"Dali" Visualization System
This is a high end visualization workstation also suitable for large memory data processing jobs. Various visualization and HPC applications are available on this system. We encourage users to visit the DAL to use this system for visualization tasks. The following page gives information about the hardware and software available on dali and also how to book and access the system.
Avizo 8.0 installed in linux. This is now the default version. Use avizo or avizo8 in a shell.
- Fiji image processing (based on ImageJ) installed in linux
ParaView 3.14.1 installed in linux
Avizo 7.1 installed in linux. Use avizo7 in a shell
- AVS/Express is no longer available due to expiry of campus-wide licence.
- Matlab r2011a (v7.12.0) 64bit installed in linux
- Matlab r2010a (v7.10.0) 64bit installed on linux
AMD FirePro V7800 GPU now replaces the Nvidia Quadro FX4600 GPU.
- AMD APP SDK v2.4 for OpenCL development installed. Please contact us if you wish to try the tools (profiler, kernel analyser) that come with the AMD SDK.
- Intel Fortran Compiler v11.1.064 (default) and v11.0.083 for Linux available.
ParaView 3.10.0 for Vista now available.
VolView 3.2 now available under Vista.
Avizo 6.3 (linux) installed (run using avizo6)
Nvidia 260.19 Driver installed for Cuda 3.2 (note this does not support OpenCL 1.1)
- Nvidia 258.19 Beta driver installed for OpenCL 1.1
- OpenCL 1.1 demos available.
- Intel C/C++ Compiler v11.0.074 for Linux available.
- Vascular Modeling Toolkit (VMTK) and Insight Toolkit (ITK) available.
- Avizo 6.2 installed.
CUDA 3.2 toolkit, sdk, profiler
CUDA 2.1 toolkit, sdk, profiler
- SPSS installed v 16.0
- Abaqus 6.10-1 has been installed under Vista 64bit
- Abaqus 6.8-2 has been installed under Vista 64bit
Remote Desktop access with full OpenGL (3D acceleration) support added
ParaView 3.4.0 is available under both Vista and Linux
- AVS/Express 7.2.1 (SE) has been installed for Linux (no longer available due to licence expiry)
- Scientific Linux 5.2 is now installed. This is the default operating system
- An ssh demon is now running on this machine under Vista so you can ssh to Dali.
- Mathematica 7 (linux) is available now available
A complete list of installed software is available below.
- 8 Cores (2 x 3GHz Quad Core Xeon X5472 Harpertown), 64bit
- 64GB RAM
- 0.5TB /home and 2TB /scratch disks
AMD FirePro V7800 2GB GPU
- The Nvidia 768MB Quadro FX4600 previously available may be restored in future. The FireGL card has been made available by AMD for an OpenCL training course and so may not be permenantly available.
FirePro driver v22.214.171.124 Linux 64bit
- OpenGL v4.1.10792
- Windows Vista x64 and Linux (Scientific Linux 5.2)
- Wacom Intuos3 A4 Graphics Tablet
To request an account on dali, please contact email@example.com giving details of your intended use. We will determine whether you qualify for an account or whether an alternative RCS resource is more appropriate.
New users are added using their Central Service (LDAP) login name though the login does not use LDAP and so the passwords can be different.
Dali can be accessed via ssh. Hostname: dali.rcs.manchester.ac.uk
We do not operate a job scheduling system on dali. Instead users wishing to use the system for interactive use or for running large memory jobs must book the machine in advance. We reserve the right to kill jobs run by users that have not booked dali in advance.
If you have any problems please contact firstname.lastname@example.org
Remote Graphics and CUDA/OpenCL Access (Linux only)
Please read the page on Dali's Remote OpenGL Facilities for details on using OpenGL applications remotely. These applications will not run without certain system permissions being granted. This also applies to users wishing to use CUDA/OpenCL.
Once you have the required permissions to run CUDA/OpenCL, our community wiki has a few hints on getting started with CUDA/OpenCL:
Dali does not operate a batch queueing system or disk usage quota. However, resources are finite and so we expect users to follow a few basic rules:
- Never shutdown or reboot the machine. Do log out when finished.
- You must book dali via the calendar for significant work (e.g., using Avizo or other package) whether visiting RCS or accessing dali remotely.
- Do not use dali as a dataset archive. You may transfer datasets to dali over the network or via USB disk brought to RCS. Data can reside on dali while you require it for processing (e.g., in Avizo). If you need to work on the dataset over several days or weeks then leave the data on dali to avoid repeatedly transferring it. However, once you are sure you have finished with the dataset please remove it from dali. You should archive your datasets using your own USB disk, departmental server, desktop system etc.
- Keep disk usage down. Do you need a dataset stored in both .raw and .tif format? Once you have determined the best format for your needs, remove the other format.
- NOTE that NO BACKUPS of dali are made. All data is stored at YOUR OWN RISK.
A high quality Wacom Inutos3 A4 tablet primarily for segmentation is now available. This has been configured to work both under Vista and Linux. See Mary McDerby for the pen if you want to try it out.
Under windows you can toggle between screens using the left dippled button on the tablet. This can be configured in Settings->Wacom Tablet.
