Stuff that should be running on every server...

Base software

Libraries

yum install tk tcl tix

Graphviz

http://www.graphviz.org

yum install graphviz graphviz-devel graphviz-graphs graphviz-gd

yum install libjpeg libjpeg-devel

Lapack

yum install lapack-devel lapack
yum install blas blas-devel
 yum install atlas-devel atlas

yum install libymal libyaml-devel

• Libraries:
  • Graphviz ()
• 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

  • iperf (http://sourceforge.net/projects/iperf/)

  • fio (http://freecode.com/projects/fio)

  • ganglia-gmond
• Python 2.7
  • Nose ()

  • Pyyaml (http://pyyaml.org/)

  • Numpy (http://www.numpy.org/)

  • Scipy (http://www.scipy.org/)

  • BeautifulSoup (http://www.crummy.com/software/BeautifulSoup/)

  • Matplotlib (http://matplotlib.org/)

  • NetworkX (http://networkx.github.com/)

  • Nltk (http://nltk.org/)

  • Pygraphviz (http://networkx.lanl.gov/pygraphviz/)

  • Cvxopt (http://abel.ee.ucla.edu/cvxopt/)

  • Scikit-learn (http://scikit-learn.org/stable/)

Utilities

p7zip

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

yum install iperf

Fio

yum install fio

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

PIL

easy_install-2.7 PIL

==== PyYAML ===

easy_install-2.7 pyyaml

Nose

easy_install-2.7 nose

PyGraphViz

easy_install-2.7 pygraphviz

Numpy

easy_install-2.7 numpy

Scipy

easy_install-2.7 scipy

Matplotlib

easy_install-2.7 matplotlib

NetworkX

easy_install-2.7 networkx

Nltk

easy_install-2.7 nltk

Scikit-learn

easy_install-2.7 scikit-learn

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

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