[Midas] ParaView Web support for Midas
Sebastien Jourdain
sebastien.jourdain at kitware.com
Wed Nov 6 14:02:05 EST 2013
The issue might be related to the fact that you should add the "-f"
argument to the command line as Jetty may think that the process is not
started yet.
The -f will force to flush the output of the python process. This was added
lately to prevent the +++++ to show up when running from the command line.
Hope that helps.
Seb
On Wed, Nov 6, 2013 at 11:56 AM, BRIAN E CHAPMAN <Brian.Chapman at utah.edu>wrote:
> Progress but not quite there. I do now actually get an attempt to launch
> Paraview but a timeout occurs:
>
> Starting ParaviewWeb instance
>
> Waiting for binding on port 9000...
> Instance creation failed: Instance did not bind to port within 5 seconds.
>
> Log content: Traceback (most recent call last):
> File "/usr/local/src/Midas3/modules/pvw/apps/midas.py", line 19, in
> from paraview.web import protocols, wamp
> ImportError: cannot import name protocols
>
>
> I’ll have to check configuration this afternoon.
>
> Brian
>
>
> On 11/6/13, 11:04 AM, "Zach Mullen" <zach.mullen at kitware.com> wrote:
>
> >Ok, good to know. I packaged up the correct www dir and attached it to
> >this email, dump that directory into the module's public dir as a
> >directory named "import" (apps, ext, and lib should be directly
> >underneath import). That should hopefully fix the issue.
> >
> >Thanks,
> >
> >Zach
> >
> >On Wed, Nov 6, 2013 at 1:00 PM, BRIAN E CHAPMAN <Brian.Chapman at utah.edu>
> >wrote:
> >> Yes. I¹m using the packaged binary. I was having a difficult time
> >>getting
> >> Paraview to compile on my machine.
> >>
> >> Brian
> >>
> >> On 11/6/13, 10:56 AM, "Zach Mullen" <zach.mullen at kitware.com> wrote:
> >>
> >>>After looking into it, it looks like this is actually only the case
> >>>with the packaged version of ParaView, not one built from source.
> >>>Brian, are you using the downloaded paraview package or building from
> >>>source?
> >>>
> >>>On Wed, Nov 6, 2013 at 7:10 AM, Zach Mullen <zach.mullen at kitware.com>
> >>>wrote:
> >>>> This is indeed the issue I discovered yesterday. Some files were moved
> >>>> within ParaView and it broke compatibility with the Midas plugin. I
> >>>>should
> >>>> have a fix committed to next branch this morning.
> >>>>
> >>>> Thanks,
> >>>>
> >>>> Zach
> >>>>
> >>>>
> >>>> On Tue, Nov 5, 2013 at 11:32 PM, Patrick Reynolds
> >>>> <patrick.reynolds at kitware.com> wrote:
> >>>>>
> >>>>> Brian,
> >>>>>
> >>>>> This looks like it could be related to the symbolic link of the
> >>>>>vtkweb
> >>>>> javascript. This may be related to an issue that Zach is tracking.
> >>>>>
> >>>>> --
> >>>>> Patrick Reynolds
> >>>>> Technical Leader
> >>>>> Kitware, Inc.
> >>>>> 919 869 8848
> >>>>>
> >>>>> On Tuesday, October 29, 2013 at 5:15 PM, BRIAN E CHAPMAN wrote:
> >>>>>
> >>>>> Patrick,
> >>>>>
> >>>>> I've been toggling the dynamic help and looking at the logs (apache
> >>>>>and
> >>>>> midas/log/dev.log). Here is what I am getting without and with
> >>>>>dynamic
> >>>>>help
> >>>>> turned on
> >>>>>
> >>>>> Dynamic help off:
> >>>>>
> >>>>> [Tue Oct 29 15:06:08.706120 2013] [:error] [pid 25319] [client
> >>>>> 155.100.62.145:54950] PHP Warning: Unknown: function 'NULL' not
> >>>>>found
> >>>>>or
> >>>>> invalid function name in Unknown on line 0,
> >>>>> referer:http://155.100.62.142/midas/pvw/paraview/volume?itemId=1
> >>>>>
> >>>>> 2013-10-29 17:06:08 WARN (4): URL:
> >>>>>
> >>>>>
> http://155.100.62.142/midas/modules/pvw/public/import/lib/js/vtkweb-al
> >>>>>l.
