[kepler-users] Kepler 2.3 and MATLAB

Christopher Brooks cxh at eecs.berkeley.edu
Tue Apr 24 17:07:27 PDT 2012 

Reimplementing the Matlab interface to use JNA instead of JNI directly 
would mean that we would not have to have a separate Ptolemy/Kepler 
Matlab-specific dll.  This *might* remove some of the platform 
dependency issues.  JNA is released under the GNU Lesser GPL.  I've been 
using JNA as an interface to C-based Functional Mock-up Unit (FMU) code 
and it works well.

In theo

Another issue is 32 vs. 64 bit width.  Many tools (Dymola) are only 
32-bit.   At least Mac OS X has a way of bundling both 32 and 64 bit 
shared objects in one file.  I don't believe Windows has such a facility.

JNA would help us get out of the business of building shared libraries 
for linux32, linux64, darwin32, darwin64, win32 and win64.

_Christopher

On 4/23/12 10:18 AM, Wade Sheldon wrote:
> I agree with you Edward, but I figured it was worth a try. I think 
> tool chaining is more sustainable than integration in the long run, so 
> data interchange formats and standards are more important than program 
> hooks.
>
> To follow up on my subsequent note, and reinforce your point, the JNI 
> for Matlab in Kepler 2.3 breaks in 2010a and 2011b, but works in 
> 2009a. I don't use COM-based or command line calls to Matlab for 
> anything else, so I'll keep 2009a configured in the path for Kepler 
> and continue to use 2011b for my normal work.
>
> Thanks.
>
> Wade
>
>
> On 4/23/2012 12:59 PM, Edward A. Lee wrote:
>>
>> If it's any consolation, my experience is that "tool integration"
>> is almost impossible to achieve, in practice... Even if you get
>> it working once, it will break when something changes...
>> There is clearly a technical challenge here.
>>
>> Edward
>>
>> On 4/23/12 9:08 AM, 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
>>>>>>
>>>>>
>>>>
>>>>
>>>
>

-- 
Christopher Brooks, PMP                       University of California
CHESS Executive Director                      US Mail: 337 Cory Hall
Programmer/Analyst CHESS/Ptolemy/Trust        Berkeley, CA 94720-1774
ph: 510.643.9841                                (Office: 545Q Cory)
home: (F-Tu) 707.665.0131 cell: 707.332.0670

More information about the Kepler-users mailing list