Hi Anil,
It's weird. If you can start Kepler 2.3, please click 'File->Open'
button. The default directory should be
$HOME/KeplerData/workflows/MyWorkflows/. You can change the directory to
be $HOME/KeplerData/workflows/module/outreach-2.2.0/demos/ from there.
Please let me know what you have. BTW: $HOME and ~ in mac both means
your home directory.
Best wishes
Sincerely yours
Jianwu Wang, Ph.D.
[email protected]
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 6/1/12 12:03 PM, Anil Deane wrote:
Hi Jianwu
There is no ~/KeplerData folder on my mac created with the latest 2.3 code.
Hmm..
WRT to Matlab - let me see if there is any issue - I just bundled the question in
with this in case this was done& you recalled. BTW the above is a FYI for the
distribution of the code. I can certainly just copy over the demos from my past
version.
Anil
On Jun 1, 2012, at 2:54 PM, Jianwu Wang wrote:
Hi Anil,
You can find the demo folders at
~/KeplerData/workflows/module/outreach-2.2.0/demos/. When Kepler 2.x
start, it will automatically create a KeplerData directory and copy demo
workflows of each Kepler module to that directory.
I looked over of the discussions in our previous emails ( it has
been 2 years! :) ), to know your Matlab question. Would you please let
us know your current specification (version and bit info of matlab,
java), and whether you can run Matlab demo workflows correctly?
Best wishes
Sincerely yours
Jianwu Wang, Ph.D.
[email protected]
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 6/1/12 7:12 AM, Anil Deane wrote:
Hi Jianwu, Dan:
I just downloaded version 2.3 on Mac and while it works fine, I don't see the demo
directory and the documentation talks about KeplerData folder etc. All I got was
the Keler folder& the Kepler Modules folders in /Applications. There is no
other reference on the website regarding demo folders and perhaps additional
downloads.
And has the 64 bit java issue been changed so that Matlab can work without
invoking 32bit java?
Thanks,
ANil
On Feb 17, 2010, at 4:09 PM, Jianwu Wang wrote:
Hi Anil,
Thanks for your information. Now we know Java 1.6 in Mac 10.6.x has
both 32 bit and 64 bit. I remember the java 1.6 in my Mac 10.5.x only
has 64 bit.
Best wishes
Sincerely yours
Jianwu Wang
[email protected]
http://users.sdsc.edu/~jianwu/
Scientific Workflow Automation Technologies (SWAT) Laboratory
San Diego Supercomputer Center
University of California, San Diego
San Diego, CA, U.S.A.
On 2/17/2010 4:04 PM, Anil Deane wrote:
This java version is
"1.6.0_17"
Java(TM) SE Runtime Environment (build 1.6.0_17-b04-248-10M3025)
Java HotSpot(TM) Client VM (build 14.3-b01-101, mixed mode)
In the Java Preferences I put 32 bit choice first so this must be 32 bit (The
preference just give 1.6 choices for 32 or 64 bit, and I just dragged and
changed the order).
I am using the default libptmatlab.dylib, not the 64 bit version you sent. The
3 steps are:
Default Kepler setup release version 1.0
Change of Java preference to start 32 bit version
DYLD_LIBRARY_PATH pointing to Matlab.../maci.
Anil
On Feb 17, 2010, at 3:46 PM, Jianwu Wang wrote:
Hi Anil,
Great news. Thanks for your test!
Are you using java 1.6.0_17 32 bit? It is usually said that java 1.6 on Mac
only have 64 bit and users have to choose 1.5 to use 32 bit java.
Also which libptmatlab.dylibare you using now? The default one along with
Kepler 1.0 or the one I sent you?
Best wishes
Sincerely yours
Jianwu Wang
[email protected]
http://users.sdsc.edu/~jianwu/
Scientific Workflow Automation Technologies (SWAT) Laboratory
San Diego Supercomputer Center
University of California, San Diego
San Diego, CA, U.S.A.
On 2/17/2010 2:32 PM, Anil Deane wrote:
Daniel,
That did the trick!!
I changed the order of running of Java from 64 then 32 in Java Preferences app,
to the other way around and then voila it works very well.
Specifically, I have Matlab 2008b, 32 bit, running on MacPro (Nehalem) Mac OS
10.6.2 with Java in 32 bit (version 1.6.0_17) and Kepler 1.0.0 - the MatLab
expressions example.
Thank you both for your help,
Anil
On Feb 17, 2010, at 1:53 PM, Daniel Crawl wrote:
Hi Anil,
Do you have java 1.5 on your Mac? You can see which versions
of java are installed, and change the version, by running
/Applications/Utilities/Java Preferences.app.
