Blogging meets Computational Chemistry
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Transcript of Blogging meets Computational Chemistry
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BLOGGING MEETS COMPUTATIONAL CHEMISTRYDr Kieron TaylorUniversity of Southampton*
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Grid computing + lab notebooks
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Managing concurrent jobs and handling the results. Paper notebooks are a disaster for
multiple computational jobs. Users must log file paths and job names by hand.
Simulation archive must be “synchronized” with the lab notebook.
Science is only as good as the record-keeping, particularly after significant time has elapsed.
It is easier to re-run than it is to figure out what happened to the answers!
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Build a database? No! Job management systems already exist e.g.
eMinerals RMCS, but they only operate on one system. No help for trial runs on private hardware.
Chemistry simulations can generate gigabytes of data each. A complete archive is unmanageable, but we must keep the data while we process it.
Processing trajectories is often custom and not always suitable for Grids.
Management system still does not provide contextual scientific discourse.
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Computational chemistry is one ongoing experiment Simulations are not guaranteed to finish. Parameters must be tweaked. Surprisingly little real time is spent in
“production”. Failures often need careful examination
before they can be fixed. Data is static, but analysis and opinion
can change over time. It is super-important to know what conditions a simulation was performed under.
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Enter the Blog Southampton University chemistry
Bloggers attempt to extend blogging into a useful experimental tool. Autoblogging laser rigs
http://blogs.chem.soton.ac.uk/shg Open science experimental blogs from
peoplehttp://blogs.chem.soton.ac.uk/neutral_drift
Now computational chemistry toohttp://blogs.chem.soton.ac.uk/kierons_flog
Blogging must be worth the effort!
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Blogging computational experiments
Writing a Blog entry requires thought and some presentational effort. This is irritating, but very useful in retrospect. Daily digest.
Computational jobs have input decks and result files that must be kept with the observations. Inter-Blog links do this well, but uploading files is a significant problem. Trajectories?
The Blog is useful for presenting progress to others. The work is already done.
Writing a Blog is easy. Writing a useful Blog is not.
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Autoblogging eases the task
Manual Blog User submits job User collects results User writes Blog entry User uploads result files to Blog User (maybe) assigns metadata
Autoblog User submits job Job submission system Blogs automatically at start. Job submission system Blogs at end of job.
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Blog-supported Grid computing
Private RepositoryBlog API
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Merits and limitations of Blogs
Blogs are stupid. Blog posts are automatically chronological. Writing a blog post forces the user to order their
thoughts and present them on a regular basis. Boss can easily see what people are getting up
to. Restricted access allows collaboration without
global disclosure. User defined tagging allows management of
discrete experiments in addition to finding data by timestamp.
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Better BlogsBlog API allows read and write, so we can
write helper-tools to do additional actions for us.
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The Future Meta-Blog interface to collect together
posts from different Blogs into one coherent report about an experiment.
Clever storage management on- and off-Grid. When is data truly dispensable?
Lablog 3.0, a better Blogging platform. Easier Grid use for molecular
simulations. Researchers who can tell you what they
did last year!
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Acknowledgments NGS staff: Jonathan Churchill, Gordon
Brown, Keir Hawker DL_POLY author: Dr William Smith
(Daresbury) DL_POLY user: Robert Hawtin (unknown) Blog coder: Andrew Milsted
(Southampton)