Installing GraphLab on Fedora Core 16

FOR LAZY USERS: You can use Amazon EC2 image: ami-1510d87c
As instructed here.

0) Login into your FC 16 machine.
On amazon EC2 - you can launch instance ami-0316d86a

1) Installing libboost

yum install boost boost-devel

2) Installing itpp
Note: For FC 15 and earlier it is easy to setup itpp, see packages here: http://koji.fedoraproject.org/koji/packageinfo?packageID=2142 and explanation on http://sourceforge.net/apps/wordpress/itpp/download/
Using the command:

yum install itpp itpp-devel itpp-doc

Here I will explain how to install itpp manually, for FC 16

yum install lapack autoconf autogen libtool
ln -s /usr/lib64/liblalpack.so.3 /usr/lib64/liblapack.so
ln -s /usr/lib64/libblas.so.3 /usr/lib64/libblas.so

yum groupinstall "Development Tools"
wget http://sourceforge.net/projects/itpp/files/itpp/4.2.0/itpp-4.2.tar.gz
tar xvzf itpp-4.2.tar.gz
cd itpp-4.2
./autogen.sh 
./configure --enable-debug --without-fft --with-blas=/usr/lib64/libblas.so.3  --with-lapack=/usr/lib64/liblapack.so.3 CFLAGS=-fPIC CXXFLAGS=-fPIC  CPPFLAGS=-fPIC
make && make install

Note: future version of lalpack may have different library name, check your /usr/lib64
dir for the correct lapack/blas lib names.

3) Install Mercurial

yum install mercurial

4) Install cmake

yum install cmake

5a) Install graphlab from mercurial
Go to graphlab download page, and follow the download link to the mercurial repository.
copy the command string: "hg clone..." and execute it in your ubuntu shell.


or 5b) Install graphlab from tgz file
Go to graphlab download page, and download the latest release.
Extract the tgz file using the command: "tar xvzf graphlabapi_v1_XXX.tar.gz"
where XXX is the version number you downloaded.

6) configure and compile

./configure --bootstrap --itpp_include_dir=/usr/local/include/  --itpp_dynamic_link_dir=/usr/local/lib/libitpp.so  --itpp_lapack_dir=/usr/lib64/
cd graphlabapi
cd release/
make -j4

7) Test Graphlab

cd tests
export LD_LIBRARY_PATH=/usr/local/lib/
./runtests.sh

8) Optional (but recommended): install Octave.

yum install octave

Installing GNU Octave

GNU Octave is a Matlab like open source math environment. Recently, while talking to many companies, many of them have expressed their dissatisfaction with Maltlab license. In this post I will explain how to install Octave instead, for all the open source lovers.

After breaking my head most of today, I found out that the easiest way
to install Octave on Linux is found here.

Specifically for Fedora, you just need to do

sudo yum install octave-forge

On Ubuntu, you need to

sudo apt-get install octave3.2

For MAC OS it is also easy: you can download dmg file here

If you want to work really hard, you can try to compile the
sourcess.
However, this is really not recommended!!!

After you download the tgz file, you need to run ./configure
you may get this error:

configure: error: You are required to have BLAS and LAPACK libraries

point to the right blas/lapack libs:

./configure --with-lapack="-llapack -L/usr/lib64/atlas/" --with-blas="-lblas -L/usr/lib64/atlas/" --prefix=/mnt/bigbrofs/usr6/bickson/octave/ --without-qhull

when compiling I got this error:

Range.cc:440: error: 'floor' is not a member of 'gnulib'

by reading on the web, it seems it is some gcc bug:
http://lists.gnu.org/archive/html/octave-bug-tracker/2011-02/msg00262.html

The way to resolve it, is either update gnulib version, or add
the appropriate header file
#include
and change gnulib::floor to floor

Next you will get about 20 such erros in different files that needs to be
setup manually.
dir-ops.cc: In member function 'bool dir_entry::open(const std::string&)':
dir-ops.cc:61: error: 'strerror' is not a member of 'gnulib'
make[3]: *** [liboctave_la-dir-ops.lo] Error 1

#include<stdlib.h>

file-ops.cc: In function 'int octave_mkdir(const std::string&, mode_t, std::string&)':
file-ops.cc:378: error: 'strerror' is not a member of 'gnulib'

file-ops.cc: In function 'int octave_rename(const std::string&, const std::string&, std::string&)':
file-ops.cc:502: error: 'rename' is not a member of 'gnulib'
make[3]: *** [liboctave_la-file-ops.lo] Error 1

lo-mappers.cc: In function 'double xtrunc(double)':
lo-mappers.cc:48: error: 'trunc' is not a member of 'gnulib'
lo-mappers.cc: In function 'double xfloor(double)':
lo-mappers.cc:53: error: 'floor' is not a member of 'gnulib'
lo-mappers.cc: In function 'double xround(double)':
lo-mappers.cc:59: error: 'round' is not a member of 'gnulib'
lo-mappers.cc: In function 'float xtrunc(float)':
lo-mappers.cc:267: error: 'truncf' is not a member of 'gnulib'
lo-mappers.cc: In function 'float xround(float)':
lo-mappers.cc:273: error: 'round' is not a member of 'gnulib'
make[3]: *** [liboctave_la-lo-mappers.lo] Error 1

lo-utils.cc: In function 'void octave_putenv(const std::string&, const std::string&)':
lo-utils.cc:93: error: 'malloc' is not a member of 'gnulib'
lo-utils.cc: In function 'std::string octave_fgets(FILE*, bool&)':
lo-utils.cc:121: error: 'malloc' is not a member of 'gnulib'
lo-utils.cc:136: error: 'realloc' is not a member of 'gnulib'

oct-env.cc: In member function 'void octave_env::error(int) const':
oct-env.cc:534: error: 'strerror' is not a member of 'gnulib'
make[3]: *** [liboctave_la-oct-env.lo] Error 1
make[3]: Leaving directory `/mnt/bigbrofs/usr7/bickson/octave-3.4.2/liboctave'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/mnt/bigbrofs/usr7/bickson/octave-3.4.2/liboctave'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/mnt/bigbrofs/usr7/bickson/octave-3.4.2'

ct-md5.cc: In function 'std::string oct_md5_file(std::string)':
oct-md5.cc:73: error: 'fclose' is not a member of 'gnulib'
make[3]: *** [liboctave_la-oct-md5.lo] Error 1

oct-time.cc: In constructor 'octave_time::octave_time(const octave_base_tm&)':
oct-time.cc:62: error: 'mktime' is not a member of 'gnulib'
oct-time.cc: In member function 'void octave_strptime::init(const std::string&, const std::string&)':
oct-time.cc:269: error: 'strptime' is not a member of 'gnulib'
oct-time.cc:276: error: 'mktime' is not a member of 'gnulib'

ANOTHER ERROR I GOT:
build-aux/bootstrap: libtoolize -c -f ...
libtoolize: $pkgltdldir not a directory: `/usr0/software/libtool/share/libtool'
SOLUTION: make clean, and this error disappeared

ANOTHER ERROR:
./liboctave/.libs/liboctave.so: undefined reference to `METIS_NodeComputeSeparator'
SOLUTION:
setenv LIBS "-lmetis -L/usr/cs/lib/"
and then ./configure again and compile again