date:20151203

[Paraview] Compiling 5.0.0-RC1 vit VisItBridge linking failure on Fedora 23

2015-12-03 Thread Jiri Vyskocil

Hello,

I'm trying to compile Paraview with MPI and VisIt bridge on Fedora 23 with 
OpenMPI. Paraview compiles, and runs fine without VisitBridge. If I enable the 
PARAVIEW_USE_VISITBRIDGE option (I'm using ccmake), I get the following error:

[ 26%] Linking CXX shared library ../../../lib/libvtkIOVisItBridge-pv5.0.so
CMakeFiles/vtkIOVisItBridge.dir/vtkVisItChomboReader.cxx.o: In function 
`MPI::Win::Set_name(char const*)':
vtkVisItChomboReader.cxx:(.text._ZN3MPI3Win8Set_nameEPKc[_ZN3MPI3Win8Set_nameEPKc]+0x5):
 undefined reference to `MPI_Win_set_name'
CMakeFiles/vtkIOVisItBridge.dir/vtkVisItChomboReader.cxx.o: In function 
`MPI::Win::Set_attr(int, void const*)':
vtkVisItChomboReader.cxx:(.text._ZN3MPI3Win8Set_attrEiPKv[_ZN3MPI3Win8Set_attrEiPKv]+0x5):
 undefined reference to `MPI_Win_set_attr'
.
snip a couple hundred similar lines
.
vtkVisItChomboReader.cxx:(.text._ZNK3MPI9Intracomm6CreateERKNS_5GroupE[_ZNK3MPI9Intracomm6CreateERKNS_5GroupE]+0x6e):
 undefined reference to `ompi_mpi_comm_null'
CMakeFiles/vtkIOVisItBridge.dir/vtkVisItChomboReader.cxx.o:(.data.rel.ro._ZTVN3MPI8DatatypeE[_ZTVN3MPI8DatatypeE]+0x78):
 undefined reference to `MPI::Datatype::Free()'
CMakeFiles/vtkIOVisItBridge.dir/vtkVisItChomboReader.cxx.o:(.data.rel.ro._ZTVN3MPI3WinE[_ZTVN3MPI3WinE]+0x48):
 undefined reference to `MPI::Win::Free()'
collect2: error: ld returned 1 exit status
Utilities/VisItBridge/databases/CMakeFiles/vtkIOVisItBridge.dir/build.make:8485:
 recipe for target 'lib/libvtkIOVisItBridge-pv5.0.so.1' failed
make[2]: *** [lib/libvtkIOVisItBridge-pv5.0.so.1] Error 1
CMakeFiles/Makefile2:13468: recipe for target 
'Utilities/VisItBridge/databases/CMakeFiles/vtkIOVisItBridge.dir/all' failed
make[1]: *** 
[Utilities/VisItBridge/databases/CMakeFiles/vtkIOVisItBridge.dir/all] Error 2
Makefile:149: recipe for target 'all' failed
make: *** [all] Error 2


Any ideas how to fix this?
___
Powered by www.kitware.com

Visit other Kitware open-source projects at 
http://www.kitware.com/opensource/opensource.html

Please keep messages on-topic and check the ParaView Wiki at: 
http://paraview.org/Wiki/ParaView

Search the list archives at: http://markmail.org/search/?q=ParaView

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/paraview

Re: [Paraview] Catalyst: simulation steering during In-Situ visualization

2015-12-03 Thread Alexandre Ancel

Hello,

@Tim:
Thanks for the nice tips regarding to queue systems and signals on HPC
clusters, I wasn't aware of that. I'll look into it on our local cluster,
and we have a stop/restart method in our library, so it could work !

@Andy:
Indeed I was aware of the UserData member, I already used it in fact.
Do you have something specific in mind, when you say that there may be a
simple hack for the live connection to pass information from the GUI back
to Catalyst ? The main interest I see with using a plugin is to have
flexibility regarding what the user can provide to the simulation. He could
directly use the option format we define in the library and define those as
graphical elements in the plugin.
I'll definitely have at look at the code behind the Catalyst GUI, I guess
the answer is behind.
Thanks you !

