E-CAM Quarterly Supporting HPC Simulation in Industry and Academia
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E-CAM Quarterly Supporting HPC simulation in industry and academia October 2016 -January 2017 1 Table of Contents E-CAM Events 2017 2 E-CAM New Management Biographies 2 E-CAM ESDW’s: a Pragmatic Response to Challenges facing Computational Science 4 Does our simulation community need EXASCALE ? 7 Second E-CAM General Assembly 10 E-CAM Deliverables Ocober 2016 to January 2017 12 E-CAM Update: October 2016 - January 2017 E-CAM has ramped up its output since October 2016. industry. The Second E-CAM General Assembly took place in November 2016 at the A multitude of deliverables have been submitted to the European Union, and Maison de la Simulation, Saclay. some 30 sofware modules have been uploaded to the E-CAM repository. An Extended Software Development Workshop (ESDW) on Trajectory Sampling was held in Traunkirchen, Austria 14th - 25th November 2016. The photograph above was taken from the location of the meeting. Read on for further details, in this fifth issue of the E-CAM newsletter. Two key changes in E-CAM management have take place with the E-CAM ESDW model is a big deal, seeking as it does to address 3 key challenges appointments of Ana Catarina F. Mendonça as Project Coordinator, and toIn computationaladdition, two piecesscience. have And beenthe second specially piece, written. written The by Davidfirst arguesCeperley, that poses the Ignacio Pagonabarraga as the Technical Manager, due to the retirement the question “Does our simulation community need EXASCALE”, and offers his of Dominic Tildesley, who, will continue to lead our interactions with perspective. 2 competitive access to Mare Nostrum and PRACE E-CAM EVENTS projects. He has secured funding from the Cat- alan Government, the Spanish Government, and the European Union, as well as from industrial E-CAM Extended Software Development Workshops companies and private foundations. He has led 54 scientific projects competitively funded. Ignacio Meso and multiscale methods, 3-14 July, 2017 , CECAM-ES is a member of: the Scientific PRACE Committe; the Scientific Panel of the Regional Government of Quantum MD, 17-28 July, 2017 July, CECAM-IRL Castilla-Leon (Spain); the External Council Board of the School of Mathematics and Physics of the Classical MD, 14-25 August, 2017, CECAM-NL University of Lincoln (UK). Meso and multiscale modeling 18-29, September 2017, CECAM-DE-MMS Since November 2016, Dr. Ana Catarina Mendonça is the E-CAM Project Co-ordinator. She obtained a degree in chemistry in 2008 from the Technical E-CAM State of the Art Workshops University of Lisbon - Instituto Superior Técnico. In 2009 she started a Marie Meso and Multiscale Modelling, 29-31 May, 2017, CECAM-IRL Curie PhD fellowship in the European Project MINILUBES, where she investi- gated the structure and interactions of ionic liquids at metallic surfaces using MD codes. In 2013 she E-CAM Industry Scoping Workshops was engaged as a post-doc for two years at CECAM HQ (EPFL) under the supervision of Prof. Dominic Solubility Prediction, 10-12 July, 2017, CECAM-FR-RA Tildesley, the CECAM Director at the time, where she focused on Monte-Carlo simulations of grafted From the atom to the molecule, 18-20 Sept. 2017, CECAM-UK-JCMAXWELL polymer brushes. She then decided to turn her ca- reer around, and in 2015 was appointed to the po- E-CAM NEW MANAGEMENT BIOGRAPHIES sition of CECAM Administrative Manager. At the same time, she also pursued a programe of advanced studies in project management, and was awarded a diploma on that topic in February 2017. Since January 2017, Professor-Ignacio-Pagonabarraga is the E-CAM Tech- nical Manager, and director of CECAM HQ at EPFL. Before assuming these posts, he was Full Professor in Condensed Matter Physics at the University of Barcelona. He has developed and exploited mesoscopic computational meth- ods to model the dynamics of soft matter and complex fluids. Recently he has also extended his interests to study the behavior of biological systems at molec- ular and cellular scales. He has expertise in the development of computation- al codes for their use in supercomputing facilities. He has gained continued, 3 E-CAM ESDW’s : a Pragmatic Response to Challenges facing Computational Science Donal Mac Kernan - University College Dublin tory[3]. At a practical level, an E-CAM sofware module must be developed usingshould the be E-CAMcertified Gitlab as such service by E-CAM and include to become three part elements of its sofware in addition reposi to Three Challenges that face computational science the code itself: The challenges that face computational science are well known and in- • documentation; clude: • a recipe for building the software and any dependencies it may have; • • unit tests (including