Bob, Could you expand on your comment that “Jmol uses typed arrays when possible"?
I am in the habit of initializing arrays with a line like: a=array() Should I be doing something else? Does the array get “typed” after I add an entry? Matt On Dec 16, 2015, at 3:48 PM, Robert Hanson <hans...@stolaf.edu<mailto:hans...@stolaf.edu>> wrote: Jmol uses typed arrays when possible. Parsing of scripts is relatively slow. Rolf, if you want to give me something to try, I will be happy to play with it and see what I can learn. On Wed, Dec 16, 2015 at 12:30 PM, Paul PILLOT <paulpil...@gmail.com<mailto:paulpil...@gmail.com>> wrote: Hi Rolf, my experience in this area is not JSmol related, but when I had to deal with big tables in javascript (for a multiple sequence alignment script, aligning 2 sequences of 5000 signs, requires at least 1 table of 5000 rows and 5000 columns), I noticed that : - using integers only tables is fastest - opting for one dimensional array instead of two dimensional didn’t make a noticeable difference - using typed arrays in some cases improved significantly the performance ( see https://developer.mozilla.org/en/docs/Web/JavaScript/Typed_arrays ). This was 2 years ago, and the browsers’ engine landscape can be quickly moving... When you parse your data from your TSV file, are the fields stored as text ? My 2 cents, Paul Le 16-12-2015 à 13:12, Rolf Huehne <rhue...@leibniz-fli.de<mailto:rhue...@leibniz-fli.de>> a écrit : Hi all, I am looking for some speedup tips for Jmol scripting in JSmol/HTML5. The speed difference between JSmol/Java and JSmol/HTML5 for graphical operations like rotation and zooming seems to be about 10 times or less in Firefox and Chrome (if you don't consider the recent rotation speed problems in Chrome). Unfortunately the difference for Jmol scripting seems to be much higher in my experience: about 50-70 times. If I load for example 3 TSV (tab separated value) format files with overall about 34,000 lines, JSmol/Java needs about 26 seconds for laoding and parsing the data and putting it into a multi-level hash structure. JSmol/HTML5 needs about 1700 seconds instead. I already tried to write the final data structure into a file with 'write VAR ...' and read it in again as a script (after adding a proper variable assignment) but this already took in Java endlessly (I stopped waiting after more than an hour...). Q: Does anyone have any other ideas that might speed up this process? Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205<tel:%2B49%203641%2065%206205> Fax: +49 3641 65 6210<tel:%2B49%203641%2065%206210> E-Mail: rhue...@leibniz-fli.de<mailto:rhue...@leibniz-fli.de> Website: http://www.leibniz-fli.de<http://www.leibniz-fli.de/> Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Burkhard Zinner VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 ------------------------------------------------------------------------------ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net<mailto:Jmol-users@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------------ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net<mailto:Jmol-users@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Department of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ------------------------------------------------------------------------------ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net<mailto:Jmol-users@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------------ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
