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So I am writing a script to build and install Netcdf, but when I source it, it seems like some of the lines just are not running or are being skipped and I am unsure why. When I run the code line by line manually however, it works fine. Here is the script:

module purge
module load gnu/5.1.0
module load mvapich2/2.1
module load hdf5/1.8.9

export SRC_DIR=/usr/local/src/netcdf/netcdf-4.3.3.1
export BUILD_DIR=$SRC_DIR/build-gnu
export INSTALL_DIR=/usr/local/netcdf/gnu/5.1/mvapich2/2.1/4.3.3.1/

mkdir -p $INSTALL_DIR
mkdir -p $BUILD_DIR
cd $BUILD_DIR

CC=mpicc CXX=mpicxx FC=mpif90 CFLAGS='-DpgiFortran -fPIC' CPPFLAGS=-I$HDF5_HOME/include \
 FCFLAGS='-DpgiFortran -fPIC' LDFLAGS=-L$HDF5_HOME/lib \
../configure --prefix=$INSTALL_DIR --enable-shared --with-hdf5=$HDF5_HOME

make
make check
make install
make clean

It seems to just skip straight to the configure command. I run the script by sourcing it using the following command:

. build-netcdf-gnu-5.1 |& tee build-netcdf-gnu-5.1.log

but when I run it none of the modules have been loaded and I am still in the directory where I started the script when I should have changed to the build directory. The weird thing is if i copy and paste the code line by line it works fine. Why isn't this script running as expected? Is there anything simple I am just overlooking? thanks for any help, it is greatly appreciated.

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