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EasyBuild at Jülich Supercomputing Centre

(author: Alan O'Cais, Jülich Supercomputing Centre)

General info

The Jülich Supercomputing Centre (JSC, https://www.fz-juelich.de/ias/jsc) at Forschungszentrum Jülich has been operating the first German supercomputing centre since 1987, and with the Jülich Institute for Advanced Simulation it is continuing the long tradition of scientific computing at Jülich. JSC operates one of the most powerful supercomputers in Europe (JUWELS), and computing time at the highest performance level is made available to researchers in Germany and Europe by means of an independent peer-review process.

Staff & user base

About 200 experts and contacts for all aspects of supercomputing and simulation sciences work at JSC. JSC's research and development concentrates on mathematical modelling and numerical simulation, especially parallel algorithms for quantum chemistry, molecular dynamics and Monte-Carlo simulations. The focus in the computer sciences is on cluster computing, performance analysis of parallel programs, visualization, computational steering and federated data services.

In cooperation with hardware and software vendors like IBM, Intel and ParTec, JSC meets the challenges that arise from the development of exaflop systems - the computers of the next supercomputer generation. As a member of the German Gauss Centre for Supercomputing, JSC has also coordinated the construction of the European research infrastructure "PRACE - Partnership for Advanced Computing in Europe" since 2008.

Resources

JSC currently manages 3 primary systems (in addition to a number of other development clusters):

JUWELS is a milestone on the road to a new generation of ultra-flexible modular supercomputers targeting a broader range of tasks. It currently has 10.6 (CPU) + 1.7 (GPU) Petaflop per second peak performance. In the coming months, JUWELS will become the first supercomputer equipped with NVIDIA A100 GPU, when a new GPU module providing an additional 58 Petaflops will be installed. This module will make JUWELS the most powerful supercomputer in Europe.

JURECA is the precursor system to JUWELS and currently has 2 modules: the JURECA DC Module with 3.54 (CPU, AMD EPYC) + 14.98 (GPU, NVIDIA A100) Petaflop per second peak performance, and the JURECA Booster Module with 5 (KNL) Petaflop per second peak performance.

JUSUF combines an HPC cluster and a cloud platform in a single system with homogeneous hardware such that resources can be flexibly shifted between the partitions. The JUSUF compute nodes are equipped with two AMD EPYC Rome CPUs, each with 64 cores. One third of the compute nodes are furthermore equipped with one NVIDIA V100 GPU. The JUSUF cluster partition will provide HPC resources for interactive workloads and batch jobs. The cloud partition will enable co-location of (web) services with these resources to enable new workflows and support community platforms.

Usage of EasyBuild within JSC

As a large site with multiple systems and diverse requirements, JSC takes advantage of how easily EasyBuild can be extensively configured according to site policies, ranging from the software installation prefix to all aspects of the module naming scheme being used for the modules being generated.

JSC maintains a public repository of the customisations and development environment for EasyBuild that we use in our production environment. Below we highlight some particular cases of these customisations.

Custom toolchains

As of June 2020, there are a total of 15 unique toolchain definitions in use at JSC, which reflect multiple combinations of compilers (GCCcore, GCC, Intel and PGI), MPI runtimes (ParaStationMPI, OpenMPI, IntelMPI and MVAPICH2) and mathematical libraries (MKL).

Given the proliferation of toolchains required at our site, JSC has put a lot of effort into increasing the capabilities of the --try-toolchain option and has recently introduced the --try-update-deps experimental option to more easily adopt upstream changes and adapt them to our environment.

Custom module naming scheme

By default EasyBuild includes both the flat and hierarchical module naming schemes and these can be leveraged as examples for custom schemes. JSC employs such a custom scheme (based closely on the standard hierarchical scheme) to control the exact structure of the hierarchy and the naming of some specific modules (such as the compilers and MPI runtimes).

