Abel Newsletter #1, 2018

Spring course week, application deadline for CPU time through Notur, interesting conferences and external courses, along with the usual list of updated tools and applications now available on Abel or in the Lifeportal.

  • USIT Underavdeling for IT i forskning ITF(NO), or Division for research computing RC(EN), is responsible for delivering IT support for research at University of Oslo.
  • The division's groups operate infrastructure for research, and support researchers in the use of computational resources, data storage, application portals, parallelization and optimizing of code, and advanced user support.
  • The Abel High Performance Computing (HPC) cluster, Notur, and the NorStore storage resources are central components of the USIT IT support for researchers.
  • Announcement of this newsletter is done on the abel-users mailing list. All users with an account on Abel are automatically added to the abel-users list. This is mandatory. The newsletter will be issued at least twice a year.


News and announcements

HPC course week

This March our HPC training course starts on the 21.03.18. The course is designed for Notur as well as local users. This event is especially suitable for scientists who wish to learn more about how they can use  Abel computer cluster and the high performance facilities of Tjenester for Sensitive Data (TSD) for their research.

All participants are expected to have a very basic working knowledge of Unix. If you are new to UNIX, please participate in one of the Software carpentry (http://www.uio.no/english/for-employees/support/research/research-data/training/carpentry/) seminars before the start of the course.

Registration: Registration will open 01-02-2018 after the schedule is finalized. Please check programme page for more details

Schedule: http://www.uio.no/english/services/it/research/events/hpc_for_research_march_2018.html

Questions? Ideas? Contact hpc-drift@usit.uio.no.

NeIC training calendar

Looking for more training events? NeIC is maintaining a shared calendar for training events in the Nordics, see https://neic.no/training/ for more information.

New Notur allocation period 2018.1, application deadline 9 February 2018 (Including TSD)

The Notur period 2018.1 (01.04.2018 - 30.09.2018) is getting nearer, and the deadline for applications for CPU hours, storage and TSD is February 9th. 
NB : As the text indicates 6 MCPUhrs and 1PiB storage is now available in TSD for RFK to hand out to applicants pr year.

Kindly reminder: If you have many CPU hours remaining in the current period, you should of course try to utilize them asap, but since many users will be doing the same there is likely going to be a resource squeeze and potentially long queue times. The quotas are allocated according to several criteria, of which publications registered to Cristin is an important one (in addition to historical usage). The quotas are based on even use throughout the allocation period. If you think you will not be able to spend all your allocated CPU hours, it is highly appreciated to notify sigma2@uninett.no so that the CPU hours may be released. You may get extra hours if you need more later. For those of you that have run out of hours already, or are about to run out of hours, you may contact sigma2@uninett.no and ask for a little more. No guarantees of course.



to list project accounts you are able to use.


cost -p


cost -p nn0815k

to check your allocation (replace 0815 with your project's account name).


cost -p nn0815k --detail

to check your allocation and print consumption for all users of that allocation.

Norstore->NIRD data migration

Most of the projects have been migrated to NIRD. The few remaining projects (those having a service running on Norstore) will be migrated during February.


Support of Linux Containers on Abel

Linux containerization is an operating system level virtualization technology that offers lightweight virtualization. An application that runs as a container has its own root file-system, but shares kernel with the host operating system. Abel supports Singularity, a user friendly tool for building, running, and managing containers on HPC systems. The user guide is here. If you are more familiar with Docker containers, Singularity offers conversion of Docker containers, but this feature is not yet mature, i.e. not all Docker converted containers work as expected. Later we will provide full support of Docker containers on Abel.


Availability of accelerated computing resources

Intel Xeon Phi (AKA Knights Landing):

We are happy to inform that 2 nodes with Xeon Phi Knights stand alone processor with Mellanox Infiniband (EDR 100 Gbits/s) are installed and available for testing and development. Please contact us if you would like assistance with porting an application to KNL. All the Intel tools are ready for KNL.

Intel developer site provide more information on products for HPC development.

freebio - first ARM based server

Freebio is a new class of HPC capable ARM based systems. The well known ARM processor architecture from mobile phones, pads, TVs, cars, Raspberry PIs, etc have now been upgraded to a high performance version. Being cost effective with a high core count these processors represent an alternative approach to many tasks. So far we have targeted the bio informatics workloads for this type of processors. However, the system is not limited to run only such tasks it can tackle all kinds of workloads. The system is installed with Ubuntu 16.04 and all software in the Ubuntu distro is available for ARM. The processor is from High Silicon, model Hi1616. The system has 64 cores, 256 GiB of memory and 36 TiB of local disk. While each core performs slightly less than an x86-64 core the higher core count compensates for this. Multithreaded programs are important as before. All Abel users can access freebio.hpc.uio.no and will find their Abel $HOME directory when logging in.