> >>>>>min.js
> >>>>> Server IP: 155.100.62.142
> >>>>> Client IP: 155.100.62.145
> >>>>> User agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_5)
> >>>>> AppleWebKit/537.36 (KHTML, like Gecko) Chrome/30.0.1599.101
> >>>>>Safari/537.36
> >>>>> Server time: 2013-10-29 17:06:08
> >>>>> RequestURI: /midas/modules/pvw/public/import/lib/js/vtkweb-all.min.js
> >>>>> Referer: http://155.100.62.142/midas/pvw/paraview/volume?itemId=1
> >>>>> <b>Message: Invalid controller specified (modules)</b>
> >>>>>
> >>>>> Trace:
> >>>>> #0 /usr/local/src/Midas3/library/Zend/Controller/Front.php(954):
> >>>>>
> >>>>>Zend_Controller_Dispatcher_Standard->dispatch(Object(Zend_Controller_R
> >>>>>eq
> >>>>>uest_Http),
> >>>>> Object(Zend_Controller_Response_Http))
> >>>>> #1
> >>>>>
> >>>>>/usr/local/src/Midas3/library/Zend/Application/Bootstrap/Bootstrap.php
> >>>>>(9
> >>>>>7):
> >>>>> Zend_Controller_Front->dispatch()
> >>>>> #2 /usr/local/src/Midas3/library/Zend/Application.php(366):
> >>>>> Zend_Application_Bootstrap_Bootstrap->run()
> >>>>> #3 /usr/local/src/Midas3/index.php(73): Zend_Application->run()
> >>>>> #4 {main}
> >>>>>
> >>>>> Request data: array (
> >>>>> 'controller' => 'modules',
> >>>>> 'action' => 'pvw',
> >>>>> 'public' => 'import',
> >>>>> 'lib' => 'js',
> >>>>> 'module' => 'default',
> >>>>> )
> >>>>>
> >>>>> Session data:
> >>>>> Dao: __PHP_Incomplete_Class::__set_state(array(
> >>>>> '__PHP_Incomplete_Class_Name' => 'UserDao',
> >>>>> '_model' => 'User',
> >>>>> 'key' => NULL,
> >>>>> '_key' => 'user_id',
> >>>>> 'saved' => true,
> >>>>> 'user_id' => '1',
> >>>>> 'firstname' => 'Brian',
> >>>>> 'lastname' => 'Chapman',
> >>>>> 'email' => 'brian.chapman at utah.edu',
> >>>>> 'thumbnail' => NULL,
> >>>>> 'company' => NULL,
> >>>>> 'hash_alg' => 'sha256',
> >>>>> 'salt' => 'uirWyLLLBDcN9udgEy2o0ZwZulN17z8s',
> >>>>> 'creation' => '2013-10-24 14:09:40',
> >>>>> 'folder_id' => '1',
> >>>>> 'admin' => '1',
> >>>>> 'privacy' => '0',
> >>>>> 'view' => '0',
> >>>>> 'uuid' => '52696264c0b08ca6ba63fc546fe5b950545d654ae59cc',
> >>>>> 'city' => '',
> >>>>> 'country' => '',
> >>>>> 'website' => '',
> >>>>> 'biography' => '',
> >>>>> 'dynamichelp' => '1',
> >>>>> ))
> >>>>>
> >>>>> Last database query: SELECT `setting`.* FROM `setting` WHERE (name =
> >>>>> 'temp_directory') AND (module = 'core') LIMIT 1
> >>>>>
> >>>>>
> >>>>> Dynamic Help ON:
> >>>>>
> >>>>> [Tue Oct 29 15:10:44.885671 2013] [:error] [pid 25321] [client
> >>>>> 155.100.62.145:55013] PHP Warning: Unknown: function 'NULL' not
> >>>>>found
> >>>>>or
> >>>>> invalid function name in Unknown on line 0,
> >>>>> referer:http://155.100.62.142/midas/pvw/paraview/volume?itemId=1
> >>>>> [Tue Oct 29 15:10:44.894376 2013] [:error] [pid 25319] [client
> >>>>> 155.100.62.145:55006] PHP Fatal error:
> >>>>>AppController::isDynamicHelp(): The
> >>>>> script tried to execute a method or access a property of an
> >>>>>incomplete
