NGS at SC'11 - round up

The UK presence was fairly significant this year at SC'11 with attendance by David Wallom, NGS Technical Director and a significant number of the leaders of research computing centres from around UK universities. This included NGS member sites @ Bristol, Leeds, Oxford, Southampton and EPCC.

In this blog post, David gives us a round up of NGS activities at this major computing event.

Having got off of the very long flight from Heathrow
to Seattle we settled onto the metro to get us  downtown. After passable sleep the following morning we headed over to the SC’11 venue – the Washington Convention Centre to collect our badges and then visit the workshop on HPC in Smart Grid, where there was UK interest from the EC FP7 HiPerDNO project being presented by Dr Stef Salvini, OeRC. Following a very productive day where we learnt the state of the art in US Smart grids, how they intend to utilize knowledge developed through the national e-infrastructure for research. We then met up with the EGI team who had an exhibition stand at the conference.

The Monday workshop, Many-Task computing on Grids and Clouds 2011,  started off with an interesting keynote from David Abramson (Monash) a long term friend of the NGS through support for their Nimrod tool which is popular with several of our biosciences users. After this there was a panel session which went slightly off topic to talk about exascale more than Many task but it still attracted several questions around the need for exascale, when we are still struggling to get a significant user base onto smaller HPC systems. Overall a good workshop though having the panel first did mean that a number of people didn’t hang around for the rest of the papers. This workshop was operating in a very competitive market with other sessions on cloud and data management which also attracted significant crowds.

The first full day of the conference allowed for the first good look around the exhibition floor alongside several interesting birds of a feather sessions There was also the  first of a number of conversations with different groups and vendors, including Microsoft, Mathworks and Adaptive Computing.  To give an idea of scale this picture is down one of the main aisles in one of the 5 rooms that were all about this size!!



Pretty impressive stands by a number of people
but the coolest was the multi projection globe on the NOAA stand.

We of course also announced
our activity with Globus Online which created a lot of interest and ended with us having a number of interesting conversations with NSF regarding future collaboration between our national e-infrastructures.





During the meeting the EGI booth was continually visited by a reasonably large number of people, we had the Real Time Monitor showing as normal (having seen a lot of 3D screens this needs to be done in 3d now for next year!). They did though give away a pretty large number of t-shirts as did a lot of stands, so I ended up as the moving poster board around down town  Seattle from 6:30-7am every morning on my morning run!

Castles, case studies and lightning

Last week I attended the Software Sustainability Institutes Collaboration Workshop in Edinburgh. As with previous meetings this event was very enjoyable with a great deal of discussion, actions and collaboration taking part.

The organisers had revamped the programme for this year’s event and one of the changes was the inclusion of “lightning talks”. The set up was interesting with each presenter having 5 minutes and one slide which shared the screen with a rather large countdown clock. It certainly kept the presenters on their toes and the attention of the audience! Unfortunately given the nature of the presentations you really had to be there to appreciate the talks but some presenters did manage to get a lot of info on their slides. In particular the slides from Taverna, STFC, software preservation, soundsoftware.ac.uk, e-science central, SPRINT, Hartree Institute and Youshare.ac.uk are worth a look. I have linked to the websites for each project where they exist but for the slides, visit the materials section.

After the a lovely lunch it was time to start what I think is the most enjoyable part of the workshops – the breakout sessions. Before the event, delegates have the opportunity to submit topics that they would like to discuss at the breakout sessions and then at the event people vote on what topics they would like to discuss. The delegates break into groups and disappear off to various parts of the building to discuss the topic. Each group has a chair, a scribe and someone who “volunteers” to report back but quite often people take on two of these roles.

I attended the session on preparing case studies to support cases for funding which was rather apt as I prepare the NGS user case studies. There were about 7 of us from a variety of backgrounds including funding council reps and the discussion covered areas such as different types of case studies, ways that case studies could contribute to REF, how to format case studies and much more. It was a very interesting hour and we did come up with several suggestions for further work for the SSI.

The second breakout session of the day took place after some caffeine had been consumed and this time I attended the session on “measuring the research impact of software”. Unfortunately the notes from this aren’t up on the SSI website yet but when they are I will make sure I update the link!

So that was day 1 at the CW11. I’m sure you don’t want to hear about the conference dinner so I’ll leave that out and write up day 2 very soon!

Are you a researcher looking for a partner?

If so then you really should consider coming to the dating event of the year! Well okay it’s not quite a dating event but matchmaking is definitely part of the plan of the Software Sustainability Institutes Collaboration Workshop.

It will be held in Edinburgh at the beginning of March and is described as “the perfect opportunity to meet the researchers, software developers, funders and other software experts that can help you advance your research”.

If you are a researcher who uses software but could do with some help from a computer scientist to make the most of your software, come along and advertise yourself and your situation / problem. You can give a lightning talk or present a poster and then work through the issue with other attendees in small break out groups.

