Glenna2/Glenna2-Newsletter-Dec-2017
Glenna2 Newsletter, December 2017
Welcome to read the newsletter of the Nordic Glenna2 cloud computing project.
Background:
Glenna2 is the continuation of the Glenna initiative and will be aligned with the efforts and roadmaps of the Nordic national e-infrastructure providers' and other involved organizations. Since these efforts are continually evolving and are still in early stages, it is important to allow a degree of agility in Glenna2 to be able to adapt to evolving national strategies. This will be effectively done within the project via 6-months short term plans and health checks.
Federated cloud collaboration is proposed as an action in the Nordic eScience Action Plan 2.0 which the Nordic Council of Ministers have requested NordForsk to follow up on. NeIC is the body that coordinates the implementation of the five concrete actions on e-Infrastructures included in the action plan.
Glenna2 aims to provide added value to the national cloud and dataintensive computing initiatives by:
1. Supporting national cloud initiatives to sustain affordable IaaS cloud resources through financial support, knowledgeexchange and pooling competency on cloud operations.
2. Using such national resources to establish an internationally leading collaboration on data intensive computing in collaboration with user communities.
3. Leveraging the pooled competency to take responsibility for assessing future hybrid cloud technology and communicate that to the national initiatives.
4. Supporting use of resources by pooling national cloud application expert support and create a Nordic support channel for cloud and big data. The mandate is to sustain a coordinated training and dissemination effort, creating training material and providing application level support to cloud users in all countries.
The project is organised into four Aims. The focus of Aims 1-3 is largely technological, while Aim 4 focuses on disseminating pooled knowledge down to end-users.
More about the four aims and the Glenna2 project can be found at: https://wiki.neic.no/w/ext/img_auth.php/7/7d/Glenna2_Project_Plan.pdf
News:
Cloudification of the HARMONIE-AROME Weather Code in Azure
As part of our MetCoOp collaboration Fredrik Robertsen from the Glenna2 team has worked on porting the HARMONIE NWP software to the MS Azure platform. We have ported the Harmonie version used in NSC:s (Linköping) benchmark suite and are happy to report success,
The larger test case in the suite executed in 162 minutes on 128 cores which seems to be a reasonable result The Azure environment specifications are: 8 nodes, Azure h16r, 2x E5-2667 V3 3.2 Ghz, 112 GB memory and FDR InfiniBand (54.54 gbit/s max)
More background about the hardware can be found at: https://azure.microsoft.com/en-us/blog/availability-of-h-series-vms-in-microsoft-azure/
In order to give this achievement some context: among low-latency interconnects for high performance computing, InfiniBand is the technology of choice in HPC. Since 2009, InfiniBand has occupied between 30 and 51 percent of every Top 500 list.
However, in the cloud, InfiniBand is hard to find. Of the three major public cloud offerings (Amazon Web Services, Google Cloud, and Microsoft Azure), only Azure currently has an InfiniBand offering. Some smaller players do as well, but it’s clear that InfiniBand doesn’t have the same traction in the general and public cloud space as it does in high performance computing.
One of the primary reasons is linked to how InfiniBand functions. Most of the work is offloaded to the hardware for performance reasons, which means routes are pretty static. In public and private clouds however there is the need to move virtual machines around and public clouds have an additional important requirement, which is providing logical separation between different customers This means the hypervisor migration that can happen transparently with traditional servers is difficult for virtual machines using InfiniBand. The time it takes to recompute and update routes ranges from several seconds to a few minutes.
Interestingly researchers at Simula Research Laboratory in Norway have developed a virtual switch model https://www.simula.no/sites/default/files/publications/files/towards_the_infiniband_sr-iov_vswitch_architecture_-_cluster2015_camera-ready.pdf for InfiniBand Single Root I/O Virtualization (SR-IOV), but it does not appear to have gained widespread recognition yet. The model allows providers to quickly reallocate resources and provide live VM migration which is a critical capability to operating a production cloud system by allowing maintenance procedures without requiring user-visible downtime.
The use of SR-IOV allows virtual machines to share a single physical host channel adapter and is a key factor in enabling cloud computing for HPC, but it does not solve the problem of updating routes. However as we can attest by porting HARMONIE to Azures HPC cloud and as earlier reported Gromacs, there has been good progress in making cloud-HPC a reality.
KubeNow - Easier Kubernetes Deployment
In the earlier November newsletter we were excited to report on our collaboration with the Pharmaceutical Bioinformatics research group at Uppsala University. The Glenna2 team is taking a close look at the groups KubeNow (https://github.com/kubenow/KubeNow) framework which is a cloud agnostic platform used for deploying a Kubernetes cluster using provisioning tools such as Terraform and Ansible on a cloud providers IaaS. It has been developed under the umbrella of the EU project PhenoMeNal (http://phenomenal-h2020.eu) and platform aims to simplify a Kubernetes deployment. KubeNow currently works on commercial clouds such as Amazon Web Services and Google Cloud Engine (GCE) as well as on private OpenStack installations.
Kubernetes is an open source platform that automates Linux container operations. It eliminates many of the manual processes involved in deploying and scaling containerized applications. Groups of hosts can be clustered together running Linux containers, and Kubernetes helps with managing those clusters. These clusters can span hosts across public, private, or hybrid clouds.Kubernetes was originally created by Google but was later donated to the Cloud Native Computing Foundation.
Kubernetes provides many services that are beneficial for conducting life science research. Since it is highly customizable it provides for a good architecture to o build on top of It is backed up by a large community and has started to gain popularity among bioinformaticians.Kubernetes is an active topic at all the Nordic e-infrastructure providers and we expect KubeNow to attract a lot of interest in the year to come.
Glenna2 - Dissemination
Members from the Glenna2 team participated in writing a section about federated cloud access in the Nordics for a book on OpenStack in science presented at the SuperComputing 2017 (SC17) conference.
The book is now officially out and is titled: The Crossroads of Cloud and HPC: OpenStack for Scientific Research: Exploring OpenStack cloud computing for scientific workloads and is available at Amazon:
https://www.amazon.com/Crossroads-Cloud-HPC-Scientific-scientific/dp/1978244703
Nordforsk has a article about Glenna: Building a cloud for Nordic researchers
NeIC AHM 2018
For all the members of the Glenna2 team don’t forget we have the NeIC All Hands Meeting January 29 - February 01, 2018 at Skeikampen, Norway coming up.
https://neicnordic.github.io/ahm18.neic.nordforsk.org/
---
About Glenna2:
Glenna2 is a three-year project to continue Nordic collaboration on cloud computing in Denmark, Finland, Iceland, Norway and Sweden. The aim of the project is to build on already existing services and infrastructure at the participating centers. The work is supported and directed by the Nordic e-infrastructure providers.
More about the project: https://wiki.neic.no/wiki/Glenna2
The name Glenna is an Icelandic name and means "Opening in the clouds"
---
The Glenna2 Newsletter is distributed to team members and affiliated parties.
Feel free to contact me for more information!
On behalf of the Glenna2 team,
Dan Still
Glenna2 Project Manager, NeIC
https://wiki.neic.no/wiki/Glenna
email: Dan.Still@csc.fi tel: +358 50 381 9037