Java 1.5 on the Mac is 32 bit and using it to run Kepler
will allow you to use the Matlab actor.
--dan
On 2/16/10 8:22 PM, Jianwu Wang wrote:
Hi Anil,
So you installed Mac 32 bit and java 64 bit on a 64 bit Mac machine. It's
interesting to know Mac 32 bit can be installed on 64 bit Mac. The default
ptmatlab.dyliblib is made for all 32 bit (Mac, Matlab and Java) and the new lib
I sent is made for all 64 bit. I think that is why both lib do not work for you.
Unfortunately, I am on vacation and do not have Mac on hand to test. Sorry
about it. Are you willing to wait for about one week? We will try to either
send you new lib or the instructions on how to make the lib next week.
Best wishes
Sincerely yours
Jianwu Wang
[email protected]
http://users.sdsc.edu/~jianwu/
Scientific Workflow Automation Technologies (SWAT) Laboratory
San Diego Supercomputer Center
University of California, San Diego
San Diego, CA, U.S.A.
On 2/16/2010 7:51 PM, Anil Deane wrote:
Hi Jianwu,
The Matlab install did not ask for a 64 or 32 bit version on install (Or I
would have picked 64).
My mac is 10.6.2
java -version
java version "1.6.0_17"
Java(TM) SE Runtime Environment (build 1.6.0_17-b04-248-10M3025)
Java HotSpot(TM) 64-Bit Server VM (build 14.3-b01-101, mixed mode)
From reading the Matlab releases, it seems that full 64 bit Matlab release was
R2009b (the 2009a was a beta). So if I really do need Matlab running in 64 bit
to use Kepler/Matlab interface, I will have to get R2009b or later. Do you
agree? Does Kepler/Matlab really need 64 bit Matlab? Seems strange, if Matlab
is running on the machine.
Matlab is running in 32 bit on my mac - because in Matlab typing "computer"
gives the machine architecture and it gives maci - indicating that it is 32 bit.
Thanks,
Anil
On Feb 16, 2010, at 5:56 PM, Jianwu Wang wrote:
Hi Anil,
If you do not have maci64 directory, usually it is because you didn't install
Matlab 64 bit version. I do not have Mac and Matlab 64 bit on hand. Yet I think
you should be able to see '64 bit' signal when you start Matlab. Or you can
check it after you start Matlab.
Another to check I think is your Mac version. You get know your Mac version
by steps at http://www.apple.com/support/mobileme/en/os_version.html. If your
Mac version is 10.5.x, your Mac is 32 bit. If it is 10.6.x, you Mac should be
64 bit.
Can you also check your java version by typing 'java -version' at console? Is
it 64 bit or 32 bit?
It is dependent on these information to know which Matlab library is needed
by Kepler to invoke Matlab library. So please let us know your detailed
configuration.
P.S.: We are creating a web page on Kepler-project web site to explain these
stuff. Hopefully, it can be online soon.
Best wishes
Sincerely yours
Jianwu Wang
[email protected]
http://users.sdsc.edu/~jianwu/
Scientific Workflow Automation Technologies (SWAT) Laboratory
San Diego Supercomputer Center
University of California, San Diego
San Diego, CA, U.S.A.
On 2/16/2010 5:13 PM, Anil Deane wrote:
Ok, thanks for the dev version tip. I will do this.
But in following the first part - there is no
/Applications/MATLAB_R2008b.app/bin/maci64, although Matlab works fine on my
Mac (Nehalem). Is this library needed to be separately installed from mathworks
or ???
Anil
On Feb 16, 2010, at 12:13 AM, Jianwu Wang wrote:
Hi Anil,
The exception is still 64 bit problem. To work with Matlab 64 bit,
DYLD_LIBRARY_PATH need to be export as
/Applications/MATLAB_R2008b.app/bin/maci64, not the usual
/Applications/MATLAB_R2008b.app/bin/maci. Please re-export DYLD_LIBRARY_PATH
and try Kepler again.
Also from the exception message, you used the latest release Kepler version,
namely 1.0, not the latest developing version which can be gotten by
instructions in
https://dev.kepler-project.org/developers/teams/build/systems/build-system/extension-build-system.
I'm not quite sure the location of the libptmatlab.dylib in Kepler 1.0. Please
first replace the new libptmatlab.dylib I attached last email with the
/Applications/Kepler-1.0.0/Kepler.app/Kepler/lib/libptmatlab.dylib. If it
doesn't work, try create a new directory, namely ptolemy/matlab/, in
$Kepler/lib and put the new libptmatlab.dylib there.
