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Linux Software

Linux is a robust and powerful open source operating system.

Due to its stability, the OS is deployed on high performance, mission critical servers worldwide, including many here at the Weizmann Institute.

Linux can also be installed on desktop computers. Much like Windows and Mac OS, it offers users a modern and intuitive GUI (Graphical User Interface) and supports a range of productivity, Internet and graphics software applications.

A range of Linux “distros” (distributions) are available, including Fedora, Ubuntu, OpenSUSE, RedHat, SLES and many more, a number of which we support. Please feel free to contact us should you require any assistance in making Linux-based PC purchasing decisions, or in installing and making the most of your Linux OS.

See details below on software applications available to Weizmann Institute Linux-based computers.

Cygwin

Cygwin is a Linux-like environment for Windows that makes it possible to port software running on POSIX systems (such as Linux, BSD and Unix) to Windows. For more information, see the Cygwin Web site.

FTP

The Weizmann Institute FTP server is at your disposal, primarily for the following uses:

Upload or download files for your own use.
Upload or download files for and from external users, for data sharing and/or collaboration purposes.

Using the FTP Server for Your Own Purposes

To upload and download files for your own use:

Access the FTP server (typically, via the command line ftp ftp.weizmann.ac.il command).
Log in with your Weizmann user ID and password.
Access your FTP folder via the cd /var/ftp/pub/[user_ID] command.
To upload and download files, use the put [file name] and get [file name] commands, respectively. To upload and download multiple files with wildcards, use the mput [partial file name]* and mget [partial file name]* commands.

Using the FTP Server for External Data Sharing and Collaboration

External users may use the FTP server to share files with you, by performing the following:

Accessing the FTP server (typically, via the command line ftp ftp.weizmann.ac.il command).
Logging in with the user name anonymous, and entering the recipient’s Weizmann Institute e-mail address as the password.
Accessing the incoming FTP folder via the cd incoming command.
Using the put [file name] and get [file name] commands, respectively, to upload and download files, and using the wildcard mput [partial file name]* and mget [partial file name]* commands to upload and download multiple files.

Note: the Weizmann Institute FTP server serves as a “data in transfer” machine. All data older than 7 days will automatically be deleted, without notice

Mathematica

Mathematica is a powerful software tool serving scientific research, engineering analysis and modeling, technical education and quantitative method application, with support for simple calculations, as well as for large-scale programing and interactive document preparation. For more information on the application, visit the Wolfram Web site.

Prerequisites

Mathematica requires CIFS support to be installed, as follows:

On Debian and Ubuntu, install CIFS support via the sudo apt-get install cifs-utils command.
On CentOS and Fedora, install CIFS via the yum install cifs-utils command.

Mathematica Installation

To install Mathematica (run the following commands as root or use sudo):

Mount the NFS location with the command mount smb://wisfiler.weizmann.ac.il/collaboration/Software/Mathematica/Mathematica_13.2.1 /mnt.
Create a mount point for the ISO file via sudo mkdir /media/iso.
Mount the ISO file inside /mnt using mount -o loop /mnt/Mathematica_13.2.1_BNDL_LINUX.iso /media/iso.
Run the installer via sudo bash /media/iso/Unix/Installer/MathInstaller. Perform the following during the installation:
- Press Enter to start installation, and again to complete it.
- Select Other ways to activate.
- Select Connect to a network license server.
- Enter license.weizmann.ac.il as the server name and click Activate.
- Accept the license agreement and click OK to complete installation.
Unmount /mnt via the umount /mnt command when done.

MATLAB

MATLAB is a high-level language and interactive environment for numerical computation, visualization and programming. Using MATLAB, you can analyze data, develop algorithms, and create models and applications.

The MATLAB language, tools and built-in math functions enable you to explore multiple approaches and reach solutions faster than you normally would with spreadsheets or such traditional programming languages as C/C++ and Java.

To install MATLAB:

Access the MATLAB portal.
Click Sign in to get started.
Create a Mathworks account with your Weizmann e-mail address (if you already have a Mathworks account, log into it). An Individual license will be linked to the account automatically.
Download the MATLAB installer.
During installation, use your Mathworks login credentials to activate the software.

For detailed instructions, see the PDF manual.

To renew the license of an existing MATLAB installation:

On the Home tab, in the Resources section, click Help > Licensing > Update Current Licenses. MATLAB displays a list of all your MathWorks licenses on this computer, with their status.
Select the Individual license and click Update. MATLAB contacts MathWorks to retrieve the most current version of the license file for the license.

If you require further assistance, please contact the IT Service Desk at extension 4444.

PGI

PGI offers a range of optimizing multi-core x64 compilers for Linux, Mac OS and Windows, with support for debugging and profiling of local MPI processes. It also provides a complete OpenMP/MPI SDK for high performance computing on the latest Intel and AMD CPUs.

For further information, visit the PGI Web site.

Prophy

Prophy is a software package designed to help analyze texts, such as papers and proposals, and suggest reviewers for these texts. Furthermore, the software can evaluate a researcher profile, compare a researcher to relevant peers, and suggest reviewers for this researcher.

The software is available to Weizmann users under an Institute site license, and its use will be free of charge during the first year.

For instructions on how to register and use the software, review the Prophy software user guide.

For information on the basics of operating Prophy, see the Prophy Software how to guide.

PyMOL

PyMOL is an open source molecular graphics system for visualization, animation, editing and publication-quality imagery generation. The system is Windows-, macOS- and Linux-compatible, is scriptable and can be extended using the Python language.

Please note that PyMOL can only be installed on computers owned by the Weizmann Institute.

To register for a PyMOL license, access the IT Service Catalog.

TeX

TeX, a sophisticated digital typographical system, is a popular means for typesetting complex mathematical formulae. It has largely displaced Unix troff, another favored formatter, in numerous Unix installations, and is also used for many other typesetting tasks, especially in the form of LaTeX and other template packages.

Contact:

IT Service Desk

Phone: 4444