Stuff that should be running on every server...

== Base software ==

=== Libraries ===

==== libnuma ====

{{{
sudo apt-get install numactl libnuma-dbg libnuma-dev libnuma1
}}}

==== Graphviz ====

http://www.graphviz.org

{{{
yum install graphviz graphviz-devel graphviz-graphs graphviz-gd
}}}

==== Libjpeg ====

{{{
yum install libjpeg libjpeg-devel
}}}

==== Lapack, Blas, Atlas ====

{{{
yum install lapack lapack-devel blas blas-devel atlas atlas-devel
}}}

==== Yaml ====

{{{
yum install libyaml libyaml-devel
}}}

==== dvipng ====

{{{
yum install dvipng
}}}

=== Utilities ===

==== p7zip ====

http://p7zip.sourceforge.net/

 * p7zip from EPEL does NOT include RAR support which we need
 * Use RPMs from /afs/cs/group/infolab/software

{{{
scp akrevl@madmax:/afs/cs/group/infolab/software/p7*.rpm ./
rpm -Uvh p7zip-9.20.1-3.el6.x86_64.rpm
}}}

==== Ganglia ====

{{{
yum install ganglia-gmond
}}}

==== Iperf ====

http://sourceforge.net/projects/iperf/

{{{
yum install iperf
}}}

==== Fio ====

http://freecode.com/projects/fio

{{{
yum install fio
}}}

==== iftop ====

{{{
yum install iftop
}}}


==== nethogs ====

{{{
yum install nethogs
}}}


==== Tcl/Tk ====

{{{
yum install tk tk-devel tcl-devel tix-devel
}}}

=== Python 2.7 ===

{{{
curl -O http://www.elders.princeton.edu/data/PU_IAS/6.3/x86_64/os/Computational/python27-2.7.3-6.2.puias6.x86_64.rpm
curl -O http://www.elders.princeton.edu/data/PU_IAS/6.3/x86_64/os/Computational/python27-setuptools-0.6.27-2.puias6.noarch.rpm
curl -O http://www.elders.princeton.edu/data/PU_IAS/6.3/x86_64/os/Computational/python27-tools-2.7.3-6.2.puias6.x86_64.rpm
curl -O http://www.elders.princeton.edu/data/PU_IAS/6.3/x86_64/os/Computational/python27-libs-2.7.3-6.2.puias6.x86_64.rpm
curl -O http://www.elders.princeton.edu/data/PU_IAS/6.3/x86_64/os/Computational/tkinter27-2.7.3-6.2.puias6.x86_64.rpm
curl -O http://www.elders.princeton.edu/data/PU_IAS/6.3/x86_64/os/Computational/python27-devel-2.7.3-6.2.puias6.x86_64.rpm

rpm -Uvh python27-*.rpm tkinter27-2.7.3-6.2.puias6.x86_64.rpm
}}}

==== PyTables ====

{{{
sudo easy_install-2.7 Cython
sudo easy_install-2.7 numexpr
sudo yum install h5py27-221-188.x86_64 python-tables hdf5 hdf5-188-gcc hdf5-devel
sudo easy_install-2.7 tables
}}}

==== PIL ====

{{{
easy_install-2.7 PIL
}}}

==== PyYAML ====

http://pyyaml.org/

{{{
easy_install-2.7 pyyaml
}}}

==== Nose ====

{{{
easy_install-2.7 nose
}}}

==== BeautifulSoup ====

http://www.crummy.com/software/BeautifulSoup/

{{{
easy_install-2.7 beautifulsoup4
python2.7
from bs4 import BeautifulSoup
}}}

==== Numpy ====

http://www.numpy.org/

{{{
easy_install-2.7 numpy
}}}

==== Scipy ====

http://www.scipy.org/

{{{
easy_install-2.7 scipy
}}}

==== Matplotlib ====

http://matplotlib.org/

{{{
easy_install-2.7 matplotlib
}}}

==== NetworkX ====

http://networkx.github.com/

{{{
easy_install-2.7 networkx
}}}

==== PyGraphViz ====

http://networkx.lanl.gov/pygraphviz/

{{{
easy_install-2.7 pygraphviz
}}}

==== Nltk ====

http://nltk.org/

{{{
easy_install-2.7 nltk
}}}

==== Scikit-learn ====

http://scikit-learn.org/stable/

{{{
easy_install-2.7 scikit-learn
}}}

==== Cvxopt ====

http://abel.ee.ucla.edu/cvxopt/

This package has the setup.py in the wrong directory which confuses easy_install-2.7.

{{{
curl -O "http://abel.ee.ucla.edu/src/cvxopt-1.1.5.tar.gz"
tar xvfz cvxopt-1.1.5.tar.gz
cd cvxopt-1.1.5/src/
python2.7 setup.py install
}}}

==== Tornado ====

http://www.tornadoweb.org/en/stable/

{{{
sudo easy_install-2.7 tornado
}}}



=== Python 3.3 ===

{{{#!wiki warning
This package is not yet a part of the standard installation.
}}}


{{{
curl -O http://springdale.math.ias.edu/data/puias/computational/6/x86_64/python3-3.3.0-1.puias6.x86_64.rpm
curl -O http://springdale.math.ias.edu/data/puias/computational/6/x86_64/python3-debug-3.3.0-1.puias6.x86_64.rpm
curl -O http://springdale.math.ias.edu/data/puias/computational/6/x86_64/python3-debuginfo-3.3.0-1.puias6.x86_64.rpm
curl -O http://springdale.math.ias.edu/data/puias/computational/6/x86_64/python3-devel-3.3.0-1.puias6.x86_64.rpm
curl -O http://springdale.math.ias.edu/data/puias/computational/6/x86_64/python3-libs-3.3.0-1.puias6.x86_64.rpm
curl -O http://springdale.math.ias.edu/data/puias/computational/6/x86_64/python3-test-3.3.0-1.puias6.x86_64.rpm
curl -O http://springdale.math.ias.edu/data/puias/computational/6/x86_64/python3-tkinter-3.3.0-1.puias6.x86_64.rpm
curl -O http://springdale.math.ias.edu/data/puias/computational/6/x86_64/python3-tools-3.3.0-1.puias6.x86_64.rpm

rpm -Uvh python3-*.rpm
}}}

=== Java ===

==== Oracle Java ====

http://www.oracle.com/technetwork/java/index.html

{{{
# scp the file from somewhere because of the annoying license agreement
rpm -Uvh jdk-7u15-linux-x64.rpm
/usr/java/default/bin/java -version
}}}

==== Apache Ant ====

http://ant.apache.org/

{{{
yum install ant
}}}

==== Apache Maven ====

http://maven.apache.org/

{{{
curl -O "http://www.trieuvan.com/apache/maven/maven-3/3.0.4/binaries/apache-maven-3.0.4-bin.tar.gz"
tar xvfz apache-maven-3.0.4-bin.tar.gz
mv apache-maven-3.0.4 /usr/local/apache-maven
scp akrevl@iln29:/etc/profile.d/maven.sh /etc/profile.d/
}}}

==== R-project ====

http://www.r-project.org/

{{{
yum install R
}}}


==== Matlab ====

http://www.mathworks.com/products/matlab/

License server(s):

 * rocky.stanford.edu
 * eel.stanford.edu

== User assignments ==

 * sudo users:
  * akrevl, rok, jure

== Kernel parameters for big memory machines ==

{{{
#/etc/sysctl.conf

vm.overcommit_ratio = 100
vm.overcommit_memory = 2
}}}