Note to self: think before posting. Thanks,
On Jun 30, 2011, at 11:29 AM, Daniel Crawl wrote:
>
> Hi Joe,
>
> The Matlab installer most likely created the symlink; the Kepler
> installer does not.
>
> --dan
>
>
> On 6/30/11 6:25 AM, Joe Futrelle wrote:
>> Interesting ... I have no such symlink in /usr/bin, but that must be because
>> I installed Kepler by dragging the app into my Applications folder, and
>> perhaps you installed it some other way (e.g,. building from source)?
>>
>> On Jun 29, 2011, at 2:15 PM, Daniel Crawl wrote:
>>
>>>
>>> Hi Joe,
>>>
>>> In Kepler, you can see what $PATH contains by using the
>>> Expression Evaluator in the Tools menu. Run this:
>>>
>>> getenv('PATH')
>>>
>>> On my mac, $PATH does not contain /Applications/Matlab...,
>>> but does have /usr/bin, which has a symlink to the Matlab
>>> binary. Matlab probably created the link when it installed.
>>> If you can't edit $PATH, you could make a symlink in a
>>> directory in $PATH.
>>>
>>> --dan
>>>
>>>
>>> On 6/29/11 9:28 AM, Joe Futrelle wrote:
>>>> Further results. My advice upthread "use launchctl to set [PATH]" is not
>>>> correct.
>>>>
>>>> Putting Matlab on your path so that Kepler can invoke it turns out to be a
>>>> different process depending on whether you are running Kepler from a shell
>>>> prompt, or whether you're double-clicking the application icon.
>>>>
>>>> As of Snow Leopard, it appears that the only way to set the PATH variable
>>>> seen by GUI applications when they are launched from the Finder/Dock is
>>>> using ~/.MacOSX/environment.plist.
>>>>
>>>> However this approach is somewhat problematic in that in environment.plist
>>>> variable references (i.e., $PATH) are not expanded, so there is no
>>>> non-kludgy way I've found to *append* the Matlab executable's path to the
>>>> PATH seen by GUI applications, using environment.plist.
>>>>
>>>>
>>>> The PATH approach that does work is using ordinary shell methods to append
>>>> the Matlab bin directory to the path, and then invoking Kepler from that
>>>> shell, like so:
>>>>
>>>> $ launchctl getenv DYLD_LIBRARY_PATH
>>>> /Applications/MATLAB_R2011a.app/bin/maci64
>>>> $ export PATH=$PATH:/Applications/MATLAB_R2011a.app/bin
>>>> $ echo $PATH
>>>> /opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/Applications/MATLAB_R2011a.app/bin
>>>> $ open /Applications/Kepler-2.2/Kepler.app/
>>>>
>>>> Can anyone advise how I might be able to get this working for launching
>>>> Kepler from Finder/Dock? Obviously I can just stick with the shell
>>>> approach, but I'd really like to be able to launch Kepler from the Dock.
>>>>
>>>> On Jun 28, 2011, at 3:48 PM, Joe Futrelle wrote:
>>>>
>>>>> OK, this thread resolved all of my issues. Thanks a lot guys! :)
>>>>>
>>>>> To summarize:
>>>>>
>>>>> DYLD_LIBRARY_PATH must include the Matlab libraries. Setting them with
>>>>> launchctl works, but don't expect to see them as shell environment
>>>>> variables unless you export them to the shell.
>>>>>
>>>>> The Matlab executable (from its app package's bin directory) must be in
>>>>> your path. (Again, use launchctl to set).
>>>>>
>>>>> I get different results when I use "open" from the command line to launch
>>>>> Kepler (works!) and when I double-click Kepler's app icon (doesn't), but
>>>>> I hypothesize that if I put both the DYLD_LIBRARY_PATH and PATH settings
>>>>> in /etc/launchd.conf and reboot, that it'll work. Unconfirmed as of yet.
>>>>>
>>>>> Hopefully the above account is accurate and not confused ...
>>>>>
>>>>> On Jun 28, 2011, at 3:20 PM, Daniel Crawl wrote:
>>>>>
>>>>>>
>>>>>> The matlab binary must be in your $PATH.
>>>>>>
>>>>>> --dan
>>>>>>
>>>>>> On 6/28/11 12:12 PM, Joe Futrelle wrote:
>>>>>>> This works.
>>>>>>>
>>>>>>> And it gets me past the stack trace I was getting before! :)
>>>>>>>
>>>>>>> Here's the transcript. I combined advice from two posts upthread.
