[Midas] ParaView Web support for Midas
BRIAN E CHAPMAN
Brian.Chapman at utah.edu
Wed Nov 6 19:25:06 EST 2013
Looking at the paraview python source files ParaView-4.0.1-Linux-64bit/lib/paraview-4.0/site-packages/paraview/web.py, there is no “protocols” to import. Do we have a version mismatch between what Midas is expecting and the binary Paraview download?
Brian
From: Sebastien Jourdain <sebastien.jourdain at kitware.com<mailto:sebastien.jourdain at kitware.com>>
Date: Wednesday, November 6, 2013 at 12:02 PM
To: Brian Chapman <brian.chapman at utah.edu<mailto:brian.chapman at utah.edu>>
Cc: Zach Mullen <zach.mullen at kitware.com<mailto:zach.mullen at kitware.com>>, "midas at public.kitware.com<mailto:midas at public.kitware.com>" <midas at public.kitware.com<mailto:midas at public.kitware.com>>
Subject: Re: [Midas] ParaView Web support for Midas
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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<tel:919%20869%208848>
>>>>>
>>>>> 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<http://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<mailto: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<http://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<http://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<mailto:patrick.reynolds at kitware.com>>
>>>>> Date: Tuesday, October 29, 2013 1:28 PM
>>>>> To: Brian Chapman <Brian.Chapman at utah.edu<mailto:Brian.Chapman at utah.edu>>
>>>>> Cc: "midas at public.kitware.com<mailto:midas at public.kitware.com>" <midas at public.kitware.com<mailto: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<tel:919%20869%208848>
>>>>>
>>>>> 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<mailto:zach.mullen at kitware.com>>
>>>>> Date: Thursday, October 17, 2013 11:54 AM
>>>>> To: Brian Chapman <Brian.Chapman at utah.edu<mailto:Brian.Chapman at utah.edu>>
>>>>> Cc: Patrick Reynolds <patrick.reynolds at kitware.com<mailto:patrick.reynolds at kitware.com>>,
>>>>> "midas at public.kitware.com<mailto:midas at public.kitware.com>" <midas at public.kitware.com<mailto: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<mailto: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<mailto:patrick.reynolds at kitware.com>>
>>>>> Date: Thursday, October 17, 2013 11:12 AM
>>>>> To: Brian Chapman <Brian.Chapman at utah.edu<mailto:Brian.Chapman at utah.edu>>
>>>>> Cc: "midas at public.kitware.com<mailto:midas at public.kitware.com>" <midas at public.kitware.com<mailto: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<tel:919%20869%208848>
>>>>>
>>>>> 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<mailto:Midas at public.kitware.com>
>>>>> http://public.kitware.com/cgi-bin/mailman/listinfo/midas
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Midas mailing list
>>>>> Midas at public.kitware.com<mailto:Midas at public.kitware.com>
>>>>> http://public.kitware.com/cgi-bin/mailman/listinfo/midas
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Zach Mullen
>>>>> R & D Engineer
>>>>> Kitware Inc.
>>>>> 919-869-8858<tel:919-869-8858>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Zach Mullen
>>>> R & D Engineer
>>>> Kitware Inc.
>>>> 919-869-8858<tel:919-869-8858>
>>>
>>>
>>>
>>>--
>>>Zach Mullen
>>>R & D Engineer
>>>Kitware Inc.
>>>919-869-8858<tel:919-869-8858>
>>
>
>
>
>--
>Zach Mullen
>R & D Engineer
>Kitware Inc.
>919-869-8858<tel:919-869-8858>
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