NetCDF 4.3.3

Basic information

Tested on (Requirements)

  • OS base: CentOS (x86_64) \(\boldsymbol{\ge}\) 6.6 (Rocks 6.2)
  • Dependencies:
    • mpich2 v3.2.1
    • HDF5 v1.8.15-patch-1
    • PNetCDF/1.6.1

Installation

  1. Load required modules.

    module load gcc/5.5.0
module load mpich2/3.2.1_gcc-5.5.0
module load hdf5/1.8.15-patch1_gcc-5.5.0_mpich2-3.2.1
module load pnetcdf/1.6.1_gcc-5.5.0_mpich2-3.2.1

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

    export CC=mpicc
export CXX=mpicxx
export FC=mpif90
export F77=mpif90
export F90=mpif90
export CPPFLAGS="-I$HDF5/include -I$PNET/include"
export CFLAGS="-I$HDF5/include -I$PNET/include"
export CXXFLAGS="-I$HDF5/include -I$PNET/include"
export FCFLAGS="-I$HDF5/include -I$PNET/include"
export FFLAGS="-I$HDF5/include -I$PNET/include"
export LDFLAGS="-L$HDF5/lib -L$PNET/lib"
HDF5=/
PNET=/

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

    cd /home/mgomezzul/apps/netcdf/src/
wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.3.tar.gz
tar -xvf netcdf-4.3.3.tar.gz

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

    cd netcdf-4.3.3

./configure --prefix=/share/apps/netcdf/4.3.3/gcc-5.5.0_mpich2-3.2.1 --build=x86_64-redhat-linux --enable-large-file-tests --enable-parallel-tests --enable-largefile

make -j 10 2>&1 | tee netcdf-make.log
make check 2>&1 | tee netcdf-make-check.log
sudo mkdir -p /share/apps/netcdf/4.3.3/gcc-5.5.0_mpich2-3.2.1
sudo chown -R mgomezzul.apolo /share/apps/netcdf/4.3.3/gcc-5.5.0_mpich2-3.2.1
make install 2>&1 | tee netcdf-make-install.log
sudo chown -R root.root /share/apps/netcdf/4.3.3/gcc-5.5.0_mpich2-3.2.1

  5. Generate the module with the following environment variable:

    setenv          PNET                    $topdir
sudo moduleGenerator

Module

#%Module1.0####################################################################
##
## module load netcdf/4.3.3_gcc-5.5.0_mpich2-3.2.1
##
## /share/apps/modules/netcdf/4.3.3_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 netcdf-4.3.3\
                \nin the shared directory /share/apps/netcdf/4.3.3/gcc-5.5.0_mpich2-3.2.1\
                \nbuilded with gcc-5.5.0, mpich2-3.2.1, hdf5-1.8.15-patch1, pnetcdf/1.6.1."
}

module-whatis "(Name________) netcdf"
module-whatis "(Version_____) 4.3.3"
module-whatis "(Compilers___) gcc-5.5.0, mpich2-3.2.1"
module-whatis "(System______) x86_64-redhat-linux"
module-whatis "(Libraries___) zlib-1.2.11, szip-2.1.1, hdf5-1.8.15-patch1, pnetcdf-1.6.1"

# for Tcl script use only
set         topdir        /share/apps/netcdf/4.3.3/gcc-5.5.0_mpich2-3.2.1
set         version       4.3.3
set         sys           x86_64-redhat-linux

conflict netcdf
module load mpich2/3.2.1_gcc-5.5.0
module load hdf5/1.8.15-patch1_gcc-5.5.0_mpich2-3.2.1
module load pnetcdf/1.6.1_gcc-5.5.0_mpich2-3.2.1

setenv          NETCDF                  $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

prepend-path    PKG_CONFIG_PATH         $topdir/lib/pkgconfig

prepend-path    MANPATH                 $topdir/share/man

Use

module load netcdf/4.3.3_gcc-5.5.0_mpich2-3.2.1

Author

  • Andrés Felipe Zapata Palacio