While writing news articles, I had to look up HTML symbols for modifier keys. Here is the full list.
| Character | HTML code | Description |
|---|---|---|
| ↦ | ↦ | Tab (mapsto symbol) |
| ^ | ^ | Control |
| ⌘ | ⌘ | Command (Apple) |
| ⇑ | ⇑ | Shift |
| ↵ | ↵ | Enter (carriage return arrow) |
| Character | HTML code | Description |
|---|---|---|
| & | & | Ampersand |
| > | > | Greater than | < | < | Less than |
All other keyboard symbols should render as entered.
The following instructions are for those trying to install ROOT on OS X 10.7 Lion with python bindings (PyROOT) and numpy, scipy, and matplotlib. For example, in a python script, one can import (a sample from one of my scripts)…
# Root imports from ROOT import TH1F, TFile, THStack, TF1, TCanvas, TLegend from ROOT import kRed, kBlue, kWhite from ROOT import gStyle, gPad # SciPy and Numpy import scipy as sp import numpy as np import matplotlib as plt
Altogether, it’s a highly flexible environment for scientific computing.
Note: The below instructions are only valid if you have XCode installed (see my post on Mac Setup, Part 1)
We will take the following route:
It is assumed that you have XCode installed. If not, please see my earlier post.
One of the trickiest parts of the installation was finding a compatable version of python. There were three issues.
I wanted to compile and install a 64 bit ROOT installation. The 2.7 Python installer from Python.org installs both 32 and 64 bit versions of Python (e.g. python2.7 and python2.7-32). One can compile ROOT with Python support using the standard Python.org 2.7 distribution with minimal effort. Everything will work well, but you will not have access to numpy, scipy, and matplotlib. These packages must be installed separately.
Most of my problems arose because of scipy and numpy. Building numpy from source requires Python 2.4, 2.5, or 2.6, but not 2.7. The package installer for 2.7 is only for 32 bit Python. I was not able to find a compatible version of Scipy and Numpy from the Scipy.org web site that worked with my 64 bit tandem install of python 2.7 and ROOT.
Luckily, the Enthought Python Distribution (EPD) provided a 64bit, Python 2.7 framework install that included numpy and scipy. The EPD 64bit distribution is, however, only free for academics. EPD Free (free for anyone) is so far 32 bit only for Apple and Windows platforms.
The 64 bit EPD Framework install is located at /Library/Frameworks/EPD64.framework/Versions/7.1/. Both 32 and 64 bit EPD distributions can be concurrently installed. The 32 bit version is located at /Library/Frameworks/Python.framework/Versions/7.1/.
Root requires a fortran compiler. This is neither provided by a stock install of 10.7 nor XCode. There are three sources for free Fortran compilers online, and they are all uncompatable. Install only one version. I have used the version provided by AT&T's R research page. Follow their instructions.
Create a directory to store the ROOT installation binaries, libraries, and other files.
sudo mkdir /usr/local/root
Download the latest ROOT source code from their download page. For Lion, the latest development version, as of early September 2011, was the 5.30/01 patch. The professional version 5.30/00 compiled with problems. Recently, the production (Pro) version has been updated to 5.30/02 and I now recommend that version.
After your download, unpack the files in your ROOT directory, i.e.
gzip -dc root_<version>.source.tar.gz | tar -xf -
Two types of installation are possible:
I chose the location independent version. Before configuring your installation through ./configure, set your environment variables. Because we are compiling with python support, you must point to the location of the python version you want married to ROOT. For me, this was the 64 bit Enthought distribution located at /Library/Frameworks/EPD64.framework/Versions/Current/.
The required environment variables needed for ./configure for a location independent install with python support are listed below. Please keep in mind that these are specific to my installation of Python and the location I wanted my ROOT distribution to reside.
export ROOTSYS=/usr/local/root/5.30.01 export PYTHONDIR=/Library/Frameworks/EPD64.framework/Versions/Current/
From your ROOT folder, run the configuration script for your OS X 64 bit system.
./configure macosx64
Python support is included by default. After a successful configuration, compile through make
sudo make -j4
The -j4 flag indicates my system has four cores. Compilation will go much faster when you can simultaneously run four instances of your fortran or c compiler. There is no sudo make install. We have chosen a location independent install. Your binaries will be located under $ROOTSYS/bin. make install moves your files to a --prefix path specified in your ./configure. We did not specify such a path.
