Renewals available now!

Hopefully you'll have already seen the announcement on one of our many communication channels such as our website, Facebook page or Twitter feed but if not then read on.

Many of you will remember the changes we brought in last year in April 2011.  Due to funding restrictions, we had to reduce the CPU allocation of all users to a maximum of 2000 free cpu hours in one year.  You can read the original announcement on our website.  As we are now a year on, all NGS users can apply for another free 2000 cpu hours.

If you are looking for some proof of concept computing, a "sand pit" area for your PhD students or to test concepts before purcahsing more hours etc then this is an ideal opportunity.

If you have any queries at all then don't hesitate to contact the NGS helpdesk.

"hello, science\n"

It is worth pondering how scientific programming is different from other programming. Last year I gave an introductory talk on specialised languages used for science (in which I include Fortran but mainly covered R, APlus, and suchlike). How do you do "hello, world" in science?  It has to be floating point, so I picked calculating the length of a vector.

Let's just digress for a second to do that. Say I want to calculate the length of (v_i); I can then start with s=0 and loop over i, adding v_i², and finally take the square root of the sum:

my $s=0; foreach (@v) {$s+=$_*$_;} return sqrt($s);

Or we can do it more functionally, creating a new vector of squares ("map"), the elements of which are then added together ("reduce"):

(sqrt (reduce #'+ (map 'list (lambda (x) (* x x)) v)))

... which is the origin of the MapReduce paradigm, but it has the disadvantage of creating a temporary copy (here a list) of the squares. But. If you are doing them in parallel, with each task squaring its own entry (which you might if v is large), in this case you do need to keep the intermediate results anyway.

Then there are questions of precision and suchlike, for which David Goldberg's paper is still one of the best introductions. This is in contrast to "normal" programming, where one should read Zen and the Art of Motorcycle Maintenance (but see also 10 papers).

We can then ask how science use of * is different from normal use of * (where * is anything). Do scientists use the cloud in a different way from non-scientists?

With this in mind, JISC and STFC co-organised a workshop on scientific computing in the cloud (and grids.) Funded by EPSRC, and with about 75 registered participants and 15 speakers from the UK and beyond, it focused on the science use of cloud (and grid) resources. There were a number of discussions on cost effectiveness, cost models, and the true cost of doing science in clouds compared to your own (university's) resources. How careful should you be about putting your data "in the cloud" - and here we are just talking about analysis of data, not long term storage. How do you convince sceptical users?

It seems that some of the lessons learned from the grid carry over to the cloud world: the use of gateways and portals is a useful way to get researchers started using the cloud, but then someone needs to build these things for the research communities - and they will in general be domain specific. And building these cannot just be a proof of principle; they have to be production ready and supported.

Of course e-scientists have scientific applications, specialised libraries, and repositories of libraries - and every e-science programmer should know their BLAS and LAPACK... on the other hand, the presence of gateways and portals brings hope to the "ordinary" researchers who want to make the most of the brave new world of the fourth paradigm but are not themselves programmers and choose (rightly) to focus on their science.

Science use of clouds may have learnt from science use of grids, but clouds also introduce new issues. We agreed at the workshop that it was worth pursuing the case studies. There was no single "pain point" for everyone, but everyone learnt from each other. Supporting scientific research in the clouds (and grids) is a research topic in its own right, bringing together computing, science, best practices, usability, security, performance, and more - and as long as we continue to share experiences, the researchers who use the infrastructure will benefit.

NGS at the EGI Community Forum, Munich

You can tell it’s been conference season over the past few weeks – lots of travelling, lack of sleep and notes written in cryptic language on my laptop from various sessions and presentations.

