Access to HellasGrid infrastructure

In order to get access to HellasGrid infrastructure, you have to:

  1. Obtain a Digital Certificate from the HellasGrid Certification Authority.
  2. Get an account at a HellasGrid User Interface.
  3. Join a Virtual Organization.
  4. Import your Digital Certificate to the User Interface you obtained a personal account.

Obtain a Digital Certificate from the HellasGrid Certification Authority

In order to acquire a Digital Certificate you have to visit the following web page: https://access.hellasgrid.gr/. By clicking at the first choice, you can request a personal Digital Certificate. You have first to complete a form with your personal information (first name, last name, organization, department, etc). Once you have completed this form an informative e-mail will be sent at your personal e-mail account informing you that your personal information has been registered at HellasGrid database and request to confirm the reception of the e-mail. In case you do not confirm the e-mail reception in seven days, your registration will be removed from the HellasGrid data base.

Once you confirmed the reception of the e-mail you can proceed with the certification request procedure. Initially you will be asked to install at your web browser the certificate of the HellasGrid Certification Authority. For the Greek users the responsible authority is the HellasGrid Certification Authority (HellasGrid-CA) operated by the Department of Physics at the Aristotle University of Thessaloniki. Consequently you must generate your private key and certificate signing request at the web browser. The private key and certificate signing request will be automatically sent at HellasGrid-CA.

Once your certificate signing request has been sent at the HellasGrid-CA an informative email will be sent to you. With this email you will be requested to visit in person your appropriate Registration Authority and present the following documents:

  1. Your identification card or your passport.
  2. One document which will confirm your affiliation with your organization.
  3. A printing of the received e-mail.

A list of the existing Registration Authorities for the Greek Users can be found at the following site. In the case you can not be served by an existing Registration Authority you must contact the Catch-all Registration Authority, operated by GridAUTH (mailto:hg-catch-all (at) grid.auth.gr).

You can regularly check the status of your certificate signing request. Once the status of your request changes to “signed” you have to install the certificate at your web browser (the same used for the procedure obtaining the certificate) and accept the terms of its use.

Get an account at a HellasGrid User Interface

A User Interface (UI) is nothing more and nothing less than a Linux box having installed all the required client software, APIs and tools for developing and running applications in the Grid. In practice everyone can install and setup a UI with the required EGEE tools following the instructions in the GLITE-3 Installation Guide.

There is also a chance that your institute may already have setup a UI machine so you can ask from your local administrator to create an account for you there.
Till now, six User Interfaces has been installed to serve the HellasGrid users:

  • three in Athens (ui01.isabella.grnet.gr, ui02.isabella.grnet.gr, ui01.marie.hellasgrid.gr),
  • one in Thessaloniki (ui01.afroditi.hellasgrid.gr),
  • one in Heraklion (ui01.ariagni.hellasgrid.gr) and
  • one in Patras (ui01.kallisto.hellasgrid.gr).

You can request access to the appropiate UI according to the location of your organization by following the second choice at the web page https://access.hellasgrid.gr. If you do not have access to a User Interface or you cannot (or do not want to) install your own UI, you may request via the second option of the web page https://access.hellasgrid.gr/ for an account at the Isabella catch-all UI hosted in the GRNET site, which is located at Athens; provided of course that you have already obtained a digital certificate issued by the HellasGrid Certification Authority. In order to connect at the User Interface at which you have an account you must use an ssh client program, for example putty, a free program which can be downloaded from the link http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html.

Join a Virtual Organization

To be authorized to use the Grid and do useful work with it you have to belong to a Virtual Organization (VO); A Virtual Organization (VO) is a group of grid users with similar interests and requirements who are able to work collaboratively with other members of the group and/or share resources (data, software, expertise, CPU, storage space, etc.) regardless of geographical location. A list of existing EGEE VOs is available here.

In order to make life easier for the South Eastern Europe users (including the HellasGrid users), speed up and simplify the process of new application induction, EGEE-SEE has established its own VO called SEE-VO. This VO will be the most adequate for SEE users that do not fit in any of the existing EGEE VOs or are not able to create their own EGEE-wide VO. To join the SEE-VO as a HellasGrid user you have to request it via the third option of the site https://access.hellasgrid.gr. Please note that this page has to be visited using the browser on which you have already loaded your digital certificate otherwise the process cannot be completed.

