Category Archives: Scientific computing

Does Denmark need a science cloud?

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cloud1

4 years ago we, the ScienceCloud group at DeIC, launched the scientific data-management service data.deic.dk.

It was a first attempt at building something like this out of open-source components: FreeBSD, ZFS, Apache, ownCloud/Nextcloud and involved engaging with similar projects in other countries (Switzerland, Australia, Germany, Holland) and open-source environments (Nextcloud, CS3).

Today this service hosts about 100 TB of … Read the rest

Sciencedata open for testing

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sciencedata_front

This is the intended replacement for our old workhorse, data.deic.dk. Those who would like to try out new features targeted at researchers, please give it a try. You’ll need to be able to log in via wayf/edugain, i.e. you need to be affiliated with a European research institution.

The new features we’re exploring are:

- ORCID integration
- Zenodo… Read the rest

What’s worse than ODBC?

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TheHomer

The classic “Process (aka Designing the Stop Sign)” nails the problem of (Over-) Design By Committee.

But is the real problem here using a committee? Can design not be meaningfully accomplished by group of people working together?

I claim the answer is yes and that typical problem is not the committee per se, but the clueless committee – regardless … Read the rest

Booting Ubuntu-14.04 cloud images without a cloud

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Ubuntu-trusty

So, Ubuntu-14.04, Trusty Tahr, is out; and booting the cloud images requires a bit more hacking than booting the 12.04 cloud images. Here goes:

Get the image, resize and loop-back mount it:

wget cloud-images.ubuntu.com/trusty/current/trusty-server-cloudimg-amd64-disk1.img
qemu-img convert -c -O qcow2 trusty-server-cloudimg-amd64-disk1.img trusty-server-cloudimg-amd64-disk1_30GB.qcow2
qemu-img resize trusty-server-cloudimg-amd64-disk1_30GB.qcow2 30G
sudo modprobe nbd
sudo qemu-nbd -c /dev/nbd0 `pwd`/trusty-server-cloudimg-amd64-disk1_30GB.qcow2
ls image || mkdir image
sudo … Read the rest

Does Denmark need a supercomputer?

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The more precise question is:

Do researchers at Danish universities need a supercomputer on the top-500 list?

A bit of background is useful:

The funding model for HPC in Danish academia, employed since ~2000, described in a previous post, has resulted in a decentralized HPC infrastructure which AFAIK is quite unique in Europe (other European countries have a

… Read the rest

Booting Ubuntu-12.04 cloud images without a cloud

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images

I was recently asking myself why the P2V concept has not been more fully embraced by the open-source community – and generalized to V2C, virtual machine to cloud instance. From a scientific computing perspective, it would be ideal to seamlessly be able to prototype a data analysis in a virtual machine on a laptop and then run large-scale data … Read the rest

3PGCIC-2011

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Back in Barcelona to present a paper at 3PGCIC-2011 – a well organized and pleasant conference with a varied program. Good discussions on distributed computing. Excellent social arrangements including the reception banquet at the charming Institut d’Estudis Catalans and a visit to the Mare Nostrum supercomputer of the BSC – located in a former chapel.

.… Read the rest

Taking citizen cyberscience a step further

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Citizen Science

Recently I’ve stumbled upon the terms citizen science and citizen cyberscience. The last term was apparently invented by Shuttleworth Fellow Francois Grey as a label for BOINC-based distributed computing projects like seti@home, folding@home and his own lhc@home. Grey is also behind the Citizen Cyberscience Centre in Geneva – on the web pages of which there’s more information to be … Read the rest

CERN School of Computing 2011 was… awesome

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LectureNyhavnCSCCanoeing

As exemplified on the pictures above (from the photo gallery of one of the students), CERN School of Computing includes a good deal of extracurricular activities. Which probably goes a long way in explaining the good and humorous atmosphere in the classroom.

Having spent a lot of energy preparing the exercise with the great CSC team, it really was great … Read the rest

The vision of GridFactory

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factory_c

In this post I’ll try to explain the vision behind a software suite I wrote at the Niels Bohr Institute, University of Copenhagen, 2009-11.

The ideas for the software arose from my dual involvement with the high energy physics and the e-science groups. Some of the code originated in previous projects, including distributed computing efforts of the ATLAS experiment at … Read the rest

CERN School of Computing 2011 – Exercise 2

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In this exercise we’ll solve the same assignment as in exercise 1, but using a prepackaged GridPilot application.

  • Download and install GridPilot
  • Start GridPilot and answer the initial questions – enable only the computing system “GridFactory” and set the submission host to gridfactory.nbi.dk
  • Import the app “ttbar_exercise”
  • Select the application/dataset “ttbar_exercise-100k-events” and click “Run”
  • Select the application/dataset “ttbar_exercise-merge” and

    • … Read the rest

CERN School of Computing 2011 – Exercise 1

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pT diboson distribution.

pT diboson distribution.


This exercise was created for the 2011 CERN CERN School of Computing, hosted by the Niels Bohr Institute, University of Copenhagen.

Credits: physics content of this exercise by Jørgen Beck Hansen from the Niels Bohr Institute.

LHC Monte Carlo event generation and analysis

… Read the rest

Browser certificate and key export

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This is a follow-up post to my previous post “Front door locks”.

I’m happy to announce a little utility that exports TCS certificate/keys to the hard disk – more precisely to your “.globus” directory where grid tools expect to find them.

Here follows instructions on how to use it:

First, you of course need to have some TCS credentials … Read the rest