Under Linux the tablet is mapped to a single screen at a time to move between the screens tab the very edge of the tablet. This does make grabbing anything at the edge where the screens meet tricky.
By default the tablet is not plugged in. Please use the USB ports on the side of the left hand monitor.
Lists of significant applications and software installed under Scientific Linux 5.2 and Windows Vista64 are given below.
Third party and significant packages are not available to run by default. Your environment can be configured to run these packages by loading the appropriate module. A module will set up the various shell environment variables required by each package.
The following module commands can be issued in a shell on dali:
to see a list of available modules
to see a brief description of each module
module load module/you/want
to load a module. This does not run the actual application but simply sets up your shell environment. You can then run the application using the command required by that application.
module help module/you/want
to see module-specific help text
Where you see the phrase (default) after a module listed by module avail you can omit the version number in the module load command. For example, the following will also load express/dev/7.2.1:
module load express/dev
- AMD APP SDK v2.4 for OpenCL development
Avizo 7.1 - GWL (available by default, no module - simply type avizo7 to run)
Avizo 7.0.1 - JSP (available by default, no module - simply type avizo701 to run)
Avizo 6.3 - GWL (available by default, no module - simply type avizo to run)
Note: If accessing Dali remotely use vglrun avizo7 for example when running graphics apps
- Avizo 6.2 - JSP
- AVS/Express 7.2.1 Standard Edition - JSP (no longer available for use)
- AVS/Express 7.2 Parallel Edition - JSP (no longer available for use)
- cmake 2.6.4 - GWL
- CUDA 3.2 - GWL
- CUDA 2.1 - GWL
- Fiji (ImageJ with plugins) - GWL
- Intel C/C++ Compiler v11.0.074 - GWL
- Intel Fortran Compiler v11.1.064 (default) and v11.0.083 - LML
- ImageJ (image analysis) - GWL
- ITK 3.18 - GWL
- Mathematica - GWL
Please read: ITS Mathematica Licencing regarding your obligations for using Mathematica.
- matlab R2011a with default toolboxes, using network/site licence - GWL
- matlab R2010a with default toolboxes, using network/site licence - GWL
- matlab R2008a with default toolboxes, using network/site licence - GWL
- Merlin (genome) - GWL
- Modules (env) - JSP
- !OpenCL 1.1 - GWL
ParaView 3.14.1 - GWL
ParaView 3.4.0 - JSP
ParaView 3.4.0 with MPICH2 1.0.8 support compiled in - GWL
- Qt 4.3.5 libraries - GWL
- R - JSP
- VirtualGL/TurboVNC - GWL
- VMTK 0.8 - GWL (module will also load VTK 5.6.0 and ITK 3.18 modulefiles)
- VTK 5.2.1 - RH
- VTK 5.6.0 (default) - GWL
Modules is not used on Windows
- Abaqus 6.10-1 64bit - LML
- Abaqus 6.8-2 64bit - LML
- Adobe Master Collection CS4 - MT
- Photoshop CS4 Extended
- Illustrator CS4
- Acrobat 9 Pro
- Flash CS4 Professional
- Dreamweaver CS4
- Fireworks CS4
- Contribute CS4
- After Effects CS4
- Adobe Premiere Pro CS4
- Soundbooth CS4
Adobe OnLocation CS4
- Encore CS4
- Adobe Bridge CS4
- Adobe Device Central CS4
- Dynamic Link
- Version Cue CS4
- AMD APP SDK v2.4 for OpenCL development
- AMOS 16.0 - MT
- AVS/Express 7.3 Standard Edition - JSP
- Chimera (molecular viz) - JSP
Cygwin 1.7.8-1 (incl: ImageMagick, Xwin, gcc, sshd, rxvt) - JSP/LML
- emacs-21 - JSP
- ImageJ (image analysis) - JSP
IrfanView (image viewer) - JSP
- Java (SDK and JRE)- JSP
- MATLAB Version 126.96.36.1992 (R2007b) (Visual Studio Compiler chosen) - MT
- Simulink Version 7.0 (R2007b)
- Bioinformatics Toolbox Version 3.0 (R2007b)
- Fuzzy Logic Toolbox Version 2.2.6 (R2007b)
- Image Processing Toolbox Version 6.0 (R2007b)
- MATLAB Compiler Version 4.7 (R2007b)
- Optimization Toolbox Version 3.1.2 (R2007b)
- Signal Processing Toolbox Version 6.8 (R2007b)
- Statistics Toolbox Version 6.1 (R2007b)
- Virtual Reality Toolbox Version 4.6 (R2007b)
- MPICH2 - JSP
ParaView 3.10.0 - LML
- SAS 9.2 - ?
- SPSS 16.0 - MT
16.0.1 16.0.2 Windows Patches, 188.8.131.52 HotFix
- SPSS Data Access Pack 4.5
- Softimage XSI 7.0 - GWL
- Visual Studio (C/C++/C#) 2005 (v8) SP1 + Vista Update - JSP
- Visual Studio (C/C++/C#) 2008 (v9) - JSP
VolView 3.2 - LML
WinMerge 2.12.4 (GUI diff comparison/merge tool)- LML
- WinSCP 4.3.2 (GUI sftp/ftp tool) - LML