ParallelNetCDF 1.6.1

Table of Contents

• ParallelNetCDF 1.6.1
  • Basic information
  • Tested on (Requirements)
  • Installation
  • Module
  • Use
  • Resources
  • Author

Basic information

• Official Website: http://cucis.ece.northwestern.edu/projects/PnetCDF/
• License: Copyright (c) 2003 Northwertern University and Argonne National Laboratory. All rights reserved.
• Installed on: Apolo II and Cronos
• Installation date: 13/02/2018

Tested on (Requirements)

• OS base: CentOS (x86_64) \(\boldsymbol{\ge}\) 6.6 (Rocks 6.2)

• Dependencies:

  • GNU GCC >= 5.5.0
  • MPICH2 >= 3.2.1

Installation

1. Load required modules.

   module purge
   module load gcc/5.5.0
   module load mpich2/3.2.1_gcc-5.5.0
   

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

   $ export F77=mpif90
   $ export CFLAGS='-O2 -fPIC'
   $ export CXXFLAGS='-O2 -fPIC'
   $ export FFLAGS='-fPIC'
   $ export FCFLAGS='-fPIC'
   $ export FLDFLAGS='-fPIC'
   $ export F90LDFLAGS='-fPIC'
   $ export LDFLAGS='-fPIC'
   

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

   cd /home/mgomezzul/apps/pnetcdf/src/
   wget http://cucis.ece.northwestern.edu/projects/PnetCDF/Release/parallel-netcdf-1.6.1.tar.gz
   tar -xvf parallel-netcdf-1.6.1.tar.gz
   

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

   cd parallel-netcdf-1.6.1
   
   ./configure --prefix=/share/apps/pnetcdf/1.6.1/gcc-5.5.0_mpich2-3.2.1 --build=x86_64-redhat-linux --enable-fortran --enable-largefile --with-mpi=/share/apps/mpich2/3.2.1/gcc-5.5.0 2&1 | tee pnetcdf-conf.log
   make -j 10 2>&1 | tee pnetcdf-make.log
   make check 2>&1 | tee pnetcdf-make-check.log
   sudo mkdir -p /share/apps/pnetcdf/1.6.1/gcc-5.5.0_mpich2-3.2.1
   sudo chown -R mgomezzul.apolo /share/apps/pnetcdf/1.6.1/gcc-5.5.0_mpich2-3.2.1
   make install 2>&1 | tee pnetcdf-make-install.log
   sudo chown -R root.root /share/apps/pnetcdf/1.6.1/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 pnetcdf/1.6.1_gcc-5.5.0_mpich2-3.2.1
##
## /share/apps/modules/pnetcdf/1.6.1_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 pnetcdf-1.6.1\
                \nin the shared directory \
                \n/share/apps/pnetcdf/1.6.1/gcc-5.5.0_mpich2-3.2.1\
                \nbuilded with gcc-5.5.0 and mpich2-3.2.1."
}

module-whatis "(Name________) pnetcdf"
module-whatis "(Version_____) 1.6.1"
module-whatis "(Compilers___) gcc-5.5.0_mpich2-3.2.1"
module-whatis "(System______) x86_64-redhat-linux"
module-whatis "(Libraries___) "

# for Tcl script use only
set         topdir        /share/apps/pnetcdf/1.6.1/gcc-5.5.0_mpich2-3.2.1
set         version       1.6.1
set         sys           x86_64-redhat-linux

conflict pnetcdf
module load mpich2/3.2.1_gcc-5.5.0

setenv          PNET                    $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 pnetcdf/1.6.1_gcc-5.5.0_mpich2-3.2.1

Resources

• http://cucis.ece.northwestern.edu/projects/PnetCDF/download.html

Author

• Andrés Felipe Zapata Palacio