Best wishes
Sincerely yours
Jianwu Wang
[email protected]
http://users.sdsc.edu/~jianwu/
Scientific Workflow Automation Technologies (SWAT) Laboratory
San Diego Supercomputer Center
University of California, San Diego
San Diego, CA, U.S.A.
On 2/15/2010 10:06 PM, Anil Deane wrote:
Hi Jianwu,
thanks for the response. I did just that, and it didn't work. I also copied it
to the suitable Matlab directory (the place that the UG says to make the link
to). And the error says:
ptolemy.kernel.util.IllegalActionException: There was a problem invoking the
Ptolemy II Matlab interface.
The interface has been tested under Windows and Linux.
The interface requires that Matlab be installed on the local machine and that
the ptmatlab shared library available.
Refer to $PTII/ptolemy/matlab/makefile for more information.
in .MatlabExpression.MatlabExpression
Because:
Did not find 'ptmatlab' in path, searched user.home
(/Applications/Kepler-1.0.0/Kepler.app/Kepler) user.dir (/Users/deane) and the
classpath for 'ptmatlab.dylib', but that was not found either.
classpath was: .:./configs:./lib:./lib/images:./build/kepler.jar:./build/kepler-icons.jar
Also tried loadLibrary("ptmatlab", exception for loadLibrary was:
java.lang.UnsatisfiedLinkError:
/Applications/Kepler-1.0.0/Kepler.app/Kepler/lib/libptmatlab.dylib: Library not loaded:
@loader_path/libeng.dylib Referenced from:
/Applications/MATLAB_R2008b.app/bin/maci/libptmatlab.dylib Reason: no suitable image
found. Did find: /Applications/MATLAB_R2008b.app/bin/maci/libeng.dylib: mach-o, but
wrong architecture /Applications/MATLAB_R2008b.app/bin/maci/libeng.dylib: mach-o, but
wrong architecture /Applications/MATLAB_R2008b.app/bin/maci/libeng.dylib: mach-o, but
wrong architecture
at ptolemy.matlab.Expression.preinitialize(Expression.java:205)
at ptolemy.actor.Director.preinitialize(Director.java:865)
at ptolemy.domains.sdf.kernel.SDFDirector.preinitialize(SDFDirector.java:527)
at ptolemy.actor.CompositeActor.preinitialize(CompositeActor.java:1103)
at ptolemy.actor.Manager.preinitializeAndResolveTypes(Manager.java:913)
at ptolemy.actor.Manager.initialize(Manager.java:578)
at ptolemy.actor.Manager.execute(Manager.java:321)
at ptolemy.actor.Manager.run(Manager.java:1071)
at ptolemy.actor.Manager$3.run(Manager.java:1112)
Caused by: java.lang.UnsatisfiedLinkError: Did not find 'ptmatlab' in path,
searched user.home (/Applications/Kepler-1.0.0/Kepler.app/Kepler) user.dir
(/Users/deane) and the classpath for 'ptmatlab.dylib', but that was not found
either.
classpath was: .:./configs:./lib:./lib/images:./build/kepler.jar:./build/kepler-icons.jar
Also tried loadLibrary("ptmatlab", exception for loadLibrary was:
java.lang.UnsatisfiedLinkError:
/Applications/Kepler-1.0.0/Kepler.app/Kepler/lib/libptmatlab.dylib: Library not loaded:
@loader_path/libeng.dylib Referenced from:
/Applications/MATLAB_R2008b.app/bin/maci/libptmatlab.dylib Reason: no suitable image
found. Did find: /Applications/MATLAB_R2008b.app/bin/maci/libeng.dylib: mach-o, but
wrong architecture /Applications/MATLAB_R2008b.app/bin/maci/libeng.dylib: mach-o, but
wrong architecture /Applications/MATLAB_R2008b.app/bin/maci/libeng.dylib: mach-o, but
wrong architecture
at ptolemy.data.expr.UtilityFunctions.loadLibrary(UtilityFunctions.java:894)
at ptolemy.matlab.Engine.<clinit>(Engine.java:176)
at ptolemy.matlab.Expression.preinitialize(Expression.java:202)
... 8 more
Caused by: java.lang.UnsatisfiedLinkError: Expecting an absolute path of the
library: ptolemy/matlab/ptmatlab
at java.lang.Runtime.load0(Runtime.java:767)
at java.lang.System.load(System.java:1020)
at ptolemy.data.expr.UtilityFunctions.loadLibrary(UtilityFunctions.java:781)
... 10 more
Caused by: java.lang.UnsatisfiedLinkError: Did not find 'ptmatlab' in path,
searched user.home (/Applications/Kepler-1.0.0/Kepler.app/Kepler) user.dir
(/Users/deane) and the classpath for 'ptmatlab.dylib', but that was not found
either.
