date:20151019

Re: [Paraview] Select which fields to load when loading .vtm multi-block

2015-10-19 Thread Deij-van Rijswijk, Menno

For future reference, the request can be found here 
http://www.paraview.org/Bug/view.php?id=15789

Best wishes,


Menno Deij – van Rijswijk


From: Berk Geveci [mailto:berk.gev...@kitware.com]
Sent: dinsdag 22 september 2015 16:54
To: Deij-van Rijswijk, Menno
Cc: paraview@paraview.org
Subject: Re: [Paraview] Select which fields to load when loading .vtm 
multi-block

Hmmm. It doesn't look like there is support for array selection in that reader. 
We should add it... Can you make a feature request in the bug tracker?

Thanks,
-berk

On Tue, Sep 22, 2015 at 6:40 AM, Deij-van Rijswijk, Menno  
wrote:
Anyone?

From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Deij-van 
Rijswijk, Menno
Sent: vrijdag 18 september 2015 16:06
To: paraview@paraview.org
Subject: [Paraview] Select which fields to load when loading .vtm multi-block

Hi,

I noticed that when I load a .vtm file, I cannot select which data fields to 
load. This requires me to load the entire file into memory, after which the 
Pass Arrays filter allows me to take the required data field forward in the 
pipeline. If I load other formats (e.g. CGNS and .vtu) I can choose which field 
to load.

Maybe I’m missing something obvious? Should there be metadata on the fields in 
the vtm file that is missing?

Thanks and best wishes,


Menno Deij – van Rijswijk


dr. ir. Menno A. Deij-van Rijswijk
Researcher / Software Engineer

Maritime Simulation & Software Group



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Re: [Paraview] VTK Data File Scalars Analysis

2015-10-19 Thread Cory Quammen

VTK and ParaView have many reader classes. Did you have a particular format
in mind?If not, then I suggest to navigate to VTK/IO/ and look at the
source code contained therein.

HTH,
Cory



On Mon, Oct 19, 2015 at 10:02 AM, Guillermo Giraldo  wrote:

> Thanks, now it's clear.
>
> If I'd like to find the actual VTK file reading process, where in the
> repository should I look?
>
> El vie., 16 de oct. de 2015 a la(s) 4:12 p. m., Cory Quammen <
> cory.quam...@kitware.com> escribió:
>
>> Guillermo,
>>
>> vtkSplitColumnComponents assigns the names based on a guess that
>> 3-component arrays are vectors with X, Y, Z components and 6-component
>> arrays represent symmetric 3x3 matrices, i.e.
>>
>> XX XY XZ
>> XY YY YZ
>> XZ YZ ZZ
>>
>> See ParaView/ParaViewCore/VTKExtensions/Core/vtkPVPostFilter.cxx, lines
>> 147-174.
>>
>> HTH,
>> Cory
>>
>> On Fri, Oct 16, 2015 at 12:28 PM, Guillermo Giraldo <
>> guillegira...@gmail.com> wrote:
>>
>>> Hi,
>>>
>>> I'd like to know how Paraview analyses scalar data from a VTK data file.
>>> Specially, how it extracts the components of a scalar and assigns names for
>>> color plots. For example if numComp is 3 they are named "Magnitude, X, Y
>>> and Z2, but if numComp is 6 they are named "Magnitude, XX, YY; ZZ, XY, XZ
>>> and YZ". How is this determined?
>>>
>>> Some questions I'd like to answer are: can this be done with only the
>>> VTK library? If not, are there any other library that can do it (e.g.
>>> paraview python)?
>>>
>>> Pointing to the specific code file in the git repository should be
>>> enough, but an explanation would be great!
>>>
>>> Thanks in advance and greetings.
>>> --
>>> Por favor confirmar recepción.
>>>
>>> Atte.
>>>
>>> Guillermo E. Giraldo Fernandez
>>> Cel. 301 628 6730
>>> Colombia - Suramérica
>>>
>>> ___
>>> 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.
>>
> --
> Por favor confirmar recepción.
>
> Atte.
>
> Guillermo E. Giraldo Fernandez
> Cel. 301 628 6730
> Colombia - Suramérica
>



-- 
Cory Quammen
R Engineer
Kitware, Inc.
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Re: [Paraview] VTK Data File Scalars Analysis

2015-10-19 Thread Guillermo Giraldo

Thanks, now it's clear.

