PLGrid Infrastructure Solutions For Computational Chemistry

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1 PLGrid Infrastructure Solutions For Computational Chemistry Mariola Czuchry, Klemens Noga, Mariusz Sterzel ACC Cyfronet AGH 2 nd Polish- Taiwanese Conference From Molecular Modeling to Nano- and Biotechnology, Opole, 27 VIII 2015

2 Agenda ACC Cyfronet AGH computing centre of excellence PLGrid Infrastructure What is PLGrid? PL- Grid Consortium Available and solutions and resources Access to Infrastructure Who is fit to free access PLGrid Users Portal How to apply for resources

3 ACC Cyfronet AGH

4 Main activity areas

5 PLGrid Infrastructure

6 PLGrid is... Computing Infrastructure for polish science which gives access to information technologies and services at well established and guaranteed level

7 PLGrid Consortum Academic Computer Centre CYFRONET AGH, Kraków (Coordinator) Tricity Academic Computer Centre, Gdańsk Poznan Supercomputing and Networking Center, Poznań Interdisciplinary Centre for Mathematical and Computational Modelling, Warszawa Wroclaw Centre for Networking and Supercomputing, Wrocław

8 PLGrid Infrastructure Nearly 3000 users use infrastructure There are more than 1000 articles in highly cited scientific journals with acknowledgments to PLGrid Infrastructure Infrastructure is used by 700 Histogram showing number of scientific articles conducted with help of PLGrid Infrastructure sorted by rank of journal Universities and research institutes staff members PhD students Undergraduate students other people involved in polish scientific projects funded by National Science Centre and National Centre for Research and Development

9 PLGrid development New generation domain- specific services in the PL- Grid infrastructure for Polish Science Competence Centre in the Field of Distributed Computing Grid Infrastructures

10 Offer for scientists

11 Main services

12 PL- Grid Infrastructure Hardware 588,02 TFLOPS cores 107,9 TB RAM 5.8 PB storage

13 TOP 500 June 2015 HPC systems from Poland 49 - Prometheus (ACC Cyfronet AGH) - 1,65 PFLOPS (PLGrid) 126 Tryton (TASK) 0,63 PFLOPS (partially in PLGrid) 135 Bem (WCSS) 0,63 PFLOPS (partially in PLGrid) ŚWIERK COMPUTING CENTRE 0,49 PFLOPS 269 Zeus (ACC Cyfronet AGH) 0,37 PFLOPS (PLGRrid) 380 Orion (ICM) 0,20 PFLOPS 418 Nostromo (ICM) 0,19 PFLOPS

14 PL- Grid Infrastructure Hardware ,5+ PFLOPS cores 300+ TB RAM 15+ PB storage

15 PL- Grid Infrastructure Hardware 2015 Available CPUs Intel Xeon 4-, 6-, 12- core (up to 24 cores on node), new Haswell microarchitecture AMD Opteron 6-, 12-, 16- core (up to 64 cores on node) Computational coprocessors GPGPU NVidia Tesla and Kepler (up to 8 units per node), Intel Xeon Phi (up to 2 coprocessors per node) Various nodes configurations 8-64 cores per node up to 512 GB RAM per node vsmp (Intel Xeon) up to 6TB RAM and 768 cores Detailed resources description

16 Access to resources and services PLGrid enables various ways to interact with Infrastructure Local queuing systems on clusters (CLI oraz GUI) grid middleware (UNICORE, QosCosGrid, glite) virtual machines webportals (InSilicoLab, Rimrock, PLG- Data, DataNet,...) Access management through PLGrid Users Portal ( Portfolio of services general services - domain specific services -

17 PLGrid - software Chemistry & Biology: ADF, AMBER, CFOUR, CP Dalton, GAMESS, Gaussian, Molcas, Molpro, MOPAC, NWChem, Open Babel, TURBOMOLE, AutoDock/AutoGrid, BLAST, Clustal, Siesta, Quantum Espresso, VASP (user s own license required), CPMD, Gromacs, NAMD Physics: FLUENT, Meep, OpenFOAM Nanotechnology: ABINIT, Quantum Espresso, NAMD Multipurpose: Mathematica, MATLAB Development: Intel, PGI, GNU compilers, MKL, CUDA, MPI, OpenMP, Alinea, Python, R, Ruby Databases Sequential, Parallel (MPI, OpenMP), interactive runs possible Users own licences could be used

18 Rimrock Rimrock Robust Remote Process and Job Controller Rimrock application simplify the way of interaction with the remote servers It allows to execute application in batch mode or start interactive application application output can be fetched online input can be send using simple REST interface 18

19 PLG- Data Access to data through web browser

20 InSilicoLab Complete workspace in web browser for a scientists who wishes to perform quantum chemistry calculations Assist with preparing input to various scientific applications performing computations on grid infrastructure controlling complex and recurrent jobs collecting output files analysis of obtained results (also from many calculations at once) 20

21 InSilicoLab Available scientific domains Chemistry Astrophysics Geophysics chemical computations using Gaussian, GAMESS, Turbomole and Terachem Trajectory Sculptor - advanced tool for manipulation of Molecular Dynamics trajectories automatic extraction of relevant parts of the input structure (based on user choices) automatic processing frames chosen by user results easily reused in quantum chemical calculations hydrodynamics calculations with finite element methods computations for Cherenkov Telescope Array (CTA) consortium digital research space for induced seismicity research in IS- EPOS project 21

22 Tools enhancing project management Adobe Connect - integrated platform for teleconference services Confluence - "wiki- style software for knowledge aggregation JIRA - tool for planning scientific or IT projects and tracking its progress Stash - Version Control with Git

23 Access to infrastructure

24 PLGrid Users Portal On- line registration through PLGrid Users Portal ( User verification based on Polish Science Database ( polska.pl/) On PLGrid Users Portal user can manage access to tools and services monitor utilization of resources manage their computational grants and grid certificates Access to all PLGrid resources through one account and one passphrase (or grid certificate)

25 Requesting for resources Computational grants in PLGrid Resources for good start personal grant Computational grants all necessary documents and forms through web portal clear and simple methods of evaluation guarantee of access to negotiated resources security of data guarantee

26 Users Support Trainings e- Learing - or hands- on with trainers info at Domain experts help through Helpdesk PLGrid service system Users Manual Available online: Users Forum

27 Registration: ext. 312

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