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Acquisition of the Central Computational Equipment for the Laboratory of Computational Chemistry and Biochemistry

English title Acquisition of the Central Computational Equipment for the Laboratory of Computational Chemistry and Biochemistry
Applicant Röthlisberger Ursula
Number 164011
Funding scheme R'EQUIP
Research institution Laboratoire de chimie et biochimie computationnelles EPFL - SB - ISIC - LCBC
Institution of higher education EPF Lausanne - EPFL
Main discipline Physical Chemistry
Start/End 01.10.2016 - 30.09.2017
Approved amount 135'520.00
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Keywords (2)

PC cluster; hardware

Lay Summary (German)

Lead
Anschaffung der zentralen Rechenausrüstung für das Laboratorium der rechengestützen Chemie und Biochemie
Lay summary

Die Forschung des “Laboratoire de Chimie et Biochimie Computationelles” (LCBC) umfasst die Entwicklung und Anwendung von Methoden in der ab initio und gemischten, quantenmechanisch/molekularmechanischen Molekulardynamik (MD) auf Basis von (zeitabhängiger) Dichtefunktionaltheorie in einem breiten Gebiet aus Chemie, Biologie und Materialwissenschaften. LCBC wurde 2002 gegründet und umfasst 15-20 Mitarbeiter. Da LCBC sich mit rein theoretischer und angewandter rechnergestützter Forschung beschäftigt, ist ein ausreichendes Mass an ständig und spezifisch der Gruppe zu Verfügung stehender Computerressourcen unabdingbar. Die für die Forschung zentralen Computerprogramme stellen hohe Anforderungen an Prozessoren, (Arbeits-)Speicher und Kommunikation zwischen Komponenten.

Wir schlagen hier den Kauf von 40 Knoten mit je zwei Intel Haswell-CPU zu 12 Kernen und je 64 GB RAM vor, verbunden via Infiniband. Diese werden Bestandteil einer zentralisierten Installation sein, die von SCITAS an der EPFL gewartet wird. SCITAS stellt Unterbringung, Hochleistungsverbindungen zwischen den Knoten, Speicherplatz, Systemadministration und technischen Support zur Verfügung. LCBC wird Zugang zum ganzen Cluster gewährt, wobei ein Gebrauchsequivalent von 40 Knoten garantiert wird. Dies ermöglicht maximale Flexibilität, da Berechnungen verglichen zu einem rein privaten Cluser auf mehr Knoten durchgeführt werden können, wobei gleichzeitig der Aufwand für Administration für LCBC minimiert wird, da dies Aufgabe der SCITAS ist.

Da LCBC in Zusammenarbeit mit verschiedenen Experimental- und theoretischen Forschungsgruppen steht (Majed Chergui-EPFL, Paul Dyson-EPFL, Michael Graetzel-EPFL, Thomas Rizzo-EPFL, Stefan Goedecker-UniBasel, Anatole von Lilienfeld-UniBasel, Ursula Keller-ETHZ, Hans-Jakob Woerner- ETHZ, Jean-Pierre Wolf-UniGeneva) und an zwei NCCR (MUST und MARCEL) und einem NRP70 Projekt teilnimmt, werden diverse Schweizer Forschungsgruppen ebenfalls indirekt von dieser Beschaffung profitieren.

Direct link to Lay Summary Last update: 28.01.2016

Responsible applicant and co-applicants

Publications

Publication

Collaboration

Group / person Country
Types of collaboration
Thomas Rizzo/EPFL Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Michael L. Klein/ Univ. Pennsylvania United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Michael Graetzel/EPFL Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Ursula Keller/ETHZ Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Leonardo Guidoni/La Sapienza Rome Italy (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Stefan Goedecker/UniBasel Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Paolo Carloni/ Juelich Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Hansjakob Woerner/ETHZ Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Mauricio Countinho-Neto/ UNiv. Fed ABC Sao Paulo Brazil (South America)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Jean-Pierre Wolf/UniGeneva Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Vassily Hatzimanikatis/EPFL Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Alessandra Magistrato Italy (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Exchange of personnel
Nigel Richards, Indiana and Purdue University United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Paul Dyson/EPFL Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Juerg Hutter/ Univ. Zurich Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Majed Chergui/EPFL Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Carme Rovira/Univ. of Barcelona Spain (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Anatole vonLilienfeld/UniBasel Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
International meeting on "Coupling Quantum Mechanics and Molecular Mechanics: Developments and Applications" Talk given at a conference Next Generation First-Principles Based QM/MM Simulations 05.09.2017 Manchester, Great Britain and Northern Ireland Röthlisberger Ursula;
SBDD Meeting Talk given at a conference De novo Design of Metalloenzymes and Biomimetic Systems 05.09.2017 Lausanne, Switzerland Röthlisberger Ursula;
11EUCO-TCC - European Conference on Theoretical and Computational Chemistry Talk given at a conference When Computational Chemistry Meets Artificial Intelligence 04.09.2017 Barcelona, Spain Röthlisberger Ursula;
WATOC2017 Talk given at a conference Next Generation First-Principles Based Multiscale Simulations: Computational Chemistry Meets Artificial Intelligence 28.08.2017 Munich, Germany Röthlisberger Ursula;
17th International Conference on Density FUnctional Theory and ist Applications Talk given at a conference Nature Knows Best: Computational Strategies for the Design of Biomimetic Systems 21.08.2017 Taellberg, Sweden Röthlisberger Ursula;
PASC17 Talk given at a conference Computational Studies of Perovskite Solar Cell Materials 27.06.2017 Lugano, Switzerland Röthlisberger Ursula;
CECAM School on Hybrid Quantum Mechanics / Molecular Mechanics (QM/MM) Approaches to Biochemistry and Beyond Talk given at a conference Interaction between QM and MM Subsystem 15.05.2017 Lausanne, Switzerland Röthlisberger Ursula;


