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Python for Scientific Gateways Development Randy Heiland1, Sean D. Mooney1, Keith Jackson2, Joshua Boverhof2, Maciek Swat1, Ariel Balter1, Marcus Christie1, Joseph Insley3 GCE Workshop Supercomputing 2007 1-Indiana University, 2-Lawrence Berkeley Lab, 3-Argonne National Lab Gateway Development: A landscape of technologies Blogs Web Services Java Web 2.0 C# Globus OGCE GridSphere XML iGoogle Background and Motivation • http://communitygrids.blogspot.com/2007/02/rethinking-science-gateways.html “Rethinking Science Gateways” …many science gateways would undoubtedly benefit from “agile development” rather than “enterprise development” practices. This is because many science teams cannot afford specialized Web and Grid developers. They would instead like to build gateways themselves. Such would-be gateway developers typically possess a great deal of programming knowledge but are more likely to be driven by practical applications rather than the desire to build elegantly architected software. … Gateway Development: A landscape of technologies Blogs Python Java Web Services Web 2.0 C# Globus OGCE GridSphere XML iGoogle Python • Released in 1991 by Guido van Rossum (at Google since Dec ‘05; 50% time on Python) • • • • • • • Dynamically typed, Strongly typed, Auto memory mgt High-level lng; Syntax (minimal, clean) Interpreted; Interactive ( rapid prototyping/development) Glue-iness, Wrap-ability (e.g., www.swig.org) CiSE Introspection May/June 2007 History with science apps Vibrant communities and evolving language Gateways: Two basic approaches • Web browser-based • Application, client-server TeraGrid Science Gateway is defined as “a community interface that enables access to high end resources, usually through a web portal or desktop client server arrangement” Some Python-related tools for a scientific gateway NumPy UCSF Chimera, VMD, PyMOL CompuCell3D ZSI, pyGlobus, pyGridWare SciPy Biopython VTK, ParaView, matplotlib TurboGears, django SWIG, SIP Pyrex VisTrails Numerical module providing array objects Molecular graphics and modeling Environment for cell-based modeling Web services toolkit, Interface to GT, WSRF toolkit Science and engineering modules Tools for computational molecular biology Scientific visualization, 2D plotting Web development frameworks Tools for wrapping code in Python Tool for writing extension modules in C Scientific workflow system Application Client-Server using Web services (SOAPpy, ZSI) chembiogrid.org lifescienceweb.org Web browser gateway: TurboGears - Web dev framework (in Python) • Open source Model-View-Controller • AJAX w/ MochiKit • Model: SQLObject • JSON • View: Kid templating • Controller: CherryPy • Apache HTTP, MySQL In addition to TurboGears, may also try django, another Python Web dev framework. Getting started - trivial $ tg-admin quickstart - prompted for proj name $ start-<proj>.py TurboGears “extras” - usual widgets: input fields, checkboxes, tables, etc. - more complex widgets ZSI - Python Web services • Python pkg implementing SOAP 1.1 spec • Generates stubs for client & server, from a WSDL: $ wsdl2py $ wsdl2dispatch (refer to Nws example in paper) CompuCell3D - NIH funded project • Cell-based tissue simulation environment Testbed for parameter sweeps on HPC via gateway(s) Security • Out-of-the-box solution using Grid Security Infrastructure (GSI) authentication • Assumes: GSI file systems (e.g. /etc/grid-security) on host computer, a newer version of M2Crypto (>=0.16) installed, client certificate exists and has been imported into browser Non-Python components using AJAX • Javascript widgets (MochiKit, Yahoo UI, Dojo, etc.) talk to Java backend • Apache HTTP server ~ Apache Tomcat • (rf. paper) Conclusion • Python (+pkgs) provides viable options for building scientific gateways. • Because Python is already being used by many scientific communities, these researchers can build/maintain their own, lightweight, focused gateways. • But wait, there’s more… Python and Education • OLPC project bundled with Python 2.5 • Potential new generation of Python programmers worldwide • ~1M/month in 2008 laptopgiving.org Thanks! Acknowledgements: Partial funding through the IPCRES Initiative grant from the Lilly Endowment. Addendum • For a Python IDE, we recommend using Eclipse with the PyDev plugin. • Other options include Wing (commercial) and IDLE (bundled w/ Python)