[kepler-users] Kepler 2.3 and MATLAB

Wade Sheldon sheldon at uga.edu
Mon Apr 23 09:53:54 PDT 2012 

Well I'll be darned - I got it working. I decided to Google that last error message and found a page that described the same issue with a JNI application caused by loading of the wrong dll from elsewhere in the path (http://stackoverflow.com/questions/159846/unsatisfiedlinkerror-the-specified-procedure-could-not-be-found). I moved the matlab paths to right after the windows paths, and the workflow started to run then alerted me that I had to run matlab /regserver to set up the COM registry entries to load a matlab engine. After I did that, it ran fine. I didn't track down the individual dll conflict, though, so hopefully I haven't hosed another application but that's a problem for another day.

I'll see if I can run it under R2011b now, but at least I have it up under R2009a for testing.

Sorry for the drama, but this is definitely something to add to the troubleshooting steps. Here's my revised path FYI:

PATH=C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\MATLAB\R2009a\bin;C:\MATLAB\R2009a\bin\win32;C:\Python25;C:\Program Files\WinZip;C:\Program Files\Bitvise Tunnelier;C:\Program Files\Microsoft SQL Server\80\Tools\Binn;C:\ArcGIS\arcexe9x\bin;C:\Program Files\cURL;C:\Program Files\TortoiseSVN\bin;C:\Program Files\R\R-2.15.0\bin;C:\Program Files\Common Files\Roxio Shared\DLLShared\;C:\Program Files\Common Files\Roxio Shared\9.0\DLLShared

