Diff for "BaseSoftware"

Differences between revisions 16 and 17

Stuff that should be running on every server...

Base software

=== Libraries ===

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 libymal libyaml-devel

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

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

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

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

-  ⇤ ← Revision 16 as of 2013-02-21 02:34:15 → 
  Size: 5259
  Editor: akrevl
  Comment:
+   ← Revision 17 as of 2013-02-21 02:45:23 → ⇥
  Size: 5204
  Editor: akrevl
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 5:
-=== Libraries ===
yum install tk tcl tix
+=== Libraries ===
-Line 16:
+Line 15:
+==== Libjpeg ====

{{{
-Line 17:
+Line 19:
-==== Lapack ====

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

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

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

==== Yaml ====

{{{
-Line 28:
+Line 31:
- * 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/)
+}}}
-Line 55:
+Line 36:
+http://p7zip.sourceforge.net/

 * p7zip from EPEL does NOT include RAR support which we need
 * Use RPMs from /afs/cs/group/infolab/software
-Line 69:
+Line 55:
+http://sourceforge.net/projects/iperf/
-Line 75:
+Line 63:
+http://freecode.com/projects/fio
-Line 77:
+Line 67:
+}}}

==== Tcl/Tk ====

{{{
yum install tk tk-devel tcl-devel tix-devel
-Line 92:
+Line 88:
-Line 103:
+Line 96:
+http://pyyaml.org/
-Line 113:
+Line 108:
+==== 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
}}}
-Line 115:
+Line 152:
+http://networkx.lanl.gov/pygraphviz/
-Line 119:
+Line 158:
-==== Numpy ====

{{{
easy_install-2.7 numpy
}}}

==== Scipy ====

{{{
easy_install-2.7 scipy
}}}

==== Matplotlib ====

{{{
easy_install-2.7 matplotlib
}}}

==== NetworkX ====

{{{
easy_install-2.7 networkx
}}}
-Line 145:
+Line 160:
+http://nltk.org/
-Line 151:
+Line 168:
+http://scikit-learn.org/stable/
-Line 156:
+Line 175:
+http://abel.ee.ucla.edu/cvxopt/