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0s and 1s in marine molecular research: a regional HPC perspective
Zafeiropoulos, H.; Gioti, A.; Ninidakis, S.; Potirakis, A.; Paragkamian, S.; Angelova, N.; Antoniou, A.; Danis, T.; Kaitetzidou, E.; Kasapidis, P.; Kristoffersen, J.B.; Papadogiannis, V.; Pavloudi, C.; Ha, Q.V.; Lagnel, J.; Pattakos, N.; Perantinos, G.; Sidirokastritis, D.; Vavilis, P.; Kotoulas, G.; Manousaki, T.; Sarropoulou, E.; Tsigenopoulos, C.S.; Arvanitidis, C.; Magoulas, A.; Pafilis, E. (2021). 0s and 1s in marine molecular research: a regional HPC perspective. GigaScience 10(8): giab053. https://dx.doi.org/10.1093/gigascience/giab053
In: GigaScience. Oxford Academic: Oxford. e-ISSN 2047-217X
Peer reviewed article  
Available in  Authors 
Keyword
    Marine/Coastal
Author keywords
    marine research; high performance computing; containerization; computational requirements; high-throughput sequencing; research infrastructures; biodiversity; biotechnology; aquaculture
Authors  Top 
  • Zafeiropoulos, H.
  • Gioti, A.
  • Ninidakis, S.
  • Potirakis, A.
  • Paragkamian, S.
  • Angelova, N.
  • Antoniou, A.
  • Danis, T.
  • Kaitetzidou, E.
  • Kasapidis, P.
  • Kristoffersen, J.B.
  • Papadogiannis, V.
  • Pavloudi, C.
  • Ha, Q.V.
  • Lagnel, J.
  • Pattakos, N.
  • Perantinos, G.
  • Sidirokastritis, D.
  • Vavilis, P.
  • Kotoulas, G.
  • Manousaki, T.
  • Sarropoulou, E.
  • Tsigenopoulos, C.S.
  • Arvanitidis, C., more
  • Magoulas, A.
  • Pafilis, E.
Abstract
    High-performance computing (HPC) systems have become indispensable for modern marine research, providing support to an increasing number and diversity of users. Pairing with the impetus offered by high-throughput methods to key areas such as non-model organism studies, their operation continuously evolves to meet the corresponding computational challenges. Here, we present a Tier 2 (regional) HPC facility, operating for over a decade at the Institute of Marine Biology, Biotechnology, and Aquaculture of the Hellenic Centre for Marine Research in Greece. Strategic choices made in design and upgrades aimed to strike a balance between depth (the need for a few high-memory nodes) and breadth (a number of slimmer nodes), as dictated by the idiosyncrasy of the supported research. Qualitative computational requirement analysis of the latter revealed the diversity of marine fields, methods, and approaches adopted to translate data into knowledge. In addition, hardware and software architectures, usage statistics, policy, and user management aspects of the facility are presented. Drawing upon the last decade’s experience from the different levels of operation of the Institute of Marine Biology, Biotechnology, and Aquaculture HPC facility, a number of lessons are presented; these have contributed to the facility’s future directions in light of emerging distribution technologies (e.g., containers) and Research Infrastructure evolution. In combination with detailed knowledge of the facility usage and its upcoming upgrade, future collaborations in marine research and beyond are envisioned.
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