InSilicoLab – Grid Environment for Supporting Numerical Experiments in Chemistry Joanna Kocot, Daniel Harężlak, Klemens Noga, Mariusz Sterzel, Tomasz Szepieniec ACC CYFRONET AGH, ul. Nawojki 11, Kraków, Poland

What is required for numerical experiments in Chemistry? Computational resources To get the results of the computations in reasonable time Chemistry packages Applications that realize the computation – e.g. Gaussian, GAMESS etc. 2 EGI User Forum, April 2011

What is available? Computational resources Grid resources in European computing centres Chemistry packages Applications (Gaussian, GAMESS etc.) installed on the Grid resources in these centers Made available to some Virtual Organizations 3 EGI User Forum, April 2011

Sample scenario: Chemistry experiment on Grids 4 EGI User Forum, April Obtaining a Grid certificate 2.Registration in a Virtual Organization 3.Proxy generation 4.Specification of the experiment input parameters 5.Execution 6.Experiment monitoring 7.Result analysis 8.Reusing the result or input data

Sample scenario: Chemistry experiment on Grids 1.Obtaining a Grid certificate 2.Registration in a Virtual Organization 3.Proxy generation 4.Specification of the experiment input parameters 5.Execution 6.Experiment monitoring 7.Result analysis 8.Reusing the result or input data EGI User Forum, April 2011 There are several on-line tools facilitating this process 5 This step has to be performed only once.

Sample scenario: Chemistry experiment on Grids 1.Obtaining a Grid certificate 2.Registration in a Virtual Organization 3.Proxy generation 4.Specification of the experiment input parameters 5.Execution 6.Experiment monitoring 7.Result analysis 8.Reusing the result or input data EGI User Forum, April 2011 voms-proxy-init The user has to store their certificate and private key in the.globus directory (with proper directory permissions set) Needs to know the command syntax. 6

Sample scenario: Chemistry experiment on Grids EGI User Forum, April Obtaining a Grid certificate 2.Registration in a Virtual Organization 3.Proxy generation 4.Specification of the experiment input parameters 5.Execution 6.Experiment monitoring 7.Result analysis 8.Reusing the result or input data External visual editor (the resulting file has to be copied to the access machine – additional operation!) Text editor Creating multiple files might be necessary 7

Sample scenario: Chemistry experiment on Grids EGI User Forum, April Obtaining a Grid certificate 2.Registration in a Virtual Organization 3.Proxy generation 4.Specification of the experiment input parameters 5.Execution 6.Experiment monitoring 7.Result analysis 8.Reusing the result or input data Creating a job description file (JDL) In case of multiple jobs – creating many files is necessary glite-wms-job-submit 8

Sample scenario: Chemistry experiment on Grids 1.Obtaining a Grid certificate 2.Registration in a Virtual Organization 3.Proxy generation 4.Specification of the experiment input parameters 5.Execution 6.Experiment monitoring 7.Result analysis 8.Reusing the result or input data EGI User Forum, April 2011 glite-wms-job-status Refresh only on demand 9

Sample scenario: Chemistry experiment on Grids 1.Obtaining a Grid certificate 2.Registration in a Virtual Organization 3.Proxy generation 4.Specification of the experiment input parameters 5.Execution 6.Experiment monitoring 7.Result analysis 8.Reusing the result or input data EGI User Forum, April 2011 Large result files have to be downloaded from LFC: glite-wms-job-output Result files in text form Usually many result files. 10

Sample scenario: Chemistry experiment on Grids 1.Obtaining a Grid certificate 2.Registration in a Virtual Organization 3.Proxy generation 4.Specification of the experiment input parameters 5.Execution 6.Experiment monitoring 7.Result analysis 8.Reusing the result or input data EGI User Forum, April Finding the right part of the result Repeating previous actions

What is the probem? Need to combine multiple tools to perform a simple scenario Difficult result management Multiple files The files are usually stored in the LFC Catalogue The files are in text format: Human-readable but very large and hardly legible Difficult to process by computer Difficult data management – results and inputs 12 EGI User Forum, April 2011

What should the solution be? Create a virtual unified space Easy access to all the results and collected data ‼Adjust, when the user wants to use the infrastructure in the traditional way Guide the user throughout the whole process of experimentation Communicate with the users in the language the language of their scientific domain 13 EGI User Forum, April 2011

Existing Layers Domain layer – the space managed by the user, Concerning terms (vocabulary) familiar to the user Grid resource layer – the part of the system providing access to e-infrastructures And the computational packages available on them To create an effective, yet intuitive tool, we need to join two layers: … and make the result available to the user EGI User Forum, April 2011

New Layer: Glue Joins the user-domain space with the resource access layer Is responsible for: Executing the experiment’s logic Automatic parallelization Execution monitoring Storing the user’s data Creating metadata – annotations, tags InSilicoLab introduces an additional layer – support layer, that: EGI User Forum, April 2011

Support Layer – Details Experiment Logic: Transforming the user’s input to Grid jobs Automatic initial analysis of the jobs’ results Automatic parallelization Automatically creates many jobs for parameter study experiments Execution engine Submits the generated jobs to the Grid Manages and monitors the experiment 16 EGI User Forum, April 2011

Support Layer – Details Metadata model Reports from result analysis summarizing the experiment Associates the experiment results with the input data Provenance tracking Data structure Storage of the molecules with their properties Unified format with export to supported application Annotations, tagging: Facilitate description and management of the data 17 EGI User Forum, April 2011

New Layer: Domain Portal Is an interface operating on the domain layer – on the concepts from the specific domain of science Enables access to the user’s space (work environment) and data stored by the user, from every computer connected to the Internet The communication between InSilicoLab with the user is realized through Web portal, that: EGI User Forum, April 2011

Grid Features Support for Grid certificates Proxy generation or upload MyProxy support LFC catalogue management Browser Input files uploaded directly from LFC LFC location assigned to experiment and its jobs Grid jobs management Submission and status monitoring Automatic output processing 19 EGI User Forum, April 2011

InSilicoLab: How it works? 20 EGI User Forum, April 2011

InSilicoLab: Ready for Use The portal is up and running Available to all users registered in Gaussian VO and vo.plgrid.pl Virtual Organizations. Supported applications: Gaussian, GAMESS, TURBOMOLE 21 EGI User Forum, April

Work in progress Support for new domains of science: Based on the same design Biochemisry: Gromacs and PDB databases Astronomy: support of the design phase of CTA Advanced data management Improving reliability and performance 22 EGI User Forum, April 2011

Summary InSilicoLab offers access to Grid resources following e-Science ideas Helps the user in managing the complexity of their experiments Generic design facilitates integration of tools from many domains of science The portal is available at: Contact: 23 EGI User Forum, April 2011

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