If I'd like to find the actual VTK file reading process, where in the
repository should I look?

El vie., 16 de oct. de 2015 a la(s) 4:12 p. m., Cory Quammen <
cory.quam...@kitware.com> escribió:

> Guillermo,
>
> vtkSplitColumnComponents assigns the names based on a guess that
> 3-component arrays are vectors with X, Y, Z components and 6-component
> arrays represent symmetric 3x3 matrices, i.e.
>
> XX XY XZ
> XY YY YZ
> XZ YZ ZZ
>
> See ParaView/ParaViewCore/VTKExtensions/Core/vtkPVPostFilter.cxx, lines
> 147-174.
>
> HTH,
> Cory
>
> On Fri, Oct 16, 2015 at 12:28 PM, Guillermo Giraldo <
> guillegira...@gmail.com> wrote:
>
>> Hi,
>>
>> I'd like to know how Paraview analyses scalar data from a VTK data file.
>> Specially, how it extracts the components of a scalar and assigns names for
>> color plots. For example if numComp is 3 they are named "Magnitude, X, Y
>> and Z2, but if numComp is 6 they are named "Magnitude, XX, YY; ZZ, XY, XZ
>> and YZ". How is this determined?
>>
>> Some questions I'd like to answer are: can this be done with only the VTK
>> library? If not, are there any other library that can do it (e.g. paraview
>> python)?
>>
>> Pointing to the specific code file in the git repository should be
>> enough, but an explanation would be great!
>>
>> Thanks in advance and greetings.
>> --
>> Por favor confirmar recepción.
>>
>> Atte.
>>
>> Guillermo E. Giraldo Fernandez
>> Cel. 301 628 6730
>> Colombia - Suramérica
>>
>> ___
>> 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.
>
-- 
Por favor confirmar recepción.

Atte.

Guillermo E. Giraldo Fernandez
Cel. 301 628 6730
Colombia - Suramérica
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Re: [Paraview] VTK Data File Scalars Analysis

2015-10-19 Thread Guillermo Giraldo

The VTK file format.

El lun., oct. 19, 2015 9:20 AM, Cory Quammen 
escribió:

> VTK and ParaView have many reader classes. Did you have a particular
> format in mind?If not, then I suggest to navigate to VTK/IO/ and look at
> the source code contained therein.
>
> HTH,
> Cory
>
>
>
> On Mon, Oct 19, 2015 at 10:02 AM, Guillermo Giraldo <
> guillegira...@gmail.com> wrote:
>
>> Thanks, now it's clear.
>>
>> If I'd like to find the actual VTK file reading process, where in the
>> repository should I look?
>>
>> El vie., 16 de oct. de 2015 a la(s) 4:12 p. m., Cory Quammen <
>> cory.quam...@kitware.com> escribió:
>>
>>> Guillermo,
>>>
>>> vtkSplitColumnComponents assigns the names based on a guess that
>>> 3-component arrays are vectors with X, Y, Z components and 6-component
>>> arrays represent symmetric 3x3 matrices, i.e.
>>>
>>> XX XY XZ
>>> XY YY YZ
>>> XZ YZ ZZ
>>>
>>> See ParaView/ParaViewCore/VTKExtensions/Core/vtkPVPostFilter.cxx, lines
>>> 147-174.
>>>
>>> HTH,
>>> Cory
>>>
>>> On Fri, Oct 16, 2015 at 12:28 PM, Guillermo Giraldo <
>>> guillegira...@gmail.com> wrote:
>>>
 Hi,

 I'd like to know how Paraview analyses scalar data from a VTK data
 file. Specially, how it extracts the components of a scalar and assigns
 names for color plots. For example if numComp is 3 they are named
 "Magnitude, X, Y and Z2, but if numComp is 6 they are named "Magnitude, XX,
 YY; ZZ, XY, XZ and YZ". How is this determined?

 Some questions I'd like to answer are: can this be done with only the
 VTK library? If not, are there any other library that can do it (e.g.
 paraview python)?