classpath was: .:./configs:./lib:./lib/images:./build/kepler.jar:./build/kepler-icons.jar
Also tried loadLibrary("ptmatlab", exception for loadLibrary was:
java.lang.UnsatisfiedLinkError:
/Applications/Kepler-1.0.0/Kepler.app/Kepler/lib/libptmatlab.dylib: Library not loaded:
@loader_path/libeng.dylib Referenced from:
/Applications/MATLAB_R2008b.app/bin/maci/libptmatlab.dylib Reason: no suitable image
found. Did find: /Applications/MATLAB_R2008b.app/bin/maci/libeng.dylib: mach-o, but
wrong architecture /Applications/MATLAB_R2008b.app/bin/maci/libeng.dylib: mach-o, but
wrong architecture /Applications/MATLAB_R2008b.app/bin/maci/libeng.dylib: mach-o, but
wrong architecture
at ptolemy.data.expr.UtilityFunctions.loadLibrary(UtilityFunctions.java:894)
at ptolemy.matlab.Engine.<clinit>(Engine.java:176)
at ptolemy.matlab.Expression.preinitialize(Expression.java:202)
at ptolemy.actor.Director.preinitialize(Director.java:865)
at ptolemy.domains.sdf.kernel.SDFDirector.preinitialize(SDFDirector.java:527)
at ptolemy.actor.CompositeActor.preinitialize(CompositeActor.java:1103)
at ptolemy.actor.Manager.preinitializeAndResolveTypes(Manager.java:913)
at ptolemy.actor.Manager.initialize(Manager.java:578)
at ptolemy.actor.Manager.execute(Manager.java:321)
at ptolemy.actor.Manager.run(Manager.java:1071)
at ptolemy.actor.Manager$3.run(Manager.java:1112)
Caused by: java.lang.UnsatisfiedLinkError: Expecting an absolute path of the
library: ptolemy/matlab/ptmatlab
at java.lang.Runtime.load0(Runtime.java:767)
at java.lang.System.load(System.java:1020)
at ptolemy.data.expr.UtilityFunctions.loadLibrary(UtilityFunctions.java:781)
... 10 more
Kepler runs fine otherwise (ie. other than the Matlab).
Anil
On Feb 15, 2010, at 6:05 PM, Jianwu Wang wrote:
Hi Anil,
So you have Mac OS 10.6 Snow Leopard and Kepler downloaded from Kepler
repository by instructions of
https://dev.kepler-project.org/developers/teams/build/systems/build-system/extension-build-system?
So your java and Matlab is also 64 bit?
As far as I know, Mac 10.6 is 64 bit system and Kepler mainly support 32 bit
system. We met the similar problem when running Matlab actor on a Mac Snow
Leopard machine, which is because of the library compiled in 32 bit system does
not work with Matlab 64 bit.
We got the lib working with 64 bit system (see attachment). Please replace this
lib with the one in $Kepler/common/lib/ptolemy/matlab/ and try again.
Please let me know whether it works for you. Thanks.
Best wishes
Sincerely yours
Jianwu Wang
[email protected]
http://users.sdsc.edu/~jianwu/
Scientific Workflow Automation Technologies (SWAT) Laboratory
San Diego Supercomputer Center
University of California, San Diego
San Diego, CA, U.S.A.
On 2/15/2010 5:13 PM, Anil Deane wrote:
[First Post. I have looked in the user guide and in the Kepler matlab example]
Could anyone please tell me how to get Kepler run a Matlab example on the Mac.
The example and the user guide indicate that one just needs to have the dynamic
library path (to maci) set properly. But that doesn't do it. I do have Matlab
able to be run from the command prompt incidentally.
I searched and found - quite inscrutable - "directions" for patches that someone contributed
(because Mac's install of Java is "nonstandard"). I have the latest Mac OS, and the latest Kepler.
There are references to Ptolemy and a ptmatlab file when Kepler fails - but nowhere does Kepler user guide or
site say that you need to install Ptolemy or that an installation of "ptmatlab" is needed.
Thanks in advance,
Anil Deane
[IntelMac 10.6.2]
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