Quick Links Applications Helix Python

The Biowulf cluster compute nodes and login node will transition from the RHEL6/CentOS6 to the RHEL7/CentOS7 operating system on June 4, 2018.

Below is a summary of user-visible changes associated with the OS upgrade.

Application installations and updates on the RHEL6/CentOS6 system will be frozen until the transition. The HPC staff is tied up with rebuilding several hundred applications for CentOS7, so no new apps will be installed and no applications will be updated on the current CentOS6 system.

Most scientific applications have been ported to CentOS7 and will be available just as they are now. However, only the latest version(s) of each application have been built for CentOS7. After the transition, you can check which versions are available with module avail appname. If your scripts specify loading an older version than is available, you may need to update your scripts. If you absolutely require an older version of an application, let us know.

Specific application changes:

• SAS: Under Rhel7, SAS requires 'module load SAS' to run the application.
• Comsol: Under Rhel7, Comsol requires 'module load Comsol' to run the application.

If you have compiled your own versions of an application which link older libraries, you may need to recompile them on CentOS7. Performance-sensitive applications (e.g. parallel molecular simulations) should be recompiled. If you need to build or test some applications, contact us and we will give you early access to the CentOS7 partition.

On June 4, Helix will transition to an 'interactive data transfer node' and only data transfer applications such as scp, Aspera transfers, and wget/curl will be available on Helix.

If you ran any scientific applications interactively on Helix in the past, you will now need to get an interactive session on Biowulf. e.g.:

[user@biowulf] sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ .... run your interactive commands here ...

Helix cron jobs

Helix will be dedicated to data transfer after June 4. User cron jobs on Helix can remain unchanged if they perform data transfer tasks. If the cron jobs run any applications, those apps will probably not be available on Helix after June 4. (see above). Those cron jobs should be migrated to Biowulf. If they are CPU or memory-intensive, set them up as a batch script.

Along with the update of the Biowulf operating system there were several changes to the python setup:

• The python/2.7.X environments and modules were retired. The python/2.7 module is still available and will provide the latest 2.7 version.
• The Anaconda/X environments and modules were retired.
• conda itself is not exposed to users any more. Please use a private installation of conda to build your own environments.
• OMP_NUM_THREADS is set to 1. To make use of implicit multithreading in the numerical packages this environment variable has to be set explicitly to a value greater than 1.
• User environments that were using symbolic links to the central package cache likely were broken during the transition and will have to be rebuilt.

The webpage Python on Biowulf (RHEL7) is a preview of the Python setup on the RHEL7/Centos7 cluster. Remember: the setup described on this webpage will not be in effect until the transition.