During my process of discovering how to install ROOT, I messed up my configuration several times. Even after a make clean I was getting errors like
No rule to make target `XrdOucFactoryBonjour.hh', needed by > > > `../../obj/XrdOucBonjour.o'. Stop.
on my next build. These errors were cleared by issuing
make distclean-xrootd make all-xrootd
after my make clean and before ./configure macosx64.
Before running ROOT or important ROOT objects into python, you need to set a few more environment variables. From my .zshrc (instructions are identical for .bashrc),
# ROOT Data Analysis Framework #export ROOTSYS=/usr/local/root/5.30.01 export ROOTSYS=/usr/local/root/current/ export LD_LIBRARY_PATH=$ROOTSYS/lib:$LD_LIBRARY_PATH export DYLD_LIBRARY_PATH=$ROOTSYS/lib:$DYLD_LIBRARY_PATH export SHLIB_PATH=$ROOTSYS/lib:$SHLIB_PATH export LIBPATH=$ROOTSYS/lib:$LIBPATH export MANPATH=$ROOTSYS/man:$MANPATH export PYTHONPATH=$ROOTSYS/bindings/pyroot:$PYTHONPATH export PYTHONPATH=$ROOTSYS/lib:$PYTHONPATH export PYTHONDIR=/Library/Frameworks/EPD64.framework/Versions/Current/
That should be it. ROOT can be run through the terminal
root
To test pyroot, launch the 64bit Enthought Python executable /Library/Frameworks/EPD64.framework/Versions/Current/bin/python (I've created a symbolic link to the binary called epython64 and placed the symbolic link in ~/bin) and import ROOT
➜ ~ epython64 Enthought Python Distribution -- www.enthought.com Version: 7.1-2 (64-bit) Python 2.7.2 |EPD 7.1-2 (64-bit)| (default, Jul 27 2011, 14:50:45) [GCC 4.0.1 (Apple Inc. build 5493)] on darwin Type "packages", "demo" or "enthought" for more information. >>> import ROOT >>>
No errors are reported. The install was a success.
These are the steps I followed for installing and customizing ZSH on 10.7 Lion.
OS X Lion comes with a newer version of zsh (4.3.11) in /bin, but if you want to maintain a current version, you can install it from MacPorts (or Fink or Homebrew depending on which package manager you prefer). The syntax is similar. For MacPorts,
sudo port install zsh-devel +mp_completion +examples +dec +pcre
MacPorts will install zsh in /opt/local/bin/zsh. Unfortunately, OS X will not recognize zsh as a login shell until /etc/shells is edited to include /opt/local/bin/zsh. My /etc/shells reads
# List of acceptable shells for chpass(1). # Ftpd will not allow users to connect who are not using # one of these shells. /bin/bash /bin/csh /bin/ksh /bin/sh /bin/tcsh /bin/zsh /opt/local/bin/zsh
/etc/shells is a protected file and can only be edited with admin or root privaleges.
sudo gvim /etc/shells
Alternatively,
sudo sh -c "echo '/opt/local/bin/zsh' >> /etc/shells
Option 1 (preferred): In Terminal.app, execute
chsh -s /opt/local/bin/zsh
Option 2: You should also be able to make the change through System Preferences -> Users & Groups. Unlock the pane (lower left corner). Right click on your account and select “Advanced Options…” (note: if the pane is not unlocked, the contextual menu will not appear).
Your default shell can be changed from the opened dialog
These are the steps I followed for installing and customizing ZSH on 10.7 Lion.
There are two main template packages that can be added to zsh. These packages extend the default functionality of ZSH. Please see their documentation for further information. The packages:
I originally tried using zsh-templates-osx. The instructions are simple: a custom /private/etc/zshrc and /private/etc/zshenv are downloaded and written with appropriate root permissions. These files are sourced with new login shells (see this article).
cd /private sudo svn co http://zsh-templates-osx.googlecode.com/svn/trunk/etc
The template files are added to /Library/init/zsh.
cd /Library sudo svn co http://zsh-templates-osx.googlecode.com/svn/trunk/Library/init
I had a few problem with the install, including problems with the order of my bin directories in $PATH (zsh-templates-osx sets variables through path_helper), environment variables, and the sourcing of etc/zshrc and etc/zshenv. I’m assuming that the error lies on my end. If you have an idea, please leave me a comment.
