Install netCDF-C#

  1. Download netCDF-C from the following website https://www.unidata.ucar.edu/downloads/netcdf/index.jsp

wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-c-4.7.0.tar.gz

  1. Untar the file

tar -xzvf netcdf-c-4.7.0.tar.gz

  1. Change directories into the package

cd netcdf-c-4.7.0

  1. Verify that no modules are currently loaded using module commands.

module list

  1. See what modules are available on your compute server use the command:

module avail

  1. Load module environment for a compiler (Intel|GCC|PGI) and mpi package corresponding to that compiler (e.g. openmpi).

module load intel18.2
module load openmpi_3.1.4/intel_18.2

  1. Review the installation instructions for netcdf-c-4.7.0 for building netCDF

more INSTALL.md

  1. Create a target installation directory that includes the loaded module environment name.

mkdir $cwd/netcdf-c-4.7.0-intel18.2

  1. Run the configure –help command to see what settings can be used for the build.

./configure --help

  1. Set the Compiler environment variables

First find the path to the CC compiler on your system using the which command

which icc

Next, replace the following path in the setenv command below to use the path to your CC compiler

setenv CC /urs/local/apps/intel/18.2/bin/icc

Find the path to the Fortran compiler on your ssystem using the which command

which ifort

Next, replace the following path in the setenv command below to use the path to the Fortran compiler on your system

setenv FC /urs/local/apps/intel/18.2/bin/ifort

Find the path to the CXX compiler on your system using the which command

which icpc

Next, replace the following path in the setenv command below to use the path to the CXX compiler on your system:

setenv CXX /urs/local/apps/intel/18.2/bin/icpc

  1. Run the configure command

./configure --prefix=$cwd/../netcdf --disable-dap

Building netCDF without the compression capabilities of netCDF4 can be done using the command

./configure --prefix=$cwd/../netcdf --disable-netcdf-4 --disable-dap

This simpler installation can work for some applications, but the CMAQ ecosystem increasingly includes netCDF4 compression. For example, the cracmm1_aq 2018 benchmark and the MEGAN 3.2 preprocessor both require netCDF4. The error “Attempt to use feature that was not turned on when netCDF was built” suggests that your workflow requires netCDF4.

  1. Check that the configure command worked correctly

make check install |& tee make.install.log.txt

  1. Verify that the following message is obtained at the end of your make.install.log.txt file

| Congratulations! You have successfully installed netCDF!    |

Install netCDF-Fortran#

  1. Download netCDF-Fortran from the following website https://www.unidata.ucar.edu/downloads/netcdf/index.jsp

wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-4.4.5.tar.gz

  1. Untar the tar.gz file

tar -xzvf netcdf-fortran-4.4.5.tar.gz

  1. Change directories to netcdf-fortran-4.4.5

cd netcdf-fortran-4.4.5

  1. Make an install directory that matches the name of your loaded module environment

mkdir $cwd/netcdf-fortran-4.4.5-intel18.2

  1. Review the installation document http://www.unidata.ucar.edu/software/netcdf/docs/building_netcdf_fortran.html

  2. Set the environment variable NCDIR

setenv NCDIR $cwd/netcdf-c-4.7.0-intel18.2

  1. Set the CC environment variable to use the intel compilers

First find the path to the CC compiler on your system using the which command

which icc

Next, replace the following path in the setenv command below to use the path to your CC compiler

setenv CC /urs/local/apps/intel/18.2/bin/icc

Find the path to the Fortran compiler on your ssystem using the which command

which ifort

Next, replace the following path in the setenv command below to use the path to the Fortran compiler on your system

setenv FC /urs/local/apps/intel/18.2/bin/ifort

Find the path to the CXX compiler on your system using the which command

which icpc

Next, replace the following path in the setenv command below to use the path to the CXX compiler on your system:

setenv CXX /urs/local/apps/intel/18.2/bin/icpc

  1. Set your LD_LIBRARY_PATH to include the netcdf-C library path for netCDF build

setenv NCDIR /home/netcdf-c-4.7.0-intel18.2
setenv LD_LIBRARY_PATH ${NCDIR}/lib:${LD_LIBRARY_PATH}