Other hardware needs

Are you in need of particular types of hardware (fancy GPUs, kunluns, dragons, etc.) not provided through Abel, please do contact us (hpc-drift@usit.uio.no), and we'll try to help you as best we can.

Also, if you have a computational challenge where your laptop is too small but a full-blown HPC solution is a bit of an overkill, it might be worth to check out UH-IaaS.

Abel operations

Follow operations

If you want to be informed about day-to-day operations you can subscribe to the abel-operations list by emailing "subscribe abel-operations <Your Name>" to sympa@usit.uio.no. You can also follow us on twitter abelcluster: http://twitter.com/#!/abelcluster

New and updated software packages

The following is a list of new or updated software packages available on Abel with the module command.

=== asciinema 1.2.0 ===
module load asciinema/1.2.0
=== bwa 0.7.17 ===
module load bwa/0.7.17
=== cellprofiler 2.2 ===
module load cellprofiler/2.2
=== cgetools 20171009 ===
module load cgetools/20171009
=== circleator 1.0.0 ===
module load circleator/1.0.0
=== dfnworks 2.0 ===
module load dfnworks/2.0
=== easybuild 3.3.1 ===
module load easybuild/3.3.1
=== easybuild 3.4.0 ===
module load easybuild/3.4.0
=== fenics 2017.1.0.1 ===
module load fenics/2017.1.0.1
=== gatk 3.8 ===
module load gatk/3.8
=== gcc 7.2.0 ===
module load gcc/7.2.0
=== idr 2.0.4 ===
module load idr/2.0.4
=== igblast 1.5.0 ===
module load igblast/1.5.0
=== igblast 1.8.0 ===
module load igblast/1.8.0
=== intel 2018.0 ===
module load intel/2018.0
=== intel 2018.1 ===
module load intel/2018.1
=== intel 2018.beta ===
module load intel/2018.beta
=== jags 4.3.0 ===
module load jags/4.3.0
=== julia 0.5.2 ===
module load julia/0.5.2
=== julia 0.6.1 ===
module load julia/0.6.1
=== matlab R2017a ===
module load matlab/R2017a
=== maxquant ===
module load maxquant/
=== mono 20171222 ===
module load mono/20171222
=== nco 4.6.9 ===
module load nco/4.6.9
=== netcdf.intel 4.5.0 ===
module load netcdf.intel/4.5.0
=== openifs 40r1v1 ===
module load openifs/40r1v1
=== parsync 1.69 ===
module load parsync/1.69
=== parsyncfp 1.45 ===
module load parsyncfp/1.45
=== pear 0.9.11 ===
module load pear/0.9.11
=== penncnv 1.0.4 ===
module load penncnv/1.0.4
=== perf-reports 7.0.6 ===
module load perf-reports/7.0.6
=== pflotran 2017.09.07 ===
module load pflotran/2017.09.07
=== pgi 17.9 ===
module load pgi/17.9
=== picard-tools 2.16.0 ===
module load picard-tools/2.16.0
=== porechop 0.2.2 ===
module load porechop/0.2.2
=== quast 4.6.0 ===
module load quast/4.6.0
=== singularity 2.3.2 ===
module load singularity/2.3.2
=== singularity 2.4 ===
module load singularity/2.4
=== spades 3.11.0 ===
module load spades/3.11.0
=== spades 3.11.1 ===
module load spades/3.11.1
=== stacks 1.46 ===
module load stacks/1.46
=== tensorflow 1.0.1 ===
module load tensorflow/1.0.1
=== trim-galore 0.4.4 ===
module load trim-galore/0.4.4
=== wrf-hydro 3.0 ===
module load wrf-hydro/3.0


Puh! Questions? Contact hpc-drift@usit.uio.no.

Publication tracker

USIT Division for Research Computing (RC) is interested in keeping track of publications where computation on Abel (or Titan) or usage of any other RC services are involved. We greatly appreciate an email to:


about any publications (including in the general media). If you would like to cite use of Abel or our other services, please follow this information.

Abel Operations mailing list

To receive extensive system messages and information please subscribe to the "Abel Operations" mailing-list. This can be done by emailing "subscribe abel-operations <Your Name>" to sympa@usit.uio.no.

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Publisert 29. jan. 2018 15:07 - Sist endret 30. jan. 2018 09:51