I settled on oh-my-zsh. Installation was also simple. Directly from their website:
Step 1: Clone the repository. Templates files are copied to a hidden directory ~/.oh-my-zsh in your $HOME directory.
git clone git://github.com/robbyrussell/oh-my-zsh.git ~/.oh-my-zsh
Step 2: Backup your ~/.zshrc
cp .zshrc .zshrc_backup
Step 3: Copy their .zshrc to your $HOME.
cp ~/.oh-my-zsh/templates/zshrc.zsh-template ~/.zshrc
Step 4: Add back any customizations from your original .zshrc (now .zshrc_backup) file back to their .zshrc.
Oh-my-zsh actives the wonderful tab-completion, history, and directory navigation features of ZSH by default. Any further changes to your user experience is straight forward: themes and additional plugins can be loaded through ~/.zshrc and further modifications can be added to .zsh files in ~/.oh-my-zsh/lib. To change your theme and add additional plugins, edit
ZSH_THEME="robbyrussell"
to change your theme. A list of current themes is maintained here. Additional plugins can be added. Edit plugins=(list of plugins) in ~/.zshrc.
plugins=(git osx macports)
A full list of plugins is maintained here.
Additional aliases and settings are placed into ~/.oh-my-zsh/lib as a group of files with .zsh suffixes. Any file with this suffix will be sourced. These files (for example aliases.zsh) can be freely edited.
Fortunately, oh-my-zsh turns on most of features a common user will need. Most of my additions were $PATH additions for ROOT, MacPorts and X11, required environment variables, and my dircolor settings (see below).
The only noteworthy additions are the automatic ls after a cd as suggested by a post on StackOverflow, and the ordering of my PATH variables.
# Path additions
# List items in the reverse order you want them to appear in $PATH (i.e. last
# items appear first ).
PATH=/usr/X11/bin:$PATH # X11 Stuff
PATH=$ROOTSYS/bin:$PATH # ROOT Data Analysis Framework
PATH=/opt/local/bin:$PATH # MacPorts
PATH=/opt/local/sbin:$PATH # MacPorts
PATH=/usr/local/bin:$PATH # User binaries
PATH=$HOME/bin:$PATH # Personal binaries
export PATH
# List directory contents after a 'cd'
function chpwd() {
emulate -LR zsh
ls
}
Although oh-my-zsh provides a default color scheme, I prefer the greater customization provided by dircolors. dircolors is not included in the base 10.7 distribution. An integrated dircolors and ls must be installed. This combination is included an integrated component of of the GNU core utilities package (coreutils), a suite of basic file, shell, and text manipulation utilities (see GNU Operating System coreutils). coreutils can be installed through MacPorts.
Here's an overview of the procedure we will follow:
First, install coreutils
sudo port install coreutils
Please install without the +with_default_names option. +with_default_names uses the regular names for new standard unix programs rather than prefacing them with a 'g', e.g. ls instead of gls. This is a problem if MacPorts is ever updated. Please see my post here.
After the installation of coreutils, create a ~/.dir_colors file.
touch ~/.dir_colors
I have included mine below, adapted and designed for text on a black terminal. Please make sure that your TERM is included in the .dir_colors header. To see your version of TERM:
echo $TERM
For my computer the result was xterm-256color. Your Terminal type can be changed in Terminal Preferences.
