scientific linux virtual box
DESCRIPTION
Installation Guide for an almost complete free Scientific PlatformTRANSCRIPT
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SCIENTIFIC LINUX (SUX)
Minimal Data Scientist Installation + …(L)AMP Server v3.0
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Scientific Linux 7.1 Installation
Contents Why use Scienitific Linux? .............................................................................................................. 4
BIOS activate Virtualization ............................................................................................................ 6
Install Scientific Linux 7.1 ............................................................................................................... 6
Change to Wired Internet by default .......................................................................................... 39
Auto log-on ................................................................................................................................ 41
Qt C++ ............................................................................................................................................ 44
Eclipse Java, C/C++ and PHP ........................................................................................................ 50
Test C++ ..................................................................................................................................... 53
Test PHP ..................................................................................................................................... 59
PHP MySQL .................................................................................................................................. 74
Apache ........................................................................................................................................ 74
MySQL ....................................................................................................................................... 78
Install MySQL Workbench .................................................................................................... 79
PHP & PHP-mySQL .................................................................................................................. 82
MariaDB & phpMyAdmin ......................................................................................................... 88
Tomcat .......................................................................................................................................... 101
Oracle Express .............................................................................................................................. 122
WordPress/Joomla/Drupal/Typo3 ................................................................................................ 128
PostgreSQL .................................................................................................................................. 134
XML/DTD/Xpath Copy Editor .................................................................................................... 135
UML Umbrello ............................................................................................................................. 143
Install R ........................................................................................................................................ 146
OpenProj ....................................................................................................................................... 148
TeXMaker .................................................................................................................................... 154
LaTeXDraw .............................................................................................................................. 161
DropBox ....................................................................................................................................... 167
Skype ............................................................................................................................................ 168
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Aptana .......................................................................................................................................... 172
Zim ............................................................................................................................................... 174
Octave ........................................................................................................................................... 176
Others ........................................................................................................................................... 178
ToDo ............................................................................................................................................. 179
Record my desktop ................................................................................................................... 179
XMind ...................................................................................................................................... 183
Maxima ..................................................................................................................................... 185
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Why use Scienitific Linux? Scientific Linux is the worldwide reference operating system for scientific and scientific
applications!
Scientific Linux forum:
http://scientificlinuxforum.org
You can download a Virtual Box with all installed stuff detailed in this PDF here:
Password is: demo
Check Kernel version:
When you update your system (yum update) the kernel will also be updated and then when
starded your computer you will get:
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To see the liste of installed Kernel:
To remove an old Kernel juste type:
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BIOS activate Virtualization Some computers have BIOS virtualization deactivated. For this purpose you need to change this:
Install Scientific Linux 7.1 Open Virtual Box:
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Click on New:
Click Next and choose memory size (2GB recommended):
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Click Next and choose:
Click Next and choose (recommended 20 GB-30 GB):
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Click Create.
Download Scientific Linux *.iso from here:
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Select the *.iso file you selected before:
Once selected, you can Start the Virtual Machine and you will get:
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Click on the VBox screen and type Tab+Enter. After a few seconds you get:
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Choose English (United States) and click on Continue:
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Choose the GNOME Desktop with the visible package on the right:
You must select a partition to be able to continue the installation:
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Just click on Done in the upper left corner. Once you have also selected the right keyboard and
Date & Time Timezone click on Begin Installation:
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While the installation is in process, click on Root Password:
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Validate with Done and wait for the installation to finish:
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When Reboot is finish, click on Finish Configuration:
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Create a user and click Next to choose the user Timezone:
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First we connect to the Network. Through the VBox settings check that you have:
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And after in you SL (Scientific Linuy acronym) do:
Once this done go in:
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Click on Install Updates and when finished, reboot!
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Change to Wired Internet by default Each time you restart the VBox you will have to reconnect (wired) the VBox to the Internet. This
is boring. Do the following in the terminal:
You will get and click on Edit:
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Auto log-on It is boring to always log-on a virtual test machine. Therefore:
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Qt C++ As some people now I like how C++ rocks. Only one language to rule them all! Develop once for
almost everything with fastest time execution as compared to Java, C#, Python and many others.
First you go on Qt website to download:
You save the file locally:
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When download finish you go in the Properties of the file:
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In Permissions we change activate Allow executing file as a program:
Note: Process is the same to install Google Earth!
Once done, you double click on the file and the installation starts:
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Eclipse Java, C/C++ and PHP We now download and install Eclipse for JEE, C/C++ and PHP.
For this purpose you go on the following page:
You click on the 64 bit link of each of the three distribution and you save the file:
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Once the download done we extract each file (rename immediately the resulting folder with
something like eclipseJava or eclipseCpp etc. otherwise each tar.gz file we erase the previous
created folder!):
For each distribution you in the corresponding folder and double click on the eclipse icon to
check that it opens without issues:
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You will get for JEE:
Caution!!! Sometimes menu are not visible but in fact they are here but just not visible!
And for C/C++:
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Test C++ Now you can test each one… First with C++:
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PHP MySQL The purpose here is to have a LAMP with SL…
Apache First we must be connected as root user:
We install Apache:
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We start the server on we change to configuration to make it start automatically at every boot:
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Now to make the whole LAMP works correctly we must configure an iptable. We create and
iptables file:
And in the editor press Insert key to begin to write:
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When finish, write ESC + : wq and Enter to save and return to the terminal.
