9 giuseppe chain-reds guwahati larocca · saga allows creating an unique interface to different...
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Co-ordination & Harmonisation of Advanced e-Infrastructuresfor Research and Education Data Sharing
Co-funded by the European Commission under its 7th Framework Programme
Accessing GROMACS ona Science Gateway
Dr. Giuseppe La Rocca, INFN Catania
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Outline
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GROMACS in a nutshell
GROMACS users in India
GROMACS on GARUDA
Actions carried out by the project
Current achievements
Future plan and remaining issues
Conclusions
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GROMACS (GROningen MAchine for ChemicalSimulations) is a very popular molecular dynamics packageprimarily designed for simulations of proteins, lipids and nucleicacids
It was originally developed in the Biophysical Chemistrydepartment of University of Groningen (1991-2000)
GROMACS in a nutshell
Since 2001 is now developed by the Royal Institute of Technology(KTH) and the Uppsala University (UU)
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GROMACS is extremely fast For certain calculations, it is 20 to 30 times faster than TINKER
GROMACS in a nutshell (2)
GROMACS is free Starting from release 4.6 it is released under the GNU General
Public License
GROMACS can be executed both on CPUs and GPUs In parallel, using MPI or threads Can manage input and output files of different formats
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GROMACS users in India
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User Communities Researchers from Universities, Academic Institutes
and R&D laboratories from India who work closely with molecular modeling studies
Letter of Interests Department of Physics – Periyar University,
Salem, India Department of Physics – Bharathiar University,
Tamilnadu, India
Scientific Domains & Relevance Bio-informatics (molecular dynamics) Allows complex studies (e.g. protein folding)
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GROMACS on GARUDA
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Software versions used: GROMACS 4.5.5 (serial/threaded) and GROMACS 4.6.5 (MPI/threaded)
Resources used: 2 HPC clusters of GARUDA (Bangalore, Chennai)
No. of Processors used on GARUDA: 5 nodes (each with 8 processors)
Toolkit: GARUDA uses Globus Toolkit (v4.0.8) GarudaAdminVOMS is not public Starting from Java 1.7+ we have to disable older signature algorithms
SHA256withSignature Algorithm are not supported
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Actions carried out by the project
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On the 16th of May 2014, the CHAIN-REDS project and theGARUDA team organized a focused event for users’ support atthe Indian Institute of Science Education and Research
GROMACS v4.6.5 release has been successfully installed and tested on the distributed computing resources Deployed at Garuda (2), Arab (2), ROC-LA(1) and EGI (13) sites 2 distributions of Linux (SL5 & SL6)
Integrated the application in the CHAIN-REDS Gatewayusing portlet technology and the Catania ScienceGateway Framework (CSGF)
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Actions carried out by the project (2)
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The gLibrary framework, and the gLibrary DataManagement APIs, have been used to store bigoutput files on a EMI-3 DPM Storages withWebDAV interface enabled
Evaluated a JSAGA Adaptor to access theGARUDA resources and make them availablethrough the Science Gateway (see next slides)
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Simple APIs for Grid Application, a high-level application-orientedsoftware library for Grid applications specified by the Open GridForum (OGF). SAGA allows creating an unique interface to different middleware stacks Different implementation of this standard
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Starting from JSAGA (v0.9.17), the WS-GRAM Adaptor was no longer used! The JSAGA Globus Adaptor to access the Gatekeeper service
running in GARUDA has been used
Status of the JSAGA Adaptor to access GARUDA resources
Testing with pure JSAGA APIs It Works! With GlassFish 3.1 Some remaining problems currently
under investigation
gatekeeper://xn03.ctsf.cdacb.in:2119/jobmanager-gw
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11/09/2014CHAIN-REDS second periodic review, Brussels11
The GROMACS applicationon the CHAIN-REDS
Science Gateway
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GROMACS on the CHAIN-REDS Science Gateway
Authentication based on Identity Federations
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GROMACS on the CHAIN-REDS Science Gateway
GROMACS on the CHAIN-REDS Science
Gateway
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GROMACS on the CHAIN-REDS Science Gateway
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GROMACS on the CHAIN-REDS Science Gateway
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GROMACS on the CHAIN-REDS Science Gateway
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GROMACS on the CHAIN-REDS Science Gateway
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GROMACS on the CHAIN-REDS Science Gateway
Results available on EMI-3 DPM Storages
with WebDAV Interface enabled GROMACS simulations’ results can be
downloaded in the user’s workstation
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Conclusions
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CHAIN-REDS project provided technical know-how andexpertise to set-up a virtual environment for theGROMACS community
The application has been integrated to take advantagefrom DCI technologies, and allow the Indian VRC tocollaborate with the rest of the global community
The application is available in the CHAIN-REDS SG
Co-ordination & Harmonisation of Advanced e-Infrastructuresfor Research and Education Data Sharing
Co-funded by the European Commission under its 7th Framework Programme
Thank you !
www.chain-project.eu