Import your Digital Certificate to your User Interface

Till now, you have a Digital Certificate installed at your web browser. In order to use the HellasGrid infrastructure, for example to submit a job for execution, check the status of the job; get the output of the job, you have to install also your certificate to the User Interface you have an account.

First you have to export your Digital Certificate from your web browser at which it is installed. To do this at Internet Explorer you must follow the path: Tools->Internet Options->Content->Certificates->Personal->Export while to do this at Mozilla Firefox you must follow the path: Edit->Preferences->Advanced->Encryption->View Certificates->Your Certificates->Backup or Tools->Options->Advanced->Encryption->View Certificates->Your Certificates->Backup. In both cases your personal certificate must be saved with .p12 extension (PKCS#12 format). So, by following the instructions of the above links you have succesfully backed up your security certificate and private key at your machine. Now you have to copy your Digital Certificate from your machine to your home directory at the User Inteface you gained an account. Then you must create your Digital Certificate and private key in .pem format. In order to do this you must execute the following two openssl commands:

openssl pkcs12 -nocerts

         -in mycertificate.p12 
         -out ~user/.globus/userkey.pem
openssl pkcs12 -clcerts -nokeys 
        -in mycertificate.p12 
        -out ~user/.globus/usercert.pem

The first openssl command gets as input your certificate in .p12 format (mycertificate.p12) and creates your private key in .pem format (userkey.perm).The second openssl command gets as input your certificate in .p12 format (mycertificate.p12) and creates your certificate in .pem format (usercert.pem). We must mention that the ~ user should be replaced by the path to your home area. Both your private key and certificate are stored in the .globus directory.


Finally you must give the appropiate read privileges at your private key and certificate.

chmod 444 ~/.globus/usercert.pem
chmod 400 ~/.globus/userkey.pem

How fast could a T-rex run?

And, more importantly, was it fast enough to catch you?

Grid computing is helping palaeontologists to understand better how dinosaurs moved around and what roles they played in their ancient world.

With its sharp teeth and massive jaws, the T-rex is the stuff of nightmares. It’s not surprising that scientists are convinced the T-rex was a carnivorous predator but huge teeth don’t tell the whole story. Was it like the modern cheetah and catch its prey in short burst-like sprints? Or was the T-rex a sneaky stalk-and-ambush hunter like the jaguar? What was its place in the Cretaceous ecosystem?

Since we can’t see a real T-rex in action (it disappeared along with the other dinosaurs 65 million years ago), palaeontologists need to look elsewhere to understand its role as a predator. Top running speed offers good clues to solving this mystery – but how do you measure the maximum speed of an extinct animal?

If zebras were to become extinct, the palaeontologists of the future could probably use horses or donkeys as comparisons. People looking at dinosaur behaviour don’t have that luxury because there is nothing alive today quite like a T-rex. The solution is to create a detailed computer simulation of the animal’s skeleton and muscles.

Continue reading...

How fast could a T-rex run?

And, more importantly, was it fast enough to catch you?

Grid computing is helping palaeontologists to understand better how dinosaurs moved around and what roles they played in their ancient world.

With its sharp teeth and massive jaws, the T-rex is the stuff of nightmares. It’s not surprising that scientists are convinced the T-rex was a carnivorous predator but huge teeth don’t tell the whole story. Was it like the modern cheetah and catch its prey in short burst-like sprints? Or was the T-rex a sneaky stalk-and-ambush hunter like the jaguar? What was its place in the Cretaceous ecosystem?

Since we can’t see a real T-rex in action (it disappeared along with the other dinosaurs 65 million years ago), palaeontologists need to look elsewhere to understand its role as a predator. Top running speed offers good clues to solving this mystery – but how do you measure the maximum speed of an extinct animal?

If zebras were to become extinct, the palaeontologists of the future could probably use horses or donkeys as comparisons. People looking at dinosaur behaviour don’t have that luxury because there is nothing alive today quite like a T-rex. The solution is to create a detailed computer simulation of the animal’s skeleton and muscles.

Continue reading...

Enter the mascot competition and win a tablet PC

Poster of the EGI mascot competition

EGI is looking for a mascot – our characterful ambassador to feature in posters, t-shirts and other goodies and give aways.