 Pointing to the specific code file in the git repository should be
 enough, but an explanation would be great!

 Thanks in advance and greetings.
 --
 Por favor confirmar recepción.

 Atte.

 Guillermo E. Giraldo Fernandez
 Cel. 301 628 6730
 Colombia - Suramérica

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>>>
>>>
>>> --
>>> Cory Quammen
>>> R Engineer
>>> Kitware, Inc.
>>>
>> --
>> Por favor confirmar recepción.
>>
>> Atte.
>>
>> Guillermo E. Giraldo Fernandez
>> Cel. 301 628 6730
>> Colombia - Suramérica
>>
>
>
>
> --
> Cory Quammen
> R Engineer
> Kitware, Inc.
>
-- 
Por favor confirmar recepción.

Atte.

Guillermo E. Giraldo Fernandez
Cel. 301 628 6730
Colombia - Suramérica
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Re: [Paraview] VTK Data File Scalars Analysis

2015-10-19 Thread Guillermo Giraldo

Thanks, very much.

El lun., oct. 19, 2015 9:40 AM, Cory Quammen 
escribió:

> VTK/IO/Legacy contains the various VTK file readers.
>
> On Mon, Oct 19, 2015 at 10:33 AM, Guillermo Giraldo <
> guillegira...@gmail.com> wrote:
>
>> The VTK file format.
>>
>> El lun., oct. 19, 2015 9:20 AM, Cory Quammen 
>> escribió:
>>
>>> VTK and ParaView have many reader classes. Did you have a particular
>>> format in mind?If not, then I suggest to navigate to VTK/IO/ and look at
>>> the source code contained therein.
>>>
>>> HTH,
>>> Cory
>>>
>>>
>>>
>>> On Mon, Oct 19, 2015 at 10:02 AM, Guillermo Giraldo <
>>> guillegira...@gmail.com> wrote:
>>>
 Thanks, now it's clear.

 If I'd like to find the actual VTK file reading process, where in the
 repository should I look?

 El vie., 16 de oct. de 2015 a la(s) 4:12 p. m., Cory Quammen <
 cory.quam...@kitware.com> escribió:

> Guillermo,
>
> vtkSplitColumnComponents assigns the names based on a guess that
> 3-component arrays are vectors with X, Y, Z components and 6-component
> arrays represent symmetric 3x3 matrices, i.e.
>
> XX XY XZ
> XY YY YZ
> XZ YZ ZZ
>
> See ParaView/ParaViewCore/VTKExtensions/Core/vtkPVPostFilter.cxx,
> lines 147-174.
>
> HTH,
> Cory
>
> On Fri, Oct 16, 2015 at 12:28 PM, Guillermo Giraldo <
> guillegira...@gmail.com> wrote:
>
>> Hi,
>>
>> I'd like to know how Paraview analyses scalar data from a VTK data
>> file. Specially, how it extracts the components of a scalar and assigns
>> names for color plots. For example if numComp is 3 they are named
>> "Magnitude, X, Y and Z2, but if numComp is 6 they are named "Magnitude, 
>> XX,
>> YY; ZZ, XY, XZ and YZ". How is this determined?
>>
>> Some questions I'd like to answer are: can this be done with only the
>> VTK library? If not, are there any other library that can do it (e.g.
>> paraview python)?
>>
>> Pointing to the specific code file in the git repository should be
>> enough, but an explanation would be great!
>>
>> Thanks in advance and greetings.
>> --
>> Por favor confirmar recepción.
>>
>> Atte.
>>
>> Guillermo E. Giraldo Fernandez
>> Cel. 301 628 6730
>> Colombia - Suramérica
>>
>> ___
>> 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.
>
 --
 Por favor confirmar recepción.

 Atte.

 Guillermo E. Giraldo Fernandez
 Cel. 301 628 6730
 Colombia - Suramérica

>>>
>>>
>>>
>>> --
>>> Cory Quammen
>>> R Engineer
>>> Kitware, Inc.
>>>
>> --
>> Por favor confirmar recepción.
>>
>> Atte.
>>
>> Guillermo E. Giraldo Fernandez
>> Cel. 301 628 6730
>> Colombia - Suramérica
>>
>
>
>
> --
> Cory Quammen
> R Engineer
> Kitware, Inc.
>
-- 
Por favor confirmar recepción.

