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In the last months, all over the world the COVID-19 pandemic has impacted everyone's life.
In particular mobility programmes, like the HPC-Europa3 one, have been highly affected by the travel limitations in most of the countries.
The pandemic will not resolve quickly, but we are all learning to cope with the limitations and be able to continue or start fruitful international co-operations to support better research.
HPC-Europa3 has at heart the safety and protection of the visitors and had suspended visits during the most critical months but we have now started to reschedule visits fully respecting containment measures taken at national level.
- Call for proposals is open and projects will be evaluated according to the original timeline (calendar of call dates is available here)
- The situation in the different countries is highly dynamic, so once a project is approved, the HPC-Europa3 team is evaluating with the applicant on a case by case basis the situation in the origin and hosting country to better define the period of the visit. The project will be supportive and flexible in re-scheduling visits whenever necessary.
- Researchers from outside the EU are highly recommended to subscribe to health insurance for the visit.
- During the visit, researchers are requested to respect the rules of the visiting country in terms of social distancing or face mask wearing and comply with the internal rules decided by the hosting institution.
- The HPC-Europa3 team is also ready to help in case of unexpected shortening or prolongation of the visits.
Next call is confirmed to be closing on the 17th of September 2020!
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Dr. Kęstutis Aidas and Dovilė Lengvinaitė, from the Vilnius University (Lithuania), were visiting Prof. Aatto Laaksonen, in Stockholm University (Sweden), to work on theoretical modelling of nuclear quadrupolar coupling constants relevant in the field of Nuclear Magnetic Resonance (NMR) relaxation by using molecular dynamics simulations and combined quantum mechanics/molecular mechanics approaches.
Very interesting NMR measurements of water mixtures with some imidazolium based Ionic Liquids (IL) have been very recently carried out by the NMR spectroscopy group of Vilnius University. These experimental findings reflected the structural changes of the samples with changing concentration of IL and water. During their visits, Dr. Aidas and his student Lengvinaitė worked on large-scale classical molecular dynamics (MD) simulations of the IL/water systems in order to sample the phase space and record the trajectories. These have been used in the subsequent calculations of NMR shielding constants using linear response quantum mechanics/molecular mechanics approaches. The produced results shed light on the early stages of water pocket formation within the IL and gave valuable theoretical interpretation for the experimental findings.
These visits with the help of HPC-Europa3 project have secured a strong collaborative link between the two universities in the field of physics.
The research interests of Prof. Aatto Laaksonen from the Dept. of Materials and Environmental Chemistry are focused on Sustainable Chemistry. Using advanced theoretical and computational chemistry methods his group has been designing green solvents and a new generation of lubricants based on room temperature ionic liquids. The research visit of Prof. Aidas and Ms Lengvinaite within the HPC-Europa3 programme was therefore most welcome. The group of Aidas is developing and applying the high-end computational tools to study these chemical most complicated liquids with all possible molecular interactions in effect. As the number of possible ionic liquids through different combinations of molecular cations and anions can be order of 1018, in silico techniques in designing them for different applications is the only feasible way before starting to synthetize them. In our case, the HPC-Europa program was simply an ideal way to connect high-level research and high-performance computing to produce green chemistry products and application. The highly professional and extremely friendly staff at PDC did provide the perfect circumstances to perform the work.
"Simulation system of ionic liquid [C4Mim][Cl]/water mixture at χw=0.5 water concentration"
Dr. Aidas shared that computational resources provided by the PDC at KTH through the HPC-Europa3 programme were instrumental in making these expensive calculations possible. An extended visit at KTH was extremely fruitful also because they had excellent conditions for uninterrupted work and great technical support from PDC. He strongly believes that the obtained computational results lead to important insight concerning the behaviour of water molecules in the highly heterogeneous systems of ionic nature such as the ionic liquids are. The success of this project will facilitate further computational studies of ionic liquid systems.
Ms Lengvinaitė reflected “These two visits were very useful to me as a young scientist, PhD student. During this visit, I had the opportunity to work independently, to test different computing capabilities, to meet the challenges. Get acquainted with great scholars and get in touch. These let us to realize this project in much faster way and produce the expected results. The publication is under preparation, to be finished this summer.”
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EPCC, the High Performance Computing Centre at the University of Edinburgh (UK), is one of the 10 partner centres in HPC-Europa3, and co-ordinates the Transnational Access programme.
Two major upgrades have recently been carried out to the HPC facilities which are available to the centre’s HPC-Europa3 visitors.
ARCHER2
EPCC has been running ARCHER, the UK National Supercomputing Service, since 2013. This 118,080-core Cray XC30 MPP supercomputer is now due to be retired from service. It will be replaced by the new ARCHER2 facility, an HPE Cray EX supercomputing system with 5,848 compute nodes, each with dual AMD EPYC Zen2 (Rome) 64-core CPUs, giving 748,544 cores in total.
ARCHER2 will have an estimated peak performance of 28 PFLOP/s and should be capable on average of more than eleven times the science throughput of the original ARCHER system, based on benchmarks which use five of the most heavily used research software packages on the current service.
 
“Images: Greg Muir/EPCC”
ARCHER2 was originally due to enter into service in May 2020. However, transporting specialist systems of this type and getting the right people on site to install them is a logistical challenge at the best of times, and the travel restrictions due to the Covid-19 pandemic have made this even more challenging than usual. A 4-cabinet Shasta Mountain system, the first phase of the full 23-cabinet system, was eventually able to leave Cray/HPE’s factory in Chippewa Falls, Wisconsin, in July, and has now been installed at EPCC’s Advanced Computing Facility, where it is currently undergoing testing, with user access due to start in the coming weeks.
A timelapse video of the build can be found here.
Cirrus Phase II
Cirrus is a UK Tier-2 state-of-the-art advanced computing facility aimed at users with computational requirements that fall between University-level resources and the National Supercomputing Service (ARCHER / ARCHER2). It is an HPE/SGI 8600 HPC system with 280 standard compute nodes and, following a recent major upgrade, it now also has 144 NVIDIA V100 GPUs and a 256 TB high performance storage layer for the most demanding data streaming applications.
"Image: Paul Clark/EPCC"
A presentation of this upgraded system can be found here.
References:
https://www.archer2.ac.uk/
https://www.cirrus.ac.uk/
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- Next call for applicants! Apply now! 17th of September 2020
- Second users' group meeting (online event), 22-23 October 2020, more information and registration here
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