Atomistix ToolKit (ATK) and its graphical user interface Virtual NanoLab (VNL) runs on most Windows and Linux systems, on Intel/AMD PCs (i686 and x86_64 architectures).

In some cases, on Linux, you need to install a few additional libraries. If ATK or VNL fails to run on your system, it is likely that a similar problem already has been reported - and solved. The solution can then be found in the FAQ. If not, post your problem on the Forum, with as many details as you possibly can, including the exact software version (and distribution for Linux) and any error messages that appear, and we will try to find a solution.

Some specific requirements are listed below, which might help when troubleshooting installation issues.

• Hardware
• Software
  • Linux
  • Windows
• Specific requirements for the graphical user interface (VNL)

Hardware requirements

CPU

ATK runs on the following platforms:

• i686: Processors conforming to the IA32 architecture, and which support the MMX and SSE instruction sets. This includes both 32 and 64-bit processors such as
  • Intel: Pentium III, Pentium 4, Pentium M, Pentium D, Celeron M, Xeon, Pentium 4 EM64T, Xeon EM64T, Core Solo/Duo, Core 2 Solo/Duo/Quad/Extreme, etc.
  • AMD: Athlon XP, Athlon MP, Athlon 64, Athlon 64 X2, Opteron, Duron, Sempron, Turion, etc.
• x86_64: 64-bit processors, belonging either to the EM64T or AMD64 classes, such as
  • Intel: Pentium 4 EM64T, Xeon EM64T, Pentium D, Core 2 Solo/Due/Quad/Extreme
  • AMD: Opteron, Athlon 64, Turion 64

Memory

The memory required to run a calculation in ATK depends very strongly on the parameters and the system treated. To run the tutorial examples, a minimum of 2 GB physical memory is required, while a system with 4 GB should be able to run most calculations with approximately 500 atoms. Note, however, that some parameter choices can cause such calculations to require substantially more memory.

Hard drive space

To install ATK, approximately 250 MB of free space is required. When running calculations in ATK, temporary files are created and the calculated results require space. A recommended size for storage is at least 1 GB of free space.

Graphics

The operations performed in Virtual NanoLab involve rather complex 3D graphics which demand a lot of both the computer processor and memory, and not least the graphics card. It is therefore necessary to have a good graphics card with 3D hardware acceleration. Make sure to obtain the latest drivers from the card manufacturer as well. More details are available below.

Parallel support

Both the Linux and Windows versions are parallelized for MPI. To run ATK in parallel over MPI requires a MPICH2-derived library. We have successfully tested parallel operation under

• MPICH2
• MVAPICH2
• Intel MPI

In addition, ATK will thread, using OpenMP, over the cores of multicore processors. No additional software is needed for this, however some configuration might be necessary.

Linux software requirements

Distribution support

ATK has been extensively tested on

• Red Hat Enterprise Linux 5
• CentOS 5.x
• SUSE Linux Enterprise Desktop 10.x, 11.x
• Ubuntu 9.x, 10.x

However, ATK typically runs on other distributions as well without problems, provided all the latest updates have been installed.

Details

Running ATK on Linux generally requires:

• Linux kernel 2.6.x with standard features,
• ELF executable support, TCP/IP networking, etc
• The threading library NPTL (instead of LinuxThread)
• GLIBC 2.3
• libstdc++.so.6
• XFree86 4.3/X.Org Server 6.8
• FreeType 2

ATK links dynamically to a set of libraries, a list can be obtained by navigating to the ATK installation directory, and using these commands:

If a library needed by ATK is missing, it will show up in the output from these commands with the string "not found" appended to the name of the library.

This is the complete list of libraries ATK links dynamically to, and which are not included with ATK itself:

• ld-linux.so.2 (i686 version of ATK)
• ld-linux-x86-64.so.2 (x86_64 version of ATK)
• libc.so.6
• libdl.so.2
• libm.so.6
• libpthread.so.0
• libutil.so.1
• linux-vdso.so.1 (x86_64 version of ATK)
• linux-gate.so.1 (i686 version of ATK)
• libstdc++.so.6.0.3 or later

VNL has a rather complex dependence on shared libraries, and not all of these are pre-installed on all distributions. If you experience any problems starting VNL, start by looking in the FAQ. If no solution can be found there, post a new question on the Forum with all details, including the exact software version (and distribution for Linux) and the log output.

Windows software requirements

For Windows, ATK has been successfully tested on Microsoft Windows XP Professional SP2 and SP3, Windows Vista, and Windows 7, 32 and 64 bit editions.

Running ATK requires that TCP/IP network is installed. Usually, this means that one has at least one Ethernet NIC which binds with the "Internet Protocol (TCP/IP)".

It is not possible to run a terminal-based ATK session, or VNL, via a remote network connection.

Graphics requirements for VNL

• Intel/AMD processors with SSE (or SSE2, depends on ATK) instruction set
• AGP or PCIe graphics card
• Properly installed OpenGL driver

To efficiently run VNL, a hardware accelerated OpenGL driver is required. Software-emulated OpenGL usually works, but the performance is poor.

A few facts about graphics cards:

• A dedicated card is usually better than motherboard-integrated card, since the former has dedicated GPU (graphics processing unit) to release CPU from heavy 3D graphics manipulations, as such the performance is significantly improved.
• The size of VRAM is not the most important, although the bigger the VRAM, the better, since more texture objects can be stored in VRAM and be accessed faster. If the VRAM is insufficient, main RAM will be used instead.
• To effectively push the graphics performance to the card's design limit, the vendor-specific driver, which usually contains the hardware-accelerated OpenGL driver, are preferable to the generic drivers shipped with OS (such as the MesaGL drivers on Linux).

A practical recommendation for smoothly running VNL is therefore:

• ATI or NVIDIA graphics card with hardware-accelerated 3D.
• Vendor-specific driver with hardware-accelerated OpenGL support (e.g. drivers downloaded from manufacturer's website).

It is generally hard to provide exact system requirements for the graphics in VNL, because even a very old 3D graphics card with properly configured OpenGL driver can run VNL. It's a matter of performance, but it's difficult to know whether the performance of a certain card is good or not. Generally, if VNL doesn't run, most likely it is caused by the driver, not by the hardware.

On Linux you can test your OpenGL installation by running the utility glxgears. If it fails, VNL will probably not run properly on your system and you should review the system configuration.