Atte.

Guillermo E. Giraldo Fernandez
Cel. 301 628 6730
Colombia - Suramérica
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Re: [Paraview] Paraview 4.1.0: Tube filter vary radius by vector or scalar does not work properly

2015-10-19 Thread Cory Quammen

Hi Jens,

I can't think of a way to do this easily in ParaView using existing
filters. Your best bet is probably to write the scaled tube geometry to
your VTK file directly and visualize that.

Sorry to not be of more help,
Cory

On Thu, Oct 15, 2015 at 10:29 AM, Jens Laube 
wrote:

> Dear Paraview users,
>
> I am using the paraview version 4.1.0 to display forces between
> nanoparticles from a Discrete Element simulation. For the visualization I
> create vtk-files that look like the following minimal example:
>
>
> *# vtk DataFile Version 2.0*
> *Generated by lpp.py*
> *ASCII*
> *DATASET POLYDATA*
> *POINTS 2 float*
> *0.0 0.0 0.0*
> *0.0 0.0 2e-09*
> *LINES 1 3*
> *2 0 1*
>
> *CELL_DATA 1*
> *VECTORS f_pair float*
> *0.0 0.0 -2.12063e-08*
> *SCALARS f_tot float 1*
> *LOOKUP_TABLE default*
> *2.12063e-08*
>
> *POINT_DATA 2*
> *VECTORS i float*
> *0.0 0.0 0.0*
> *0.0 0.0 0.0*
> *VECTORS f float*
> *0.0 0.0 0.0*
> *0.0 0.0 0.0*
> *VECTORS omega float*
> *0.0 0.0 0.0*
> *0.0 0.0 0.0*
> *VECTORS v float*
> *0.0 0.0 0.0*
> *0.0 0.0 -0.4*
> *SCALARS radius float 1*
> *LOOKUP_TABLE default*
> *1.53e-09*
> *1.53e-09*
> *SCALARS type float 1*
> *LOOKUP_TABLE default*
> *1.0*
> *1.0*
> *SCALARS id float 1*
> *LOOKUP_TABLE default*
> *1.0*
> *2.0*
>
>
> The lines defined in this file connect the particle centers and the
> CELL_DATA VECTORS and SCALARS represent the interparticle force vector and
> the absolute force respectively.
> With this file I try to visualize the force by a tube with varying radius
> and color depending on the magnitude of the vorce vector using paraview
> 4.1.0. To this aim I use the Filters "CellDatatoPointData"-->"Tube". In the
> scalars and Vectors field of the "Tube"-filter I can choose the variables "
> *f_tot*" and "f_pair" from the vtk-file, but if I try to scale the radius
> by vector, there is no visible variation of the radius independent of the
> values in "Radius" and "Radius Factor". The only way to receive a varying
> radius is choosing the option "Vary radius By Absolute Scalar" but then I
> cannot manipulate the minimum and maximum thickness of the tube by using
> the values of "Radius" and "Radius Factor". Thus I receive a too large tube.
> Do I miss something basic here? Could anyone give me a hint how to
> customize the visualization properly?
> Thanks a lot
>
> Best Whishes
> Jens Laube
>
>
> --
> Dipl.-Ing. Jens Laube
> Hybrid Materials Interfaces Group
> Universität Bremen
> Am Fallturm 1, D-28359 Bremen
> Tel.   +49 421 218 64574
> Fax+49 421 218 64599jla...@hmi.uni-bremen.dewww.hmi.uni-bremen.de
>
>
> ___
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> Please keep messages on-topic and check the ParaView Wiki at:
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-- 
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Kitware, Inc.
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Re: [Paraview] VTK Data File Scalars Analysis

2015-10-19 Thread Cory Quammen

VTK/IO/Legacy contains the various VTK file readers.