Best regards,
Alexandre Ancel

On Wed, Dec 2, 2015 at 6:47 PM, Andy Bauer  wrote:

> Yes, it should be doable in ParaView through a plugin. The
> vtkCPDataDescription class has a UserData member that is a vtkFieldData
> pointer which can be used to pass information back and forth between the
> Catalyst pipelines and the adaptor. It's also Python wrapped so it's
> available in the Catalyst Python pipeline scripts as well. In the adaptor
> you would have to know how to process that data to your computational
> steering on the simulation side (i.e. take the Catalyst input). There may
> be a simple hack for the live connection to pass information from the GUI
> back to Catalyst in which case you might not even need a plugin. Otherwise,
> you should probably look at the code for the live connection (i.e. the
> stuff under the Catalyst GUI menu) to see how to pass other information
> back and forth between the GUI and Catalyst.
>
> On Wed, Dec 2, 2015 at 12:02 PM, Tim Gallagher 
> wrote:
>
>> Hi Alexandre,
>>
>> I don't know if this is possible or not with Catalyst, hopefully somebody
>> else comes along to answer that.
>>
>> But, we did this in our code using signal handling and POSIX signals (see
>> http://man7.org/linux/man-pages/man7/signal.7.html). We define 3
>> behaviors in our code -- reload the input file and change simulation
>> behavior accordingly; create a restart file at the next available chance
>> and keep running; create a restart file and exit immediately. We use
>> SIGUSR1 and SIGUSR2 for the first two options and then we use SIGTERM for
>> the last behavior. This is helpful because most queue systems on HPC
>> clusters will send SIGTERM 60 seconds before your wall-time is about to run
>> out, so catching that signal and using it to write a restart file and exit
>> means we always get our data right before our job runs out of time.
>>
>> Signals can be sent locally using `kill` or can be sent through PBS using
>> `qsig`. It works quite nicely.
>>
>> Tim
>>
>> --
>> *From: *"Alexandre Ancel" 
>> *To: *"paraview" 
>> *Sent: *Wednesday, December 2, 2015 11:47:59 AM
>> *Subject: *[Paraview] Catalyst: simulation steering during
>> In-Situvisualization
>>
>>
>> Hello,
>>
>> We are currently using Catalyst for In-Situ visualization in the context
>> of our finite element library and it is working very well.
>>
>> We would like to implement simulation steering while using Catalyst.
>> The idea would consist in having a ParaView plugin that we load in the
>> ParaView client. Within the code of this plugin, we would like to send data
>> to the simulation code to modify its behavior.
>>
>> First question: Is it possible to do so ?
>> Then, How would the whole process be run ?
>> The ideal scenario would be the following:
>> - Launch ParaView & connect to the distant pverver & enable Catalyst
>> - Load the plugin in ParaView
>> - Launch the simulation
>> - Receive data until timestep N then stop the simulation
>> - Send data to the simulation through the loaded plugin
>> - Continue with the simulation
>> Would it be possible to do so ? If yes, could you give me keypoints about
>> how to do this ?
>>
>> Thanks in advance for your answers,
>>
>> Best regards,
>> Alexandre Ancel
>>
>> --
>> Alexandre Ancel
>> Docteur, Ingénieur de recherche / Phd, Research Engineer
>> Cemosis  - alexandre.an...@cemosis.fr
>> Tel: +33 (0)3 68 8*5 02 06*
>> IRMA - 7, rue René Descartes
>> 67 000 Strasbourg, France
>>
>> ___
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Please keep messages on-topic and check the ParaView Wiki at:
>> http://paraview.org/Wiki/ParaView
>>
>> Search the list archives at: http://markmail.org/search/?q=ParaView
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/paraview
>>
>>
>> ___
>> Powered by www.kitware.com
>>
>>

Re: [Paraview] Paraview 4.4.0 - Plugin with a custom 3d widget

2015-12-03 Thread Cory Quammen

Andrzej,

I believe the ProxyGroup name for the widget should be set with



instead of



HTH,
Cory

On Thu, Dec 3, 2015 at 6:42 AM, Andrzej Peczak  wrote:

