<?xml version="1.0" encoding="utf-8"?><!DOCTYPE article  PUBLIC '-//OASIS//DTD DocBook XML V4.4//EN'  'http://www.docbook.org/xml/4.4/docbookx.dtd'><article><articleinfo><title>BaseSoftware</title><revhistory><revision><revnumber>27</revnumber><date>2015-02-13 20:56:57</date><authorinitials>akrevl</authorinitials></revision><revision><revnumber>26</revnumber><date>2014-07-23 18:59:37</date><authorinitials>akrevl</authorinitials></revision><revision><revnumber>25</revnumber><date>2013-08-05 21:45:15</date><authorinitials>akrevl</authorinitials></revision><revision><revnumber>24</revnumber><date>2013-04-25 23:48:18</date><authorinitials>akrevl</authorinitials></revision><revision><revnumber>23</revnumber><date>2013-04-11 01:35:27</date><authorinitials>akrevl</authorinitials></revision><revision><revnumber>22</revnumber><date>2013-04-04 01:05:05</date><authorinitials>akrevl</authorinitials></revision><revision><revnumber>21</revnumber><date>2013-04-04 01:04:42</date><authorinitials>akrevl</authorinitials></revision><revision><revnumber>20</revnumber><date>2013-03-12 02:41:21</date><authorinitials>akrevl</authorinitials></revision><revision><revnumber>19</revnumber><date>2013-02-21 02:47:00</date><authorinitials>akrevl</authorinitials></revision><revision><revnumber>18</revnumber><date>2013-02-21 02:45:31</date><authorinitials>akrevl</authorinitials></revision><revision><revnumber>17</revnumber><date>2013-02-21 02:45:23</date><authorinitials>akrevl</authorinitials></revision><revision><revnumber>16</revnumber><date>2013-02-21 02:34:15</date><authorinitials>akrevl</authorinitials></revision><revision><revnumber>15</revnumber><date>2013-02-20 22:01:13</date><authorinitials>akrevl</authorinitials></revision><revision><revnumber>14</revnumber><date>2013-02-20 21:42:13</date><authorinitials>akrevl</authorinitials></revision><revision><revnumber>13</revnumber><date>2013-02-20 21:37:37</date><authorinitials>akrevl</authorinitials></revision><revision><revnumber>12</revnumber><date>2013-02-16 06:56:30</date><authorinitials>akrevl</authorinitials></revision><revision><revnumber>11</revnumber><date>2013-02-16 06:55:33</date><authorinitials>akrevl</authorinitials></revision><revision><revnumber>10</revnumber><date>2013-02-16 06:53:42</date><authorinitials>akrevl</authorinitials></revision><revision><revnumber>9</revnumber><date>2013-02-16 06:52:44</date><authorinitials>akrevl</authorinitials></revision><revision><revnumber>8</revnumber><date>2013-02-05 08:52:09</date><authorinitials>akrevl</authorinitials></revision><revision><revnumber>7</revnumber><date>2013-01-11 09:20:32</date><authorinitials>akrevl</authorinitials></revision><revision><revnumber>6</revnumber><date>2013-01-11 09:20:17</date><authorinitials>akrevl</authorinitials></revision><revision><revnumber>5</revnumber><date>2012-10-25 18:23:56</date><authorinitials>akrevl</authorinitials></revision><revision><revnumber>4</revnumber><date>2012-10-24 16:58:21</date><authorinitials>akrevl</authorinitials></revision><revision><revnumber>3</revnumber><date>2012-10-09 22:31:29</date><authorinitials>akrevl</authorinitials></revision><revision><revnumber>2</revnumber><date>2012-09-24 22:58:17</date><authorinitials>akrevl</authorinitials></revision><revision><revnumber>1</revnumber><date>2012-09-24 22:56:09</date><authorinitials>akrevl</authorinitials></revision></revhistory></articleinfo><para>Stuff that should be running on every server... </para><section><title>Base software</title><section><title>Libraries</title><section><title>libnuma</title><screen><![CDATA[sudo apt-get install numactl libnuma-dbg libnuma-dev libnuma1]]></screen></section><section><title>Graphviz</title><para><ulink url="http://www.graphviz.org"/> </para><screen><![CDATA[yum install graphviz graphviz-devel graphviz-graphs graphviz-gd]]></screen></section><section><title>Libjpeg</title><screen><![CDATA[yum install libjpeg libjpeg-devel]]></screen></section><section><title>Lapack, Blas, Atlas</title><screen><![CDATA[yum install lapack lapack-devel blas blas-devel atlas atlas-devel]]></screen></section><section><title>Yaml</title><screen><![CDATA[yum install libyaml libyaml-devel]]></screen></section><section><title>dvipng</title><screen><![CDATA[yum install dvipng]]></screen></section></section><section><title>Utilities</title><section><title>p7zip</title><para><ulink url="http://p7zip.sourceforge.net/"/> </para><itemizedlist><listitem><para>p7zip from EPEL does NOT include RAR support which we need </para></listitem><listitem><para>Use RPMs from /afs/cs/group/infolab/software </para></listitem></itemizedlist><screen><![CDATA[scp akrevl@madmax:/afs/cs/group/infolab/software/p7*.rpm ./