My ~/.dir_colors file
# DIRCOLOR file for the mac. # Designed for a text on black terminal. # Below, there should be one TERM entry for each terminal # type that can be colored. TERM linux TERM linux-c TERM mach-color TERM console TERM con132x25 TERM con132x30 TERM con132x43 TERM con132x60 TERM con80x25 TERM con80x28 TERM con80x30 TERM con80x43 TERM con80x50 TERM con80x60 TERM dtterm TERM xterm TERM xterm-color TERM xterm-256color # Default for OS X 10.7 TERM xterm-debian TERM rxvt TERM screen TERM screen-bce TERM putty TERM screen-w TERM vt100 TERM Eterm COLOR yes # Below are the color init strings for the basic file types. # A color init string consists of one or more of the following # numeric codes: # # Attribute codes: # 00=none 01=bold 04=underscore 05=blink 07=reverse # 08=concealed # Text color codes: # 30=black 31=red 32=green 33=yellow 34=blue 35=magenta # 36=cyan 37=white # Background color codes: # 40=black 41=red 42=green 43=yellow 44=blue 45=magenta # 46=cyan 47=white NORMAL 00 # Global default FILE 00 # Normal file DIR 04;40;33 # Directory (DEFAULT: 01;34 - CHANGED S.M.) LINK 01;36 # Symbolic link. FIFO 40;33 # Pipe SOCK 01;35 # Socket DOOR 01;35 # Door BLK 40;33;01 # Block device driver CHR 40;33;01 # Character device driver ORPHAN 40;31;01 # Symlink to nonexistent file # This is for files with execute permission: EXEC 01;32 # List any file extensions like '.gz' or '.tar' that you would # like ls to colorize below. Put the extension, a space, and # the color init string (and any comments you want to add after # a '#'). # USER DEFINED # Archive files .tar 01;31 # archives or compressed (bright red) .tgz 01;31 .tar.gz 01;31 .arj 01;31 .taz 01;31 .lzh 01;31 .zip 01;31 .z 01;31 .Z 01;31 .gz 01;31 .bz2 01;31 .deb 01;31 .rpm 01;31 .jar 01;31 # Images and video .fig 01;35 .jpg 01;35 .jpeg 01;35 .gif 01;35 .bmp 01;35 .pbm 01;35 .pgm 01;35 .ppm 01;35 .tga 01;35 .xbm 01;35 .xpm 01;35 .tif 01;35 .tiff 01;35 .png 01;35 .mov 01;35 .mpg 01;35 .mpeg 01;35 .avi 01;35 .fli 01;35 .gl 01;35 .dl 01;35 .xcf 01;35 .xwd 01;35 # Audio .ogg 01;35 .mp3 01;35 .wav 01;35 .aac 01;35 # Programming *Makefile 01;33 .C 01;33 .cpp 01;33 .cc 01;33 .c 01;33 .for 01;33 .h 01;33 .tcl 01;33 .py 01;33 .sh 01;33 .o 33 .so 33 # Documents *README 01;37;41 *Readme 01;37;41 *readme 01;37;41 .tex 01;37;40 .dvi 01;37;40 .ppt 01;37;40 .pptx 01;37;40 .doc 01;37;40 .docx 01;37;40 .xls 01;37;40 .xlsx 01;37;40 .ps 01;37;40 .eps 01;37;40 .pdf 01;37;40 .txt 01;37;40 .htm 01;37;40 .xml 01;37;40 .pot 01;37;40 .nb 01;37;40 # Spectra (physics stuff) .spe 32 .spn 32 .sec 32 .asc 32 .mat 32 .spc 32 .Spc 32 .root 32 .gf2 32 .gf3 32 # Data .dat 01;04;35 .evt 01;04;35 .bin 01;04;35 # Temporary files *~ 36 .bak 36 .tmp 36 *# 36
Add the following lines to your ~/.zshrc to ensure that dircolors runs when ls or any ls variant is called.
# Color listing
eval $(dircolors ~/.dir_colors)
zstyle ':completion:*' list-colors "${(s.:.)LS_COLORS}"
ls must be called with the --color flag. Modify the ls aliases in ~/.oh-my-zsh/lib/aliases.zsh.
# List direcory contents export LS_OPTIONS='--color' alias l='ls $LS_OPTIONS' alias ll='ls $LS_OPTIONS -lh' alias lll='ls $LS_OPTIONS -alh' alias sl='ls $LS_OPTIONS' # often screw this up
Lastly, ~/.oh-my-zsh/lib/theme-and-appearance.zsh needs modified so ls is not called with the -G flag. Change alias ls='ls -G' to alias ls='ls --color, i.e.
# Enable ls colors # Edited - S.M. Changed ls -G -> ls --color. Requires dircolor to be valid. if [ "$DISABLE_LS_COLORS" != "true" ] then # Find the option for using colors in ls, depending on the version: Linux or BSD ls --color -d . &>/dev/null 2>&1 && alias ls='ls --color=tty' || alias ls='ls --color' fi
That should be all! Questions and comments can be addressed below.
I had to setup a new OS X system from scratch. The last time I did so was over a half-decade ago with my old laptop, and I’ve forgotten most of my global and software settings. Below are my notes associated with the new machine, including a description of problems I faced in my upgrade from Snow Leopard to Lion.
I’ve separated my content into two entries because of length. The first will cover software. The second will cover tweaks.
