2nd meeting of the atbi workgroup infrastructure and hpc · • >200 perl, python2, python3, r...
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2nd meeting of the ATBI workgroup infrastructure and HPC9-11 Current situation of computing in life sciences
Coffee break11-12 HRSM projects started in 2017
Exchange between computing facilities; future ideas? 12-13 Lunch break13-15 Structure and roles in the upcoming Austrian ELIXIR node
Life Science Compute Cluster (LiSC) Althanstraße+Rennweg
Life Science Compute Cluster (LiSC)
Life Science Compute Cluster (LiSC)
Life Science campus Althanstraße + Rennweg:• Microbiology and Ecosystem research• Organismal systems biology, zoology, anthropology• Botany• Ecology• Pharmacy• (Cognition biology)
16 Compute nodes A20 cores, 320G RAM, 3T tmp
30 Compute nodes B16 cores AMD, 128G RAM, 6T tmp
10 NAS-heads
FC-attached storage5 Arrays
650TB total capacity
2 Database Servers128G RAM,2 TB RAID 10
5 Login nodes: 1xGPU/MIC,8/16 core,48/196G RAM,2/7T tmp
5 Compute nodes C32..40 cores, 1T RAM, 8T tmp
Life Science Compute Cluster (LiSC)
6 Compute nodes D8 cores, 48G RAM, 3T tmp
2 VMWARE Servers 256G RAM16 virtual machines
FC-attached storage1 Array
24TB total capacity
Fanless desktops
NAGIOS Monitoring server(hw, services, backup, prov.)
ZID TSM Backup
Fedora Workstation 26
CentOS 7SLURM workload manager
LDAP user management
Support for users
• Software installation (on demand)
• Database provisioning (weekly/monthly)
• Helpdesk
• Courses
• Usage statistics
• …
http://cube.univie.ac.at/lisc
Environment modules on LiSC
• >200 perl, python2, python3, R modules• 548 modules and versions
sequenceanalysis 78ngstools 73metagenomics 25development 21phylogeny 21assembly 16amplicons 5genetics 5networktools 5visualisation 5rnatools 3machinelearning 2system 2
HRSM projects VSCBio and SOLID
Tier 1: Vienna Scientific Cluster
HRSM 2013-2017: 17 bioinformatics nodes• CPU: 2x Intel(R) Xeon(R) CPU E5-2690 v4 @ 2.60GHz (14 Cores / 28 threads per
CPU)• Storage: 4x Intel P3600 SSD 2 TB (Exported via the BINFS filesystem)• Storage: 12x Seagate ST8000NM0075 8 TB Disks (Exported via the BINFL
filesystem)• Intel Omnipath Interconnect (100 Gigabit/s)• Mellanox ConnectX3 Infiniband Controller (40 Gigabit/s to VSC-3)• 512GB for the nodes binf-01 to binf-12,• 1024GB for the nodes binf-13 to binf-16 and• the binf-17 node has a total of 1536GB of RAM (with slightly lower performance).
HRSM SOLID: 2017-2020
265 kEUR
162 kEUR
12 kEUR
220 kEUR
Tier 1
Tier 2
Tier 3
Distribution of expertiseHPC
Bioinformatics
Biology
Relevant software tools and data resources
http://bio.tools
Aim:
HPC resources easier accessible for life scientists
Concept:
Bioinformatics HPC services by experts for non-experts
SOLID team
TBI, Prof. Ivo Hofacker, Fakultät für Chemie, Universität Wien
CUBE, Prof. Thomas RaAei, Forschungsverbund CMM, Universität Wien
CIBIV, Prof. Arndt von Haeseler, MFPL, Universität Wien + MedUni Wien
Medical Epigenomics Lab, Dr. Christoph Bock, Medizinische Universität Wien
CemSIIS, BiosimulaNon and BioinformaNcs, Prof. Wolfgang Schreiner, MedUni Wien
Molekulare Ökologie, Prof. Birgit Schlick-Steiner, Universität Innsbruck
Roadmap 2017
1. Technical and administrative standards (analysis, surveys, concepts)• Homogeneity of HPC platforms• Software packaging and dependency management
2. Biological database requirements3. Software repositories, Issue tracker, Documentation
Roadmap 2018
1. Software deployment on VSC• Environment modules• Singularity containers
2. Hiring mainly Pre-Docs on 20% basis3. Presentation to users, feedback4. Quantitative usage measures, predictive planning5. Full operation in late 2018
Operation 2019/2020
• bm.wfw funding until end of 2019• In kind contributions of partners until end of 2020
Consolidation 2020: Austrian ELIXIR node
The Austrian ELIXIR node
State of the art in Austria/international
• Austria: High-performance islands, little connected, few bridges
• International:• Institutional/Company (HPC, Software, Databases, User support)• Regional/National networks/facilities (HPC, Software, Databases, Workflows,
User support)• International networks/facilities (data archives, web-based computing,
standards, …)
Advantages ELIXIR
• Develop national HPC infrastructure, participate+contribute to international (incentives for bioinformaticians to provide infrastructures)
