README_macos.md

Installation (that has worked with OSX 10.10)

Installation of the required compilers

1. Install MacPorts (port):

   • follow the instructions on the MacPorts installation page.
   • Check that /opt/local/bin and /opt/local/sbin are defined in PATH (echo $PATH in a new command window).

2. Install gcc48 (or more recent versions) with MacPorts:

   sudo port search gcc
   sudo port install gcc48
   sudo port select --list gcc
   sudo port select --set gcc mp-gcc48
   

3. Install openmpi-gcc48 (or a version compatible with your gcc) with MacPorts:

   sudo port search openmp
   sudo port install openmpi-gcc48
   sudo port select --list mpi
   sudo port select --set mpi openmpi-gcc48-fortran
   sudo ln -s /opt/local/bin/mpicxx /opt/local/bin/mpic++
   

Installation of the required libraries

1. Install the Boost C++ libraries

   1. Download version 1.55 of boost on http://www.boost.org (It is better to restart from here if you had an upgrade of your os).
   2. copy bconfigure.sh and binstall.sh from /nextsim/scripts/boost/ to your boost directory.
   3. Add the line using mpi ; at the end of the file tools/build/v2/user-config.jam (This file could also be copied in your home directory for boost from the version 1.56).
   4. type the command unset BOOST_DIR
   5. check if bconfigure.sh corresponds to your architecture.
   6. From boost directory, type: ./bconfigure.sh
   7. From boost directory, type: ./binstall.sh (sudo password is required during the process).

2. Install NetCDF

   1. instal hdf5 via macport: sudo port install hdf5
   2. download latest stable C version of netcdf on the NetCDF dowloads page and unzip it.
   3. copy configure_c.sh from /nextsim/scripts/netcdf
   4. From netcdf directory, type: ./configure_c.sh then make make check and finally sudo make install
   5. download latest stable C++ (cxx) version of netcdf on the NetCDF dowloads page and unzip it.
   6. copy configure_cxx.sh from /nextsim/scripts/netcdf
   7. From netcdf-cxx directory, type: ./configure_cxx.sh then make make check and finally sudo make install

3. Install Gmsh from source

   1. Download the source code from the Gmsh website.
   2. In the gmsh directory do

mkdir lib
cd lib
cmake -DDEFAULT=0 -DENABLE_BUILD_LIB=1 ..
make -j 32 lib
sudo make install/fast

4. Set the PATH environment variable correctly
   1. Add these lines to your .bash_profile for nextSIM in C++:

export NEXTSIMDIR=$HOME/Developer/nextsim/
export GMSH_DIR=/usr/local/

export NETCDF_DIR=/opt/local/netcdf-cxx

export BOOST_DIR=/opt/local/boost

export DYLD_LIBRARY_PATH="/opt/local/boost/lib"
export DYLD_LIBRARY_PATH=NEXTSIMDIR/lib:$DYLD_LIBRARY_PATH

Compile neXtSIM itself

1. Open a new command window

2. Either modify the Makefile to have the right link to openmpi or do the following:

sudo rm -rf /opt/local/include/openmpi-mp
sudo ln -sf /opt/local/include/openmpi-gcc48 /opt/local/include/openmpi-mp
sudo rm -rf /opt/local/lib/openmpi-mp
sudo ln -sf /opt/local/lib/openmpi-gcc48 /opt/local/lib/openmpi-mp

3. Type make in nextsim
4. For the model application (run nextsim)
5. go to nextsim/model
6. Type make

Run neXtSIM

1. type bin/nextsim.exec from the nextsim/model directory.

Create documentation

Run Doxygen with docker

cd [path to nextsim source]
docker run --rm -v $(pwd):/data -it hrektts/doxygen doxygen

This automatically uses the file Doxyfile (made originally with the doxygen gui) in the nextsim directory. Outputs go into a new folder nextsim-doc:

ls nextsim-doc/
html  latex  man  rtf  xml

You can then see the results with (eg.) firefox nextsim-doc/html/index.html &

Install Doxygen locally

• Ubuntu: sudo apt-get install doxygen graphviz doxygen-gui
• Mac OSX:
  • GUI: download .dmg image from docker website and open it to install
  • command line: sudo port install doxygen graphviz

Run locally

• Ubuntu
  • GUI: doxywizard &
  • command line:

  cp Doxyfile Doxyfile-edited.cfg
  [edit new file and change entries for INPUT and OUTPUT_DIRECTORY]
  doxygen Doxyfile-edited.cfg
  

• Mac OSX:
  • GUI: open Doxygen.app file
  • command line: same as ubuntu
  • Note that Doxygen is not fully functional on Mac OSX (graphviz not working correctly) but GUI could still be used to create a config file to run with docker