> Hi
>
> I am trying to customise a plugin with an implicit function widget. As an
> example I choose vtkPVBox class to check if I can register it under a
> different name. To do it I created a SM file as following, but the plugin
> seems not seeing the object I am registering. Can anybody explain how do I
> register my own widget ?
>
> Thanks
>
> Andrzej
>
> 
> 
>
>  name="TranslateFilter">
>  name="Input"
> panel_visibility="default">
> 
> 
> 
> 
> 
> 
> 
>  value="vtkRectilinearGrid" />
> 
> 
>  name="TranslateFilter"
> panel_visibility="default">
> 
> 
> 
> 
>  name="Translate3" />
> 
> 
> 
> 
> 
>
> 
>
> 
>  default_values="0 1 0 1 0 1" name="Bounds"
> number_of_elements="6">
> 
>  command="SetPosition"
> default_values="0.0 0.0 0.0"
> name="Position" number_of_elements="3">
> 
> 
>  command="SetRotation"
> default_values="0.0 0.0 0.0"
> name="Rotation" number_of_elements="3">
> 
> 
>  command="SetScale"
> default_values="1.0 1.0 1.0" name="Scale"
> number_of_elements="3">
> 
> 
> 
> 
> 
>  name="Position" />
>  name="Rotation" />
>  name="Scale" />
>  name="Bounds" />
> 
> 
> 
> 
>
>
> 
>  default_values="0.0 0.0 0.0"
> information_property="PositionInfo"
> label="Translate" name="Position" number_of_elements="3">
> 
> 
>  default_values="0.0 0.0 0.0" information_only="1"
> name="PositionInfo"
> number_of_elements="3" />
> 
> 
> 
> 
> 
> 
>
>
> 
> 
>
> 
>
> **
> Please consider the environment. Only print this email if absolutely
> necessary.
>
> This email contains information that is private and confidential and is
> intended only for the addressee.
> If you are not the intended recipient please delete it and notify us
> immediately by e-mailing the sender.
> Note: All email sent to or from this address may be accessed by someone
> other than the recipient, for
> system management and security reasons.
> Aircraft Research Association Ltd.  Registered in England, Registration No
> 503668 Registered Office:
> Manton Lane, Bedford MK41 7PF England VAT No GB 196351245
>
> **
> ___
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>



-- 
Cory Quammen
R Engineer
Kitware, Inc.
___
Powered by www.kitware.com

Visit other Kitware open-source projects at 
http://www.kitware.com/opensource/opensource.html

Please keep messages on-topic and check the ParaView Wiki at: 
http://paraview.org/Wiki/ParaView

Search the list archives at: http://markmail.org/search/?q=ParaView

Follow this link to

Re: [Paraview] Labels using mathtext notation

2015-12-03 Thread David Lonie

The bugfix is in master, see
https://gitlab.kitware.com/vtk/vtk/merge_requests/955.

Thanks again for the report!

On Tue, Dec 1, 2015 at 1:56 PM, David Lonie  wrote:

> Hi Steven,
>
> Thanks for the report. I've confirmed this issue and opened a bug for it:
> http://www.vtk.org/Bug/view.php?id=15859
>
> I'll try to have this fixed soon, but in the meantime, it looks like
> adding some whitespace between the $$ (e.g. "$x $") will workaround the bug.
>
> Thanks,
> Dave
>
> On Tue, Nov 24, 2015 at 12:19 PM, Hahn, Steven E.  wrote:
>
>> Hi,
>>
>> I am trying to generate a plot using ParaView v5.0.0-RC1 where the axes
>> contain mathtext labels. If the label is 2 or more characters long, then
>> everything is OK. If my label is one character only, it plots the $ signs.
>>
>> Here is a simple way to reproduce this issue:
>> - Use a sphere source.
>> - Show the axes
>> - Edit axes grid
>> - At the end of X Title string add ³$x$²
>> - At the end of Y Title string add ³$yy$²
>>
>> The X axis title is ³X Axis $x$². The Y axis title is ³Y Axis yy² where yy
>> is italic.
>>
>> Best,
>> Steven Hahn
>>
>> ___
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Please keep messages on-topic and check the ParaView Wiki at:
>> http://paraview.org/Wiki/ParaView
>>
>> Search the list archives at: http://markmail.org/search/?q=ParaView
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/paraview
>>
>
>
___
Powered by www.kitware.com

Visit other Kitware open-source projects at 
http://www.kitware.com/opensource/opensource.html

Please keep messages on-topic and check the ParaView Wiki at: 
http://paraview.org/Wiki/ParaView

Search the list archives at: http://markmail.org/search/?q=ParaView

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/paraview

Re: [Paraview] Paraview 4.4.0 - Plugin with a custom 3d widget

2015-12-03 Thread Andrzej Peczak

Cory

I had tried to place the widget in utilities.xml under  earlier without the success. The filter sees the 
standard Box but not MyBox.

Andrzej

From: Cory Quammen [mailto:cory.quam...@kitware.com] 
Sent: 03 December 2015 14:18
To: Andrzej Peczak
Cc: paraview@paraview.org
Subject: Re: [Paraview] Paraview 4.4.0 - Plugin with a custom 3d widget

Andrzej,

I believe the ProxyGroup name for the widget should be set with

instead of 

HTH,
Cory

On Thu, Dec 3, 2015 at 6:42 AM, Andrzej Peczak  wrote:
Hi

I am trying to customise a plugin with an implicit function widget. As an 
example I choose vtkPVBox class to check if I can register it under a different 
name. To do it I created a SM file as following, but the plugin seems not 
seeing the object I am registering. Can anybody explain how do I register my 
own widget ?