Most software on this list is free. A few installs are covered in additional details below this list.
sudo install) can be easily extended to Fink or Homebrew. The differences between the three package managers are outlined in a blog post by Ted Wise. There are several GUI wrappers for MacPorts for those that prefer graphics over a command-line interface, but I haven’t used them. Note that the installation of MacPorts, and likely all of the mentioned package managers, require the installation of the latest version of XCode. Installation notes: See MacPorts update notes after this list. Please select a single package manager. The simultaneous use of several (e.g. Fink and MacPorts) can cause problems.If you bought your computer with 10.7 installed, you can ignore the text below. The following information only applies to people like me who installed MacPorts before an upgrade to 10.7. Any operating system upgrade will likely break your MacPorts installation.
Download the latest version from MacPorts, mount the dmg, and run the installer. MacPorts requires the latest version of XCode, as installed from the App Store.
After a new installation of MacPorts, try and update old packages
sudo port upgrade outdated
This upgrade process will likely fail. If so, you need to go through the processes of uninstalling and re-installing packages. The upgrade processes is outlined in the MacPorts Wiki and consists of the following steps (taken directly from their site).
The associated commands for these four steps are
port -qv installed > myoutputfile.txt sudo port -fp uninstall --follow-dependents installed sudo port clean all sudo port install portname +variant1 +variant2 …
+variant1, +variant2, etc. are the additional flags that can be passed to a package for additional functionality. For my zshell installation, for example
sudo port instal zsh-devel +mp_completion +dec +examples
For me, the process of migrating MacPorts was particularly frustrating. I installed coreutils with the +with_default_names variant. Coreutils usually installs its utilities with a ‘g’ prefix, i.e. ls becomes gls. +with_default_names removes the ‘g’ prefex. When I uninstalled all packages, /usr/local/bin was left with many of the essential and now broken coreutils programs like ls. I couldn’t figure out why my sudo port installations were failing. The problem: the uninstaller removed all the linked libraries for the core utilities, but did not remove the main binaries. A full suite of common unix utilities, which where overwriting the standard distribution utilities in /bin and /usr/bin because of the preference of /usr/local/bin in $PATH, were broken. MacPorts was trying to use broken Unix utilities to compile new software.
The lesson: After completing your MacPorts uninstall, check /usr/local for any orphaned packages beyond the standard port* binaries and remove them. When reinstalling coreutils, run the command without variants
sudo port install coreutils
The g-prefix utilities can be symlinked to their regular names.
for f in g*; do sudo ln -s $f ${f:1}; done
A list of programs I’ve installed through MacPorts
The corresponding MacPort commands
sudo port install coreutils sudo port install ctags sudo port install zsh-devel +mp_completion +examples +dec +pcre sudo port install wine sudo port install gimp-devel
My ZSH installation is addressed in a separate post.
Multiple python distributions can be installed simultaneously.
OS X provides python out of the box (installed in /usr/bin/python)—just execute python from the command line—but its recommended that one install a new Framework version (either 2.7 or 3.1) from Python.org. If you need computational or visualization packages, consider installing the Enthought Python Distribution (EPD), which bundles numpy, scipy, matplotlib, wxPython and other packages into an easy installer.
Installation of ROOT is addressed in a separated post.
Most applications on this list are free.
Update (2 Sep. 2011): The download of my thesis is now password protected. If you want a copy, please contact me and I’ll send you the password.
I’ve uploaded information on my doctoral thesis, including a complete abstract.
My thesis has been submitted to ProQuest for publication (IP limited and subscription based). Michigan State University requests that ProQuest converts all submitted theses to microfiche format (arghhh!) and the entire processes takes four to five weeks. A link and citation will be provided when available.
For those looking for a sensible pdf copy: download (right click and save as…). The file is 20.5 MB in size. I have purchased and reserved the copyright in my name. Although the file is currently available for anyone to download, access restrictions may be installed in the future. Enjoy!
I have also updated the pdf copy of my resume. It now agrees with the posted version. For those who downloaded an older version, please also note that my current address has changed.
I added a publications page under ‘Resume and CV‘, and updated my CV to reflect new articles in press.
I have added information about my work at the NSCL and my thesis project, “A study of complementary reactions: single-proton knockout and single-proton pickup.” I have now pointed my old websites, hosted by the MSU physics and astronomy department and the NSCL to automatically redirect to this domain.
I have uploaded my resume and CV. They are posted in both HTML and PDF form. If you are interested in additional details, you can contact me.
Initial creation of the personal website of Sean M. McDaniel. Please bear with me as I upload and update content.
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