After we must install a package that can read and use the previous file:
Once installation done, you will have troubles with the existing firewall. We need to stop it and
deactivate it for each boot:
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Now go in your favorite Internet Browser and type http://localhost:
MySQL The purpose now is to install MySQL RDBMS:
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Install MySQL Workbench
First you go on the following website:
Double click:
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PHP & PHP-mySQL The purpose now is to install PHP engine with the PHP-mySQL connector:
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To test that everything work, first method is to use the defaults Linux visual editor. But first we
need writing rights on the main Apache root folder:
Now we can create a PHP file:
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We can do the same with Eclipse PHP. We create a project:
We create a simple script:
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And when you click on Run you get:
Now to use mySQL with PHP we need:
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MariaDB & phpMyAdmin Now we want to install phpMyAdmin to manage more easily MySQL tables. First we need to
install a fedora repo:
And after:
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To be sure that everything will work we do and update of all packages:
Now we can install phpMyAdmin:
Remarque: With this you can also install thunderbird (yum install thunderbird)
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Once this done, you restart Apache:
And now you can check if it works through your browser:
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But you will not be able to access to the admin console. For this we need to install MariaDB
packages (Oracle is devil…):
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Now we start MariaDB services and we launch mysql secure installation wizard:
Now we can finally secure our mysql-phpMyAdmin installation:
!!! Just type ENTER for current root password. And follow the below answers:
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To set root password above we have chosen password as password…
We continue…:
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Now we configure MariaDB to start automatically on each reboot:
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If and only if you can't still access to phpMyAdmin do the following:
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So we can change the following file:
And you change:
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And also:
We need to change back the access rules to read only:
Restart computer.
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Tomcat To create Java server pages we need to install the tomcat server: for this purpose:
After:
Once done this has created a tomcat7 folder where we need to change the default port 8080 to
something else otherwise we will be in conflict with our apache server:
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To change this file we do:
And in the file we search:
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And we get:
Now we can test it. First open Java Eclipse and go into:
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Click on Finish.
Now we can try to create a JSP page:
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Oracle Express Major tool to learn PL/SQL!
First download Oracle Database Express Edition for Linux x64:
Once file download extract it on place:
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Open the terminal in folder Disk1 of the resulting extraction and after type:
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WordPress/Joomla/Drupal/Typo3 Install WordPress and Joomla is very very easy stuff in SE Linux once the above steps all done.
But for Drupal it is a little bit more difficult. Once the zip file unpacked in the
var/www/html/drupal do the following:
And create the following folder:
And do:
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So when you got before the following error message:
By clicking on proceed with the installation you get:
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And now just continue as for WordPress and Joomla!
For Typo3 take care!!! The message:
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XML/DTD/Xpath Copy Editor To install XML Copy Editor. First download:
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UML Umbrello To install UML Umbrello Editor the process is quite easy:
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Install R As we all know, R is actually the most complete statistical software in the world. So we need it
for number analysis
Therefore first thanks to the fedora repo:
We make an update to be sure to have the last version:
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Now we launch R by typing just… R… (not userfriendly but terribly efficient access):
After you just have to read my R 1'300 pages book on R ;-)
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OpenProj We all know that project management has become increasingly normative these last decades.
Having a project management software is a minimum nowadays.
So let's run with OpenProj.
First we download:
And we need to install the downloaded file:
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Therefore you need first to install JRE:
If the Java Platform does not appear it means (most of time) that its already installed.
After we edit the following file:
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And we change this part:
Now we can open… OpenProj:
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TeXMaker A very important tool for every scientist and engineer that must write high quality scientific
documents (papers and books):
First we use the CRAN installation file:
This tool need and MD5 Checksum to be installed. Therefore we need to install MD5 checksum
Perl packages:
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After we write in the terminal:
sudo ./install-tl
That brings us to:
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Wait… almost 3000 modules (LaTeX packages/*.sty) to install…
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To install TeXMaker on SL 7.1 we will need to recompile TeXMaker code source. Then before
we install QT4 compiler!:
yum install pkg-config qt-devel qt-webkit-devel poppler-qt4-devel gcc-c++ make rpmdevtools
zlib1g-dev
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And we download TeXMaker code source:
Once the download done we extract the package:
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And by security we install the following packages:
Now we compile the sources:
After a few minutes you can finally write:
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Now to be able to install and update packages do each time the two following lines:
LaTeXDraw To install LaTeXDraw first download:
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Skype Until today it is still not easy to install Skype on SL x64. Here are the different steps:
We start with:
And after:
yum install alsa-lib.i686 fontconfig.i686 freetype.i686 glib2.i686 libSM.i686 libXScrnSaver.i686
libXi.i686 libXrandr.i686 libXrender.i686 libXv.i686 libstdc++.i686 pulseaudio-libs.i686 qt.i686
qt-x11.i686 zlib.i686 qtwebkit.i686
We install some additional modules:
Now we download Skype:
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Now we unpack:
Now we create launcher:
We create now a file with a specila content:
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Once downloaded just unzip and double click:
You will get:
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If you get an error message about Chromium. Just reboot computer.
Zim You like OneNote/EverNote and don't want use the web version? Here is the way to do it:
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Octave Octave is a Maple/Matlab like scientific software. To install it:
You get:
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Others After from the Software installer wizard you can install easily also:
VLC media player
Audacity
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ToDo Write procedure for DraftSight, Google Earth, XMinder, Aptana
Record my desktop