On Mon, Oct 19, 2015 at 10:33 AM, Guillermo Giraldo  wrote:

> The VTK file format.
>
> El lun., oct. 19, 2015 9:20 AM, Cory Quammen 
> escribió:
>
>> VTK and ParaView have many reader classes. Did you have a particular
>> format in mind?If not, then I suggest to navigate to VTK/IO/ and look at
>> the source code contained therein.
>>
>> HTH,
>> Cory
>>
>>
>>
>> On Mon, Oct 19, 2015 at 10:02 AM, Guillermo Giraldo <
>> guillegira...@gmail.com> wrote:
>>
>>> Thanks, now it's clear.
>>>
>>> If I'd like to find the actual VTK file reading process, where in the
>>> repository should I look?
>>>
>>> El vie., 16 de oct. de 2015 a la(s) 4:12 p. m., Cory Quammen <
>>> cory.quam...@kitware.com> escribió:
>>>
 Guillermo,

 vtkSplitColumnComponents assigns the names based on a guess that
 3-component arrays are vectors with X, Y, Z components and 6-component
 arrays represent symmetric 3x3 matrices, i.e.

 XX XY XZ
 XY YY YZ
 XZ YZ ZZ

 See ParaView/ParaViewCore/VTKExtensions/Core/vtkPVPostFilter.cxx, lines
 147-174.

 HTH,
 Cory

 On Fri, Oct 16, 2015 at 12:28 PM, Guillermo Giraldo <
 guillegira...@gmail.com> wrote:

> Hi,
>
> I'd like to know how Paraview analyses scalar data from a VTK data
> file. Specially, how it extracts the components of a scalar and assigns
> names for color plots. For example if numComp is 3 they are named
> "Magnitude, X, Y and Z2, but if numComp is 6 they are named "Magnitude, 
> XX,
> YY; ZZ, XY, XZ and YZ". How is this determined?
>
> Some questions I'd like to answer are: can this be done with only the
> VTK library? If not, are there any other library that can do it (e.g.
> paraview python)?
>
> Pointing to the specific code file in the git repository should be
> enough, but an explanation would be great!
>
> Thanks in advance and greetings.
> --
> Por favor confirmar recepción.
>
> Atte.
>
> Guillermo E. Giraldo Fernandez
> Cel. 301 628 6730
> Colombia - Suramérica
>
> ___
> 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.

>>> --
>>> Por favor confirmar recepción.
>>>
>>> Atte.
>>>
>>> Guillermo E. Giraldo Fernandez
>>> Cel. 301 628 6730
>>> Colombia - Suramérica
>>>
>>
>>
>>
>> --
>> Cory Quammen
>> R Engineer
>> Kitware, Inc.
>>
> --
> Por favor confirmar recepción.
>
> Atte.
>
> Guillermo E. Giraldo Fernandez
> Cel. 301 628 6730
> Colombia - Suramérica
>



-- 
Cory Quammen
R Engineer
Kitware, Inc.
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Re: [Paraview] About ParaView catalyst

2015-10-19 Thread Andy Bauer

Hi Jun,

I'm a bit confused. Do you mean Cetus at Argonne? Also, are you talking
about the Intel compilers or the IBM XL compilers? I'm not familiar with
any Intel XL compilers.

Assuming that you're talking about the IBM XL compilers on a BG/Q, I know
that there were some issues with that but they may have been resolved in
the ParaView superbuild (http://www.paraview.org/Wiki/ParaView/Superbuild),
which includes Catalyst. If you try it out and have issues though, please
email the mailing list so that we can try and fix them.

FYI: ParaView has also been built with the Intel compilers on many
platforms but I'm not sure about a BG/Q.

Regards,
Andy

On Mon, Oct 19, 2015 at 3:54 PM, Jun Fang  wrote:

> Hello,
>
> Here I have some questions about the in-situ library support. Does anyone
> know if the ParaView catalyst is now supported by Intel XL compilers or
> not? Based on my recent scaling test on INL Cetus, the XL compilers are
> almost twice efficient compared to the GNU compilers for the identical
> source codes, compilation flags (-O2), simulation case set-up (16,385
> cores) and input parameters. Therefore, it becomes a tough decision for me
> to choose either "GNU+in-situ capability" or "XL without in-situ". The
> perfect situation is that XL compilers can also support insitu
> visualization (i.e. ParaView catalyst), but I am not sure about that.
>
> Thanks a lot,
> Jun
>
> --
> Jun Fang
> Department of Nuclear Engineering
> North Carolina State University
> Phone: (919) 592-2233
>
> ___
> 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
>
>
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Re: [Paraview] About ParaView catalyst