The EGI Community Forum was held in Munich, Germany at the end of March and consisted of 4 days of conferencing and various workshops on the Monday morning.  As well as helping to look after the UK NGI exhibition stand, I also attended a wide variety of interesting sessions including:

• Sustaining the EGIInfrastructure
• Impact of e-Infrastructures: Theories and practices ofassessment methodologies
• Community-tailored Services
• Communication: the key to future funding

Each session had its highlights – the EGI session looked at how to count the number of users that EGI actually has.  They attempted to do this through the use of VOMS (Virtual Organization Membership Service) but there were problems with the information contained being out of date or indeed missing in some cases, not all users being registered, expired users still being in the system and many more.  However at the end of the day they did eventually come up with a definitive figure which was as accurate as possible on the day it was calculated – 20706.

Also in this session was a presentation from the German national grid – D-Grid.  They presented on a business model for a sustainable Grid infrastructure.  The slides from this session are definitely worth a look for anyone interested in the next stage of national e-infrastructure.

I also presented on the NGS Campus and Community Champion initiatives at the NGS in the session on Communication.  To save me telling you all about it, I’m instead going to provide a link to a blog post written by Elizabeth Leake who wrote about her take on the session and my presentation.

A big congratulations to the local organisers who did a fantastic job – great venue and great food as well as inbuilt entertainment in the conference venue.  You may have to join our Facebook page to see evidence of this coming soon!

Munich was another great EGI event and we’re already planning and looking forward to the next one which is the EGI Technical Forumin Prague in September. 

Doing a lot of talking about software

Recently I attended the Software Sustainability Institute Collaboration Workshop (CW) which was held in a very sunny Oxford for 2 days.  It was a busy workshop for me due to being on the steering committee, being part of the events team, chairing a session, giving a lightning talk and scribing for some of the sessions as well!

If you’ve never been to a CW before then the best way to describe it is a conference but not as you know it!  In most conferences people sit and listen to one person giving a demo or PowerPoint presentation at the front of a lecture theatre.  At a CW people pick the topics they want to discuss and head off into break out rooms to have stimulating and interactive discussions about these topics.  Everyone then reconvenes in the main lecture theatre and all the groups report back to inform all delegates of the points and issues raised as well as some possible solutions!

However before the breakout sessions there were some lightning talks – short presentations done against the clock.  Simon Hettrick from SSI makes sure that there are no misunderstandings as a large countdown timer is projected up on the screen along with the one and only slide you are allowed.  I have done lightning talks before at SSI events but this time Simon had raised the bar by only giving each delegate a mere 3 mins.  As I had to present on both the Campus and Community champs in this time it was a tall order but I made it – just!

After the adrenaline rush of the lightning talks we moved onto the more sedate business of breakout sessions.  During the two days I attended several sessions -

•    Building research and communication networks across disciplines
•    How to blog, and how to run a blog 
•    Bringing together representatives of the research community: Institute's Agents and SSAs, and the SeIUCCR Community and Campus Champions
•    Using the internet and social media to increase your impact and publicise research to the public and research community 

From each of these sessions the 5 most important points learnt during the session were recorded and reported back along with -

•    What are the problems, and are there solutions?
•    What further work could be done, and who should do it?
•    Are there any useful resources that people should know about?

All the notes from all the sessions are available through the Collaborations Workshop 2012 Google Group – you don’t need a Google account to view the information.  They make for some very interesting reading particularly if you are a research software engineer or a researcher who uses software!

Photos from the event are also available which prove just how nice the weather really was before we descended back into winter this week!

Radio silence

It's gone a bit quiet over here at the NGS blog lately mainly because I was completely caught up in writing a bid which took over my life for a few weeks.  As it was all I did for a couple of weeks I didn't have much to blog about.  Hopefully the bid will be successful and we'll have some exciting news for you in the near future!

Apart from that I have been working with colleagues at SSI in preparation for their Collaborations Workshop which will take place on the 21st - 22nd of March.  There has been a great response with maximum attendance and a great range of people attending.  One of the purposes of the workshop is to get researchers and software engineers working networking to find where they can help each other out. There aren't many conferences out there where the aim is to get everyone talking to each other all day instead of just a few people doing the talking!

