Traditional access to HPC systems is provided through batch jobs submitted directly by users. Today, an increasing number of biological software is made accessible through web portals. This improved ease of use has led towards a democratization of access to computational resources, allowing scientists without computational backgrounds to carry out data- and compute-intensive analyses. However, these persistent services do not integrate well into a classical batch oriented HPC system such as MENDEL. This shift in requirements for emerging services demands a re-evaluation of infrastructure planning and deployment. We will present our ongoing efforts to fulfil these requirements in our existing system, and how we plan to address them in a next generation data analysis platform.

1. The past, present, and future of HPC in life sciences
Erich Birngruber, Ümit Seren
Gregor Mendel Institute for Molecular Plant Biology (GMI)
AHPC17

2. Who we are
- Basic research institute in plant sciences
- 9 independent research groups
- Employees 100 + 20 (scientific + admin)
- HPC Operations Team: 2 + 1 (engineer + lead)

3. Past: Beginnings as traditional HPC
Scientific computing at GMI
- Started in 2010
- SGI ICE-X since 2013 (MENDEL)
(72 nodes, 144 today)
- SGI UV2000
- Rich software environment
(EasyBuild, lmod)
- Keeping up with current
developments
Machine specs
3 generations of nodes:
- 72x 16c E5-2609, 192gb mem
- 18x 20c E5-2680, 256gb mem
- 54x 24c E5-2650, 256gb mem,
230gb ssd
UV2000: 96c E5-4617, 2tb mem
IB FDR interconnect (1 fabric)
Storage: Lustre 300tb, NetApp >1pb

4. Past: System architecture

5. Present: GMI site specifics
- Services: customers are biologists
- On campus initial training
- Consulting and support (w/ ticket system, intranet wiki)
- Software installations
- Provided as modules: different versions, repeatability
- This is getting harder with the demand for more complex software
- Monitoring software usage

6. Present: Monitoring software usage
- Software in env modules
- 460 software packages
in 1297 versions
- Monitoring module usage
(load, unload)
- Reporting by user, job, project

7. Present: Monitoring system activity
Monitoring and metrics
The foundation for all future decisions
- Resource consumption
- Capacity planning
- Software, technology usage
- Auditing
Alerting

8. Nodestatus

9. Jobresources

10. Present: Applications & Appliances
Phenobox (in development)
- Web-interface, API
- MySQL (DB)
- DSLR, RaspberryPi
- HPC (computer vision, storage)
GWA-Portal (https://gwas.gmi.oeaw.ac.at)
- Web-interface, API
- Elasticsearch (fulltext search)
- PostgreSQL (DB)
- Docker (Python microservices)
- HPC (analysis, storage)
Galaxy (https://galaxyproject.org/)
- Web-interface, API
- MySQL (DB)
- Visualization
- HPC (analysis, storage)
PacBio SMRT Link
(https://github.com/PacificBiosciences/SMRT-Link)
- Web-interface, API
- MySQL (DB)
- HPC (analysis, storage)
Own developments: 3rd party software:

11. Present: new developments
Deployment of OpenStack (IaaS):
- Cross-vendor open source project
- On-premises cloud
- Provision VMs and containers
- Deploy classic application services
- Enables self-service for customers
Consequences:
- More heterogeneous use-cases
- Customer base is increasing
- Non-human “customers” of HPC
- Services are more complex and
distributed over subsystems

12. Past: System architecture

13. Present: MENDEL, Openstack

14. Present: Problem 1: maintenance
- VMs are difficult to maintain
- Wrong abstraction for the use-case
- What is the next step?
- Containers?
- Container Orchestration Engines?
- Provide Software as a Service (SaaS)?
Fact is: the field is evolving

15. Present: MENDEL, Openstack

16. Future: Problem 2: integration
Applications sit on different islands:
HPC vs. Cloud
Drawbacks:
- Hard to maintain (infra)
- Hard to debug (app)
Vision: converged compute platform.
Unified infrastructure to schedule all
types of tasks
New challenges:
- Networking - Storage
- IDM - Accounting
What do others do?
Container Orchestration Engine (Google
Kubernetes, Docker Swarm, Apache Mesos)
First steps:
- Containers for HPC
- Biocontainers http://biocontainers.pro
- Singularity http://singularity.lbl.gov
- Current status: test deployment

17. Contact / References:
Erich Birngruber <erich.birngruber@gmi.oeaw.ac.at>, @ebirn
Ümit Seren <uemit.seren@gmi.oeaw.ac.at>, @timeu_s
GMI on Github:
https://github.com/Gregor-Mendel-Institute
Total recall: holistic metrics for broad systems performance and user experience visibility in a
data-intensive computing environment
https://dl.acm.org/citation.cfm?id=2835001

18. Acknowledgements
Gregor Mendel Institute
of Molecular Plant
Biology
Dr Bohr-Gasse 3
1030 Vienna, Austria

19. EOF