These Frequently Asked Questions are currently being developed. Please send us your comments, requests or suggestions.
Broadly speaking, eResearch is the application of advanced Information and Communication Technologies (ICT) to the practice of research. This can be considered as somewhat analogous to the application of e-Commerce to the commercial sector- new tools and techniques open up new possibilities as well as new ways of doing what has always been done. We now take for granted ways of shopping, of making payments, that were not feasible previously.
The range of areas in which eResearch methods can be applied is vast. A very few such examples are
That is eResearch can help you obtain, store, analyse and interpret your data. It can keep you in touch and working with your colleagues no matter where they may be. In short, it helps you do research. Some of these possibilities may have been previously conceptualised- but were not practicable. Some of them are more effective and efficient ways of doing things that have long been done. In all cases, though, we may expect benefits to the way in which our research progresses as a result.
Eventually, there will not be "eResearch" as something distinct in its own right- it will just be part of the way we undertake research, an assumed and relied-upon suite of capabilities that form an integral component of how researchers do their work.
PC
eResearch SA is a Member of the national Australian Research Collaboration Service (ARCS), along with related state-based organisations in the other capital cities. eResearch SA, its fellow MARCS, and ARCS, endeavour to provide Australian researchers with access to eResearch facilities and services that are necessary for the effective conduct of contemporary and future research.
eResearch SA, through its relationship with ARCS as well as other national eResearch bodies such as ANDS, acts as the South Australian focus for such activities. Thus, it aims primarily to assist local (i.e. South Australian) researchers, whilst taking part also in the devleopment and deployment of these activities on a national level. This leads to a consistency and robustness of service, since the same tools, techniques and methodologies are being applied locally and nationally.
eResearch SA provides access to eResearch facilities and practical support and guidance to South Australian researchers from all disciplines.
Talk to us about your research project and how eResearch SA can help you with:
Most of our services are free for university researchers.
Yes. These are held annually, over the period late November to February. Please see here for further information.
The ITS Divisions of the eResearch SA members support corporate, desktop and teaching applications. In keeping with normal practice in large organisations, these services are highly standardised in order to deliver consistent service quality across each institution.
While this approach is very cost-effective, it is not always well suited to the needs of researchers seeking to use ICT as a research tool.
eResearch SA, on the other hand, provides researcher-oriented IT tools and services that focus on flexibility and performance and are often highly specialised to specific applications.
See our current employment opportunities
The best way to contact us is by sending an email to: helpdesk@ersa.edu.au. In your email please specify your contact details, your area of research and all the relevant details about your problem i.e. product, release, error messages etc. The more detailed your email is, the faster we'll be able to provide the appropriate assistance.
eResearch SA's facilities may be divided into the following broad categories:
Generally, these facilties and services are available to Australian researchers. For university-based, "pure" research, use of these is, for the main part, free of charge.
Use within commercial, industrial and Government spheres is subject to charges.
Thus, if you are involved with research, eRSA's facilities and services are here to assist you in that research. However, please do be aware that, depending on circumstances, some usage may be subject to fees and charges.
Please see the Charges page for an outline of costs associated with certain facilities and services.
For circumstances not covered by that information, or where discussion is required, please contact our Direcetor.
To gain access to the eRSA facilities, you require an eRSA account. Please fill in the membership form here to apply for one: http://www.eresearchsa.edu.au/membership_form
We would like to think so! Please contact us
High-performance Computing (HPC) is the use of specially-designed hardware systems (and associated software) that allow computational operations to be undertaken at higher speed than is possible with "typical" computers.
Typically, HPC systems consist of many individual compute nodes that are connected together in such a way as to make the overall system much faster at computational jobs than any of the individual nodes alone would be. Thus, the combined nodes (dozens, to hundreds or even thousands in number) can work togther to undertake tasks that would take a single node a prohibitively long time.
This relies on not only a large number of compute nodes- the way they pass data between eachother, the way they access common data, and the way the software that is run makes use of the many compute nodes, is of vital importance. So, while an individual node may be no faster than a good contemporary laptop or desktop machine, it is the overall capability of the entire system (multiple compute nodes, their interconnection, data and memory access, and optimised software) that gives the increase in performance.
Such systems are quite complex in terms of hardware, management software and maintenance, and they also require purpose-built rooms with air-conditioning, mains power conditioning and similar non-trivial support infrastructure.
However, without the sort of number-crunching capacity enabled by facilities such as eResearch SA's HPC systems, many of the problems encountered in today's research areas would not be able to be investigated.
Details coming!
Details coming!
