Nugroho's blog.

Thursday, December 15, 2011

Install GCC 4.6.2 on OS X Lion (success)

Still failed, for not able to access gcc-4.6.2 automatically (have to access ~/gcc462/bin), I install binary GCC from HPC. So I'm extracted gcc-lion.tar.gz. For my surprise, it's extracted with some hierarchy like usr/local/bin, usr/local/include, … and I supposed to copy it to root folder. In that case, my Xcode4.2's gcc would still intact because it's in /usr/bin .

I wonder if all gcc compilation result'll stored to /usr/local if we didn't pass any parameter, so I checked my /usr/local/bin directory

Nugrohos-MacBook-Pro:/ nugroho$ cd usr/local/bin/
Nugrohos-MacBook-Pro:bin nugroho$ ls
2to3gfortran                  python-config    smtpd.py
2to3-2.7    idle     python2.7    smtpd2.7.py
c++     idle2.7     python2.7-32    x86_64-apple-darwin11.2.0-c++
cpp     jcf-dump    python2.7-config   x86_64-apple-darwin11.2.0-g++
g++     pydoc     pythonw     x86_64-apple-darwin11.2.0-gcc
gcc     pydoc2.7    pythonw-32    x86_64-apple-darwin11.2.0-gcc-4.6.2
gcj     python     pythonw2.7    x86_64-apple-darwin11.2.0-gcj
gcov     python-32    pythonw2.7-32    x86_64-apple-darwin11.2.0-gfortran

There is gcc in it. Is in gcc-4.2?

Nugrohos-MacBook-Pro:bin nugroho$ ./gcc --version
gcc (GCC) 4.6.2
Copyright (C) 2011 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Yes, it is gcc-4.6.2? So, I replace gcc symlink previously pointed to /usr/bin/llvm-gcc to /usr/local/bin/gcc

Nugrohos-MacBook-Pro:bin nugroho$ which gcc
/usr/bin/gcc
Nugrohos-MacBook-Pro:bin nugroho$ which llvm-gcc
/usr/bin/llvm-gcc
Nugrohos-MacBook-Pro:bin nugroho$ sudo ln -s gc
gcc   gcj   gcov  
Nugrohos-MacBook-Pro:bin nugroho$ sudo ln -s gcc /usr/bin/gcc
Password:
ln: /usr/bin/gcc: File exists
Nugrohos-MacBook-Pro:bin nugroho$ sudo mv /usr/bin/gcc /usr/bin/gccOLD
Nugrohos-MacBook-Pro:bin nugroho$ sudo ln -s gcc /usr/bin/gcc
Nugrohos-MacBook-Pro:bin nugroho$ gcc
gcc: fatal error: no input files
compilation terminated.
Nugrohos-MacBook-Pro:bin nugroho$ gcc --version
gcc (GCC) 4.6.2
Copyright (C) 2011 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Nugrohos-MacBook-Pro:bin nugroho$

Hooray, HPC binary is left untouched, :)

Ubuntu 11.10 Oneiric Ocelot on OS X Lion via Virtual Box

It's long time since my MacBook Pro had ubuntu installed. Curious about new release of ubuntu, I decided to download .iso file via torrent network and installed it on my Mac via VirtualBox as I don't want to dual booting my Mac again (the way I did several years ago).

I downloaded 64-bit version of Oneiric Ocelot and it's installed without problem.

From screenshot below, we know ubuntu team has improved their installation method. While the system is busy copying file, we're prompted to fill our detail of instalation; keyboard, time zone, username. Such an efficient method.

From Blogsy Photos

Wednesday, December 14, 2011

Installing GCC 4.6.2 on OSX Lion

After searching how to's, compiling from source, installing Snow Leopard version of Xcode (on its DVD) and installing light alternate gcc 4.2 version without success (or success but not satisfied), I installed Xcode 4.2 on my OS X Lion. Alas, Apple ship its own GCC compiler, llvm-gcc, instead GCC. So I download tar.gz version of GCC-4.6.2 from GNU and try to install it

From Blogsy Photos

check to know what dependencies I don't have by typing

./configure

the result is

 
…
configure: error: Building GCC requires GMP 4.2+, MPFR 2.3.1+ and MPC 0.8.0+.
…

So, I download it mpc (http://www.multiprecision.org/index.php?prog=mpc&page=download), mpfr(http://www.mpfr.org/mpfr-current/#download) and gmp(http://gmplib.org/). I don't know why gmp's download always ended by error, duh. Trying to 'torrenting' it via burnbit but still get error. I was forced to use ftp connection via Finder (Command-K) and done. Installing these dependencies is easy task, just unzip/untar these archive, cd to its directory and type three magical UNIX installation words.