>>>>>>>
>>>>>>> bash-3.2# DYLD_LIBRARY_PATH=/Applications/MATLAB_R2011a.app/bin/maci64/
>>>>>>> env | grep DYLD
>>>>>>> DYLD_LIBRARY_PATH=/Applications/MATLAB_R2011a.app/bin/maci64/
>>>>>>> bash-3.2# open /Applications/Kepler-2.2/Kepler.app
>>>>>>>
>>>>>>> Now I'm getting a different stacktrace. I have a properly-licensed
>>>>>>> Matlab instance running and csh is @ /bin/csh.
>>>>>>>
>>>>>>> ptolemy.kernel.util.IllegalActionException: matlabEngine.open(null) :
>>>>>>> can't find Matlab engine. Try starting Matlab by hand as an application
>>>>>>> to verify that Matlab is set up properly and the license is correct.
>>>>>>> Under Windows, try running "matlab /regserver", the Matlab C API
>>>>>>> communicates with Matlab via COM, and apparently the COM interface is
>>>>>>> not automatically registered when Matlab is installed. Under Linux and
>>>>>>> other types of UNIX, csh must be installed in /bin/csh.
>>>>>>> at ptolemy.matlab.Engine.open(Engine.java:280)
>>>>>>> at ptolemy.matlab.Engine.open(Engine.java:232)
>>>>>>> at ptolemy.matlab.Expression.preinitialize(Expression.java:303)
>>>>>>> at ptolemy.actor.Director.preinitialize(Director.java:1010)
>>>>>>> at ptolemy.actor.Director.preinitialize(Director.java:991)
>>>>>>> at
>>>>>>> ptolemy.domains.ct.kernel.CTDirector.preinitialize(CTDirector.java:748)
>>>>>>> at
>>>>>>> ptolemy.domains.ct.kernel.CTMultiSolverDirector.preinitialize(CTMultiSolverDirector.java:637)
>>>>>>> at
>>>>>>> ptolemy.actor.CompositeActor.preinitialize(CompositeActor.java:1735)
>>>>>>> at
>>>>>>> ptolemy.actor.Manager.preinitializeAndResolveTypes(Manager.java:983)
>>>>>>> at ptolemy.actor.Manager.initialize(Manager.java:643)
>>>>>>> at ptolemy.actor.Manager.execute(Manager.java:340)
>>>>>>> at ptolemy.actor.Manager.run(Manager.java:1164)
>>>>>>> at ptolemy.actor.Manager$3.run(Manager.java:1217)
>>>>>>>
>>>>>>>
>>>>>>> On Jun 28, 2011, at 3:02 PM, Sean Riddle wrote:
>>>>>>>
>>>>>>>> I can't get launchd.conf to set DYLD_LIBRARY_PATH, but for some reason
>>>>>>>> it doesn't set anything else either. But DYLD_LIBRARY_PATH is
>>>>>>>> settable, at least in some ways:
>>>>>>>>
>>>>>>>> dhcp33-gc5:~ sean$ DYLD_LIBRARY_PATH=hello env | grep
>>>>>>>> "DYLD_LIBRARY_PATH"
>>>>>>>> DYLD_LIBRARY_PATH=hello
>>>>>>>>
>>>>>>>> I would recommend trying the support including in the build system for
>>>>>>>> setting environment variables. Create a file
>>>>>>>> kepler/module-info/environment.txt and specify the value there. You
>>>>>>>> can look at r/module-info/environment.txt for an example. Note that as
>>>>>>>> in the example, you can (and possible must, I'm not sure) specify
>>>>>>>> separate values for all three of the platforms that Kepler supports.
>>>>>>>>
>>>>>>>> - Sean
>>>>>>>>
>>>>>>>> On Tue, Jun 28, 2011 at 11:27 AM, Joe Futrelle<[email protected]>
>>>>>>>> wrote:
>>>>>>>>> I tried that, didn't work.
>>>>>>>>>
>>>>>>>>> Again, I have no problem setting system-wide environment variables in
>>>>>>>>> launchd.conf. If I set "foo" to "bar" then "foo" is set to "bar" in
>>>>>>>>> my environment. But if I set DYLD_LIBRARY_PATH to anything, it's like
>>>>>>>>> I didn't set it at all.
>>>>>>>>>
>>>>>>>>> Exactly the same behavior with environment.plist. It seems to me like
>>>>>>>>> DYLD_LIBRARY_PATH is on some kind of blacklist.