Thanks

Andrzej

**
Please consider the environment. Only print this email if absolutely necessary.

This email contains information that is private and confidential and is 
intended only for the addressee.
If you are not the intended recipient please delete it and notify us 
immediately by e-mailing the sender.
Note: All email sent to or from this address may be accessed by someone other 
than the recipient, for
system management and security reasons.
Aircraft Research Association Ltd.  Registered in England, Registration No 
503668 Registered Office:
Manton Lane, Bedford MK41 7PF England VAT No GB 196351245

**
___
Powered by www.kitware.com

Visit other Kitware open-source projects at 
http://www.kitware.com/opensource/opensource.html

Please keep messages on-topic and check the ParaView Wiki at: 
http://paraview.org/Wiki/ParaView

Search the list archives at: http://markmail.org/search/?q=ParaView

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/paraview

-- 
Cory Quammen
R Engineer
Kitware, Inc.

**
Please consider the environment. Only print this email if absolutely necessary.

This email contains information that is private and confidential and is 
intended only for the addressee.
If you are not the intended recipient please delete it and notify us 
immediately by e-mailing the sender.
Note: All email sent to or from this address may be accessed by someone other 
than the recipient, for
system management and security reasons.
Aircraft Research Association Ltd.  Registered in England, Registration No 
503668 Registered Office:
Manton Lane, Bedford MK41 7PF England VAT No GB 196351245

**
___
Powered by www.kitware.com

Visit other Kitware open-source projects at 
http://www.kitware.com/opensource/opensource.html

Please keep messages on-topic and check the ParaView Wiki at: 
http://paraview.org/Wiki/ParaView

Search the list archives at: http://markmail.org/search/?q=ParaView

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/paraview

[Paraview] Varying distance between threshold values plot over time in paraview

2015-12-03 Thread Saideep Pavuluri

Hi guys;

I would like to collect data of specific varying distance between two threshold 
values in paraview varying over time. How can I do that?
Using a ruler for each time step looks to be a tedious job.

Any suggestions..

thanks,
Saideep



- 
We invite research leaders and ambitious early career researchers to 
join us in leading and driving research in key inter-disciplinary themes. 
Please see www.hw.ac.uk/researchleaders for further information and how
to apply.

Heriot-Watt University is a Scottish charity
registered under charity number SC000278.

___
Powered by www.kitware.com

Visit other Kitware open-source projects at 
http://www.kitware.com/opensource/opensource.html

Please keep messages on-topic and check the ParaView Wiki at: 
http://paraview.org/Wiki/ParaView

Search the list archives at: http://markmail.org/search/?q=ParaView

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/paraview

[Paraview] Error while building, H5_SIZEOF_SIZE_T is undefined

2015-12-03 Thread Thomas Oliveira

Dear all,

When building paraview, master branch, commit
d00c2cfed216bd07122f8b38c41329c40b510b50, I get the error:
/opt/paraview/VTK/ThirdParty/hdf5/vtkhdf5/src/H5public.h:166:5: error:
#error "nothing appropriate for ssize_t"

The context of it is:

#if H5_SIZEOF_SSIZE_T==0
/* Undefine this size, we will re-define it in one of the sections below */
#undef H5_SIZEOF_SSIZE_T
#if H5_SIZEOF_SIZE_T==H5_SIZEOF_INT
#ifdef WIN32
#undef ssize_t
#endif
typedef int ssize_t;
#   define H5_SIZEOF_SSIZE_T H5_SIZEOF_INT
#elif H5_SIZEOF_SIZE_T==H5_SIZEOF_LONG
typedef long ssize_t;
#   define H5_SIZEOF_SSIZE_T H5_SIZEOF_LONG
#elif H5_SIZEOF_SIZE_T==H5_SIZEOF_LONG_LONG
typedef long long ssize_t;
#   define H5_SIZEOF_SSIZE_T H5_SIZEOF_LONG_LONG
#else /* Can't find matching type for ssize_t */
#   error "nothing appropriate for ssize_t"
#endif
#endif


Checking the value of some variables with  #pragma message, I verified that
at the beginning of this part, not only *H5_SIZEOF_SSIZE_T is undefined*, *but
also* *H5_SIZEOF_SIZE_T is undefined.*

I wasn't able to diagnose the problem further than that. Would you have any
suggestion? Is there some configuration of CMake that I am doing wrong?