$./configure
$make
$sudo make install

OK, now it's GCC time. Extract GCC zipped file, cd to its directory

./configure
make 
sudo make install

You can add make command to make -j 4 if you have multicore processor and want to make process processed in parallel. "Make" process is very long time process.
Look at gnumake, cc1 , sh , and llvm-gcc-4.2 processes. They're processed in parallel.

From Blogsy Photos

OMG, after long awaiting time, I got an error, something about libgfortran. (update: it's succeed indeed despite of error, it actually compiled gcc but not in Lion path, so Lion's still use llvm-gcc version , I post the update here) After a minute of thinking, I decide to compile just C for now, and build on separate directory and output-ed it on my home directory

Nugrohos-MacBook-Pro:gcc-4.6.2 nugroho$ mkdir build
Nugrohos-MacBook-Pro:gcc-4.6.2 nugroho$ cd build
Nugrohos-MacBook-Pro:build nugroho$ ../configure --prefix=$HOME/gcc462 --enable-languages=c

These command will build GCC on 'build' directory and store the compilation result on gcc462 directory on my home folder. If you are interested in building only a limited set of languages, just like me, you could also specify this option in the configure line. For example if you need only C, C++ and Fortran just append this to the above line: --enable-languages=c,c++,fortran

First Impression of Portable Python

I'm curious about Portable Python I found several days ago even I don't have windows machine. So I borrowed my mom's Pentium III Dynabook Satellite with XP installed, and installed Portable Python in my 8GB Transcend JetFlash USB pendrive. Pathetic though; why do I installed it to pen drive if I already have Windows machine? Yeah, because it can't be installed via my MacBook Pro with Lion of course. Anyway here's some screenshot

From Blogsy Photos

Portable Python can be acessed interactively via command prompt like this

From Blogsy Photos

or throught PyScripter, but we'll face "coud not connect to the python engine server. The remote interpreter and debugger is not available" error because windows's blocking pythonw like this

From Blogsy Photos

Clicking unblock will allow PyScripter run

From Blogsy Photos

Monday, December 12, 2011

Lorenz Attractor using Python 2.7 and Vpython Module on Mac OS X Lion

From Blogsy Photos

Lorenz attractor's generated by three nonlinear simultaneous equation.

x1=x0+h*a*(y0-x0)
y1=y0+h*(x0*(b-z0)-y0)
z1=z0+h*(x0*y0-c*z0)

where

a=10
b=28
c=8./4.

We can play with a,b and c to see the effect.

Here the code to visualize Lorenz attractor on Python. We need VPython module to visualize it.

from visual import *
from operator import mod
jl=1.
h=0.01
a=10
b=28
c=8./4.
x0=0.1
y0=0
z0=0
n=10000.
r=1.
while jl < n:
    rate(1000)
    rd=mod(n,jl)/1000
    sphere(pos=(x0,y0,z0),radius=r, color=(rd,1,rd))
    x1=x0+h*a*(y0-x0)
    y1=y0+h*(x0*(b-z0)-y0)
    z1=z0+h*(x0*y0-c*z0)
    jl=jl+1
    x0=x1
    y0=y1
    z0=z1

Since Vpython's not support 64bit platform, we must execute the code using 32-bit python like this

Nugrohos-MacBook-Pro:cellular nugroho$ python2.7-32 lorenz.py

Here the result

From Blogsy Photos

The Journey of Installing Matplotlib Python on Mac OS X Lion (continued)

To install Matplotlib, I have to install numpy first. To install numpy, I need GCC. Lion installer package didn't come with XCode, it has to be downloaded separately from MacAppStore for free. I don't dare to even trying it with my sluggish itnternet connection, so I tried others possibility without success untill I found my SnowLeopard DVD.