Knowledge transfer events



Self-organised

Title Date Place
CECAM School on Hybrid Quantum Mechanics / Molecular Mechanics (QM/MM) Approaches to Biochemistry and Beyond 15.05.2017 Lausanne, Switzerland

Awards

Title Year
Ron Hides Award 2017 of the American Society of Mass Spectrometry for the paperInfrared spectroscopy of mobility-selected H+ Gly-Pro-Gly-Gly (GPGG), JASMS DOI: 10.1007/s13361-015-1172-4 (2015) by A. Masson, M. Z. Kamrath, M. A. S. Perez, M. S. Glover, U. Rothlisberger, D. E. Clemmer, and T. R. Rizzo 2017

Associated projects

Number Title Start Funding scheme
140865 Rational design of organo-ruthenium anticancer compounds with novel modes of action 01.04.2012 Project funding (Div. I-III)
146645 Multiscale Simulations for Biological Signaling and Biomimetic Design 01.05.2013 Project funding (Div. I-III)

Abstract

The research activity of the Laboratory of Computational Chemistry and Biochemistry (LCBC) focuses on the development and the application of first-principles and mixed quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) methods based on density functional and time-dependent density functional theories to a variety of scientific problems in chemistry, biology and materials science. The group is involved in several national projects (two SNF-NCCR projects, MUST and MARVEL and a NRP70 project) at the forefront of theoretical/computational research and in close collaboration with experimentalists. LCBC was formed in 2002 and typically consist of 15-20 members. As the group is involved in purely theoretical and computational research, sufficient and permanently usable, “dedicated” computational resources are absolutely essential for our work. The group's key codes are CPU, memory and communication intensive. The basic computational equipments needed for our research are: i) personalized workstations with high floating point performance that serve as working place for each group member for code development, test calculations, data processing and as terminals to remote machines. GPGPU enabled workstations are also used for special projects or for local testing of calculations to bring on larger GPGPU computer facilities for production (renewed on a as-needed basis via the labs' yearly running budget).ii) purpose-specific small to medium size high performance compute clusters as shared resources of the group for dedicated number crunching, i.e. productions runs for medium sized systems. In addition, local resources are the perfect and necessary complement to large national and international facilities to cope with the fast evolution of research themes. Urgent and highly competitive projects especially in cutting edge research, can often not wait for the allocation of computer resources by supercomputing centres (with typically of the order of six months or more between request and start of the grant).Currently, the LCBC has a ~ 6 years-old 50 nodes dual socket-quad cores Intel Xeon E5520 with 24 GB RAM per node, connected via an Infiniband switch (named Dalco3) that serves as mid size compute cluster. Dalco 3 was purchased in 2009 financed via a SNF R’equip grant (206021_128752) augmented by 50% EPFL matching funds. During the last 6 years, Dalco 3 has been running throughout at full load. As can be expected from an intensely used 6-years old computer, hardware failures (defect ventilators, hard disks etc.) are becoming more and more frequent. Furthermore, the provided computational power is no longer competitive with today's needs. Due to the ever-increasing maintenance costs and the loss of computational power, it has become necessary to buy a new computer facility for the group. Here, we propose to buy a 40 nodes dual socket-twelve cores Intel Haswell with 64 GB RAM per node, connected via an Infiniband switch. This hardware will be part of a centralized machine acquired and maintained by the SCITAS department at EPFL. SCITAS provides housing, high performance interconnect among the nodes, storage, system administration and general support. We are granted access to the entire cluster with a guaranteed usage equivalent corresponding to 40 nodes. This solution gives us high flexibility, where we can run our calculations also on more nodes than what would be possible on a fully private cluster, and at the same time minimize the effort of the group for the management of the machine as this is the responsibility of the SCITAS at EPFL. Since LCBC is involved in many collaborations with experimental and theoretical groups (Majed Chergui-EPFL, Paul Dyson-EPFL, Michael Graetzel-EPFL, Thomas Rizzo-EPFL, Stefan Goedecker-UniBasel, Anatole vonLilienfeld-UniBasel, Ursula Keller-ETHZ, Hans-Jakob Woerner- ETHZ, Jean-Pierre Wolf-UniGeneva) and participates in two NCCRs (MUST and MARVEL) as well as in a NRP70 project, several Swiss research groups will indirectly profit from this acquisition too.
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