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HPC SIG: IT4Innovations Ostrava - Supercomputer visit notes

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] <a href="https://docs.it4i.cz/salomon/hardware-overview/" title="https://docs.it4i.cz/salomon/hardware-overview/">https://docs.it4i.cz/salomon/hardware-overview/</a>
[2] <a href="https://github.com/hpcugent/easybuild" title="https://github.com/hpcugent/easybuild">https://github.com/hpcugent/easybuild</a>
[3] <a href="http://singularity.lbl.gov/" title="http://singularity.lbl.gov/">http://singularity.lbl.gov/</a>