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Hi Michal,<br>
<br>
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.<br>
<br>
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.<br>
<pre class="moz-signature" cols="72">Best wishes
Sincerely yours
Jianwu Wang, Ph.D.
<a class="moz-txt-link-abbreviated" href="mailto:jianwu@sdsc.edu">jianwu@sdsc.edu</a>
<a class="moz-txt-link-freetext" href="http://users.sdsc.edu/~jianwu/">http://users.sdsc.edu/~jianwu/</a>
Assistant Project Scientist
Scientific Workflow Automation Technologies (SWAT) Laboratory
San Diego Supercomputer Center
University of California, San Diego
San Diego, CA, U.S.A. </pre>
<br>
On 5/25/12 1:21 AM, Michal Owsiak wrote:
<blockquote cite="mid:4FBF4108.2030101@man.poznan.pl" type="cite">Hello
Matt,
<br>
<br>
I have prepared patch for the trunk version. File is attached to
the e-mail.
<br>
<br>
I have tested it with most recent Kepler version (trunk version
from SVN).
<br>
<br>
I hope you will find it useful and will incorporate it into main
release.
<br>
<br>
To apply it, simply execute:
<br>
<br>
patch Run.java < Run.java.trunk.patch
<br>
<br>
inside
<br>
<br>
kepler/build-area/src/org/kepler/build
<br>
<br>
Regards
<br>
<br>
Michal
<br>
<br>
<blockquote type="cite">Michal,
<br>
<br>
This change looks fairly innocuous and seems to be a reasonable
change.
<br>
Thanks. Please let us know how your testing against trunk goes,
and if it
<br>
goes well, it seems reasonable to commit it so that it can be
part of the
<br>
Kepler 2.4 release.
<br>
<br>
Matt
<br>
<br>
On Thu, May 24, 2012 at 3:25 AM, Michal Owsiak
<br>
<a class="moz-txt-link-rfc2396E" href="mailto:michal.owsiak@man.poznan.pl"><michal.owsiak@man.poznan.pl></a>wrote:
<br>
<br>
<blockquote type="cite">Hello Kepler team,
<br>
<br>
it looks like Kepler has a bug in Run.java file.
<br>
<br>
In this description I refer to Kepler 2.2 - as I have patch
for this
<br>
version.
<br>
<br>
At the moment it is not possible to spawn Kepler with custom
HOME
<br>
location. This is due to bug in file:
<br>
<br>
./build-area/src/org/kepler/**build/Run.java
<br>
<br>
Inside this file new Java process is spawn. However, user.home
property is
<br>
not correctly passed to this sub-process. That means, even
though user
<br>
executes Kepler following way:
<br>
<br>
java -D"user.home"="$USER_HOME/**kepler_local" -classpath
<br>
$KEPLER/build-area/lib/ant.**jar:$KEPLER/kepler.jar
<br>
org.kepler.build.runner.Kepler
<br>
<br>
these settings are not passed to new process and new Java
process uses
<br>
original $HOME location instead of location specified by
-Duser.home - in
<br>
that case
<br>
<br>
-D"user.home"="$USER_HOME/**kepler_local"
<br>
<br>
To make it possible to run Kepler in custom HOME locations,
one must
<br>
update Run.java with the patch attached to the e-mail.
<br>
<br>
As soon as I test this solution for trunk version I will post
the message
<br>
to the group with proper patch.
<br>
<br>
Why this bug exists:
<br>
<br>
Java Virtual Machine doesn't use $HOME environment variable to
set
<br>
user.home. Instead it gets it from system directly. Each new
Java Virtual
<br>
Machine must be provided with user.home variable set in order
to change
<br>
default settings.
<br>
<br>
Regards
<br>
<br>
Michal
<br>
<br>
--
<br>
Michal Owsiak<a class="moz-txt-link-rfc2396E" href="mailto:michal.owsiak@man.poznan.pl"><michal.owsiak@man.poznan.pl></a>
<br>
<br>
Institute of Bioorganic Chemistry PAS
<br>
Poznan Supercomputing and Networking Center
<br>
Noskowskiego 12/14, 61-704 Poznan, POLAND
<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.man.poznan.pl">http://www.man.poznan.pl</a>
<br>
<br>
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<br>
<br>
<br>
</blockquote>
<br>
</blockquote>
<br>
<br>
<br>
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</blockquote>
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