2015-10-19 Thread David E DeMarle

Back in the day, with bluegene-P I was able to get ParaView compiled with
xlc working so it should be possible. (And before that others did it on
BGL.) However - I struggled with xl compilers on the mira@anl installs for
several days (see the dreaded -mminimal-toc error below). Despite great
help from the alcf support guys, and trying many many things, I eventually
gave up and went with the gnu compilers. But ... sometime after those few
terrible days that I do not care to repeat, Todd Gamblin at llnl
contributed a BGQ platform file to CMake. With that and latest cmake, there
is some hope that the xlc compile will just work.

/bgsys/drivers/ppcfloor/gnu-linux/powerpc64-bgq-linux/bin/ld:
/bgsys/drivers/V1R2M0/ppc64/comm/sys/lib/libpami.a(component-pami--CAPI.cnk.o)(.text._ZNSt8_Rb_treeIjSt4pairIKjjESt10_Select1stIS2_ESt4lessIjESaIS2_EE8_M_eraseEPSt13_Rb_tree_nodeIS2_E[_ZNSt8_Rb_treeIjSt4pairIKjjESt10_Select1stIS2_ESt4lessIjESaIS2_EE8_M_eraseEPSt13_Rb_tree_nodeIS2_E]+0xbc):
sibling call optimization to
`_ZNSt8_Rb_treeIjSt4pairIKjjESt10_Select1stIS2_ESt4lessIjESaIS2_EE8_M_eraseEPSt13_Rb_tree_nodeIS2_E'
does not allow automatic multiple TOCs; recompile with -mminimal-toc or
-fno-optimize-sibling-calls, or make
`_ZNSt8_Rb_treeIjSt4pairIKjjESt10_Select1stIS2_ESt4lessIjESaIS2_EE8_M_eraseEPSt13_Rb_tree_nodeIS2_E'
extern



David E DeMarle
Kitware, Inc.
R Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909

On Mon, Oct 19, 2015 at 5:13 PM, Andy Bauer  wrote:

> Hi Jun,
>
> I'm a bit confused. Do you mean Cetus at Argonne? Also, are you talking
> about the Intel compilers or the IBM XL compilers? I'm not familiar with
> any Intel XL compilers.
>
> Assuming that you're talking about the IBM XL compilers on a BG/Q, I know
> that there were some issues with that but they may have been resolved in
> the ParaView superbuild (http://www.paraview.org/Wiki/ParaView/Superbuild),
> which includes Catalyst. If you try it out and have issues though, please
> email the mailing list so that we can try and fix them.
>
> FYI: ParaView has also been built with the Intel compilers on many
> platforms but I'm not sure about a BG/Q.
>
> Regards,
> Andy
>
> On Mon, Oct 19, 2015 at 3:54 PM, Jun Fang  wrote:
>
>> Hello,
>>
>> Here I have some questions about the in-situ library support. Does anyone
>> know if the ParaView catalyst is now supported by Intel XL compilers or
>> not? Based on my recent scaling test on INL Cetus, the XL compilers are
>> almost twice efficient compared to the GNU compilers for the identical
>> source codes, compilation flags (-O2), simulation case set-up (16,385
>> cores) and input parameters. Therefore, it becomes a tough decision for me
>> to choose either "GNU+in-situ capability" or "XL without in-situ". The
>> perfect situation is that XL compilers can also support insitu
>> visualization (i.e. ParaView catalyst), but I am not sure about that.
>>
>> Thanks a lot,
>> Jun
>>
>> --
>> Jun Fang
>> Department of Nuclear Engineering
>> North Carolina State University
>> Phone: (919) 592-2233
>>
>> ___
>> 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
>
>
___
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Re: [Paraview] About ParaView catalyst

2015-10-19 Thread Jun Fang

Hi Andy,

Thank you so much for the prompt reply and the corrections. Yes, you are
totally right, I made some stupid typos and mistakes. Cetus is a BG/Q HPC
machine at Argonne National Lab for small test cases (along with Mira for
production runs). The XL compiler I mentioned is from IBM, not Intel.