-Wade


On 4/23/2012 12:08 PM, Wade Sheldon wrote:
> Hi folks,
>
> Thanks for all the advice last week, but I'm throwing in to towel unless someone has a radically new idea. I installed Matlab 2009a and that also failed to run the demo, but with a different error message: "Caused by: java.lang.UnsatisfiedLinkError: C:\Program Files\Kepler-2.3\common-2.3.0\lib\ptolemy\matlab\ptmatlab.dll: The specified procedure could not be found ...". I also tried R2007b (mentioned in help files) and had the same result as 2009a. So R2010a and R2011b error with "...The
> operating system cannot run %1" and R2007b and R2009a error with the above procedure call error, in case that's of any diagnostic value. I also installed Kepler on a different workstation run WinXP and had the same issues.
>
> To eliminate potential Java version issues, I wiped Kepler 2.3 and all the settings files, uninstalled an old version of the JDK I had on the box (1.6_18), installed a matching JDK to the Java libraries previously installed (1.6.0_31-b05) and reinstalled Kepler. Same result. I also added C:\Program Files\Kepler-2.3\common-2.3.0\lib\ptolemy\matlab to the path (based on Ptolemy Matlab troubleshooting guidelines) but that didn't help either.
>
> I then tried to follow the build instructions from the url Dan sent, spending most of the weekend setting up the software and source code and ironing out cygwin and mingw configurations and dependencies (the instructions on the reference page are out of date, and the mingw shell scripts described are not online and no mention is made of what libraries are needed for cygwin, so I had to guess and reinstall several times to get what was needed). After climbing down ever darker rabbit holes I managed to get a working build system set up, but then hit syntax errors with the .config files (apparently due to line terminator issues) and never could successfully build a dll.
>
> I concluded that this process is really untenable for someone not already set up to do Java development and use the entire Kepler build system, so at this point I rolled back my system and dumped the gig of software I spent all weekend messing with. So it was an informative, but ultimately futile, exercise.
>
> Thanks anyway. For my work it will be more productive to generate delimited files from Kepler and pick them up in Matlab, but I wanted to kick the tires and see if I could roll our Matlab code into native workflows. I'm about to rebuild that system using Win7/64 dual booting with Ubuntu, so I may try again if I feel adventurous.
>
> -Wade
>
>
> On 4/21/2012 4:48 PM, Daniel Crawl wrote:
>>
>> I can run the MatlabExpression workflow with Kepler 2.3 on
>> WinXP SP3 (32bit) using Matlab 2009A and Java 1.6.0_31-b05.
>>
>> Your PATH looks ok (assuming you installed Matlab in C:\ and
>> not the default C:\Program Files). It's possible that ptmatlab.dll
>> is not compatible with newer versions of Matlab. You can find
>> instructions on building ptmatlab.dll here:
>>
>> https://kepler-project.org/developers/teams/build/matlab-lib-build-instructions-in-kepler-for-matlab-actor/
>>
>>   --dan
>>
>> On 4/21/12 4:17 AM, Wade Sheldon wrote:
>>> Hi Derek,
>>>
>>> Here you go:
>>>
>>> PATH=C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Python25;C:\Program
>>> Files\WinZip;C:\Program Files\Bitvise Tunnelier;C:\Program
>>> Files\Microsoft SQL
>>> Server\80\Tools\Binn;C:\ArcGIS\arcexe9x\bin;C:\MATLAB\R2011b\bin;C:\MATLAB\R2011b\bin\win32;C:\Program
>>> Files\cURL;C:\Program Files\TortoiseSVN\bin;C:\Program
>>> Files\R\R-2.15.0\bin;C:\Program Files\Common Files\Roxio
>>> Shared\DLLShared\;C:\Program Files\Common Files\Roxio Shared\9.0\DLLShared
>>>
>>>
>>> I have several versions of MATLAB on this box for code testing, but I
>>> made sure only one is present in the path each time I tested (currently
>>> 2011b). I also confirmed that the target "libmex.dll" is present in
>>> \bin\win32.
>>>
>>> I don't have cygwin installed to test Christopher's idea about building
>>> a new .dll, but I may play with that option over the weekend if I get
>>> ambitious. Based on Matt's comment that may ultimately prove necessary
>>> if the problem doesn't come down to path handling.
>>>
>>> Thanks for your input.
>>>
>>> -Wade
>>>
>>>
>>> On 4/20/2012 11:30 PM, Derik Barseghian wrote:
