Scientific Linux

Scientific Linux Installation Guide

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Scientific Linux

v4.3 (2017-07-31)


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Scientific Linux 7.1 Installation

1 Contents

2 Why use Scientific Linux? ....................................................................................................... 4

2.1 Updates .............................................................................................................................. 5

3 BIOS activate Virtualization .................................................................................................... 7

4 Install Scientific Linux 7.1 ....................................................................................................... 7

4.1 Change to Wired Internet by default ............................................................................... 40

4.2 Auto log-on ...................................................................................................................... 42

5 Programming/Development ................................................................................................... 45

5.1 Qt C++ ............................................................................................................................. 45

5.2 Eclipse Java, C/C++ and PHP ......................................................................................... 51

5.2.1 Test C++ ................................................................................................................... 56

5.3 Aptana .............................................................................................................................. 61

5.4 XML/DTD/Xpath Copy Editor ....................................................................................... 64

5.5 UML Umbrello ................................................................................................................ 72

5.6 PHP MySQL .................................................................................................................... 75

5.6.1 Apache ...................................................................................................................... 75

5.6.2 MySQL ..................................................................................................................... 80

5.6.3 PHP & PHP-mySQL ................................................................................................ 84

5.6.4 MariaDB & phpMyAdmin ....................................................................................... 90

5.7 Tomcat ........................................................................................................................... 102

5.8 Python ............................................................................................................................ 124

5.9 Code::Blocks and Fortran .............................................................................................. 127

5.10 Oracle Express ............................................................................................................... 130

5.11 PostgreSQL .................................................................................................................... 137

6 Content Management Server ................................................................................................ 138

6.1 Drupal ............................................................................................................................ 138

6.2 Typo 3 ............................................................................................................................ 140

7 Science ................................................................................................................................. 143

7.1 R..................................................................................................................................... 143

7.1.1 R Studio .................................................................................................................. 145

7.1.2 Test PHP ................................................................................................................. 146

7.2 TeXMaker ...................................................................................................................... 160

7.2.1 TeXLive ................................................................................................................. 168

7.2.2 LaTeXDraw ............................................................................................................ 169

7.2.3 Tex2Html ............................................................................................................... 175

7.3 Octave ............................................................................................................................ 175

7.4 Scilab ............................................................................................................................. 177


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7.5 FreeCAD ........................................................................................................................ 181

7.6 Salome ........................................................................................................................... 183

7.7 Maxima .......................................................................................................................... 187

7.8 KiCAD ........................................................................................................................... 188

8 Office .................................................................................................................................... 190

8.1 Qalculate ........................................................................................................................ 190

8.2 OpenProj ........................................................................................................................ 191

8.3 DropBox ........................................................................................................................ 196

8.4 Skype ............................................................................................................................. 198

8.5 Zim................................................................................................................................. 201

8.6 VYM (View Your Mind/Mind Mapping) ..................................................................... 203

8.7 Vokoscreen (screen recorder) ........................................................................................ 204

8.8 Dia ................................................................................................................................. 206

9 Others ................................................................................................................................... 208

10 ToDo..................................................................................................................................... 209

10.1 XMinder......................................................................................................................... 209

10.2 DraftSight ...................................................................................................................... 210


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2 Why use Scientific Linux?

Scientific Linux is the worldwide reference operating system for scientists and scientific

applications at this beginning of the 21st century and created in 2004!

among a lot of other distributions:

Scientific Linux forum:

http://scientificlinuxforum.org

You can download the complete 31 Gigabytes Scientific Linux Virtual Box (vdi file) here1:

https://www.dropbox.com/s/g1p1rymql4x45o4/ScientificLinux7.vdi?dl=0

with all installed stuff detailed in this PDF here:

1 The password of the Virtual Machin account is: password

http://scientificlinuxforum.org/

https://www.dropbox.com/s/g1p1rymql4x45o4/ScientificLinux7.vdi?dl=0


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https://fr.scribd.com/document/278466634/Scientific-Linux-Virtual-Box

If necessary you can check the kernel version with the following command:

2.1 Updates

When you update the applications of your system (yum update) the kernel will also be updated

and then when start your computer you will get:

To see the list of installed Kernel:

https://fr.scribd.com/document/278466634/Scientific-Linux-Virtual-Box


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To remove an old Kernel just type:

Upgrades between major versions (from SL 5 to SL 6, or SL 6 to SL 7) are not supported!!!


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3 BIOS activate Virtualization

Some computers have BIOS virtualization deactivated. For this purpose you need to change this:

4 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:



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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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Now go in the Settings… of the VBox:


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And choose:


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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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The following window appears:


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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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And type a password (never forget it!):


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Validate with Done and wait for the installation to finish:


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When installation is finish click on Reboot:


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When Reboot is finish, click on Finish Configuration:


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Wait a few minutes to get:


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Click Next:


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Choose above your language and click Next:


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Create a user and click Next to choose the user Timezone:


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And… it's obvious… not need to comment:


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You will get:


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In VirtualBox go in:


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Click on Run:


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Type your password to continue the installation:


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And wait for the installation process to finish:


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When finish, restart the VBox:


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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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You will get almost 200 updates:


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Click on Install Updates and when finished, reboot!


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4.1 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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And activate:


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4.2 Auto log-on

It is boring to always log-on a virtual test machine. Therefore:


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Something that may be important to know in Linux is how to open the file explorer with

administrative rights:


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5 Programming/Development

5.1 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:


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You save the file locally:


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When download finish you go in the Properties of the file:

In Permissions we change activate Allow executing file as a program:


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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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You click on Next:


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On Next:

On Next again:


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On Next again and we wait:

5.2 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:


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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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5.2.1 Test C++

Now you can test each one… First with C++:

After:


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And:


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After:


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After:


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After:


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After:

5.3 Aptana

Just download first:


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It's a zip file:

Once downloaded just unzip and double click:


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You will get:


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If you get an error message about Chromium. Just reboot computer.