• Services (licensing possible, see KEGG):• 13 compute• 71 database (including essential)• 12 interoperability• 45 tools• 8 training
• International network integration now review criterion for international projects (EU) in life science (early data access, mio EUR!)• PANGEA: MSCA-ITN via ELIXIR Italy, SmartBioMaps failed, DECIDE-Sys failed,
• Solution to• Bridging users and specialists of life science HPC• Sustainability problem in bioinformatics
ELIXIR node structure
Mission1. ELIXIR Austria supports Austrian bioinformaticians and provides
excellent bioinformatics services to Austrian life scientists via ATBI, which will function as the Austrian hub for all ELIXIR activities.
2. ELIXIR Austria provides bioinformatics training for life scientists in Austria through ATBI-coordinated training activities.
3. The ELIXIR Austria node will foster cooperation within the Austrian bioinformatics community and with international networks for bioinformatics.
ELIXIR node structure
Structure and topics• Section “Services”• Orchestrating the organization of existing bioinformatics hardware (funded by
HRSM, FFG and research institutions, startup funding to new professors and others) into a collaborative framework.• Provisioning and support of comprehensive bioinformatics software and
biological database services on the Austrian High-Performance Computing (HPC) resources.• Identification, maintenance and further development of Austrian core
resources (hardware, software and databases for life sciences) with the goal of achieving long-term sustainability.
ELIXIR node structure
Structure and topics• Section “Training”• Improvement of undergraduate and graduate bioinformatics education in
Austria (e.g. synchronization of special courses between Universities, e-learning material).• Improvement of post-graduate bioinformatics training in Austria (from PhD-
level to on-the-job training).• Development of training offers for Austrian core resources via Summer
Schools etc..
ELIXIR node structure
Structure and topics
• Section “Collaboration”• Maintaining the connections between Austrian life scientists,
bioinformaticians and ELIXIR Austria (e.g. through conferences, workshops, meetings and a jointly organized new Summer School program).• Identification of areas of shared interest with de.NBI (Germany’s Next
Generation Bioinformatics Platform; http://www.denbi.de), SIB (the Swiss Institute of Bioinformatics; http://www.sib.swiss) and other ELIXIR nodes, creation of links between these entities and ELIXIR Austria.
ELIXIR node implementation
Phase 1: initiation
• The initial phase should be coordinated by ATBI, which will represent the Austrian bioinformatics community with regards to ELIXIR. The main tasks of this phase are:• Collection and provision of information about Austrian infrastructure resources
for life science data (mainly through a central website, which serves as starting point for life scientists seeking solutions for their computational and data analysis problems).• Establishment of the core of the three aspects (Service Provision, Training and
Collaboration) by identifying relevant bioinformaticians and infrastructure-related projects in Austria.• Negotiation of the contractual requirements for full membership of Austria with
ELIXIR.
ELIXIR node implementa1on
Phase 2: full operation
• Austrian ELIXIR node should then serve as a “one-stop-shop” for
Austrian life scientists with regard to computational infrastructure
• Develop support mechanisms and facilities for exchange
• Financial resources:
• annual fees to ELIXIR (estimated 200k EUR p.a.)
• Operational costs of ELIXIR Austria (mainly project-based).
• In addition, funding for a country-wide bioinformatics collaboration also
needs to be identified to make an ELIXIR node fully functional.
Funds for ELIXIR (institutes/ministry/university)• Swiss model:• SIB is federally funded and elixir node Switzerland• Institutions pay for SIB membership• Membership benefits: e.g. infrastructure access, SIB funded positions for
developing core resources• Austrian model:• Membership (162 kEUR in 2018) ?• Structural costs (1-2 positions) ?• Operational costs (scientific/technical/training activities) ?
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