I will check the link you sent and see if I can resolve the compatibility
issue b/w XL compilers and catalyst.

Again, thank you so much.
Jun

On Mon, Oct 19, 2015 at 5:13 PM, Andy Bauer  wrote:

> Hi Jun,
>
> I'm a bit confused. Do you mean Cetus at Argonne? Also, are you talking
> about the Intel compilers or the IBM XL compilers? I'm not familiar with
> any Intel XL compilers.
>
> Assuming that you're talking about the IBM XL compilers on a BG/Q, I know
> that there were some issues with that but they may have been resolved in
> the ParaView superbuild (http://www.paraview.org/Wiki/ParaView/Superbuild),
> which includes Catalyst. If you try it out and have issues though, please
> email the mailing list so that we can try and fix them.
>
> FYI: ParaView has also been built with the Intel compilers on many
> platforms but I'm not sure about a BG/Q.
>
> Regards,
> Andy
>
> On Mon, Oct 19, 2015 at 3:54 PM, Jun Fang  wrote:
>
>> Hello,
>>
>> Here I have some questions about the in-situ library support. Does anyone
>> know if the ParaView catalyst is now supported by Intel XL compilers or
>> not? Based on my recent scaling test on INL Cetus, the XL compilers are
>> almost twice efficient compared to the GNU compilers for the identical
>> source codes, compilation flags (-O2), simulation case set-up (16,385
>> cores) and input parameters. Therefore, it becomes a tough decision for me
>> to choose either "GNU+in-situ capability" or "XL without in-situ". The
>> perfect situation is that XL compilers can also support insitu
>> visualization (i.e. ParaView catalyst), but I am not sure about that.
>>
>> Thanks a lot,
>> Jun
>>
>> --
>> Jun Fang
>> Department of Nuclear Engineering
>> North Carolina State University
>> Phone: (919) 592-2233
>>
>> ___
>> 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
>>
>>
>


-- 
Jun Fang
Department of Nuclear Engineering
North Carolina State University
Phone: (919) 592-2233
___
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[Paraview] segmentation fault with netCDF when loading state file

2015-10-19 Thread Ryan Abernathey

Hello,

I am extremely frustrated and stuck on this problem. Any advice would be
appreciated.

I am working with a dataset of 2400 sequentially numbered netCDF files
(generic & CF conventions).

In a fresh pipeline, Paraview is able to recognizes these files as a single
source and load them correctly. I then create a standard pipeline involving
various filters (contour, etc., nothing funny) and save a state file.

When I attempt to load the state file, I get the following segmentation
fault. Further down you can see a ncdump of the offending file.

Would appreciate any advice on how to debug / overcome this issue. Is it a
bug? It sure feels like one...

Best,
Ryan Abernathey


ERROR: In
/home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/IO/NetCDF/vtkNetCDFReader.cxx,
line 822
vtkNetCDFCFReader (0x55c0620): netCDF Error: NetCDF: Index exceeds
dimension bound


ERROR: In
/home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx,
line 784
vtkPVCompositeDataPipeline (0x5be23d0): Algorithm
vtkFileSeriesReader(0x4c0c3e0) returned failure for request: vtkInformation
(0x8141700)
  Debug: Off
  Modified Time: 05
  Reference Count: 1
  Registered Events: (none)
  Request: REQUEST_DATA
  FORWARD_DIRECTION: 0
  FROM_OUTPUT_PORT: 0
  ALGORITHM_AFTER_FORWARD: 1




ERROR: In
/home/kitware/Dashboards/MyTests/NightlyMaster/ParaViewSuperbuild-Release/paraview/src/paraview/VTK/Common/ExecutionModel/vtkExecutive.cxx,
line 784
vtkCompositeDataPipeline (0x744fde0): Algorithm
vtkPVGeometryFilter(0x7436500) returned failure for request: vtkInformation
(0x5737250)
  Debug: Off
  Modified Time: 43
  Reference Count: 1
  Registered Events: (none)
  Request: REQUEST_DATA_OBJECT
  FORWARD_DIRECTION: 0
  FROM_OUTPUT_PORT: 0
  ALGORITHM_AFTER_FORWARD: 1