>>>>>>>>>
>>>>>>>>> On Jun 28, 2011, at 2:15 PM, Sean Riddle wrote:
>>>>>>>>>
>>>>>>>>>> I always heard that if you wanted to set environment variables for
>>>>>>>>>> GUI
>>>>>>>>>> applications in OS X, you needed to edit the environment.plist file.
>>>>>>>>>> A
>>>>>>>>>> stackoverflow thread
>>>>>>>>>> (http://stackoverflow.com/questions/135688/setting-environment-variables-in-os-x)
>>>>>>>>>> says it can be set on a per-user basis at
>>>>>>>>>> ~/.MacOSX/environment.plist.
>>>>>>>>>> However, that thread also says that launchd.conf also works for GUI
>>>>>>>>>> applications. Maybe try setting it in environment.plist to see if
>>>>>>>>>> that
>>>>>>>>>> makes a difference.
>>>>>>>>>>
>>>>>>>>>> - Sean
>>>>>>>>>>
>>>>>>>>>> PS - Property List Editor in Utilities is what creates and edits
>>>>>>>>>> .plist files.
>>>>>>>>>>
>>>>>>>>>> On Tue, Jun 28, 2011 at 11:09 AM, Joe Futrelle<[email protected]>
>>>>>>>>>> wrote:
>>>>>>>>>>> Hi, I'm trying to run Matlab codes from Kepler in Mac OS (Snow
>>>>>>>>>>> Leopard). As an inexperienced user I'm simply firing up the
>>>>>>>>>>> prepackaged Mac OS distribution of Kepler and double-clicking on
>>>>>>>>>>> the app icon.
>>>>>>>>>>>
>>>>>>>>>>> It's no problem constructing a workflow with a "Matlab expression"
>>>>>>>>>>> in it, but when I run I get a stacktrace about the Matlab libraries
>>>>>>>>>>> not being on the DYLD_LIBRARY_PATH.
>>>>>>>>>>>
>>>>>>>>>>> I'm having no trouble finding those libraries manually; they're
>>>>>>>>>>> right where they should be in my Matlab install, and they're 64
>>>>>>>>>>> bit, and everything seems in order.
>>>>>>>>>>>
>>>>>>>>>>> Setting DYLD_LIBRARY_PATH doesn't seem possible in Mac OS; I can
>>>>>>>>>>> set environment variables in launchd.conf, but launchd appears to
>>>>>>>>>>> silently ignore DYLD_LIBRARY_PATH; maybe it's special-casing it for
>>>>>>>>>>> some reason.
>>>>>>>>>>>
>>>>>>>>>>> I'm having trouble finding a previous post on this list, or a bug
>>>>>>>>>>> in Kepler's bugzilla database, or a documentation section or FAQ
>>>>>>>>>>> entry that explains how to solve this. It's clear that some people
>>>>>>>>>>> have had problems with this in the past, but I don't see a clear
>>>>>>>>>>> description of what I should be doing. Any and all advice welcome.
>>>>>>>>>>>
>>>>>>>>>>> Mac OS version: 10.6.7
>>>>>>>>>>> Java version: 1.6.0_24 (Java HotSpot(TM) 64-Bit Server VM (build
>>>>>>>>>>> 19.1-b02-334, mixed mode))
>>>>>>>>>>> Kepler version: 2.2
>>>>>>>>>>> Matlab version: R2011a
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> Joe Futrelle
>>>>>>>>>>> Woods Hole Oceanographic Institution
>>>>>>>>>>> [email protected]
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> Kepler-users mailing list
>>>>>>>>>>> [email protected]
>>>>>>>>>>> http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Joe Futrelle
>>>>>>>>> Woods Hole Oceanographic Institution
>>>>>>>>> [email protected]
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Joe Futrelle
>>>>>>> Woods Hole Oceanographic Institution
>>>>>>> [email protected]
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Kepler-users mailing list
>>>>>>> [email protected]
>>>>>>> http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
>>>>>>>
>>>>>>
>>>>>
>>>>> --
>>>>> Joe Futrelle
>>>>> Woods Hole Oceanographic Institution
>>>>> [email protected]
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Kepler-users mailing list
>>>>> [email protected]
>>>>> http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
>>>>>
>>>>
>>>> --
>>>> Joe Futrelle
>>>> Woods Hole Oceanographic Institution
>>>> [email protected]
>>>>
>>>>
>>>>
>>>>
>>>
>>
>> --
>> Joe Futrelle
>> Woods Hole Oceanographic Institution
>> [email protected]
>>
>>
>>
>>
>
--
Joe Futrelle
Woods Hole Oceanographic Institution
[email protected]
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