From: Lorand S. <lo...@il...> - 2011-06-15 16:14:02
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Dear CDK developers, I am Lorand Szakacs, research intern at the University of Illinois at Urbana-Champaign. Currently my colleagues and I are working on ways to efficiently parallelize sequential code, specifically, by using automated tools that we are building, one of which is ReLooper. ReLooper (http://refactoring.info/tools/ReLooper ) is a refactoring tool that enables Java programmers to parallelize loops over arrays or vectors using Java's upcoming ParallelArray framework. We would like to help you make CDK more efficient by making computationally intensive loops run in parallel. Since you are developers on CDK, you know (much better than us) if it could benefit from parallelization. In case you consider so, please let us know. We will then make an in-depth analysis of CDK and attempt to parallelize parts of it - while, of course, checking thread safety. Although your help would not be required at that stage, we would greatly appreciate your guidance in identifying computationally-intensive sections and overcoming any difficulties. Our benefit from this is that by applying ReLooper on real programs (including CDK), we can make the tool more robust. In exchange, you get a free parallel implementation, which scales when adding more cores. We are looking forward to hearing from you, ReLooper Team -- Lorand Szakacs city: Urbana-Champaign country: Illinois, USA -------------------------- "Science is a way of trying not to fool yourself. The principle is that you must not fool yourself, and you are the easiest person to fool." - Richard Feynman |
From: Egon W. <ego...@gm...> - 2011-06-16 04:27:10
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Dear Lorand, On Wed, Jun 15, 2011 at 6:13 PM, Lorand Szakacs <lo...@il...> wrote: > I am Lorand Szakacs, research intern at the University of Illinois at > Urbana-Champaign. Currently my colleagues and I are working on ways to > efficiently parallelize sequential code, specifically, by using automated > tools that we are building, one of which is ReLooper. I am very interested, and threading has come up. The CDK is not particularly written to support threading, and some things require serious hacking, so all your input is most welcome. I am listening in on the Jmol thread too, and looking forward to an analysis on the CDK source code. Egon -- Dr E.L. Willighagen Postdoctoral Researcher Institutet för miljömedicin Karolinska Institutet (http://ki.se/imm) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers |
From: Christoph S. <ste...@eb...> - 2011-06-16 09:34:31
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Hi Lorand, I second what Egon said. We are highly interested in this. Thread-safty is the most important issue in the beginning. We did a lot of work in the past years to ensure thread-safty, but we never got around to do a systematic analysis of the CDK with respect to this, but this would be very interesting. Cheers, Chris -- Dr. Christoph Steinbeck Head of Chemoinformatics and Metabolism European Bioinformatics Institute (EBI) Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD UK Phone +44 1223 49 2640 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. On 15 Jun 2011, at 17:13, Lorand Szakacs wrote: > Dear CDK developers, > > I am Lorand Szakacs, research intern at the University of Illinois at Urbana-Champaign. Currently my colleagues and I are working on ways to efficiently parallelize sequential code, specifically, by using automated tools that we are building, one of which is ReLooper. > > ReLooper (http://refactoring.info/tools/ReLooper ) is a refactoring tool that enables Java programmers to parallelize loops over arrays or vectors using Java's upcoming ParallelArray framework. We would like to help you make CDK more efficient by making computationally intensive loops run in parallel. > > Since you are developers on CDK, you know (much better than us) if it could benefit from parallelization. In case you consider so, please let us know. We will then make an in-depth analysis of CDK and attempt to parallelize parts of it - while, of course, checking thread safety. Although your help would not be required at that stage, we would greatly appreciate your guidance in identifying computationally-intensive sections and overcoming any difficulties. > Our benefit from this is that by applying ReLooper on real programs (including CDK), we can make the tool more robust. In exchange, you get a free parallel implementation, which scales when adding more cores. > > We are looking forward to hearing from you, > > ReLooper Team > > -- > Lorand Szakacs > city: Urbana-Champaign > country: Illinois, USA > -------------------------- > "Science is a way of trying not to fool yourself. The principle is that you must not fool yourself, and you are the easiest person to fool." - Richard Feynman > > ------------------------------------------------------------------------------ > EditLive Enterprise is the world's most technically advanced content > authoring tool. Experience the power of Track Changes, Inline Image > Editing and ensure content is compliant with Accessibility Checking. > http://p.sf.net/sfu/ephox-dev2dev_______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel |