Annual Scientific Report 2015

Systems Applications
The Systems Applications team manages EMBL-EBI’s core IT applications,
which include virtualisation, cloud technologies including Embassy Cloud,
e-mail, authentication and desktop systems. We also provide database
administration, for example for Oracle and MySQL, and provide basic services
to EMBL-EBI staff as well as external collaborations.
Major achievements
Virtualisation and cloud
The virtual infrastructure that supports more than 2000
virtual machines (VMs) continues to provide a solidly
reliable service, with 100% uptime. We completed
virtualisation of existing services and shifted focus
to supporting new services. EMBL-EBI’s technical
infrastructure remained within acceptable capacity
figures despite the linear growth in usage. We retired
several old hypervisors and storage systems,
migrating their virtual machines to other systems
without downtime.
Embassy Cloud work focused on commissioning the new
OpenStack infrastructure and maintaining it through
its first six months of usage, during which it provided
robust, high-performance service.
We moved EMBL-EBI’s contribution to the PanCancer
Analysis of Whole Genomes (PCAWG) initiative to the
OpenStack infrastructure, supporting the scientists
by providing more high-performance compute to the
project (n.b. CPU utilisation peaked at upwards of 80%
over 1000 cores during processing). We transferred the
Cloud resources to the internal EMBL teams working
on the next phase of the PCAWG initiative, for which
the Embassy Cloud continued to provide a highperformance
compute environment.
Open Targets (formerly CTTV), which is hosted on
the Embassy Cloud, continued to grow in resource
usage, which we accommodated through maintenance
and expansion of the Cloud. Working with eMedLab
partners our team enabled the EMBL-EBI contribution
to the eMedLab project, functioning as an active part of
their Operations team. We will further support eMedLab
by managing the transfer and maintenance of selected
EMBL-EBI datasets on the eMedLab infrastructure for
access by their tenant users.
In 2015 we began to join The Embassy Cloud to the
European Grid Infrastructure, putting significant efforts
into an initial proof-of-concept implementation of their
Federated Cloud software. This will progress to a trial in
2016 to support ELIXIR.
Best Data Centre Project of the Year’ award from the Computer Weekly
European User Awards 2015, for work on Delphix architecture planning
for public-facing technical infrastructure, a project led by Systems
Applications team member Manuela Menchi.
Databases
We completed the consolidation of all database
instances from hundreds of individual physical servers
with dedicated SAN storage systems to VMs and a
shared infrastructure. This consolidation reduced
the data-centre capacity required for databases,
provides additional flexibility in updating the
underlying hardware without impacting services,
and reduces EMBL-EBI’s exposure to licence costs
that are calculated on physical core count. This work
included the retirement of obsolete hardware, database
infrastructure activities such as backup, data protection
and software upgrades to the database management
system (i.e. MySQL, MongoDB, Vertica, Oracle, MS
SQL Server), a review of monitoring systems, testing
and support – all in conjunction with the migration of
the EMBL-EBI internal authentication system from
Network Information Service (NIS) to Lightweight
Directory Access Protocol (LDAP).
We contributed to wider projects involving the IT
infrastructure and data centres, reviewing the Database
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2015 EMBL-EBI Annual Scientific Report