Commercially-licensed (or paid for) software can also be installed on our systems by eRSA staff. However it is up to the user to pay for a valid license for the product. Please note that we will not install software on our systems that in any way violates a usage or licensing policy.
Upgrading of software is done based on the resources and effort required. Upgrade licenses for software are the responsibility of the user.
Custom-written user code can be installed and compiled on our systems; please note that we can only provide limited support for custom-written user code.
Details coming!
Details coming!
We make use of the Linux Operating System on our HPC Facilities and as such cannot support native Windows code.
We do not place any hard limits on HPC usage, however our HPC facilities are a shared resource and as such we ask users keep their usage to a reasonable level.
- Submission of more than 50 jobs to the queue in a single run - Requesting large amounts of wall time on a large number of queued jobs (Submitting 50 jobs to the queue and requesting 300 hours wall time per job)
This depends heavily on the type of jobs you are running and what the application you are using supports. It is best to contact the help desk if you need help selecting the best supercomputer for your job. As a rule of thumb:
Job start times vary based on a number of criteria. These include
During busy times you may have to wait 2 or 3 days for your jobs to start.
If you think your job has been queued for an excessively long time, contact the Service Desk and let us know.
Details coming!
There are two ways to find this information.
When logged-in to one of the eRSA systems, use the module avail command for an up-to-date list of installed modules on that system. Note that this must be done on each system individually. Refer here to help decide which system is most applicable to the type of job you're considering running.
Details coming!
Details coming!
Details coming!
Details coming!
Details coming!
Details coming!
/home - Storage for your program code, submission scripts. This is network-based storage. (25GB / user)
/data - This is a storage area for application input and output files. This is network-based storage. (50GB / user)
/scratch - High performance storage used for storing temporary input and output files while a job is running. This is local node storage.
Reading input or writing output files to /home is strictly prohibited.
For MPI jobs please use /data.
For sequential jobs please make use of scratch storage. Scratch storage is much faster than network storage, so jobs will complete quicker.
We currently do not offer a database hosting solution, however, we are able to offer custom solutions. Contact the help desk for details.
Quotas.
What the heck is a Quota?
A quota is a restriction that is placed on the amount of data an account may use.
A quota consists of a soft/hard quota and a grace period.
A soft quota is a predetermined level where a warning email is sent out. This however does not prevent you writing more data until the grace period is reached.
A grace period is the amount of time you are allowed to go over the soft limit before the system blocks your ability to write more data.
A hard quota is a predetermined level where the system blocks your ability to write more data. You will still however be able to read your data.
Could I have an example of the Quota system?:
Scenario 1 -
I have 20GB of data in my home directory. I copy another 10GB to my home directory.
So I now have 30GB of data which means I'm 5GB over the soft limit. I receive an email stating I have gone over the quota.
A counter is now started on the server which is called the grace period.
I now have 7 days to reduce my data back down below 25GB (the soft limit). However I can still keep my data at 30GB safely for a week.
Scenario 2 -
I have 30GB of data in my home directory and I decide to copy another 25GB. As soon as I reach 50GB of usage on my home directory, the system stops me writing anymore data.
The copy / scp / rsync command would return an error "quota has been exceeded".
Scenario 3 -
I have 30GB of data in my home directory and I forget to reduce the data below 25G. The 7 day grace period then expires.
The 25GB soft limit now becomes a hard limit. I will be unable to write anymore data to my home directory until I reduce my usage below 25GB.
There are two parts to this issue... depending on the desired nature of the website. We support three applications in this area.
1) Drupal and Plone : these are examples of Content Management Systems, which allow groups of people to contribute to the development and maintenance of a website, and largely through a browser-based interface. They can provide a visually rich environment for the site (so that it is pleasing to the eye, informative and content-rich) and are a good option when a collaborative and configurable site with a strong public-facing side is required. Site-member roles and permissions may be managed at a fine level.
2) Sakai : originally developed for the educational sector, Sakai is useful for developing group-maintained, information-rich collaborative sites. The emphasis is more on ways to organise groups of people and share information, than on producing visuallly-rich sites with a strong public face. A Sakai site is configured with a number of selectable Tools which have a collaborative theme- Calendar, Schedule, Announcements, Forums, Wiki, Resouces (file utility), and others- and the overall intent is that the site is an aid to effective research collaboration. There can be public display of content- but this is in a quite simple, textual format. As with Drupal, site-member roles and permissions may be controlled.
So- if you're after what is more generally thought of as a website, then Drupal or Plone may well be the preferred option. If you are after a site (a "project site", in Sakai parlance) that primarily will be used as an aid for organising your research group, then Sakai may be more applicable.