> >>>>> object. Please ensure that the class definition "UserDao"
> >>>>>of
> >>>>>the
> >>>>> object you are trying to operate on was loaded _before_ unserialize()
> >>>>>gets
> >>>>> called or provide a __autoload() function to load the class
> >>>>>definition
> >>>>> in
> >>>>> /usr/local/src/Midas3/core/AppController.php on line 424,
> >>>>> referer:http://155.100.62.142/midas/pvw/paraview/volume?itemId=1
> >>>>>
> >>>>> 2013-10-29 17:10:44 CRIT (2): Fatal Error: Array
> >>>>> (
> >>>>> [type] => 1
> >>>>> [message] => AppController::isDynamicHelp(): The script tried to
> >>>>> execute a method or access a property of an incomplete object. Please
> >>>>>ensure
> >>>>> that the class definition "UserDao" of the object you are
> >>>>>trying
> >>>>> to operate on was loaded _before_ unserialize() gets called or
> >>>>>provide
> >>>>>a
> >>>>> __autoload() function to load the class definition
> >>>>> [file] => /usr/local/src/Midas3/core/AppController.php
> >>>>> [line] => 424
> >>>>> [typeText] => E_ERROR
> >>>>> )
> >>>>>
> >>>>>
> >>>>> URL:
> >>>>>
> >>>>>
> http://155.100.62.142/midas/modules/pvw/public/import/lib/js/vtkweb-al
> >>>>>l.
> >>>>>min.js
> >>>>>
> >>>>> Server IP: 155.100.62.142
> >>>>> User agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_5)
> >>>>> AppleWebKit/537.36 (KHTML, like Gecko) Chrome/30.0.1599.101
> >>>>>Safari/537.36
> >>>>> Server time: 2013-10-29 17:10:44
> >>>>> Referer: http://155.100.62.142/midas/pvw/paraview/volume?itemId=1
> >>>>> Parameters (post): Array
> >>>>> (
> >>>>> )
> >>>>> Parameters (get): Array
> >>>>> (
> >>>>> )
> >>>>>
> >>>>>
> >>>>> Brian E. Chapman, Ph.D.
> >>>>> Associate Professor
> >>>>> Department of Radiology
> >>>>> University of Utah
> >>>>>
> >>>>>
> >>>>> From: Patrick Reynolds <patrick.reynolds at kitware.com>
> >>>>> Date: Tuesday, October 29, 2013 1:28 PM
> >>>>> To: Brian Chapman <Brian.Chapman at utah.edu>
> >>>>> Cc: "midas at public.kitware.com" <midas at public.kitware.com>
> >>>>> Subject: Re: [Midas] ParaView Web support for Midas
> >>>>>
> >>>>> Brian,
> >>>>>
> >>>>> Are you able to get to the admin page and disable dynamic help?
> >>>>>
> >>>>> That should yield an improved error message.
> >>>>>
> >>>>> --
> >>>>> Patrick Reynolds
> >>>>> Technical Leader
> >>>>> Kitware, Inc.
> >>>>> 919 869 8848
> >>>>>
> >>>>> On Thursday, October 24, 2013 at 6:58 PM, BRIAN E CHAPMAN wrote:
> >>>>>
> >>>>> Hi Zach, et al.,
> >>>>>
> >>>>> I'm making progress here. I looked at Sebastien's suggestion of using
> >>>>> VirtualGL but decided to go back and build a VM with X11 support.
> >>>>>I've
> >>>>>got
> >>>>> Midas running and ParaView web configured as per the web site and
> >>>>>Zach's
> >>>>> instructions. When I got to view an object (a 3D CT stored in .mha
> >>>>>format) I
> >>>>> get a blank canvas with "Volume rendering: pe0017s4.mha" on the top
> >>>>>and a
> >>>>> bunch of control widgets on the right.
