Sharing notes from a visit in IT4Innovations center in Ostrava.
Supercomputer parameters info are available at [1] - mixture of Xeon, Xeon Phi and graphic card cores. Two clusters - Anselm runs RHEL 6, Salomon runs CentOS 6.
Each node runs on a specific piece of a hardware. If a project is built on a builder of a different hardware, it is built with different flags and configuration and the resulting binaries are not properly optimized. Some projects need special features of compilers in order to run efficiently. Some of the features are available only in the latest versions of compilers. By the time the latest versions get into builders, it is usually to late. Or a project needs to be built with a proprietary compiler that is not publicly available. Or given each project needs different version of system libraries in general, the HPC infrastructure needs to offer various versions of the same library. The software needs to be available in many flavors. It means the same software to be built with multiple compilers and multiple versions. Different versions have different properties/features. Different compilers accent/provide different optimizations. Thus, a matrix of software to provide the users with. At the end a software needs to be built for the end-system architecture so it can use all the available instructions not to slow down the computation. For that reason (and many others) all the projects need to be built locally inside the cluster. That makes most of the binary packages in CentOS distribution unusable for the HPC use cases.Only usecase for rpm as proof of concepting on devel laptops is useful, not for final deployments.Currently, the EasyBuild project [2] is used as a replacement for rpm based spec files.Operators use Fedora upstream monitoring tool to monitor latest&greatest software (atm. ~400+ projects). Infiniband is usedfor connection of the nodes, sometimes issues with 3rd party SW drivers (Bull/Atos and/or HPE).
Other notes: - Lot of service providers are still running on CentOS 6, which blocks upgrade to CentOS 7- shutdown of cluster not possible, infra for clusters changed between RHEL 6 and RHEL 7. - Puppet and Ansible used to deploy clusters (Ansible for disk-free nodes, Puppetfor nodes with disks). Still, each deployment is unique (e.g. unexpected situations) and thus not fully automated.For Ansiblepart,there is no roleusedfromthe AnsibleGalaxy - just Core modules and custom roles and playbooks - Experiments with containers as well via Singularity [3] (Docker is not fully supported on CentOS 6, needs privileged user account) - Demand on packaging and providing tooling for HPC rather than libraries themselves. If possible, provide full HPC stack that is upstream and distribution supported/maintained (including full stack upgrades). CI/CD supported as well. - HPC community is unfortunately security free, security fix deployment can take several months, dependencies on specific minor releases or kernel versions. Kernel KABI whitelist should be advised to 3rd party vendors of drivers to prevent hard version deps - Each assigned set of nodes is expected to be vanilla new. Given it takes some time before a node is rebooted (order of minutes), all the tooling running inside a node must clean everything a user task left. Thus, minimize a number of times a node is really rebooted.
[1] https://docs.it4i.cz/salomon/hardware-overview/ [2] https://github.com/hpcugent/easybuild [3] http://singularity.lbl.gov/