In the first instance, contact the Help Desk for more information.
Certainly. eRSA supports (and uses!) two applications in this area:
1) EVO http://evo.arcs.org.au
2) Access Grid http://accessgrid.org.au
Both applications allow simple face-to-face conversation with audio and video, but have extended functionality such as shared desktop, shared whiteboard, file transfer, text chat, multiple video/camera sources, and more.
It also is possible to hold meetings that are accessible simultaneously both to EVO and Access Grid users (so-called bridged meetings).
See the eRSA pages on EVO and Access Grid, and also for information on eRSA's Meeting Room. See here for the relevant booking form if you would like to make use of our video collaboration facilities.
eRSA provides Service Desk support to Australian research users of these tools, and can advise on getting the applications running as well as hardware requirements for various levels of installations.
Please contact the Service Desk for initial inquiries as well as user support.
The EVO video-collaboration tool has a facility whereby people may use a phone to connect to an EVO Meeting via audio only. This can be very handy when travelling, or when network or other issues preclude attending via EVO proper.
When one has joined the Meeting via the Phone Bridge (as it is called), one will hear the audio from all the other participants, and they will hear you.
To use the EVO Phone Bridge, follow these steps
Each EVO Meeting has a unique ID number. If a password has been set for the Meeting, it will also have a Phone Bridge password (actually a number). Thus, before being able to connect via the Phone Bridge, you will need to obtain the Meeting ID (and password/passnumber if required) from someone who has that information (such as the person who booked the Meeting, or someone who has EVO running and can see the Meeting information).
Note that it is possible to use EVO as a "hub" between muliple people joining via the Phone Bridge. This effectively makes an EVO Meeting into a conference call, but only at the cost of a local call for each participant (if they use a phone number which is local to their area). To do so, book an EVO Meeting and distribute the details to the intended participants. They can each then join the Meeting via the Phone Bridge, and have a multi-way phone conversation via the EVO Meeting's audio. The number of available lines is limited, so this approach cannot be scaled too far.
It is not actually necessary in this case for anyone to use EVO itself to join the Meeting, although this could provide a useful monitoring tool during the Meeting. Even if no-one joins the Meeting via EVO proper, the Meeting will open and the Phone Bridge can be used.
See here for further documentation on using the Phone Bridge.
Fundamentally, these video collaboration tools are intended to enable the same basic activity- online, video- and audio-based meetings between people who are in different locations. Both applications allow meeting participants to see and hear eachother.
Further, both applications have functionality beyond just "see and hear". There is text chat, the ability to send desktop content as a video stream, multi-way connectivity, the ability to use multiple cameras, file-sharing, etc.
Whilst either may be used in situations ranging from a single-user with a desktop/laptop to room-based installations for groups of people, EVO is intended to be straightforward for individual users to get running, and to do so with little or no support. Apart from ensuring that Java is on your machine, EVO does not need the user to install any software. A common example of use is for easy, rapid one-to-one or small group meetings, with the capability to share some or all of a participant's desktop as a video stream.
Access Grid, whilst requiring user installation and a slightly higher level of configuration, is Open Source, and consequently has a greater range of extra features that can be added and used. Whilst it certainly can be used on a personal basis, it is particularly well suited to meetings with larger numbers of participants. Items such as VNC, VPCScreenCapture and various Shared applications allow a high level of participation between AG users in a Meeting. Extended uses include remote teaching, online conferences, remote instrument control.
In short, EVO is quick to get going, and is very handy for convenient, frequent meetings. Access Grid can require more work for installation and configuration, but has a wider range of extra features and is more adpatable to a wider range of uses.
Perhaps we can split this into two questions.
Firstly, what is data visualisation? This is the activity of presenting data (from whatever source, in whatever field of study) into some sort of visual format that enhances - or even allows- one's ability to interpret those data. This can range from a simple two-dimensional graph, to a fully immersive, virtual-reality-based environment involving advanced soiftware, multiple projectors, haptics devices and real-time computational steering. In short, presenting data in such a way that allows us to use our eyes, and the brain's associated visual processing, to look for patterns and relationships in data.
Second, what is visualisation, in a more general context? This is a wider and less defined concept. It is, perhaps, the development or presentation of some idea or concept in a visual form. This can range from a presentation of an architectural design via a sketch or, more commonly these days, as a three-dimensional image; to computer-generated imagery that is used in the film industry. The source (i.e. that which is to be visualised) does not need to be data (which we most often think of as being numerical data); it is just something which needs to be, or is better expressed or presented, in a visual form.