>>>> Sorry this hasn't been easy, and no help from me yet -- I'm trying to
>>>> get Matlab and a license for my 32bit XP box so that I can try to
>>>> replicate, hopefully on Monday. It seems to me it should work on your
>>>> XP box. The last commit message for ptmatlab.dll says it's 32bit:
>>>> --------------
>>>> r24053 | crawl | 2010-04-29 13:30:49 -0700 (Thu, 29 Apr 2010) | 2 lines
>>>>
>>>> updating matlab jni library for 32 bit windows
>>>> based on ptmatlab.cc r57728.
>>>> --------------
>>>>
>>>> Interesting to hear about the error on 64bit AMD, sounds like we have
>>>> an (additional) problem there.
>>>>
>>>> Can you send your PATH?
>>>> Derik
>>>>
>>>> On Apr 20, 2012, at 8:14 PM, Wade Sheldon wrote:
>>>>
>>>>> No joy under Win7/64 either with a clean install of Kepler 2.3 and
>>>>> the proper Matlab paths (albeit R2010a 64bit). However this time I
>>>>> get an error related to running 32bit libraries on the system:
>>>>> C:\Program Files
>>>>> (x86)\Kepler-2.3\common-2.3.0\lib\ptolemy\matlab\ptmatlab.dll: Can't
>>>>> load IA 32-bit .dll on a AMD 64-bit platform
>>>>>
>>>>> (This is an Intel Core i7, not AMD cpu, BTW).
>>>>>
>>>>> Sigh. Harder than I'd hoped. Python and R work fine as on WinXP/32 -
>>>>> the problem is just related to the MatlabExpression actor, which is
>>>>> what I'm particularly interested in using.
>>>>>
>>>>> -Wade
>>>>>
>>>>>
>>>>> On 4/20/2012 10:41 PM, Wade Sheldon wrote:
>>>>>> Also, I updated Java to the latest version (1.6.0_31-b05),
>>>>>> uninstalled Kepler, and reinstalled from a full admin account. Same
>>>>>> results. From what I can find on the web, that "The operating system
>>>>>> cannot run %1" is a generic error that implies a path issue.
>>>>>> Anything I can check regarding the Kepler classpath or libraries
>>>>>> come to mind?
>>>>>>
>>>>>> Thanks again for your help.
>>>>>>
>>>>>> -Wade
>>>>>>
>>>>>> On 4/20/2012 10:02 PM, Wade Sheldon wrote:
>>>>>>> Thanks, Christopher. I had already perused the mailing list
>>>>>>> archives via Google and just saw references to the same issue
>>>>>>> without solutions. I confirmed that the JVM bit width is 32 (Java
>>>>>>> version 1.6.0_20).
>>>>>>>
>>>>>>> I set up a simpler workflow with just a SDF director,
>>>>>>> MatalbExpression actor and text display actor, and configured the
>>>>>>> expression: "rand(100,1);", but I got the same error. Here's the
>>>>>>> trace from the first time it was invoked, which yielded a little
>>>>>>> more info as you indicated, specifically "C:\Program
>>>>>>> Files\Kepler-2.3\common-2.3.0\lib\ptolemy\matlab\ptmatlab.dll: The
>>>>>>> operating system cannot run %1". Hope that points to a specific issue.
>>>>>>>
>>>>>>> Thanks.
>>>>>>>
>>>>>>> -Wade
>>>>>>>
>>>>>>> complete stack dump:
>>>>>>> ptolemy.kernel.util.IllegalActionException: There was a problem
>>>>>>> invoking the Ptolemy II Matlab interface.
>>>>>>> The interface has been tested under Linux, Mac OS X, and Windows.
>>>>>>> The interface requires that Matlab be installed on the local
>>>>>>> machine and that the ptmatlab shared library available.
>>>>>>> * Under Linux, you must have the LD_LIBRARY_PATH environment
>>>>>>> variable set to include the directories that contain libmx.so and
>>>>>>> libptmatlab.so.
>>>>>>> * Under Mac OS X, you must have the DYLD_LIBRARY_PATH environment
>>>>>>> variable set to include the directories that contain libmx.dylib
>>>>>>> and libptmatlab.jnilib.
>>>>>>> * Under Windows, you must have your PATH set to include the Matlab
>>>>>>> bin/win32 or equivalent directory so that libmex.dll is found and
>>>>>>> the directory that contains libptmatlab.dll. In addition, if you
>>>>>>> are running under Windows from the Cygwin bash prompt, then you
>>>>>>> must start Vergil with the -jni argument: $PTII/bin/vergil -jni.
>>>>>>> For details, see $PTII/jni/package.html.
>>>>>>> Refer to $PTII/ptolemy/matlab/makefile for more information.
>>>>>>> in .Unnamed1.MatlabExpression
>>>>>>> Because:
>>>>>>> C:\Program
>>>>>>> Files\Kepler-2.3\common-2.3.0\lib\ptolemy\matlab\ptmatlab.dll: The
>>>>>>> operating system cannot run %1
>>>>>>> at ptolemy.matlab.Expression.preinitialize(Expression.java:263)
>>>>>>> at ptolemy.actor.Director.preinitialize(Director.java:1056)
>>>>>>> at ptolemy.actor.Director.preinitialize(Director.java:1035)
>>>>>>> at
>>>>>>> ptolemy.domains.sdf.kernel.SDFDirector.preinitialize(SDFDirector.java:655)
