Category Archives: Scientific computing

Does Denmark need a science cloud?


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

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


This is the intended replacement for our old workhorse, 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
- ZenodoRead the rest

What’s worse than ODBC?


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


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:

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?

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


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


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

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


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


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

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
  • 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

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

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