possibly regression tests); scale/exascale applications and multiscale/multi-paradigm methods; aswell as basic adherence to an E-CAM code writing style (basically a sim- • the increasinglack of highly difficulty skilled of computaional creating simulation scientists software well versedfit for extreme both in ple naming convention for variables names, maximum line length etc). science and in modern advanced software engineering; and, • working with the large number of codes written by the indvidual sci- entist or small group, frequently poorly documented and lacking prop- concept of hiding the internal workings of a module behind simple and er unit testing and other attributes associated with modern software The modules share with the traditional computer science definition the engineering[1]. abstraction and refactoring of useful ideas from existing codes, rather than beingwell-defined written interfaces. entirely from It is scratch. likely that Moreover, many modules due to a willheterogenous result from com the- Four elements of a pragamatic response - E-CAM extended software development workshops[2] seek to respond though the ability to use C as an interfacing language is prefered, but in- pragmatically to these challenges by combining software module gener- steadmunity, to the enforce E-CAM good software software focus programming is not to enforce practise a specific allowing language, anticipated al ation with “training by doing” bringing modern programming standards hardware developments in the near future to be easily exploited. and techniques into the work practices of the participants, in its four core 2 Assembly of a dedicated team of programmers meso/multiscale modeling. The second element of this response is the assembly by E-CAM of a small scientific areas: classical MD, electronic structure, quantum dynamics, and but dedicated team of programmers/software architects and a software 1 Definition of an E-CAM software module manager who provide the general training and quality control infrastruc- - ture for ESDW’s, and a set of postdoctoral associates (pda’s) focused on the ware module[3], and goes beyond the traditional concept of software mod- ulesThe first(i.e. elementof a piece of ofthis code response possibly is the including very definition data performing of an E-CAM logically soft discrete operations, interacting through interfaces). In essence E-CAM ex- development and use of E-CAM modules and other methods on specific 3scientific Planning, questions structure, and andapplications. running of each ESDW and test suites as well as traditional subroutines and functions. Obviously, The third element is the planning, structure, and running of each ESDW, antends E-CAM the definitionsoftware moduleto include should inter be alia of workflowpotential usescripts, to the analysis community, tools, which starts typically a year ahead of the event with the submission of an encapsulate some additional functionality, enhanced performance or im- ESDW proposal to CECAM for peer review on a reasonably focused scien- proved usability for performing computational simulations in the domain areas of interest to E-CAM. Strictly speaking, an E-CAM sofware module corresponding Workpackage coordinators and ESDW organisers will tific theme. If accepted, the E-CAM software manager, programmers, and 4 identify the software skills needed for the meeting, and associated training is completed early, a participant may choose to work on another module either with the same team or another one. After the EWDW, participants are given training material well in advance of the ESDW, so as to prepare disperse to their home labs and continue module development in remote themselvesmaterial and for documentation the meeting, specificand select to individualthe module(s) modules. they considerParticipants the collaboration for several months, until the teams meet again for a 2-3 day most interesting or relevant to their work. workshop to complete,and upload the software modules, documentation, and unit tests to the E-CAM repositry. Each ESDW typically co-locates 12-15 trainees aswell as programmers and others to work on between 6 and 9 modules for about two weeks. At the 4 Online training infrastructure that facilitate the creation of modules using programming best practic- A fourth element partially completed and still under development is an ap- es,start including of the ESDWthe demands participants and constraints are introduced likely to to bea workflow required toand achieve tools propriate online training infrastructure. The E-CAM software repository is their optimal performance on future hardware. The rest of the meeting in- the principal access point for users wishing to interact with E-CAM, includ- ing training. There, they are encouraged to download and upload software, is largely