Marion Nanosystems
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Virtual Nanolab® System Requirements
Supported platforms
There are currently two different distributions of VNL, which are compatible with the following platforms:
Platform Processor Operating system
Linux i686 LSB 1.3/2.0 C++
Windows i686 Windows XP
The processor labels are explained here.
The LSB versions refer to the Linux Standard Base list of certified Linux distributions. Note that the C++ module is needed; it is not sufficient with just the core module. For more details, see Software Requirements below.
Provided the general and specific requirements listed below are met, it is expected to run on practically all modern Linux distributions. If it anyway fails to run on some system, please contact support@atomistix.com and we will try to find a solution.
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Hardware Requirements
Graphics card
Viewing large molecules and complex geometries puts hard strain on the graphics components of your system. It is therefore necessary to have a good 3D graphics card with hardware acceleration. Make sure to obtain the latest drivers for the manufacturer as well.
Storage space
To install Virtual NanoLab you need 100-200 MB available storage space on the installation drive. However, the result files created when running the program can often become large. It is therefore recommended to have at least 500 MB available, but note that certain calculations can require gigabytes of storage space.
Memory
The analyses performed in Virtual NanoLab involve rather complex numerical calculations, which demand a lot of both the computer processor and memory. Although there is no specific minimum requirement, other than those that generally apply to running applications on each specific platform, it is highly recommended to equip the computer with a large amount of memory, with 512 MB as an absolute minimum, and 1 GB as a reasonable number for larger (but not too large) calculations.
Processor
It is a good idea to have at least a Pentium 4 or correspondingly, and certainly above 2 GHz clock frequency.
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Software Requirements
Virtual NanoLab (VNL) runs on almost all Linux and Windows systems, but there are specific requirements that must be met:
§ Running VNL requires that TCP/IP network is installed.
Linux
VNL is expected to run properly on any Linux distribution listed in the Linux Distribution Certification Register that matches the LSB version listed above.
The following system components (or newer) are required:
§ Linux kernel 2.4.8
§ XFree86 4.3/X.Org Server 6.8
§ GLibC 2.2.5
§ FreeType 2
Also g2c library is needed to run VNL.
In addition, VNL requires Xft, which is available as a package for the latest version of your Linux distribution. Most newer XFree86 servers have this library available by default. The error message "error while loading shared libraries: libXft.so.2: cannot open shared object file: No such file or directory" is displayed if Xft is not available.
Some distributions do not install libXmu.so, libGL.so and libGLU.so properly, it may be necessary to install the regular and development packages of libXmu, mesa-libGL and mesa-libGLU to correct this.
A list of commonly used libraries needed by VNL:
1. The following libraries are part of glibc:
§ ld-linux.so.2
§ libpthread.so.0
§ libdl.so.2
§ libutil.so.1
§ libc.so.6
§ libm.so.6
2. The following libraries are part of XFree86/X.Org:
§ libSM.so.6
§ libICE.so.6
§ libXext.so.6
§ libX11.so.6
§ libXi.so.6
§ libXrender.so.1
§ libXft.so.2
§ libfreetype.so.6
§ libfontconfig.so.1
§ libXt.so.6
3. The following libraries must, as discussed above, also be installed:
§ libgcc_s.so.1
§ libstdc++.so.5
§ libg2c.so.0
§ libXmu.so.6
§ libGL.so.1
§ libGL.so
§ libGLU.so.1
Windows
VNL has been successfully tested on Microsoft Windows XP Professional.
However, it is also expected to run properly on Windows 2000/2003, x64 edition and Vista.
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General compatibility issues
We are continously working on extending these lists. If you would like to run any of our programs on a specific platform not listed above, please send an e-mail to support@atomistix.com and we will try our best to compile the program for you.
Due to various issues not under our control, this may unfortunately not always be possible. This pertains, in particular, to Virtual NanoLab which is much more dependent on other software libraries.
Unfortunately, Mandrake Linux 10.1 has broken the backward compatibility for the freetype library by shipping version 2.1.9. Mandrake Linux 10.0, however, has freetype-2.1.7, and should be able to run Virtual NanoLab.
The Linux distribution Gentoo has a patched freetype 2.1.9, which has backward compatibility. Hopefully, Mandrake will offer this at some point.
While we now know what the problem is, there is not much we can do to remedy it. We are very carefull not to use any fancy new packages which may cause problems, but we cannot stop distributors from releasing operating systems that are not backward compatible. Hopefully this will be a rare problem, but still extremely annoying for those actually running Mandrake 10.1, of course
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A note on graphics handling in VNL
VNL, and particularly the NanoScope compoment, relies on OpenGL and requires heavy and quick 3D manipulations to visualize the molecular and electronic structures. The essential requirements for running VNL are:
§ 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.
VNL runs well on IBM ThinkPad X31, which is equipped with Intel Pentium M 1.4GHz and ATI Mobility Radeon 16MB VRAM. The latest Apple MacBook is also capable of running VNL, and the processor is Intel Core Duo 2.0GHz, the graphics card is the integraded Intel 945 with 64MB VRAM.
A few facts about the graphics card:
§ 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. While the VRAM is insufficient, main RAM will be used for such purpose.
§ 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 than the generic driver shipped with OS.
(This means, for instance on Linux, MesaGL is bad, one has to install ATI or Nvidia proprietary drivers). A practical recommendation for smoothly running VNL is:
§ ATI or Nvidia (almost all other graphics card vendors have died already) graphics
card with 128 MB VRAM and hardware-accelerated 3D.
(Note: 8MB cards usually do not support 3D, 16MB and better ones do);
§ Vendor-specific driver with hardware-accelerated OpenGL support (e.g. drivers
downloaded from ATI or Nvidia website).
It is generally hard to provide system requirements for 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.
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