More and more, visualisation is being achieved through software. This is especially the case for data visualistion, where many specific software applications have been written explicitly for the purpose of visualising numerical data (examples include AVS Express, Open DX, Visualisation Toolkit, and many more).
Humans have stereoscopic vision. We have two laterally-displaced eyes, and the slight differences between the left-eye and right-eye images are processed by the brain to furnish us with a sense of depth perception.
This is the natural way in which we view the world, and we intuitively use that direct depth perception as an aid to our interpretation of the world. By definition, it requires the brain to be provided with two separate images- two views of the same scene, differing due to the different locations of the imaging systems (our eyes). Most artificial scenes- be they drawings, paintings, photographs, TV screens, computer monitors- present the eyes with a single image only. Although we view that "scene object" with both eyes, there is no sterescopic imformation within that scene object. It is "flat", since both eyes see essentially an identical image of that scene object, and there is no information therein for the direct perception of depth (although other clues, such as object occlusion and lighting effects in that artificial scene are interpreted so as to provide some depth information).
Thus, in the viewing of these monoscopic artificial scenes, we are missing out on a rich source of visual information that we take for granted when viewing the natural world. What we're concerned with here is the attempt to introduce natural depth perception (stereopsis) into such artificial scenes- to imbue such scenes with a greater amount of the visual richness that we use as a matter of course in our day-to-day view of the world.
To achieve this, we must first acquire or generate the image pairs that are required. This may involve capturing real world content (i.e. photography or filming of real world scenes) or computer-generated or other artificial content- or, indeed, the combination of these.
We will look at such acquisition in the next FAQ item.
We will consider the following two broad categories :
Real world content
By this is meant the use of still photography or video/film techniques to capture natural scenes (including studio techniques such as filming elements against green/blue screen). One technique is to use a single camera that is moved horizontally between shots- this can be used when the scene to be captured is static. A more generally usable scenario is to use a pair of identical cameras, mounted in such a way to ensure that their optical axes are horizontally separated by an amount that is appropriate for the distance from the cameras to the target object.
In this context, each camera will acquire the visual content to be presented to the viewer's corresponding eye during later stereoscopic display and viewing.
The camera pair will record the left and right images simultaneously. The level of synchnronism may not be perfect, but it should be sufficient that there is no time-based difference between the two left/right images large enough to spoil the stereo effect when the images are viewed together. How the cameras are mounted depends on a number of factors, including the camera body size and shape, how close the cameras' optical axes need to be, is there a need for rapid variation of interaxial separation, etc. Mounting methods range from simple mounting bars using fixed holes, to motorised mirror-based rigs that allow arbitrary axial separation with a large variety of camera bodies.
Imaginary / non-real content
By this is meant the development, by computer-generated imagery or other techniques, of images that are not directly derived from imaging real world scenes. This could be the result of employing ray-tracing software such as POV-Ray, 3DS, Maya and a host of others; or even by carefully planned and executed drawing or painting. In a CGI example, one might render an image pair for a virtual scene, with different virtual camera locations in each scene; the virtual cameras for the virtual scene are then analogues of a real-world camera pair.
In this context, separate renders of a scene are used to generate the visual content to be presented to the viewer's corresponding eye during later stereoscopic display and viewing.
No matter how the content is obtained, the image pairs must somehow be presented in an appropriate way to the viewer. This will be discussed briefly in the next FAQ entry.
Once one has obtained some stereoscopic (a.k.a. "3D") content, how is it to be displayed? This is indeed a rapidly evolving area, with strong interest in devleoping hardware for the consumer market. Large-scale uptake is some way off yet... we will discuss some of the basic principles, as well as some hardware which is currently in use.
The basic requirement is that each of the viewer's eyes must receive the image that is intended for it- and only that image. The most common way to achieve this is via the use of glasses which somehow allow or block the left or right image as required. That is, the right eye must see oinly the image intended for the right eye; and similarly for the left eye. It is the job of the "3D glasses" to make this happen.
There are several methods for achieveing this, some of which we'll now look at briefly.
Colour separation
Anaglyph The viewer's glasses have different colour filters for each eye, a common example being red and cyan. The left and right images are processed so that their colour content matches the range of colours admitted by the corresponding eye filter. Typically, these red/cyan images can be composited into a single image, so that an anaglyph image can be presented as a single image that's encoded with the stereo information.