But what could this be? Is it an animal, a plant or a mineral? Something abstract? We don’t know so we set up the EGI Mascot Competition to find out.

Use your imagination and surprise us. Submit your idea to the competition and you might win a tablet computer and a free registration to the Community Forum in Munich (26-30 March 2012).

Here is how it’s going to work:

  • Submission of ideas opens 15 October 2011

  • Deadline for submissions is 31 December 2011

  • Online voting will take place between 11 January-8 February 2012

  • The winners will be announced on 15 February 2012

How to enter the competition

Come up with a great idea for a mascot. Tell us what it is, and why and how it represents the European Grid Infrastructure (in no more than 150 words). You can also include an optional image of any kind to support your entry – from a raw sketch to a final drawing, or even a photograph (file format: GIF, PNG or JPEG, 400 pixel maximum on the longest side). While submitting an image is not compulsory, we strongly suggest that you do, because it will help to communicate your idea, especially for the online voting.

When you have all the entry requirements, you are ready to submit. E-mail your submission to mascot@egi.eu with ‘Mascot entry’ in the subject line (this e-mail address is for submitting an entry only. For enquiries, please contact press@egi.eu). You can submit more than one entries, but each entry must be sent in a separate e-mail.
 

Enter the mascot competition and win a tablet PC

Poster of the EGI mascot competition

EGI is looking for a mascot – our characterful ambassador to feature in posters, t-shirts and other goodies and give aways.

But what could this be? Is it an animal, a plant or a mineral? Something abstract? We don’t know so we set up the EGI Mascot Competition to find out.

Use your imagination and surprise us. Submit your idea to the competition and you might win a tablet computer and a free registration to the Community Forum in Munich (26-30 March 2012).

Here is how it’s going to work:

  • Submission of ideas opens 15 October 2011

  • Deadline for submissions is 31 December 2011

  • Online voting will take place between 11 January-8 February 2012

  • The winners will be announced on 15 February 2012

How to enter the competition

Come up with a great idea for a mascot. Tell us what it is, and why and how it represents the European Grid Infrastructure (in no more than 150 words). You can also include an optional image of any kind to support your entry – from a raw sketch to a final drawing, or even a photograph (file format: GIF, PNG or JPEG, 400 pixel maximum on the longest side). While submitting an image is not compulsory, we strongly suggest that you do, because it will help to communicate your idea, especially for the online voting.

When you have all the entry requirements, you are ready to submit. E-mail your submission to mascot@egi.eu with ‘Mascot entry’ in the subject line (this e-mail address is for submitting an entry only. For enquiries, please contact press@egi.eu). You can submit more than one entries, but each entry must be sent in a separate e-mail.
 

Evaluating the impact of climate change on European air quality

Scientists from the Laboratory of Atmospheric Physics (School of Physics) and the Department of Meteorology and Climatology (School of Geology) have simulated the regional climate-air quality over Europe for two future decades (2041-2050 and 2091-2100) using the HellasGrid Infrastructure and the EGI Grid, with the support of the Scientific Computing Center at A.U.Th..

The computational models used for these simulations are the regional climate model RegCM3 and the air quality model CAMx, which have been off line coupled in this case (Figure 1). The control simulation for the decade 1991-2000 was performed twice, once externally forced by the ERA40 reanalysis and once using the global circulation model ECHAM5, in order to investigate the importance of external meteorological forcing on air quality (Katragkou et al., 2010). The RegCM3 model was forced by ECHAM5 under the A1B emission scenario for two future time slices, namely 2041-2050 and 2091-2100. These simulations served as a theoretical experiment of evaluating the impact of climate change on air pollution (Katragkou et al., 2011).

For each decadal simulation the computation consumed approximately 1000 CPU hours. CAMx simulations were performed on SMP machines as the model has been intrinsically parallelized with the OpenMP library. Using this feature of the CAMx model a significant reduction on the overall computation time was feasible.

In terms of storage, the resources required for archiving the CAMx output files are estimated to slightly more than 5TB.