> >>>>>
> >>>>> When I look at the apache2 logs I see the following.
> >>>>>
> >>>>> acces.log: 111.222.33.444 - - [24/Oct/2013:16:38:02 -0600] "GET
> >>>>> /midas/modules/pvw/public/import/lib/js/vtkweb-all.min.js HTTP/1.1"
> >>>>>500 936
> >>>>> "http://111.222.33.555/midas/pvw/paraview/volume?itemId=1"
> >>>>>"Mozilla/5.0
> >>>>> (X11; Ubuntu; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0"
> >>>>>
> >>>>> error.log [Thu Oct 24 16:38:02.468812 2013] [:error] [pid 7303]
> >>>>>[client
> >>>>> 111.222.33.444:34502] PHP Fatal error:
> >>>>>AppController::isDynamicHelp(): The
> >>>>> script tried to execute a method or access a property of an
> >>>>>incomplete
> >>>>> object. Please ensure that the class definition "UserDao"
> >>>>>of
> >>>>>the
> >>>>> object you are trying to operate on was loaded _before_ unserialize()
> >>>>>gets
> >>>>> cal
> >>>>>
> >>>>> The midas log file is as follows:
> >>>>>
> >>>>> dev.log
> >>>>> Referer: http://111.222.33.555/midas/pvw/paraview/volume?itemId=1
> >>>>> Parameters (post): Array
> >>>>> (
> >>>>> )
> >>>>> Parameters (get): Array
> >>>>> (
> >>>>> )
> >>>>>
> >>>>> Any ideas as to what is going wrong?
> >>>>>
> >>>>> Brian
> >>>>>
> >>>>> Brian E. Chapman, Ph.D.
> >>>>> Associate Professor
> >>>>> Department of Radiology
> >>>>> University of Utah
> >>>>>
> >>>>>
> >>>>> From: Zach Mullen <zach.mullen at kitware.com>
> >>>>> Date: Thursday, October 17, 2013 11:54 AM
> >>>>> To: Brian Chapman <Brian.Chapman at utah.edu>
> >>>>> Cc: Patrick Reynolds <patrick.reynolds at kitware.com>,
> >>>>> "midas at public.kitware.com" <midas at public.kitware.com>
> >>>>> Subject: Re: [Midas] ParaView Web support for Midas
> >>>>>
> >>>>> Hi Brian,
> >>>>>
> >>>>> Answered your questions inline.
> >>>>>
> >>>>>
> >>>>> On Thu, Oct 17, 2013 at 1:49 PM, BRIAN E CHAPMAN
> >>>>><Brian.Chapman at utah.edu>
> >>>>> wrote:
> >>>>>
> >>>>> Patrick,
> >>>>>
> >>>>> That saved a lot of time! A couple of dummy questions. In
> >>>>> /var/www/midas/modules there is already a pvw directory. So where am
> >>>>>I
> >>>>> supposed to create the symbolic link to
> >>>>>$PARAVIEW_ROOT/lib/paraview-4.0/www?
> >>>>>
> >>>>>
> >>>>> You should create a symlink at
> >>>>>/var/www/midas/modules/pvw/public/import,
> >>>>> and it should point to the paraview-4.0/www dir.
> >>>>>
> >>>>>
> >>>>> Also, just because I'm kind of dense, do I need to set the DISPLAY
> >>>>> environment variable. The pop-up help says "If the DISPLAY env var
> >>>>>should be
> >>>>> setŠ" I don't know if it should be.
> >>>>>
> >>>>> It depends what environment you are running in. If you plan on
> >>>>>running
> >>>>> this headlessly as a server, you will probably need to set the
> >>>>>environment
> >>>>> variable. If you are running the server within an already existing X
> >>>>> environment, you probably won't need to set it. If you open a
> >>>>>terminal
> >>>>>and
> >>>>> type
> >>>>>
> >>>>> echo $DISPLAY
> >>>>>
> >>>>> It will show you the current value of your display ID.
> >>>>>
> >>>>>
> >>>>> Finally, is there a tutorial or demo for the Midas/ParaView
> >>>>>interface?
