Suggestions for (open source) software to get for your Mac





1. Get the (Apple) Developer Tools installed, esp. XCode, X11 (get updates as available): use your distribution DVDs to get started.


2. Install MacPorts, which you should be able to download from www.macports.org (remember 'sudo port -d selfupdate'); useful commands to update what you have are 'sudo port upgrade installed' and 'sudo port clean all'.


3. Sudo port install ImageMagick (the capitalization is important) for graphics conversions


4. Sudo port install gnuplot (for plotting)


5. Sudo port install geomview (for surface viewing)


6. To have fortran available, the current recommendation is to use gfortran which you can find by searching with "high performance computing mac os x" as keywords, which should take you to hpc.sourceforge.net. Follow the installation instructions carefully. Once installed you should be able to use gfortran in your Terminal window. There is also a gfortran that you can find with "r att gfortran" as keywords. This version is compatible with XCode.

6B. Note that some libraries such as lapack and blas are already available on the Macs: use "-framework veclib" to include them in compilations.


7. Get and install Aquamacs (nice text editor for programming, recognizes C, c++, fortran etc.)


8. Get and install TexShop (for LaTex); LaTeXiT is nice for equation setting (has a library) and to go with it, TeX FoG is a handy GUI for setting up equations without having to remember all the commands.


9. Get and install paraview (for 3D viewing), www.paraview.org


10. Get and install openmpi (for running parallel programs that use MPI). On Macs, it's often convenient to install the libraries under /Users/Shared/. Be careful about how you set up $PATH (generally from .bash_profile in your home directory): since Macs come with openmpi pre-installed (but lacking in Fortran support) you have to make sure that the path to your self-installed openmpi (with Fortran support!) precedes the standard system locations (such as /usr/local). Note also that openMP is built into the Macs.

Further notes: the following should work for most machines:
./configure --prefix=/Users/Shared/openmpi F77=gfortran F90=gfortran CC=gcc CXX=g++ --enable-static 2>&1 | tee openmpi-config.out
With this configure command, the following inserted into your .bash_profile should work: export PATH=/Users/Shared/openmpi/bin:${PATH}


11. Get and install TextWrangler (good for simple text editing, although I prefer to use Aquamacs)


12. Get and install the GMT cartographic graphics package (tricky - you may need help with their installation procedure which involves both a script and a parameter file); this is useful for plotting any type of spherical data.) These days, my advice is to install GMT via mac ports, because this will deal with the dependency on netcdf.


13. Get and install Cyberduck (best SFTP program so far, although Fugu also works)


14. This costs a few bucks but DefaultFolder is v handy for keeping track of directories


15. Install the FFTW library from www.fftw.org; we find that both 2.1.5 (for its MPI implementation) and the latest v3 are useful. On Macs, it's often convenient to install the libraries under /Users/Shared/.

Further notes: the following configure command should work on most machines (note that the path to the openmpi libraries etc needs to match what you used to install your version of openmpi, above):
./configure --prefix=/Users/Shared/fftw-3.3.2 !!!OR!!! 2.1.5 CC=gcc --enable-type-prefix --with-gcc --enable-mpi F77=gfortran F90=gfortran --with-g77-wrappers LDFLAGS="-L/usr/local/lib" CPPFLAGS="-I/usr/local/include" MPILIBS="-L/Users/Shared/openmpi/lib -lmpi" CPPFLAGS="-I/Users/Shared/openmpi/lib " 2>&1 | tee fftw-config.out
Then you may need to modify any Makefile that needs to use openmpi and/or FFTW to have the correct paths to your installations. Confused ... ?!


16. Get and install GraphicConverter (graphics manipulation, movies)


17. Download and install the statistics package R from http://cran.r-project.org/bin/macosx/ Useful extra packages include e1071 (probability plots) and ggplot2 (nicer plots than the standard).

Also check out these useful URLs for suggestions on how to get going with it:

http://www.cyclismo.org/tutorial/R/

http://www.harding.edu/fmccown/R/

http://www2.warwick.ac.uk/fac/sci/moac/degrees/modules/ch923/r_introduction/histograms_etc/

http://mercury.bio.uaf.edu/mercury/R/R.html#plotting


18. I have not used it much yet, but matplotlib (http://matplotlib.sourceforge.net/) looks like a nice plotting software. I was able to install it via Mac Ports, but be careful to make sure that you have a version that is compatible with your current version of python. This requires more care, because osx comes with python, but mac ports will install a separate version (in /opt etc) which matplotlib will expect to depend on. Note: 'port' installs in /opt/local etc.


19. Get and install inkscape ; 'sudo port install inkscape' will do it. Very useful as a tool for drawings, sketches etc.


Fink installs (typically) in /sw etc.


Gcc, gfortran, g77 install in /usr/local etc.




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