[kepler-dev] Kepler - bug related to user.home settings

[Jianwu Wang]

Hi Michal,

     In Kepler trunk, if I run command like ./kepler.sh 
-D"arg1"="value1", the workflow can get the new value. You can get its 
value in the workflow by using property("arg1") in Expression actor. I 
also tried ./kepler.sh -D"user.home"="$HOME/test-home", which also works 
for me. Please try whether this way works for you.

     Your patch looks good. Just it is not general. Users may also want 
to pass other properties. Luckily, the current kepler trunk support any 
property to be set after kepler.sh. At least in my tests.

Best wishes

Sincerely yours

Jianwu Wang, Ph.D.
jianwu at sdsc.edu
http://users.sdsc.edu/~jianwu/

Assistant Project Scientist
Scientific Workflow Automation Technologies (SWAT) Laboratory
San Diego Supercomputer Center
University of California, San Diego
San Diego, CA, U.S.A.


On 5/25/12 1:21 AM, Michal Owsiak wrote:
> Hello Matt,
>
> I have prepared patch for the trunk version. File is attached to the 
> e-mail.
>
> I have tested it with most recent Kepler version (trunk version from 
> SVN).
>
> I hope you will find it useful and will incorporate it into main release.
>
> To apply it, simply execute:
>
> patch Run.java < Run.java.trunk.patch
>
> inside
>
> kepler/build-area/src/org/kepler/build
>
> Regards
>
> Michal
>
>> Michal,
>>
>> This change looks fairly innocuous and seems to be a reasonable change.
>> Thanks.  Please let us know how your testing against trunk goes, and 
>> if it
>> goes well, it seems reasonable to commit it so that it can be part of 
>> the
>> Kepler 2.4 release.
>>
>> Matt
>>
>> On Thu, May 24, 2012 at 3:25 AM, Michal Owsiak
>> <michal.owsiak at man.poznan.pl>wrote:
>>
>>> Hello Kepler team,
>>>
>>> it looks like Kepler has a bug in Run.java file.
>>>
>>> In this description I refer to Kepler 2.2 - as I have patch for this
>>> version.
>>>
>>> At the moment it is not possible to spawn Kepler with custom HOME
>>> location. This is due to bug in file:
>>>
>>> ./build-area/src/org/kepler/**build/Run.java
>>>
>>> Inside this file new Java process is spawn. However, user.home 
>>> property is
>>> not correctly passed to this sub-process. That means, even though user
>>> executes Kepler following way:
>>>
>>> java -D"user.home"="$USER_HOME/**kepler_local" -classpath
>>> $KEPLER/build-area/lib/ant.**jar:$KEPLER/kepler.jar
>>> org.kepler.build.runner.Kepler
>>>
>>> these settings are not passed to new process and new Java process uses
>>> original $HOME location instead of location specified by -Duser.home 
>>> - in
>>> that case
>>>
>>> -D"user.home"="$USER_HOME/**kepler_local"
>>>
>>> To make it possible to run Kepler in custom HOME locations, one must
>>> update Run.java with the patch attached to the e-mail.
>>>
>>> As soon as I test this solution for trunk version I will post the 
>>> message
>>> to the group with proper patch.
>>>
>>> Why this bug exists:
>>>
>>> Java Virtual Machine doesn't use $HOME environment variable to set
>>> user.home. Instead it gets it from system directly. Each new Java 
>>> Virtual
>>> Machine must be provided with user.home variable set in order to change
>>> default settings.
>>>
>>> Regards
>>>
>>> Michal
>>>
>>> -- 
>>> Michal Owsiak<michal.owsiak at man.poznan.pl>
>>>
>>> Institute of Bioorganic Chemistry PAS
>>> Poznan Supercomputing and Networking Center
>>> Noskowskiego 12/14, 61-704 Poznan, POLAND
>>>
>>> http://www.man.poznan.pl
>>>
>>> _______________________________________________
>>> Kepler-dev mailing list
>>> Kepler-dev at kepler-project.org
>>> http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-dev
>>>
>>>
>>
>
>
>
>
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