rpm -Uvh p7zip-9.20.1-3.el6.x86_64.rpm]]></screen></section><section><title>Ganglia</title><screen><![CDATA[yum install ganglia-gmond]]></screen></section><section><title>Iperf</title><para><ulink url="http://sourceforge.net/projects/iperf/"/> </para><screen><![CDATA[yum install iperf]]></screen></section><section><title>Fio</title><para><ulink url="http://freecode.com/projects/fio"/> </para><screen><![CDATA[yum install fio]]></screen></section><section><title>iftop</title><screen><![CDATA[yum install iftop]]></screen></section><section><title>nethogs</title><screen><![CDATA[yum install nethogs]]></screen></section><section><title>Tcl/Tk</title><screen><![CDATA[yum install tk tk-devel tcl-devel tix-devel]]></screen></section></section><section><title>Python 2.7</title><screen><![CDATA[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
]]><![CDATA[
rpm -Uvh python27-*.rpm tkinter27-2.7.3-6.2.puias6.x86_64.rpm]]></screen><section><title>PyTables</title><screen><![CDATA[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]]></screen></section><section><title>PIL</title><screen><![CDATA[easy_install-2.7 PIL]]></screen></section><section><title>PyYAML</title><para><ulink url="http://pyyaml.org/"/> </para><screen><![CDATA[easy_install-2.7 pyyaml]]></screen></section><section><title>Nose</title><screen><![CDATA[easy_install-2.7 nose]]></screen></section><section><title>BeautifulSoup</title><para><ulink url="http://www.crummy.com/software/BeautifulSoup/"/> </para><screen><![CDATA[easy_install-2.7 beautifulsoup4
python2.7
from bs4 import BeautifulSoup]]></screen></section><section><title>Numpy</title><para><ulink url="http://www.numpy.org/"/> </para><screen><![CDATA[easy_install-2.7 numpy]]></screen></section><section><title>Scipy</title><para><ulink url="http://www.scipy.org/"/> </para><screen><![CDATA[easy_install-2.7 scipy]]></screen></section><section><title>Matplotlib</title><para><ulink url="http://matplotlib.org/"/> </para><screen><![CDATA[easy_install-2.7 matplotlib]]></screen></section><section><title>NetworkX</title><para><ulink url="http://networkx.github.com/"/> </para><screen><![CDATA[easy_install-2.7 networkx]]></screen></section><section><title>PyGraphViz</title><para><ulink url="http://networkx.lanl.gov/pygraphviz/"/> </para><screen><![CDATA[easy_install-2.7 pygraphviz]]></screen></section><section><title>Nltk</title><para><ulink url="http://nltk.org/"/> </para><screen><![CDATA[easy_install-2.7 nltk]]></screen></section><section><title>Scikit-learn</title><para><ulink url="http://scikit-learn.org/stable/"/> </para><screen><![CDATA[easy_install-2.7 scikit-learn]]></screen></section><section><title>Cvxopt</title><para><ulink url="http://abel.ee.ucla.edu/cvxopt/"/> </para><para>This package has the setup.py in the wrong directory which confuses easy_install-2.7. </para><screen><![CDATA[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]]></screen></section><section><title>Tornado</title><para><ulink url="http://www.tornadoweb.org/en/stable/"/> </para><screen><![CDATA[sudo easy_install-2.7 tornado]]></screen></section></section><section><title>Python 3.3</title><warning><para>This package is not yet a part of the standard installation. </para></warning><screen><![CDATA[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
]]><![CDATA[
rpm -Uvh python3-*.rpm]]></screen></section><section><title>Java</title><section><title>Oracle Java</title><para><ulink url="http://www.oracle.com/technetwork/java/index.html"/> </para><screen><![CDATA[# scp the file from somewhere because of the annoying license agreement
rpm -Uvh jdk-7u15-linux-x64.rpm
/usr/java/default/bin/java -version]]></screen></section><section><title>Apache Ant</title><para><ulink url="http://ant.apache.org/"/> </para><screen><![CDATA[yum install ant]]></screen></section><section><title>Apache Maven</title><para><ulink url="http://maven.apache.org/"/> </para><screen><![CDATA[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/]]></screen></section><section><title>R-project</title><para><ulink url="http://www.r-project.org/"/> </para><screen><![CDATA[yum install R]]></screen></section><section><title>Matlab</title><para><ulink url="http://www.mathworks.com/products/matlab/"/> </para><para>License server(s): </para><itemizedlist><listitem><para>rocky.stanford.edu </para></listitem><listitem><para>eel.stanford.edu </para></listitem></itemizedlist></section></section></section><section><title>User assignments</title><itemizedlist><listitem><para>sudo users: </para><itemizedlist><listitem><para>akrevl, rok, jure </para></listitem></itemizedlist></listitem></itemizedlist></section><section><title>Kernel parameters for big memory machines</title><screen><![CDATA[#/etc/sysctl.conf
]]><![CDATA[
vm.overcommit_ratio = 100
vm.overcommit_memory = 2]]></screen></section></article>