system news

Gromacs 4.6.1 is finally installed on Abisko.

Detailed instructions for using the new features in this version is still lacking.

Thu, 2013-04-11 16:32 | Åke Sandgren

A new version with some bugfixes and new features for our batch system, slurm, has been released.

The new version has improvments in how the jobs are scheduled that will enhance utilization of the cluster and we will also change some other configurations for better throughput of jobs.

The upgrade is a major version and will require all jobs to be stopped during the upgrade.

The upgrade should be complete within an hour including testing of the new version on abisko.

Update:
System upgrade finished at 10:20.

Important updates:

Due to scheduled maintenance on the network February 4th between 22:00 and 24:00, access to all HPC2N resources will likely be sporadic and unreliable. Please plan around the time period accordingly.

Thu, 2013-01-31 17:03 | Daniel Petersen

VASP has now been upgraded to version 5.3.3 on Abisko.

It contains new features like k-point parallization and the x/y/z-restrict patch from NSC.
It will be a fair bit faster for certain types of problems.

The names of the binaries have changed (the old names still remain but will be dropped with the next release).

Please read our updated VASP documentation.

Thu, 2013-01-24 10:26 | Åke Sandgren

We are currently installing R version 2.15.2 on Abisko. The login node and about half of the compute nodes already have it installed. The other compute nodes will have it installed when currently running jobs finish. 

See /resources/software/r for information about running R at HPC2N.

Fri, 2012-12-14 14:53 | Björn Torkelsson

Amber 12 patch level 13 has now been installed on Abisko.

Wed, 2012-11-07 09:47 | Åke Sandgren

The /pfs/nobackup file system is currently over 95% full.
That is the limit for starting new jobs on Akka.

Please remove unused files from the file system.

Mon, 2012-11-05 15:07 | Åke Sandgren

Amber 11 patchlevel 23 with AmberTools 1.5 patchlevel 28 have now been installed on Akka.
It should work a bit better then the previous version and should hopefully be a bit faster.
It has also been made the default.

Tue, 2012-09-18 21:06 | Åke Sandgren

Performance on the Parallel File System has been degraded due to an increasing demand on both bandwidth and storage space. We apologize for any adverse impact this may have on our user's research work and are planning a major upgrade of both storage and bandwidth capacity later this year.

Until that time, we need to keep the amount of space used on the file system manageable. The file system is currently 93% full, which is contributing to the poor performance. Continuing to increase space usage towards 100% will make the system unusable, therefore:

The parallel debugger DDT version 3.2 is now installed on Abisko.

It is a very good debugger for parallel programs both MPI and OpenMP and can be used together with the batch system.

Thu, 2012-09-13 15:29 | Åke Sandgren