################
##
## module load hdf5/1.12_intel-19.0.4
##
## /share/apps/modules/hdf5/1.12_intel-19.0.4
## Written by Tomas Navarro & Santiago Alzate
##

proc ModulesHelp {} {
     global version modroot
     puts stderr "Sets the environment for using hdf5 1.12\
                  \nin the shared directory /share/apps/hdf5/1.12/intel-19.0.4\
                  \nbuilded with intel-17.0.1."
}

module-whatis "(Name________) hdf5"
module-whatis "(Version_____) 1.12"
module-whatis "(Compilers___) intel-19.0.4"
module-whatis "(System______) x86_64-redhat-linux"
module-whatis "(Libraries___) zlib, szip"

# for Tcl script use only
set         topdir        /share/apps/hdf5/1.12/intel-19.0.4
set         version       1.8.19
set         sys           x86_64-redhat-linux

conflict hdf5
module load intel
module load szip/2.1.1_intel_19.0.4
module load zlib/1.2.11_intel_19.0.4


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

Mode of use

$ module load hdf5/1.12_intel_19.0.4

Author

  • Tomas David Navarro
  • Santiago Alzate Cardona