  1. Check your LD_LIBRARY_PATH

echo $LD_LIBRARY_PATH

  1. Set the install directory for netCDF fortran

setenv NFDIR /home/netcdf-fortran-4.4.5-intel18.2
setenv CPPFLAGS -I${NCDIR}/include
setenv LDFLAGS -L${NCDIR}/lib

  1. check your LD_LIBRARY_PATH environment variable

echo $LD_LIBRARY_PATH

  1. Run the configure command

./configure --prefix=${NFDIR}

  1. Run the make check command

make check |& tee make.check.log.txt

Output if successful:

Testsuite summary for netCDF-Fortran 4.4.5
==========================================
# TOTAL: 6
# PASS:  6

  1. Run the make install command

make install |& tee ./make.install.log.txt

Output successful if you see:

Libraries have been installed in:
   
   /home/netcdf-fortran-4.4.5-intel18.2

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the '-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the 'LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the 'LD_RUN_PATH' environment variable
     during linking
   - use the '-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to '/etc/ld.so.conf'

  1. set your LD_LIBRARY_PATH to include the netcdf-Fortran library path for netCDF build

setenv NFDIR /home/netcdf-fortran-4.4.5-intel18.2
setenv LD_LIBRARY_PATH ${NFDIR}/lib:${LD_LIBRARY_PATH}

(may need to add the NCDIR and NFDIR to .cshrc)

Install I/O API#

Note The complete I/O API installation guide can be found at either of the following:

https://www.cmascenter.org/ioapi/documentation/all_versions/html/AVAIL.html

or

https://cjcoats.github.io/ioapi/AVAIL.html

  1. Download I/O API

git clone https://github.com/cjcoats/ioapi-3.2
cd ioapi-3.2         ! change directory to ioapi-3.2
git checkout -b 20200828   ! change branch to 20200828 for a tagged release version

  1. Change the BIN setting on line 133 of the Makefile to include the loaded module name

cd ioapi gedit Makefile

BIN        = Linux2_x86_64ifort_openmpi_3.1.4_intel18.2

  1. Change the NCFLIBS setting on line 141 of the Makefile to be

NCFLIBS    = -lnetcdff -lnetcdf

  1. Copy an existing Makeinclude file to have this BIN name at the end

cd ioapi
cp Makeinclude.Linux2_x86_64ifort Makeinclude.Linux2_x86_64ifort_openmpi_3.1.4_intel18.2

  1. Edit the Makeinclude file, lines 27 and 28 to comment out the openmmp flag

OMPFLAGS  = # -qopenmp
OMPLIBS   = # -qopenmp

  1. Set the environment variable BIN

setenv BIN Linux2_x86_64ifort_openmpi_3.1.4_intel18.2

  1. Create a BIN directory under the ioapi-3.2 directory

cd ..
mkdir $BIN

  1. Create a link to this $BIN directory for WRF-CMAQ

ln -s Linux2_x86_64ifort_openmpi_3.1.4_intel18.2 Linux2_x86_64ifort

  1. Link the netcdf-C and netcdf-Fortran library in the $BIN directory

cd $BIN
ln -s /home/netcdf-c-4.7.0-intel18.2/libnetcdff.a
ln -s /home/netcdf-fortran-4.4.5-intel18.2/libnetcdf.a

  1. Run the make command, specifying the location of the ioapi-3.2 directory path to compile and link the ioapi library

cd ioapi
make 'HOME=[your_install_path]/LIBRARIES' |& tee make.log

  1. Change directories to the $BIN dir and verify that both the libioapi.a and the m3tools were successfully built

cd $BIN
ls -lrt libioapi.a
ls -rlt m3xtract

  1. If you need to do a make clean, to rebuild the I/O API Library, specify the HOME directory at the command line as follows

cd ../ioapi
make 'HOME=[your_install_path]/LIBRARIES' clean

  1. After successfull completion of this tutorial, the user is now ready to proceed to the CMAQ Installation & Benchmarking Tutorial.