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← Revision 27 as of 2015-02-13 20:56:57 ⇥
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* Python 2.7 * scipy * numpy * matplotlib * networkX * nltk * Java * R-project (statistics) * Matlab pylab multiprocessing argparse elementtree pyQt scikit-learn sqlite3 BeautifulSoup mechanize virtualenv sip QtCreator |
== 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 }}} |
Stuff that should be running on every server...
Base software
Libraries
libnuma
sudo apt-get install numactl libnuma-dbg libnuma-dev libnuma1
Graphviz
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
- 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
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
easy_install-2.7 numpy
Scipy
easy_install-2.7 scipy
Matplotlib
easy_install-2.7 matplotlib
NetworkX
easy_install-2.7 networkx
PyGraphViz
http://networkx.lanl.gov/pygraphviz/
easy_install-2.7 pygraphviz
Nltk
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
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
yum install ant
Apache Maven
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
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