On 2/4/14, 6:28 PM, Noel O'Boyle wrote: > It would be nice to see some explicit examples of how Open Babel might > be used in this way, using one or all of these tools.
Let's say you have a file commmands.sh: --- obabel some_file1 -Osome_other_file1.other_format ... obabel some_file2 -Osome_other_file2.other_format --- With PAR, you run them like this in parallel: par -i commands.sh -v -o log # all your cores will be used by default to check the logs (in case you are really careful about what you are doing, e.g. when preparing datasets for scientific use), I recommend: sort -u log | less > - Noel > > On 4 February 2014 00:52, Francois Berenger <beren...@riken.jp> wrote: >> On 02/04/2014 12:14 AM, Maciek Wójcikowski wrote: >>> You can also use xargs. >> >> Yes, xargs with the -P option, but the command lines are not trivial then. >> >>> ---- >>> Pozdrawiam, | Best regards, >>> Maciek Wójcikowski >>> mac...@wojcikowski.pl <mailto:mac...@wojcikowski.pl> >>> >>> >>> 2014-02-03 16:10 GMT+01:00 Igor Filippov <igor.v.filip...@gmail.com >>> <mailto:igor.v.filip...@gmail.com>>: >>> >>> How is it different from GNU parallel? >>> http://www.gnu.org/software/bash/manual/html_node/GNU-Parallel.html >> >> It should be quite similar in functionality. >> >>> Igor >>> >>> >>> On Mon, Feb 3, 2014 at 1:37 AM, Francois Berenger <beren...@riken.jp >>> <mailto:beren...@riken.jp>> wrote: >>> >>> Hello, >>> >>> I do this almost everyday so I think I should share it with this >>> list. >>> >>> In case you need to execute many Open Babel commands >>> and don't want to wait, you can execute them in parallel >>> on a multi-core computer. >>> Of course, the commands should be independent, for example >>> processing different datasets. >>> >>> Let's say the commands are in a file called for_par.sh. >>> I developped a tool called PAR years ago that can do this: >>> >>> par -i for_par.sh -v -o log >>> >>> It will use all cores of the computer, display a completion >>> percentage and store all output messages in the file log. >>> >>> If your user can connect to several computers e.g. via >>> SSH then you can even run commands in a distributed manner. >>> I use it daily on Linux but know some people used it on Mac OS X >>> as well. >>> >>> The project is there: >>> >>> https://savannah.nongnu.org/projects/par >>> >>> The paper is freely available there: >>> >>> http://bioinformatics.oxfordjournals.org/content/26/22/2918.long >>> >>> -- >>> Best regards, >>> Francois Berenger. >>> >>> >>> ------------------------------------------------------------------------------ >>> Managing the Performance of Cloud-Based Applications >>> Take advantage of what the Cloud has to offer - Avoid Common >>> Pitfalls. >>> Read the Whitepaper. >>> >>> http://pubads.g.doubleclick.net/gampad/clk?id=121051231&iu=/4140/ostg.clktrk >>> _______________________________________________ >>> OpenBabel-discuss mailing list >>> OpenBabel-discuss@lists.sourceforge.net >>> <mailto:OpenBabel-discuss@lists.sourceforge.net> >>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Managing the Performance of Cloud-Based Applications >>> Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. >>> Read the Whitepaper. >>> >>> http://pubads.g.doubleclick.net/gampad/clk?id=121051231&iu=/4140/ostg.clktrk >>> _______________________________________________ >>> OpenBabel-discuss mailing list >>> OpenBabel-discuss@lists.sourceforge.net >>> <mailto:OpenBabel-discuss@lists.sourceforge.net> >>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >>> >>> >> >> >> -- >> Best regards, >> Francois Berenger. >> >> ------------------------------------------------------------------------------ >> Managing the Performance of Cloud-Based Applications >> Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. >> Read the Whitepaper. >> http://pubads.g.doubleclick.net/gampad/clk?id=121051231&iu=/4140/ostg.clktrk >> _______________________________________________ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ------------------------------------------------------------------------------ Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121051231&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