There have already been some break out group discussion topics suggested BUT one of the best things about this meeting is that the agenda constantly changes depending on the interests of the attendees, the emergence of new discussion threads and tangents. There’s never a dull moment!

I’ve attended several of these meetings and I’ve thoroughly enjoyed every single one. No death by PowerPoint and plenty of discussion and positive solutions instead! The constantly changing agenda works really well as we report back to the assembled attendees after every session and then decide on the next set of discussion topics. I’ve always met new and interesting people and came away fully enthused.

If you are a developer there are some free places up for grabs but the deadline is this Friday (18th Feb) so don’t delay!

NGS roadshow event at the University of Huddersfield

Last week saw the NGS outreach team at the University of Huddersfield for a NGS roadshow event. The local organiser was Ibad Kureshi who did a fantastic job of organising everything locally and making the day went smoothly. Ibad also did a great job of advertising the event locally meaning that we had over 30 participants at the morning roadshow and over 20 registered for the afternoon training event.

The roadshow kicked off in the usual fashion with an overview of the NGS from our Technical Director, David Wallom from the University of Oxford. Many people in the audience were not familiar with the NGS before the event or had just heard our name mentioned but were unaware of what the NGS actually does so this presentation is designed as a gentle introduction!

Following David we moved onto presentations from NGS users including Paul Martin who is a researcher at the University of Huddersfield. Paul has been using the NGS for computer modelling of thoria in order to determine its suitability for a next generation nuclear fuel. He explained how he has used DL_POLY 2 which scales very well on the NGS. Paul in particular praised the good on-line instructions/training, FAQ’s, blog and helpdesk/support which is great to hear!

Paul was followed by another user, Matt Smith from the University of Liverpool. Ibad had suggested that a presentation by an Abaqus user would go down very well due to the interest in this software package at Huddersfield. We were happy to oblige! Matt spoke about his use of Abaqus on the NGS to model lattice structures. This was a very interesting talk helped by the sample materials Matt brought along to illustrate his presentation. As Ibad had thought, Matt’s presentation prompted plenty of questions about his usage of the NGS and about his research.

David Fergusson from the training team at NeSC then elaborated on how users actually get started on the NGS and how to apply for a certificate, run jobs etc. Again there were plenty of questions showing that Huddersfield researchers are keen to use our resources!

The final presentation was by Ibad who outlined the locally available resources and how these tied in with the resources offered by the NGS. We’ve found in previous roadshows that having presentations about local resources helps the audience to visualise how the NGS fits in locally and that it is there to complement existing resources.

All the presentations from the event are available on the NGS website from the event page.

Got a problem with your software?

If so then we know who can help! Todays blog post is courtesy of Simon Hettrick from the Software Sustainability Institute (SSI).

In 2010, a crack developer was asked to join the SSI. This man promptly set up as the Institute’s software architect. Today, still wanted by a number of projects, Steve survives as a developer of fortune. If you have a problem, if no one else can help, and if you can email him, maybe you can Ask Steve!

At the SSI, whenever we have a software problem we simply ask Steve. He’s our in-house software architect and all-round guru of code. Then we got to thinking: it’s selfish to keep such a valuable resource to ourselves, we should make Steve’s knowledge available to everyone. And that’s when the idea for the Ask Steve! blog was born.

So what is Ask Steve? The idea is that anyone can email Ask Steve! with a software trouble and query. Each week or so, Steve will work on a problem and post his answer to the blog. People can comment, try out the solution or simply get back to Steve with another question. Steve will sort through the questions he is posed and answer the ones that trouble the most people.
Next time you have a software problem, visit the Ask Steve! blog.

The NGS at the centre of the universe?

I've recently been working on a number of case studies with several NGS users to highlight the different ways that the NGS is used in many different research areas.

The first case study from this batch has recently been released and is now available on the NGS website case study section. This case study highlights the work of Cristiano Sabiu from the University of Portsmouth who used the NGS to analyse the distribution of galaxies in the universe.

Cristiano made use of the freely available Gadget2 code which is installed on the NGS STFC RAL site and ran 20 full scale simulations which required approximately 100,000 cpu hours.

To find out more about Cristianos research see our user case study page. More user case studies are in the pipeline so watch this space!

Would you like a free software trial?

If you would then it's your lucky day!

For the next 3 months, the NGS partner resource at Leeds and Schrodinger are offering NGS users a free trial of the Virtual Screening workflow from Schrodinger's structure based design tools.

Schrödinger software has been used on national and regional high performance computing centers as a way of providing access to greater computing power, particularly for applications such as high throughput virtual screening. As part of this initiative they are offering a three-month evaluation of Schrödinger’s structure based design tools to all academic users accessing the NGS resources.

You don't need to be an existing user of the software - just a NGS user. Through the trial you'll gain access to an interface for full protein and ligand preparation and high throughput access to Schrödinger’s Glide docking application for screening of large datasets via your existing NGS access.