> >>>>>
> >>>>>
> >>>>> We just finished transitioning the demo application to the latest
> >>>>>version
> >>>>> of ParaViewWeb. The demo of the old capabilities is here:
> >>>>>
> >>>>>
> http://50.58.123.185/external/midas/visualize/paraview/volume?itemId=4
> >>>>>4
> >>>>>
> >>>>> There isn't much currently in the way of developer-oriented
> >>>>>documentation
> >>>>> for the module; for that you might have to just consult us with your
> >>>>> questions :)
> >>>>>
> >>>>> Thanks,
> >>>>>
> >>>>>
> >>>>> Thanks for the help.
> >>>>>
> >>>>> Brian
> >>>>>
> >>>>>
> >>>>> From: Patrick Reynolds <patrick.reynolds at kitware.com>
> >>>>> Date: Thursday, October 17, 2013 11:12 AM
> >>>>> To: Brian Chapman <Brian.Chapman at utah.edu>
> >>>>> Cc: "midas at public.kitware.com" <midas at public.kitware.com>
> >>>>> Subject: Re: [Midas] ParaView Web support for Midas
> >>>>>
> >>>>> Brian,
> >>>>>
> >>>>> You'll need to build Paraview Web from Source or download binaries.
> >>>>>It
> >>>>> comes with paraview, so you should be able to follow the instructions
> >>>>> stemming from this wiki page:
> >>>>>
> >>>>> http://www.paraview.org/Wiki/ParaViewWeb
> >>>>>
> >>>>> HTH.
> >>>>>
> >>>>> --
> >>>>> Patrick Reynolds
> >>>>> Technical Leader
> >>>>> Kitware, Inc.
> >>>>> 919 869 8848
> >>>>>
> >>>>> On Thursday, October 17, 2013 at 12:56 PM, BRIAN E CHAPMAN wrote:
> >>>>>
> >>>>> Hello Midas World,
> >>>>>
> >>>>> I'm trying to build an instance of Midas with ParaviewWeb enabled.
> >>>>>I'm
> >>>>> working on an Ubuntu 12.04 instance. Midas built fine, but I'm
> >>>>>having a
> >>>>> difficult time getting Paraview to build. Just curious if the
> >>>>> paraview-python package that is available in the ubuntu distribution
> >>>>>is
> >>>>> sufficient for this purpose? If it is, curious about the details of
> >>>>>the
> >>>>> configuration for the instructions: "Make sure to symlink the www
> >>>>>directory
> >>>>> of your ParView build directoryŠ"
> >>>>>
> >>>>> I'm suspicious of the package since when I try to run pvpython I get
> >>>>>an
> >>>>> error:
> >>>>>
> >>>>> "Error converting executable file "/usr/bin/../lib/paraview/pvpython"
> >>>>>to
> >>>>> real path: no such file or directory"
> >>>>>
> >>>>>
> >>>>> Brian E. Chapman, Ph.D.
> >>>>> Associate Professor
> >>>>> Department of Radiology
> >>>>> University of Utah
> >>>>>
> >>>>> _______________________________________________
> >>>>> Midas mailing list
> >>>>> Midas at public.kitware.com
> >>>>> http://public.kitware.com/cgi-bin/mailman/listinfo/midas
> >>>>>
> >>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> Midas mailing list
> >>>>> Midas at public.kitware.com
> >>>>> http://public.kitware.com/cgi-bin/mailman/listinfo/midas
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> --
> >>>>> Zach Mullen
> >>>>> R & D Engineer
> >>>>> Kitware Inc.
> >>>>> 919-869-8858
> >>>>>
> >>>>>
> >>>>>
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> Zach Mullen
> >>>> R & D Engineer
> >>>> Kitware Inc.
> >>>> 919-869-8858
> >>>
> >>>
> >>>
> >>>--
> >>>Zach Mullen
> >>>R & D Engineer
> >>>Kitware Inc.
> >>>919-869-8858
> >>
> >
> >
> >
> >--
> >Zach Mullen
> >R & D Engineer
> >Kitware Inc.
> >919-869-8858
>
> _______________________________________________
> Midas mailing list
> Midas at public.kitware.com
> http://public.kitware.com/cgi-bin/mailman/listinfo/midas
>
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