In completely different news I just posted an article to the NGS website from EGI.  The EGI are showcasing their users research much the same as the NGS user case studies do (wonder where they got the idea from...?).  They are doing their case studies in the form of video interviews and the first one focuses on the research of Henry Hocking of the CONCO project who used the grid to analyse naturally occurring molecules in venoms used by marine snails to immobilise their prey.  You never would have guessed that one!

On email addresses in distinguished names

Those of you who are sysadmins know we have email addresses in host certificates, in their distinguished names (DNs).  The origin of this decision is lost in the mists of time - it certainly pre-dates the UK e-Science CA - I seem to remember something about host certificates being used as clients and the email address of the contact appearing in the log file, as a forerunner of "robot" certificates - which can't quite be right because initially we did not give host certificates client extensions. But hosts have been used in this way to implement portals.

In any case, the practice is now deprecated, mainly because much of our software (strictly speaking incorrectly) depends on the string representation of the DN, and different software stringifies emailaddress in different ways. We have been meaning to get rid of it for a while, waiting only for some code changes and an update to the policy.

In fact the policy needs updating because in a (very small) number of cases we are doing things that are not consistent with the policy - but which are nonetheless wholly consistent with IGTF. Actually the only examples I can think of is that we have permitted two "software robots," a practice which is permitted by IGTF now but wasn't when our policy was written.

The proposal is now that we remove email addresses from DNs, before the policy rewrite is finished (its about 2/3 done since you ask.) Removing email addresses is clearly consistent with IGTF, but deviates from our historical practice of  preserving the end entity DN across all generations of CA certificates. Having an out of date policy is of course not consistent with IGTF...

The trouble is, how do we know whether people depend on the email address in the DN?  We have no way of knowing how the certificates are being used. Of course we could take the approach that if the certificate is being used for unsupported purposes, then you're on your own. OTOH, we have usually strived not to do that, even if grid software makes that quite difficult (see GFD.125 again, or every rollover).

So we need to leave it to the "owner" of the certificate to decide. The easiest way of doing this is JK's proposal, that we remove email address from new certificates, but keep them on renewal. For host certificates, getting a new certificate is often the same amount of work as a renewal.  Existing certificates are not affected but if you want your certificate to be affected you could revoke it and get a new one.

And of course all this applies only to hosts, there is no change for personal certificates.

Bits and pieces

It's been one of those weeks with a lot of bits and pieces going on.  Busy and varied is how I'd probably sum it up!

Tuesday was the NGS Collaboration Board meeting which was held at the University of Birmingham thanks to the kind hospitality of Paul Hatton.  The theme of the meeting was reaching out and engaging with potential new communities and existing user communities.  Mike Jones gave a presentation on SaRONGS to show how we are making it easier for people to access grid resources and I gave a presentation on the Campus and Community Champions networks.  Following on neatly from my presentation was Rebecca Notman who is one of our Community Champions.  Rebecca spoke about her role and how the NGS has played a part in her research.  There was also plenty of time for discussion with each of our Collaboration Board members updating us on new and activities from their institutions.  It seems to be a busy time in the world of research computing!

Wednesday was the next seminar in our short series.  This time it was the turn of John Kewley from STFC Daresbury who is the NGS helpdesk manager.  After a few technical issues, John spoke about the Certificate Wizard - a tool that the NGS produced to help people manage their grid certificate more easily and it seems to have worked.  There have been less helpdesk queries regarding certificates since the introduction of the tool.

Yesterday morning I took part in the steering group for the forthcoming Software Sustainability Institute Collaboration Workshop.  This is always a really enjoyable conference as it's 2 days of full interactive discussion and networking.  If you go to a conference to get peace and quiet to read your email then this isn't for you!  Every session is a group discussion session apart from when the groups report back to the conference as a whole.  There are some really interesting topics for discussion this year, all of which have been suggested by the attending delegates.  If you would like to attend and you are a software developer then have a look at this as you may be able to get a free place and a contribution towards your expenses.