If you are interested in taking advantage of this offer, please see the news item on the NGS website.

Free places at the TransferSummit

Thanks to colleagues at the OSS Watch there are a couple of free places for academics to attend this years TransferSummit.

If you haven't been before (or heard of it!), it's an opportunity for academics, the research community and business executives to talk about the requirements, challenges, and opportunities in the use, development, licensing, and future of Open Source technology.

This isn't your usual "death by PowerPoint" conference either. There will be three tracks, a Gala Dinner and a BarCamp over the 2 days ensuring that everyone has a good chance to contribute to the discussion.

If you'd like to attend then please email OSS Watch to obtain a discount code.

Who looks after your software when you've gone?

It's a familiar scenario. A PhD student creates a piece of software during their 3 years of research, it's used for their project but then they leave. What happens to the software? Who looks after it? Who maintains it?

EPSRC have also recognised this problem and have recently awarded £4.2 million to establish the UK’s Software Sustainability Institute (SSI). A team of academics and software engineers based at the University of Southampton’s School of Electronics and Computer Science, the School of Computer Science at the University of Manchester and led by EPCC at the University of Edinburgh will work together to tackle these issues.

Together with the research community they will work to manage software beyond the lifetime of its original funding, so that it is strengthened, adapted and customised to maximise its value to future generations of researchers.

The establishment of the SSI obviously has implications for the NGS as there are many pieces of software out there which could be used by the wider community on the NGS - they just need a bit of TLC!

Roaming around the EBI

Earlier this week, I was down in Cambridge at the European Bioinformatics Institute for the NMR Software Workshop.

I was there to issue certificates to users as a "Roaming RA" operator. The NGS runs the UK e-Science Certificate Authority, which issues certificates not only to the people who want to make use of NGS services and resources, but for any UK academics involved in Grid computing. The certificates are accepted and recognised across the world and can be used to enable authentication of people across different Universities - even in different continents.

Usually, certificates are authorised for someone by an operator in their own institution but this is not always available.... which is where I come in. There are a number of Roaming RA operators with the ability to issue certificates at events where there is no local provision for issuing certificates. Quite often this will be at one of the many NGS roadshows or events we attend.

If you have an event where you think people would like a convenient opportunity to get a certificate for use on the NGS or elsewhere, get in touch with us at support@grid-support.ac.uk.

After the storm

I'd like to say thank you to everyone who came along to the National Grid Service Innovation Forum '08 last week. We played host to over 120 people over 2 days at the Museum of Science and Industry (MoSI) in Manchester where delegates heard over 20 presentations ranging from services currently available to NGS users to upcoming services and the future direction of the NGS.

Thank you to everyone who has so far completed a feedback form and I'm pleased to say that the feedback so far has been extremely positive. If you still have a feedback form that you would like to submit then please contact me. The feedback has strongly indicated that we should hold a similar event at least once a year so watch this space!

It's also nice to see that reports about the event are popping up in other blogs such as this one from the ESRC National Centre for e-Social Science (NCeSS).

The slides from the presentations will be up on the NGS website very soon and nearly all the presentations were videoed by colleagues from the Lancaster University Centre for e-Science so if you couldn't attend in person, you can see what you missed!

In other news there have been further software updates at the NGS so if you are a user of any of the following please take note!

EMBOSS 6.0.1
The latest release of EMBOSS (6.0.1) will be available on the NGS node at RAL (ngs.rl.ac.uk) next week. EMBOSS (The European Molecular Biology Open Software Suite) is an analysis package specially developed for the needs of the molecular biology user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. EMBOSS also integrates a range of currently available packages and tools, for sequence analysis, into a seamless whole. Further information on running EMBOSS on NGS resources can be found here.

Scali-MPI 5.6.4
The latest version of the commercial PlatformMPI (previously known as ‘ScaliMPI Connect’) MPI libraries are available on the NGS node at RAL (ngs.rl.ac.uk). All MPI software at RAL is linked to this latest version and is the default when compiling using mpicc,mpif77,mpif90,mpic++ . It provides a number of bug fixes and, for some user codes which call ‘free()’ repeatedly, it provides a significant speedup. RAL have benchmarked these libraries up to 10% faster than equivalent open source libraries such as MPICH.

And it's closed

Registration for the National Grid Service Innovation Forum has now closed and I'm pleased to announce that we have 118 people attending over the two days. We are really pleased with the numbers that have registered and it's shaping up to be a great event. If you aren't able to attend, don't worry as colleagues from the Centre for e-Science at the University of Lancaster will be filming the presentations at the event so you can catch all the presentations at your leisure!

The latest fortnightly news bulletin from the NGS was released today and contained information about new software additions on the NGS including Gaussian 3, PC-GAMESS / Firefly 7.1.C and the expansion of the bioinformatics database provision. If you would like to receive a short fortnightly update by email from the NGS, you can subscribe here.