Francois, could you please elaborate on the "log" argument? Because, that
might be the only difference here. Using either gnu parallel or xargs
standard output and error are "FIFO", which makes them useless.
Other than that I cant see any advantage, since parallel line would be:
cat commands.sh | parallel -P 8 > log 2> error.log
(or 2>&1 if someone prefers joint log)
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2014-02-04 11:58 GMT+01:00 Francois Berenger <beren...@riken.jp>:
> 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
