Installing & Running RAxML on OS X 10.4
by James Munro
These are simply some guidelines that might be helpful. Alexis' manual for the installation and running of RAxML is very thorough and what follows is not meant to supplant his manual, rather, think of it as an "Idiots Gude"...
The author assumes no responsibility - whatsoever. Not all steps or suggested software may be necessary to run RAxML; however, this is what has worked for me. There is no implied warranty and no guarantee.
Xcode Development Tools
- Make sure you have Xcode Development Tools installed in your root directory.
- The folder ‘Developer' should be listed in your root directory when you double-click on your hard drive icon.
- Xcode is installed from the CD that came with your original software or it can be obtained from Apple.
Is Terminal Running tcsh or bash?
- Open a Terminal shell. (Applications > Utilities > Terminal).
- In the top frame, it should read ‘Terminal - bash - (window size in pixels)'.
If you have a clean installation of OS X 10.4, you should be fine and may proceed to Step #3. If you have upgraded the OS from 10.1, 10.2 or even in some cases 10.3, you may be running tcsh and not bash.
If you have a tcsh shell - proceed as follows.
- You must have administrative privileges to the computer. You need the password.
- Open NetInfo Manager (Applications > Utilities > NetInfo Manager).
- The window will have 4 panes; 3 across the top and one on the bottom.
- In the middle, top pane, select ‘users'.
- In the right, top pane, select the main users folder.
- The information that appears in the lower window will include ‘shell'.
- Click on the padlock icon and enter the administrative password.
- Select ‘shell' and edit /bin/tcsh to bin/bash.
- Select the lock and exit NetInfo Manager.
Creating the /usr/local/bin directory in the root directory
- Open a Terminal shell.
- Type: mkdir /usr
- Type: mkdir /usr/local
- Type: mkdir /usr/local/bin
- NB: you may need to use the command ‘sudo' - (superuser do). This allows you to run programs in the guise of another user (i.e. the system's superuser). If you are denied permission at any of the above steps, add ‘sudo' before ‘mkdir' and type in the administrative password when prompted.
Tip: While you have Terminal open, you might as well tweak it:
- Terminal > Window Settings > Buffer = unlimited scrollback.
- Terminal > Window Settings > Color = green on black (A personal preference. The old style green on black color scheme makes me feel like a 'real' hacker... Ha-ha).
Installing g77 binaries
- Open your web browser and be sure that in your preferences, you do NOT have ‘Open Safe Files' selected. If you do, de-select this option, completely quit the browser and open it again.
- Download the file ‘g77v3.4-bin.tar.gz' from HPC Mac OS X.
- NB: if you download files to somewhere other than your desktop, you will have to modify the following Terminal commands.
- Open a Terminal shell.
- Type: cd Desktop
- Type: gunzip g77v3.4-bin.tar.gz
- Type: sudo tar -xvf g77v3.4-bin.tar -C /
Create a .bash_profile & add the /usr/local/bin directory to your path
- Open Vi Editor to create a .bash_profile.
- Type: vi .bash_profile
- Type i for insert.
- Type the following - exactly as it is or cut 'n' paste!
if [ -f ~/.bashrc ]; then
- Hit the escape key.
- Type: a colon :
- Type: wq
- Hit the enter key.
- Completely quit Terminal (not just close) and restart a new shell.
- Type: echo $PATH
- The directory /usr/local/bin should be listed. If it is not, you screwed up your .bash_profile and need to start from the beginning - I did tell you to type it exactly as shown... (Ha-ha).
- Make sure that you have the latest version of Stuffit Expander. It is usually found in your Applications folder, but may be in Applications > Utilities.
- Alternatively, you can use Apple's native BOMArchiveHelper.app. Just ‘control-click' and ‘open with'.
Installing the standard serial/sequential version of RAxML
- Download the latest version of RAxML-VI-HPC.
- Download the manual (AWESOME manual!) .
- Use StuffIt or BOMArchiveHelper to unpack the archive RAxML-7.0.4.tar.bz2 onto your Desktop. The folder ‘RAxML-7.0.4' should appear on your Desktop.
- At this point, you may want to note tip #2 below...
- Open a Terminal shell.
- Type: cd Desktop/RAxML-7.0.4
- Type: make -f Makefile.gcc
- Drag the unpacked archive RAxML-7.0.4 from your Desktop to Applications.
- Open Terminal.
- Type: cd /Applications/RAxML-7.0.4
- Type: sudo cp raxmlHPC /usr/local/bin/raxml (personally, it is easier to type ‘raxml' than raxmlHPC when calling the program so here you re-name it)
- Completely quit Terminal, (not just close), and restart a new shell.
- cd to the location of the RAxML file you want to execute. (A folder on the Desktop that contains your PHYLIP formatted dataset works just fine).
- Type: raxml - starts the application.
- From this point on, you should refer to the manual...
1). To convert RAxML tree files to PAUP readable Nexus files, try using Matt Yoder's PERL script phase2nexus, available at jRNA Miscellaneous Downloads
2). Mike Robeson shared this tip for optimizing the Makefile.gcc for the Mac G5 PPC Intel processors. Mike noted that he gets get anywhere form 10 - 20 % speed improvements using the following compiling flags:
CFLAGS = -O3 -fast -ftree-vectorize #.... other flags
1). Prior to compiling RAxML (i.e. typing make...), open the Makefile.gcc in a text editor such as TextWrangler.
2). Add a "#" to the line that reads "CFLAGS = -O3 -fomit-frame-pointer -funroll-loops".
3). It should now look like this...
#CFLAGS = -O3 -fomit-frame-pointer -funroll-loops
4). Below that line, add the following
CFLAGS = -O3 -fast -ftree-vectorize -fomit-frame-pointer -funroll-loops
5). Save the file.
6. Proceed with the instructions above, starting from where you left off.
Mike also points out that the MrBayes MakeFile can be similarly optimized.
Check out Mike's web page at Bioinformatics Software for OSX