>>>>>>>
>>>>>>> at
>>>>>>> ptolemy.actor.CompositeActor.preinitialize(CompositeActor.java:1735)
>>>>>>> at
>>>>>>> ptolemy.actor.Manager.preinitializeAndResolveTypes(Manager.java:930)
>>>>>>> at ptolemy.actor.Manager.initialize(Manager.java:636)
>>>>>>> at ptolemy.actor.Manager.execute(Manager.java:340)
>>>>>>> at ptolemy.actor.Manager.run(Manager.java:1111)
>>>>>>> at ptolemy.actor.Manager$PtolemyRunThread.run(Manager.java:1641)
>>>>>>> Caused by: java.lang.UnsatisfiedLinkError: C:\Program
>>>>>>> Files\Kepler-2.3\common-2.3.0\lib\ptolemy\matlab\ptmatlab.dll: The
>>>>>>> operating system cannot run %1
>>>>>>> at java.lang.ClassLoader$NativeLibrary.load(Native Method)
>>>>>>> at java.lang.ClassLoader.loadLibrary0(Unknown Source)
>>>>>>> at java.lang.ClassLoader.loadLibrary(Unknown Source)
>>>>>>> at java.lang.Runtime.load0(Unknown Source)
>>>>>>> at java.lang.System.load(Unknown Source)
>>>>>>> at
>>>>>>> ptolemy.data.expr.UtilityFunctions._loadLibrary(UtilityFunctions.java:2068)
>>>>>>>
>>>>>>> at
>>>>>>> ptolemy.data.expr.UtilityFunctions.loadLibrary(UtilityFunctions.java:927)
>>>>>>>
>>>>>>> at ptolemy.matlab.Engine.<clinit>(Engine.java:176)
>>>>>>> at ptolemy.matlab.Expression.preinitialize(Expression.java:260)
>>>>>>> ... 9 more
>>>>>>> Caused by: java.lang.UnsatisfiedLinkError: C:\Program
>>>>>>> Files\Kepler-2.3\common-2.3.0\lib\ptolemy\matlab\ptmatlab.dll: The
>>>>>>> operating system cannot run %1
>>>>>>> at java.lang.ClassLoader$NativeLibrary.load(Native Method)
>>>>>>> at java.lang.ClassLoader.loadLibrary0(Unknown Source)
>>>>>>> at java.lang.ClassLoader.loadLibrary(Unknown Source)
>>>>>>> at java.lang.Runtime.load0(Unknown Source)
>>>>>>> at java.lang.System.load(Unknown Source)
>>>>>>> at
>>>>>>> ptolemy.data.expr.UtilityFunctions._loadLibrary(UtilityFunctions.java:2068)
>>>>>>>
>>>>>>> at
>>>>>>> ptolemy.data.expr.UtilityFunctions.loadLibrary(UtilityFunctions.java:927)
>>>>>>>
>>>>>>> at ptolemy.matlab.Engine.<clinit>(Engine.java:176)
>>>>>>> at ptolemy.matlab.Expression.preinitialize(Expression.java:260)
>>>>>>> at ptolemy.actor.Director.preinitialize(Director.java:1056)
>>>>>>> at ptolemy.actor.Director.preinitialize(Director.java:1035)
>>>>>>> at
>>>>>>> ptolemy.domains.sdf.kernel.SDFDirector.preinitialize(SDFDirector.java:655)
>>>>>>>
>>>>>>> at
>>>>>>> ptolemy.actor.CompositeActor.preinitialize(CompositeActor.java:1735)
>>>>>>> at
>>>>>>> ptolemy.actor.Manager.preinitializeAndResolveTypes(Manager.java:930)
>>>>>>> at ptolemy.actor.Manager.initialize(Manager.java:636)
>>>>>>> at ptolemy.actor.Manager.execute(Manager.java:340)
>>>>>>> at ptolemy.actor.Manager.run(Manager.java:1111)
>>>>>>> at ptolemy.actor.Manager$PtolemyRunThread.run(Manager.java:1641)
>>>>>>>
>>>>>>>
>>>>>>> On 4/20/2012 6:38 PM, Christopher Brooks wrote:
>>>>>>>> Hi Wade,
>>>>>>>> I don't think I have a WinXP installation at hand, but I was able
>>>>>>>> to run the MatlabExpression demo under Windows Server 2003 with a
>>>>>>>> 32-bit JVM from a clean install of Kepler-2.3. Windows Server 2003
>>>>>>>> is fairly similar to XP.
>>>>>>>>
>>>>>>>> To determine the bit width of your JVM, start up Kepler, go to
>>>>>>>> Tools -> check settings and look at the value of
>>>>>>>> sun.arch.data.model = 32
>>>>>>>>
>>>>>>>> When I start a dos shell (Start->Run->cmd), I can start matlab
>>>>>>>> from the command line, which works for you.
>>>>> -- 
>>>>> ______________________________________________________________________________
>>>>>
>>>>>
>>>>> Wade M. Sheldon
>>>>> GCE-LTER Information Manager/SIMO Database Administrator
>>>>> School of Marine Programs
>>>>> University of Georgia
>>>>> Athens, GA 30602-3636
>>>>> Email: sheldon at uga.edu
>>>>> WWW:
>>>>> http://gce-lter.marsci.uga.edu/public/app/personnel_bios.asp?id=wsheldon
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Kepler-users mailing list
>>>>> Kepler-users at kepler-project.org
>>>>> http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
>>>>
>>>
>>
>>
>

-- 
____________________________________

  Wade M. Sheldon
  GCE-LTER Information Manager/SIMO Database Administrator
  School of Marine Programs
  University of Georgia
  Athens, GA 30602-3636
  Email: sheldon at uga.edu
  WWW: http://gce-lter.marsci.uga.edu/public/app/personnel_bios.asp?id=wsheldon

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