Getting Started

What is SAMSON?

SAMSON is a software platform for computational nanoscience. Its generic, open architecture makes it suitable for material science, life science, physics, electronics, chemistry, and even education. The SAMSON application and the SAMSON SDK are developed by the NANO-D group led by Stephane Redon at INRIA. SAMSON stands for "Software for Adaptive Modeling and Simulation Of Nanosystems".

SAMSON-1YRF.png
Interactive minimization of 1YRF in SAMSON

Current version

The current version of SAMSON is 0.7.0. As the major version number indicates, this is a beta version. Please refer to Versioning for more information about version numbers.

Supported platforms

SAMSON is available on the following platforms:

  • Windows Vista
  • Windows 7
  • Windows 8
  • Windows 10
  • Linux
  • Mac OS X

Requirements

For running SAMSON, a 64-bit operating system and a graphics card supporting OpenGL 3.2 are required. Intel graphics cards may currently cause issues.

What are SAMSON Elements?

SAMSON has an open architecture which allows you to extend it, and adapt it to your needs, by downloading SAMSON Elements (modules) from the SAMSON Connect website. SAMSON Elements come in many flavors: apps, editors, controllers, models, parsers, etc., and are adapted to different application domains. SAMSON Elements help users build new models, perform calculations, run interactive or offline simulations, visualize and interpret results, and more.

Installing SAMSON

To install SAMSON, download the SAMSON installer from this page on SAMSON Connect. You will be asked to sign in, or create an account if you don't have one. When you download the installer, a key will be sent to the email address you used for registration.

Start the SAMSON installer you just downloaded, you should see following window:

SAMSONInstaller1.png
The SAMSON installer

Note: Intel graphics cards may currently cause issues. If you have one, the SAMSON installer will generate a warning. You may choose to ignore the warning, especially if you also have a non-Intel graphics card (NVIDIA or AMD).

After accepting the license agreement, you reach a page that allows you to configure a proxy, if necessary:

SAMSONInstaller2.png
Enter proxy parameters if necessary

At this point, the SAMSON installer checks that it can reach SAMSON Connect (that SAMSON needs to install SAMSON Elements). If it can, this page shows the message "SAMSON Connect reached successfully". Else, you might have to enter proxy parameters (you may have to ask your system administrator for information). Use the "Test connection" button to check that the proxy parameters you entered are valid.

Next, the installer asks you to enter the email address you used to register, and the SAMSON key that was sent to you at that address when you downloaded the installer.

SAMSONInstaller3.png
Enter your email address and the SAMSON key you received at that address

If you want, you may check the "Advanced mode" box to choose a custom installation path and specify which version of SAMSON you want to install (by default, the latest version is installed).

Then, the installer downloads SAMSON from SAMSON Connect, and installs it:

SAMSONInstaller4.png
SAMSON is being downloaded from SAMSON Connect

Finally, the last page of the installer gives you the possibility to start SAMSON and visit SAMSON Connect:

SAMSONInstaller5.png
SAMSON has been installed successfully

Starting SAMSON

Here is how you start SAMSON depending on your operating system.

Windows

On Windows, start SAMSON from the Start menu. Typing SAMSON in the search box might just lead you there. Else, SAMSON may be found in the SAMSON 0.7.0 folder.

Mac

On Mac, start SAMSON from the launchpad.

Linux

On Linux, open a terminal, go to the SAMSON installation folder path (it should be ~/NANO-D/SAMSON/0.7.0/Binaries), then execute the SAMSON-Core.sh script:

./SAMSON-Core.sh

In case you have issues on Linux with graphics cards, please refer to the Troubleshooting section.

Customizing SAMSON

The first time you start SAMSON, it downloads a set of default SAMSON Elements from SAMSON Connect. To customize your SAMSON installation from SAMSON Connect, simply sign in to your account, then go to the Elements section of SAMSON Connect to choose the SAMSON Elements you need. Please refer to this page for more information.

Troubleshooting

If you have trouble installing SAMSON and cannot find an answer below, please contact us at contact@samson-connect.net or get some help at the SAMSON Connect forum.

Running SAMSON on Linux with an AMD GPU

SAMSON requires a graphics card supporting OpenGL 3.2. To detect which GPU you have you may run several commands:

sudo lshw -c video
lspci -nn | grep VGA

SAMSON depends on libOpenGL.so and libGLX.so (to be precise, libOpenGL.so.0 and libGLX.so.0), which are not provided by SAMSON and should be installed on your system. To check whether these libraries are installed on your system, you may run the following commands:

sudo updatedb
locate libOpenGL.so
locate libGLX.so
locate libGL.so

If you have no libOpenGL.so library in your system, you can make links to either the libQt5OpenGL.so shipped with SAMSON, or to your system library, e.g. by compiz:

ln -s $HOME/NANO-D/SAMSON/0.7.0/Binaries/SAMSONQtLibs/libQt5OpenGL.so $HOME/NANO-D/SAMSON/0.7.0/Binaries/SAMSONQtLibs/libOpenGL.so.0

or

sudo ln -s /usr/lib/x86_64-linux-gnu/compiz/libopengl.so /usr/lib/x86_64-linux-gnu/libOpenGL.so.0

In the first case, you will need to create this link every time your SAMSON has been updated. If you have no libGLX.so library, you may create a link to libGL.so, e.g. depending on where you have libGL.so:

sudo ln -s /usr/lib/x86_64-linux-gnu/libGL.so /usr/lib/x86_64-linux-gnu/libGLX.so.0

or

sudo ln -s /usr/lib/x86_64-linux-gnu/mesa/libGL.so.1 /usr/lib/x86_64-linux-gnu/libGLX.so.0

Otherwise, these libraries can be installed through a GPU driver or mesa. If, for example, you have Ubuntu 14.04 (up to Xorg 1.16) you may install the fglrx driver (we refer to https://help.ubuntu.com/community/BinaryDriverHowto/AMD").

For a newer version of Ubuntu, if you have a recent AMD GPU, you may install the AMDGPU Driver or the AMDGPU-PRO Driver. Alternatively, you may install mesa:

sudo apt-get install mesa-utils libgl1-mesa-dev