5.4 XML/DTD/Xpath Copy Editor

To install XML Copy Editor. First download:


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Reboot machine and you will have:


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5.5 UML Umbrello

To install UML Umbrello Editor the process is quite easy:


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5.6 PHP MySQL

The purpose here is to have a LAMP with SL…

5.6.1 Apache

First we must be connected as root user:


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We install Apache:


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We start the server on we change to configuration to make it start automatically at every boot:

Now to make the whole LAMP works correctly we must configure an iptable. We create and

iptables file:


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And in the editor press Insert key to begin to write:

When finish, write ESC + : wq and Enter to save and return to the terminal.


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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:

Now go in your favorite Internet Browser and type http://localhost:


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5.6.2 MySQL

The purpose now is to install MySQL RDBMS:


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5.6.2.1 Install MySQL Workbench

First you go on the following website:

Double click:


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After a few seconds we get:


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And when we open:


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5.6.3 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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With a simple PHP script inside:


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After you just need to test it:


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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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5.6.4 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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Or if the above method doesn't work well:


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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 you can enter with root and password as input:


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When you click on Go we get:


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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.

5.7 Tomcat

To create Java server pages we need to install the tomcat server: for this purpose:


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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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We change to:

We start the Tomcat server a first time:


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we wait one minute… stop it:

and start it again:


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And we get:

Now we can test it. First open Java Eclipse and go into:


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After we go:


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We take:


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We click on Next to get:


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We go in our Tomcat installation folder:


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We get:


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Click on Finish.

Now we can try to create a JSP page:


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Search after for Dynamic web project:


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After we have:


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We click on Next:


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And Next again:


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And Finish:


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We get:


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5.8 Python

To install Python you run the following command:


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How do I start IDLE under Linux?


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numpy and scipy come pre-compiled with CentOS, just type:


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5.9 Code::Blocks and Fortran


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5.10 Oracle Express

Major tool to learn PL/SQL!

First download Oracle Database Express Edition for Linux x64:


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Once file download extract it on place:

Open the terminal in folder Disk1 of the resulting extraction and after type:


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Password: password


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5.11 PostgreSQL

Other details will follow…


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6 Content Management Server

6.1 Drupal

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:


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And do:

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!

6.2 Typo 3

For Typo3 take care!!! The message:


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For the database step choose socket:


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7 Science

7.1 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:


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We make an update to be sure to have the last version:

Now we launch R by typing just… R… (not userfriendly but terribly efficient access):


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It may be useful also to know how to uninstall R as sometimes it can be corrupted. Then run the

following commands:

yum uninstall R

yum uninstall R-core

yum uninstall R-devel

yum uninstall R-core-devel

If you get an error when running R for the first time saying that a file is missing in a given folder.

Just go in this folder and copy paste in an existing file in that same folder having a similar name

and just rename it as expected by the R error message!

After you just have to read my R 1'700 pages book on R ;-)

7.1.1 R Studio

To install R Studio just run the following command:


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7.1.2 Test PHP


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If necessary:

7.2 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:


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This tool need and MD5 Checksum to be installed. Therefore we need to install MD5 checksum

Perl packages:

After we write in the terminal:

sudo ./install-tl


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That brings us to:

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 write each time the two following lines:


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7.2.1 TeXLive

To install a basic package for LaTeX type the following:

and to install a specific package:


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7.2.2 LaTeXDraw

To install LaTeXDraw first download:


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Unzip:


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In the shell go into the folder:


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And a wizard appears on the screen:


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Once finished:


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Finally:


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7.2.3 Tex2Html

7.3 Octave

Octave is a Maple/Matlab like scientific software. To install it:


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You get:

Finally:


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7.4 Scilab

To install Scilab, the official way is first to download the package:


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after to extract:


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After in the shell we write:


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And Scilab opens:


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7.5 FreeCAD


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7.6 Salome

To install SALOME we go first on their webpage to select the option highlighted below:


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Once the download finish we extract the files:

Then we enter the corresponding folder:

Afterward we go in the shell, browse in the corresponding folder and launch the corresponding

bash file:


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Then we get:

And after by creating a new file and inserting objects you can create your project:


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7.7 Maxima


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7.8 KiCAD

A Cross Platform and Open Source Electronics Design Automation Suite:


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8 Office

8.1 Qalculate

A "small" calculator is always useful. Let us see how to install one that is considered as a

reference in the Linux World:


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8.2 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:


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And we need to install the downloaded file:

After OpenProj will be in the menu:


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But you will not be able to start it:


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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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8.3 DropBox

First:

And finally:


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8.4 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 special content:


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Finally:

And Skype starts:


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8.5 Zim

You like OneNote/EverNote and don't want use the web version? Here is the way to do it:

Once installed you get:


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Finally:


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8.6 VYM (View Your Mind/Mind Mapping)

To have in an easy way a Mind Mapping tool, type:

Then we get:


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Ce qui donne:

8.7 Vokoscreen (screen recorder)

To have as screen recorder we type first:

After what we get:


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This gives:


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8.8 Dia


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9 Others

After from the Software installer wizard you can install easily also:

VLC media player

Audacity


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10 ToDo

Write procedure for DraftSight, Google Earth, XMinder, Aptana

10.1 XMinder


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10.2 DraftSight


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XMinder:


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Google Earth:


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Answer Y to all questions.

Reboot and install:


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Answer Y to all questions. After:


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Date post:	22-Jan-2018
Category:	Science
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