Outline 18/12/2014. Accessing GROMACS on a Science Gateway. GROMACS in a nutshell. GROMACS users in India. GROMACS on GARUDA

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1 Outline Co-ordination & Harmonisation of Advanced e-infrastructures for Research and Education Data Sharing Accessing GROMACS on a Dr. Giuseppe La Rocca, INFN Catania 6 th CHAIN-REDS Workshop, Guwahati - India 17 December 2014 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 proj-office@chain-project.eu Co-funded by the European Commission under its 7 th Framework Programme 2 1

2 GROMACS in a nutshell GROMACS in a nutshell (2) GROMACS (GROningen MAchine for Chemical Simulations) is a very popular molecular dynamics package primarily designed for simulations of proteins, lipids and nucleic acids It was originally developed in the Biophysical Chemistry department of University of Groningen ( ) Since 2001 is now developed by the Royal Institute of Technology (KTH) and the Uppsala University (UU) GROMACS is extremely fast For certain calculations, it is 20 to 30 times faster than TINKER 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 3 4 2

3 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) GROMACS users in India GROMACS on GARUDA Software versions used: GROMACS (serial/threaded) and GROMACS (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) GarudaAdmin VOMS is not public Starting from Java 1.7+ we have to disable older signature algorithms SHA256withSignature Algorithm are not supported 5 6 3

4 Actions carried out by the project Actions carried out by the project (2) On the 16 th of May 2014, the CHAIN-REDS project and the GARUDA team organized a focused event for users support at the 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) The glibrary framework, and the glibrary Data Management APIs, have been used to store big output files on a EMI-3 DPM Storages with WebDAV interface enabled Evaluated a JSAGA Adaptor to access the GARUDA resources and make them available through the (see next slides) Integrated the application in the CHAIN-REDS Gateway using portlet technology and the Catania Science Gateway Framework (CSGF) 7 8 4

5 Status of the JSAGA Adaptor to access GARUDA resources Simple APIs for Grid Application, a high-level application-oriented software library for Grid applications specified by the Open Grid Forum (OGF). SAGA allows creating an unique interface to different middleware stacks Different implementation of this standard 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 gatekeeper://xn03.ctsf.cdacb.in:2119/jobmanager-gw Testing with pure JSAGA APIs It Works! With GlassFish 3.1 Some remaining problems currently under investigation

6 The GROMACS application on the CHAIN-REDS Authentication based on Identity Federations 11 CHAIN-REDS second periodic review, Brussels 11/09/

7 GROMACS on the CHAIN-REDS Science Gateway

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9 Results available on EMI-3 DPM Storages with WebDAV Interface enabled GROMACS simulations results can be downloaded in the user s workstation

10 Conclusions CHAIN-REDS project provided technical know-how and expertise to set-up a virtual environment for the GROMACS community The application has been integrated to take advantage from DCI technologies, and allow the Indian VRC to collaborate with the rest of the global community The application is available in the CHAIN-REDS SG Co-ordination & Harmonisation of Advanced e-infrastructures for Research and Education Data Sharing Thank you! proj-office@chain-project.eu CHAIN-REDS second periodic review, Brussels 19 11/09/ proj-office@chain-project.eu Co-funded by the European Commission under its 7 th Framework Programme 10