Finally, I am able to install GCC. I used XCode 3.2 on Snow Leopard DVD in Lion, :). So, the journey is continue…

Check (just for show off, :))

Nugrohos-MacBook-Pro:mysite nugroho$ gcc
gcc gcc-4.0 gcc-4.2 gccmakedep
Nugrohos-MacBook-Pro:mysite nugroho$ gcc

Now install numpy, oh no… look at this.

Last login: Sun Dec 11 19:11:11 from 192.168.2.2
Nugrohos-MacBook-Pro:mysite nugroho$ pip install numpy
Downloading/unpacking numpy
Downloading numpy-1.6.1.tar.gz (2.6Mb): 2.6Mb downloaded
Running setup.py egg_info for package numpy
Running from numpy source directory.non-existing path in 'numpy/distutils': 'site.cfg'
F2PY Version 2
blas_opt_info:
FOUND:
extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
define_macros = [('NO_ATLAS_INFO', 3)]
extra_compile_args = ['-faltivec', '-I/System/Library/Frameworks/vecLib.framework/Headers']
…
…
building extension "numpy.core._sort" sources
adding 'build/src.macosx-10.6-intel-2.7/numpy/core/include/numpy/config.h' to sources.
adding 'build/src.macosx-10.6-intel-2.7/numpy/core/
py/core/include/numpy/__multiarray_api.h']
building extension "numpy.core.multiarray" sources
adding 'build/src.macosx-10.6-intel-2.7/numpy/core/include/numpy/config.h' to sources.
…
…
error: could not delete '/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/__config__.py': Permission denied
…

It's look like my gcc think it's on Snow Leopard platform, :(. But, there is small hope; the error warning just mentions permission, hm, how about sudo?

ok, let's try again

Nugrohos-MacBook-Pro:mysite nugroho$ sudo pip install numpy
Password:
Downloading/unpacking numpy
Running setup.py egg_info for package numpy
Running from numpy source directory.non-existing path in 'numpy/distutils': 'site.cfg'
…
…
adding 'build/scripts.macosx-10.6-intel-2.7/f2py' to scripts
changing mode of /Library/Frameworks/Python.framework/Versions/2.7/bin/f2py to 755
Successfully installed numpy
Cleaning up...
Nugrohos-MacBook-Pro:mysite nugroho$

hm, still in doubt

Nugrohos-MacBook-Pro:mysite nugroho$ python
Python 2.7.2 (v2.7.2:8527427914a2, Jun 11 2011, 15:22:34)
[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>>

yeahh…
(don't know if it works as it compiled using GCC designed for Snow Leopard. At least no news is good news, :) )

So here it is

Nugrohos-MacBook-Pro:mysite nugroho$ pip install matplotlib
Downloading/unpacking matplotlib
Downloading matplotlib-1.0.1.tar.gz (13.3Mb): 13.3Mb downloaded
…
BUILDING MATPLOTLIB
matplotlib: 1.0.1
python: 2.7.2 (v2.7.2:8527427914a2, Jun 11 2011, 15:22:34)
[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)]
platform: darwin
REQUIRED DEPENDENCIES
numpy: 1.6.1
freetype2: found, but unknown version (no pkg-config)
* WARNING: Could not find 'freetype2' headers in any
* of '.', './freetype2'.
OPTIONAL BACKEND DEPENDENCIES
libpng: found, but unknown version (no pkg-config)
* Could not find 'libpng' headers in any of '.'
----------------------------------------
Command python setup.py egg_info failed with error code 1
Storing complete log in /Users/nugroho/.pip/pip.log
Nugrohos-MacBook-Pro:mysite nugroho$

Hm, still long way to go, have to install freetype2 and lbpng. Ugh…

Tux and Beasty

Tux is Linux mascot while Beasty is FreeBSD mascot (have same pronounciation like BSD)

Pages

Thursday, December 15, 2011

Wednesday, December 14, 2011

Monday, December 12, 2011