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Odyssey 3, The Next Generation

Summary

We are at the point where new technology requires us to update the operating system, and we have chosen to migrate the Odyssey HPC cluster to CentOS 7. This will impact all Odyssey Slurm compute and login nodes. Virtual machines used for web applications, etc. will not necessarily be impacted.

This is the first thing in a long time.

Over the next 6 months, you can follow the progress outlined below in the Status section.

In this migration, new hardware to host the software will also be installed and performance will improve in a number of areas, including module load times. Software in the new module system with at least nominal usage will be migrated, while the old, "legacy" modules will not. See Details below.

Prior to deployment of the new system, RC will host seminars to explain how to use the new CentOS 7 modules and existing CentOS 6 modules. Additional migration assistance will be provided where possible.

Status

  • Initial communication, July 2017. Completed.
  • Base CentOS 7 image
  • New build environment available
  • Core compiler and libraries built
  • Module migration list published
  • CentOS 7 modules deployed with opt-in
  • CentOS 7 re-imaging
  • CentOS 7 modules default

Details

Over the course of the next 6 months, the Odyssey-HPC cluster will be undergoing a significant hardware and software update. The general compute will be refreshed with nearly 15,000 new Intel Xeon Broadwell cores. The operating system will be updated from CentOS 6.* to CentOS 7. There are several advantages to the more modern OS:

  • Support to launch modern container at runtime (i.e. Singularity )
  • Support for new technologies such as Xeon Phi, GPU's, 3DXpoint Memory, etc.
  • Performance and power improvements
  • Security enhancements
  • Support for newer code bases

Much of the software on Odyssey is delivered via a LMOD module system that enables software built for CentOS 6.8. In many cases, this software can be migrated to CentOS 7 without any changes. However, some code and libraries, especially those that depend heavily on glibc, can be sensitive to architecture or system packages and will likely need to be recompiled. To support this transition, the modulepaths of the current system will be split into CentOS 6 and CentOS 7 branches with the default modules transitioning to CentOS 7 at a specified time.

"legacy" modules will no longer be available on Odyssey. These modules typically start with prefixes like "hpc/", "math/", or "centos6/". In many cases, these modules are more than 7 years old, based on CentOS 5, and, in the case of MPI-based code, do not work properly with our current environment. The new module system already has several thousand builds of more than 600 applications and so should be able to accommodate any computation required.

We will be attempting to consolidate some of the modules during this migration. Particularly for some compiler and MPI-dependent libraries, there are dozens of builds only a handful of which are really used (see NetCDF). We will be using our module load logging data to determine whether applications or libraries are actually used and they will be given priority.

Migration of some legacy applications can be very difficult and time-consuming. RC staff will be available at Office Hours or by appointment to assist where possible.

Check this page for updates

While this project progresses, we will be sending out periodic communications. These communications will be available from this page, so check below for new postings.


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