Off-line coupling of RegCM3 and CAMx computational models

Figure 1: A schematic illustrating an outline of the modelling system RegCM3/CAMx applied in this study (from Zanis et al., 2011)

Surface ozone simulated by RegCM3/CAMx was evaluated against ground based measurements from the European database EMEP (Zanis et al., 2011). The air quality simulations available at AUTH for the three time slices (1991-2000, 2041-2050 and 2091-2100) over Europe with a resolution of 50 Km have been provided as air quality boundaries for higher resolution air quality simulations over sub-European grids (Huszar et al., 2011).

The results suggest that changes imposed by climate change until the 2040s in surface ozone concentration during summer will be below 1 ppbv (parts per billion by volume) . By the 2090s, however, changes are foreseen to be more significant especially over south-west Europe, where the median of near surface ozone has been found to increase by 6.2 ppbv.

Near surface ozone concentrations over Europe

Figure 2: Average summer surface ozone for the control simulation 1991-2000 (left). Differences in simulated average summer ozone between 2091-2100 and control simulation (right). The grey color corresponds to non-statistical significant differences (from Katragkou et al., 2011)

The median of summer near surface temperature for Europe at the end of the 21st century was calculated at 2.7K higher than the end of the 20th century with more intense temperature increase simulated for southern Europe. A prominent outcome was the decrease of cloudiness mostly over western Europe at the end of the 21st century associated with an anticyclonic anomaly which favours more stagnant conditions and weakening of the westerly winds (Katragkou et al., 2011).

Mean temperature differences

Figure 3: Mean differences between second future decade (2091-2100) and the present decade (1991-2000) for summer in the fields of surface temperature (left) and geopotential height at 500 hPa (right).The red contours correspond to geopotential height at 500 hPa during the control decade (from Katragkou et al., 2011).

This work has been accomplished in the framework of the FP6 European Project CECILIA (Central and Eastern Europe Climate Change Impact and Vulnerability Assessment, Contract Nr 037005). The results were produced on the EGI and HellasGrid infrastructure with the support of the Scientific Computing Center at the Aristotle University of Thessaloniki (AUTH). The results of this work have been published in peer-review journals (see references), presented in several national and international conferences and awarded by the Hellenic Meteorological Society (2008), the European Association for the Science of Air Pollution (2009) and the Research Committee of the Aristotle University of Thessaloniki (2010).

Contact details:

  • Dimitris Melas (PI), Associate Professor, AUTH, melas (at) auth.gr
  • Prodromos Zanis, Assistant Professor, AUTH, zanis (at) geo.auth.gr
  • Eleni Katragkou, Lecturer, AUTH, katragou (at) auth.gr
  • Scientific Computing Center, AUTH, contact (at) grid.auth.gr

References:

  1. Huszar P., K. Juda-Rezler, T. Halenka, H. Chervenkov, D. Syrakov, B. C. Krueger, P. Zanis, D. Melas, E. Katragkou, M. Reizer, W. Trapp, M. Belda, Potential climate change impacts on ozone and PM levels over Central and Eastern Europe from high resolution simulations, Climate Research (in press), 2011
  2. Katragkou Ε., P. Zanis, I. Tegoulias, D. Melas, I. Kioutsioukis, B. C. Krüger, P. Huszar, T. Halenka, S. Rauscher, Decadal regional air quality simulations over Europe in present climate: near surface ozone sensitivity to external meteorological forcing, Atmospheric Chemistry and Physics, 10, 11805-11821, 2010
  3. Κatragkou E., P. Zanis, I. Kioutsioukis, I. Tegoulias, D. Melas, B.C. Krüger, E. Coppola, Future climate change impacts on summer surface ozone from regional climate-air quality simulations over Europe, J Geophys Res (in press), 2011
  4. Zanis P., E. Katragkou, I. Tegoulias, A. Poupkou, D. Melas, Evaluation of near surface ozone in air quality simulations forced by a regional climate model over Europe for the period 1991-2000, Atmospheric Environment, 45, 6489-6500, 2011

Biodiversity Virtual e-Laboratory launched

A groundbreaking research project which could revolutionise the study of biodiversity around the world has been launched at Cardiff University in the United Kingdom.

The Cardiff School of Computer Science and Informatics led project, worth €5 million in funding, is seeking to provide a vital service that will improve the way scientists share, analyse and present information in the growing area of biodiversity science.

Biodiversity science is the study of plants and animals that inhabit our planet and the environments they live in. Amid growing concerns over the extinction rate of certain species as their natural habitats are increasingly destroyed, and with biodiversity becoming as important as climate change on the political agenda, this new research project could not be more timely.

