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

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