Custom easyconfigs

The upgrade cycle for our software stack does not exactly match that of EasyBuild (see below for context on this). This means that the versions of software and dependencies that we provide may be slightly different than what is in the main repository (due to critical updates, releases of important software, etc.). Arising from this and the custom toolchains that we use, we maintain our own reference easyconfig repository (our Golden repository).

We are actively trying to minimise the differences between the two (see our usage of hooks below) as we recognise that this introduces an additional maintenance burden for us, and inhibits our ability to easily contribute back our easyconfigs to EasyBuild.

Hiding dependencies

While we provide an extensive set of software, we try to minimize the packages exposed to the users by hiding a large set of dependencies which users are unlikely to require directly (via the hide-deps configuration setting). There are currently over 200 such hidden dependencies.

While hidden dependencies are not visible in the module view by default, users can expose them by the use of the --show-hidden argument in Lmod:

module --show-hidden avail

Usage of hooks

The relatively new hooks feature of EasyBuild provides JSC with an opportunity to track upstream developments more closely.

We are currently integrating a new hook that provides a lot of useful functionality:

  • Facilitates userspace installations alongside system provided installations
  • EasyBuild is configured to allow both shared installations for a group and private installations (group installations are automatically picked up by Lmod for other members of the group)
  • Restricts users from installing non-supported compilers (in particular we don't want people to install their own GCCcore since this would likely lead to an avalanche of required dependencies) and MPI runtimes (since MPI installations are heavily customised)
  • Restricts users to only resolve dependencies from our Golden repository (as well as from their own installed software) but allows them to search in the upstream repositories
    • if they try to install something from the upstream repository, the hook advises them how to do this correctly for our systems
  • Customises the final module files
  • Customises the names of some modules (such as Intel over iccifort and IntelMPI over impi)
  • Injects an Lmod family in the modules of our compilers and MPI runtimes
  • Adds Lmod properties for GPU enabled applications and user installed software so that they can be easily identified in the module view
  • Adds a site_contact for all modules
  • Updates the Lmod cache when an installation is made system-wide

We see potential in the use of hooks as a great way of encouraging, documenting and automating "correct" installation processes for our system.

Upgrading and retiring software

The expected lifetime of a system like JURECA is roughly five years. Within that period one can expect updates to compilers every few months and updates to MPI implementations as the latest standards are integrated. This would mean that the entire software stack will require frequent upgrades. During such upgrades it is natural to expect that one would install the latest version of any particular software package.

The project cycles at JSC lasts 12 months with two cycles per year. When new users get access to the machine, we want them to only be exposed to the latest software with the latest compilers. Originally, we had chosen six months as our upgrade period but found this to be cumbersome as the number of supported systems and toolchains grew, our upgrade period is now every 12 months. We chose to retire outdated software versions with the same frequency. We call these software upgrades "stages". For each 'stage', we select the toolchains that we will support and rebuild the latest versions of our supported software with these toolchains. We chose a prototype toolchain as a template and, once fully populated, migrate the changes to our other toolchains.

We expect members of the support team to contribute to software installations since it is common that application software requires specific knowledge to be installed and tested appropriately. A common workflow is to create a personal installation of a package that can be tweaked, then a group installation for others to try out. Once a software package has been successfully built and tested, it is added to a Golden repository to be used in production.

The default stage visible to users is controlled by a symbolic link. Stage upgrades are prepared in a separate environment to this default. Once the upgrade has been implemented, users are given three weeks notice and the symbolic link is updated during a maintenance window. Users are provided with the capability of continuing to use a retired stage if they wish to do so. However, additional software requests are (typically) only accepted for the current default stage.

While stage upgrades may introduce some overhead for existing users (they may need to recompile their code and modules may be named differently in particular cases), there are clear benefits to using the latest compilers and software stack. In addition, these upgrades provide us with the opportunity to potentially change our module hierarchy or introduce new features related to Lmod.


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Last update: June 23, 2021