Starting in September 2011, the three-year project called Biodiversity Virtual e Laboratory (BioVeL) will establish an international e-Laboratory – the first of its kind in Europe – that will allow biodiversity scientists to jointly tackle diverse research challenges.

Experts from Cardiff University along with 15 partners from institutions across Europe (photo), hope that when completed, the BioVeL e-Laboratory will for the first time, give scientists access to multiple data, analysis and computing resources for biodiversity science through a robust e-Science infrastructure.

Coordinator of the project, Alex Hardisty of Cardiff University’s School of Computer Science and Informatics commented: “The outcomes from this project will improve the study of biodiversity. All scientists will benefit directly from the tools, knowledge and expertise assembled in this infrastructure, offering the promise of new opportunities to more easily research substantial biodiversity problems with societal impact.”

Ranked by the European Commission (EC) as top of its class from more than 60 proposals, BioVeL is funded under the EC’s FP7 e-Infrastructures programme to support the creation of the European Research Area.

Visit the BioVeL website

 

Biodiversity Virtual e-Laboratory launched

A groundbreaking research project which could revolutionise the study of biodiversity around the world has been launched at Cardiff University in the United Kingdom.

The Cardiff School of Computer Science and Informatics led project, worth €5 million in funding, is seeking to provide a vital service that will improve the way scientists share, analyse and present information in the growing area of biodiversity science.

Biodiversity science is the study of plants and animals that inhabit our planet and the environments they live in. Amid growing concerns over the extinction rate of certain species as their natural habitats are increasingly destroyed, and with biodiversity becoming as important as climate change on the political agenda, this new research project could not be more timely.

Starting in September 2011, the three-year project called Biodiversity Virtual e Laboratory (BioVeL) will establish an international e-Laboratory – the first of its kind in Europe – that will allow biodiversity scientists to jointly tackle diverse research challenges.

Experts from Cardiff University along with 15 partners from institutions across Europe (photo), hope that when completed, the BioVeL e-Laboratory will for the first time, give scientists access to multiple data, analysis and computing resources for biodiversity science through a robust e-Science infrastructure.

Coordinator of the project, Alex Hardisty of Cardiff University’s School of Computer Science and Informatics commented: “The outcomes from this project will improve the study of biodiversity. All scientists will benefit directly from the tools, knowledge and expertise assembled in this infrastructure, offering the promise of new opportunities to more easily research substantial biodiversity problems with societal impact.”

Ranked by the European Commission (EC) as top of its class from more than 60 proposals, BioVeL is funded under the EC’s FP7 e-Infrastructures programme to support the creation of the European Research Area.

Visit the BioVeL website

 

SARA and BiG Grid host HPC cloud day

BiG Grid, the Dutch National Grid Initiative, and SARA will host a special High Performance Cloud Computing Day, next Tuesday 4 October at the Science Park Amsterdam Conference Hall.

The event has a packed programme with talks and demonstrations of scientific cloud usage and it will finish with the official inauguration of the new national HPC cloud infrastructure.

Registration for the HPC cloud day is free and it is still open.

The demonstrations will be presented by scientists, who will share their HPC and cloud experiences in the Life Sciences, Earth Sciences, Finance and Linguistics, amongst others.

The national HPC cloud will be an important step in the expansion and diversification of the BiG Grid infrastructure, who manages grid computing resources used by the CERN experiments, the LOFAR telescope and life science research.

More information

 

SARA and BiG Grid host HPC cloud day

BiG Grid, the Dutch National Grid Initiative, and SARA will host a special High Performance Cloud Computing Day, next Tuesday 4 October at the Science Park Amsterdam Conference Hall.

The event has a packed programme with talks and demonstrations of scientific cloud usage and it will finish with the official inauguration of the new national HPC cloud infrastructure.

Registration for the HPC cloud day is free and it is still open.

The demonstrations will be presented by scientists, who will share their HPC and cloud experiences in the Life Sciences, Earth Sciences, Finance and Linguistics, amongst others.

The national HPC cloud will be an important step in the expansion and diversification of the BiG Grid infrastructure, who manages grid computing resources used by the CERN experiments, the LOFAR telescope and life science research.

More information