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Add singularity container definition file #222

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Add singularity container definition file #222

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90 changes: 90 additions & 0 deletions singularity_cgenie_muffin.def
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Bootstrap: docker
From: centos:7

%post
yum install -y epel-release
yum install -y net-tools
yum install -y wget
yum install -y libcurl-devel
yum install -y make
yum install -y which
yum groupinstall -y 'Development Tools'
yum install -y centos-release-scl
yum install -y devtoolset-8-gcc*
yum install -y zlib-devel
yum install -y hdf5-devel
yum install -y libxslt

# enable gcc-8
scl enable devtoolset-8 bash

# export envrionmental variables so they can be used for netcdf and cgenie muffin builds
export LD_LIBRARY_PATH=/opt/rh/devtoolset-8/root/usr/lib/gcc/x86_64-redhat-linux/8:$LD_LIBRARY_PATH
export PATH=/opt/rh/devtoolset-8/root/usr/bin:$PATH
export CXX=/opt/rh/devtoolset-8/root/usr/bin/g++
export CC=/opt/rh/devtoolset-8/root/usr/bin/gcc
export FC=/opt/rh/devtoolset-8/root/usr/bin/gfortran
export F77=/opt/rh/devtoolset-8/root/usr/bin/gfortran

# grab netcdf-c and put it in /tmp/netcdf-c
cd /tmp
mkdir netcdf-c
cd netcdf-c
wget https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.8.0.tar.gz
tar xzvf v4.8.0.tar.gz
cd netcdf-c-4.8.0

# configure and build netcdf-c
CFLAGS="$CFLAGS -I/usr/include" \
LDFLAGS="-L/usr/lib64" \
./configure --prefix=/opt/netcdf --disable-netcdf-4 --disable-dap-remote-tests
make check
make install
rm -rf /tmp/netcdf-c

export LD_LIBRARY_PATH=/opt/netcdf/lib:$LD_LIBRARY_PATH

# grab netcdf-cxx and put it in /tmp/netcdf-cxx
cd /tmp
mkdir netcdf-cxx
cd netcdf-cxx
wget https://downloads.unidata.ucar.edu/netcdf-cxx/4.2/netcdf-cxx-4.2.tar.gz
tar xzvf netcdf-cxx-4.2.tar.gz
cd netcdf-cxx-4.2

# configure and build netcdf-cxx
CPPFLAGS="$CPPFLAGS -I/usr/include -I/opt/netcdf/include" LDFLAGS="-L/usr/lib64 -L/opt/netcdf/lib" ./configure --prefix=/opt/netcdf
make check
make install
rm -rf /tmp/netcdf-cxx

# grab netcdf-fortran and put it in /tmp/netcdf-fortran
cd /tmp
mkdir netcdf-fortran
cd netcdf-fortran
wget https://downloads.unidata.ucar.edu/netcdf-fortran/4.5.3/netcdf-fortran-4.5.3.tar.gz
tar xzvf netcdf-fortran-4.5.3.tar.gz
cd netcdf-fortran-4.5.3

# configure and build netcdf-fortran
CPPFLAGS="$CPPFLAGS -I/usr/include -I/opt/netcdf/include" FFLAGS="-I/usr/include -I/opt/netcdf/include" LDFLAGS="-L/usr/lib64 -L/opt/netcdf/lib" ./configure --prefix=/opt/netcdf
make check
make install
rm -rf /tmp/netcdf-fortran

%environment
# edit command prompt so its short and shows you in a container
export PS1="Singularity > "

# add devtoolset to PATH and LD_LIBRARY_PATH
export PATH=/opt/rh/devtoolset-8/root/usr/bin:$PATH
export LD_LIBRARY_PATH=/opt/rh/devtoolset-8/root/usr/lib/gcc/x86_64-redhat-linux/8:$LD_LIBRARY_PATH

# add compilers as global variables so they can be used to compile cgenie code
export CXX=/opt/rh/devtoolset-8/root/usr/bin/g++
export CC=/opt/rh/devtoolset-8/root/usr/bin/gcc
export FC=/opt/rh/devtoolset-8/root/usr/bin/gfortran
export F77=/opt/rh/devtoolset-8/root/usr/bin/gfortran

# add netcdf to LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/opt/netcdf/lib:$LD_LIBRARY_PATH