Thank you for your attention,

Thomas Oliveira
___
Powered by www.kitware.com

Visit other Kitware open-source projects at 
http://www.kitware.com/opensource/opensource.html

Please keep messages on-topic and check the ParaView Wiki at: 
http://paraview.org/Wiki/ParaView

Search the list archives at: http://markmail.org/search/?q=ParaView

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/paraview

Re: [Paraview] Labels using mathtext notation

2015-12-03 Thread Hahn, Steven E.

Hi Dave,

Thank you for looking into and quickly fixing this issue. Will this bugfix be 
included in ParaView 5?

Best,
Steven

From: David Lonie >
Date: Thursday, December 3, 2015 at 9:14 AM
To: Steven Hahn >
Cc: "paraview@paraview.org" 
>
Subject: Re: [Paraview] Labels using mathtext notation

The bugfix is in master, see 
https://gitlab.kitware.com/vtk/vtk/merge_requests/955.

Thanks again for the report!

On Tue, Dec 1, 2015 at 1:56 PM, David Lonie 
> wrote:
Hi Steven,

Thanks for the report. I've confirmed this issue and opened a bug for it: 
http://www.vtk.org/Bug/view.php?id=15859

I'll try to have this fixed soon, but in the meantime, it looks like adding 
some whitespace between the $$ (e.g. "$x $") will workaround the bug.

Thanks,
Dave

On Tue, Nov 24, 2015 at 12:19 PM, Hahn, Steven E. 
> wrote:
Hi,

I am trying to generate a plot using ParaView v5.0.0-RC1 where the axes
contain mathtext labels. If the label is 2 or more characters long, then
everything is OK. If my label is one character only, it plots the $ signs.

Here is a simple way to reproduce this issue:
- Use a sphere source.
- Show the axes
- Edit axes grid
- At the end of X Title string add ³$x$²
- At the end of Y Title string add ³$yy$²

The X axis title is ³X Axis $x$². The Y axis title is ³Y Axis yy² where yy
is italic.

Best,
Steven Hahn

___
Powered by www.kitware.com

Visit other Kitware open-source projects at 
http://www.kitware.com/opensource/opensource.html

Please keep messages on-topic and check the ParaView Wiki at: 
http://paraview.org/Wiki/ParaView

Search the list archives at: http://markmail.org/search/?q=ParaView

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/paraview

___
Powered by www.kitware.com

Visit other Kitware open-source projects at 
http://www.kitware.com/opensource/opensource.html

Please keep messages on-topic and check the ParaView Wiki at: 
http://paraview.org/Wiki/ParaView

Search the list archives at: http://markmail.org/search/?q=ParaView

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/paraview

[Paraview] Can ParaView create "envelope" or cumulative maximums?

2015-12-03 Thread Scott, W Alan

I have a user that needs to create a new array, with each cell in the array 
holding the maximum value of each cell over all time.  I have heard this called 
a cumulative maximum for all cells.  The then wants to paint his 3d object with 
this new array.  For instance, if you have a variable array (maybe von mises 
stress), three cells and four timesteps, as follows:


Three cells:
0.0 0.0 0.0(Timestep 0)
1.0 0.0 0.0(Timestep 1)
2.0 1.0 0.0(Timestep 2)
1.0 3.0 1.0(Timestep 3)

Results, to be used to paint the object in a 3d view:
2.0 3.0 1.0(Result)


Does anyone know how to do this?  My user feels comfortable with Python and the 
Programmable filter/ Python Calculator.

Thanks,

Alan

___
Powered by www.kitware.com

Visit other Kitware open-source projects at 
http://www.kitware.com/opensource/opensource.html

Please keep messages on-topic and check the ParaView Wiki at: 
http://paraview.org/Wiki/ParaView

Search the list archives at: http://markmail.org/search/?q=ParaView

Follow this link to subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/paraview

[Paraview] Compiling 5.0.0-RC1 vit VisItBridge linking failure on Fedora 23

Re: [Paraview] Catalyst: simulation steering during In-Situ visualization

Re: [Paraview] Paraview 4.4.0 - Plugin with a custom 3d widget

Re: [Paraview] Labels using mathtext notation

Re: [Paraview] Paraview 4.4.0 - Plugin with a custom 3d widget

[Paraview] Varying distance between threshold values plot over time in paraview

[Paraview] Error while building, H5_SIZEOF_SIZE_T is undefined

Re: [Paraview] Labels using mathtext notation

[Paraview] Can ParaView create "envelope" or cumulative maximums?

9 matches

Site Navigation

Mail list logo

Footer information