Infitec A refinement of the anaglyph method, this projection method uses matched filters for the projectors and viewer's glasses. Each left or right filter covers segments of the entire visual range of colours; the transmission curve resembles a comb filter, rather than the broad block or pass of traditional anaglyph filters. Two projectors are required.
Polarised
Two projectors are used, each with a polarising filter (usually in front of the lens). The planes of polarisation of the filters are crossed. The viewer's glasses have matching filters, and thus each eye sees only the matching projector's image.
Shutter glasses
A single projector (or monitor) alternately displays the left and right images. The viewer wears glasses which contain LCD panels which are alternately opaque and clear (that is, when the left panel is opaque, the right is clear, and vice versa). The glasses operate in synchronism with the projector; when the left image is displayed, the left eye panel is clear and the right opaque, and vice versa. This is done at a rate sufficiently rapid that most people do not perceive any flickering in the image.
Glasses-free displays
Currently suited only to much smaller numbers of viewers than any of the above methods, it is possible to produce monitor displays which simultaneuosly display both the left and right images, yet ensure that each of the viewer's (or viewers') eyes see only the correct image without the use of glasses.
Yes indeed. At present, we have three sets of imaging hardware.
If you would like to make use of any of these, please contact us.
eRSA offers two visualisation suites.
The Vislab has a single 4m x 3m screen, and employs the Infitec system. Movable desks seat five comfortably, and up to around twenty may be accomodated with chairs.
The South Australian Virtual Reality Centre (SAVRC) has three 2.3m x 1.3m screens, for an overall screen of 6.9m x 1.3m (with blending between screens 1 and 2). Shutter glasses are used to enable stereo viewing. Tiered seating accomodates 23, and the room can be opened up to allow up to 100 people to use the space.
Non-visualisation use of the suites has included filming and photography locations, due to the ability to back-project images and control lighting very closely, and also as a green-screen facility.
There is a Linux PC in the Vislab which is used to run the AVS Express data visualisation package, and has 3D glasses for stereo viewing of its monitor.
eRSA also two haptics devices - see here for more information, and contact us to check on their availability.
Vislab
SAVRC
We currently host Drupal- and Sakai-based websites for Researchers.
If you are interested in hosting a site with eRSA, please contact the service desk. We are also happy to discuss the hosting of other systems with you.
Details coming!
Details coming!
Details coming!
Indeed we can. eRSA has a number of visualisation facilities:
1) eRSA Vislab
2) South Australian Virtual Reality Centre (SAVRC)
3) visualisation desktop machine (Linux Fedora Core 5, running AVS/Express for data visualisation, with shutter glasses for stereo)
4) Mac G5 (a general "workhorse" machine for Mac applications).
See the Vislab and SAVRC pages for lists of installed software. Assistance can be given in using AVS/Express for data visualisation.
Both the Vislab and SAVRC have stereo-capable displays, but please note that not all software is stereo-capable or compatible with the hardware used in those rooms, as it may not deliver the appropriate video format.
"Haptics" refers to the use of tactile sensation in human interaction with data. That is, in essence, a physical interaction with virtual content.
This is most often accomplished through the use of some electro-mechanical device which is used with the hand, both for delivering some sort of input to the virtual environment (such as the position of a virtual tool, or just a cursor position in virtual three-dimensional space) as well as providing tactile feedback to the user via resistance to hand movements or even active movement of the physical device. Often, the part of the device that is held is a pen-shaped stylus.
This allows the user to interact with the virtual environment via not only the more usual visual means, but also via tactile sensation. Thus, more of the user's senses are engaged, and the interaction with the virtual world is more involved.
Applications include virtual sculpting, teaching and training of medical procedures, remote control of physical devices, and data visualisation (extended beyond visual information only, of course).
The console output of your jobs are emailed to you and stored in your working directory (eg. jobname.o11111).
Normally error messages or crashes are captured in these files. Review these files and if you are unable to debug the problem, submit a request to the service desk.
Please attach the output file and point us to where your submission script / code is stored in your home directory.
Please use this form to reset your password: https://www.eresearchsa.edu.au/eRSAUserAcctManager/default.do
We only allow logins to our systems from the University of Adelaide, UniSA and Flinders University networks.
For networks that are outside the Universities (i.e The Internet), we can allow explicitly grant access, however you must have a static public IP address.
We cannot allow direct access from ADSL or 3G Broadband systems. If you are using an ADSL or 3G broadband system, please contact your local University ITS Helpdesk and request VPN access to a University Network.
If you can't find an answer to your question here, please send an email to: helpdesk@ersa.edu.au and one of our specialist staff will contact you as soon as possible.