Segmentation fault (core dumped)






$ ncdump -h rce_rrtm303x512dx3f20_512x512x64_3km_12s_128_000300.nc
netcdf rce_rrtm303x512dx3f20_512x512x64_3km_12s_128_000300 {
dimensions:
x = 512 ;
y = 512 ;
z = 64 ;
time = UNLIMITED ; // (1 currently)
variables:
float x(x) ;
x:units = "m" ;
float y(y) ;
y:units = "m" ;
float z(z) ;
z:units = "m" ;
z:long_name = "height" ;
float time(time) ;
time:units = "d" ;
time:long_name = "time" ;
float p(z) ;
p:units = "mb" ;
p:long_name = "pressure" ;
float zi(z) ;
zi:units = "m" ;
zi:long_name = "intfc_ht" ;
float U(time, z, y, x) ;
U:long_name = "X Wind
Component" ;
U:units = "m/s   " ;
float V(time, z, y, x) ;
V:long_name = "Y Wind
Component" ;
V:units = "m/s   " ;
float W(time, z, y, x) ;
W:long_name = "Z Wind
Component" ;
W:units = "m/s   " ;
float PP(time, z, y, x) ;
PP:long_name = "Pressure
Perturbation   " ;
PP:units = "Pa" ;
float QRAD(time, z, y, x) ;
QRAD:long_name = "Radiative heating
rate  " ;
QRAD:units = "K/day " ;
float TABS(time, z, y, x) ;
TABS:long_name = "Absolute
Temperature" ;
TABS:units = "K " ;
float QV(time, z, y, x) ;
QV:long_name = "Water
Vapor "
;
QV:units = "g/kg  " ;
float QN(time, z, y, x) ;
QN:long_name = "Non-precipitating Condensate
(Water+Ice)" ;
QN:units = "g/kg  " ;
float QP(time, z, y, x) ;
QP:long_name = "Precipitating Water
(Rain+Snow) " ;
QP:units = "g/kg  " ;
float LQRAD(time, z, y, x) ;
LQRAD:long_name = "LW Radiative heating
rate   " ;
LQRAD:units = "K/day " ;
float SQRAD(time, z, y, x) ;
SQRAD:long_name = "SW Radiative heating
rate   " ;
SQRAD:units = "K/day " ;
}
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Re: [Paraview] ParaView Environment Variables

2015-10-19 Thread Cory Quammen

Hi Bill,

This is a good project. Perhaps we can include a version of your man page
in the user's guide when it is finished?

I know about some of these environment variables:

- PARAVIEW_DATA_ROOT - used to point ParaView to a testing data repository.
This is really only used when ParaView's tests are run and likely isn't
useful to users.

- PV_NO_OFFSCREEN_SCREENSHOTS - just what it sounds like. If set, offscreen
rendering will not be used for generating screenshots, even if the ParaView
settings say that offscreen rendering should be used for generating
screenshots.

- VTK_AUTOLOAD_PATH - users shouldn't need to set this. From the
vtkObjectFactory documentation: "The first time CreateInstance is called,
all dll's or shared libraries in the environment variable VTK_AUTOLOAD_PATH
are loaded into the current process."

- VTK_RENDERER - this looks like a historical way to choose which render
window to instantiate. It doesn't look like it is used anymore.

- PV_DEBUG_LEAKS_VIEW - enables a window that shows the number of instances
of all VTK classes. Useful for debugging, not really useful for users.

-PV_DEBUG_TEST - I don't see this in the ParaView source anywhere

- PV_SETTINGS_DEBUG - turns on debugging message related to loading
ParaView's settings files, e.g., where it looked for the settings file.

- PV_PLUGIN_DEBUG - print debugging output having to do with where ParaView
looks for plugins.

- PV_PLUGIN_PATH - adds search path for plugins

- VTK_MATPLOTLIB_DEBUG - Enable verbose debugging output during
initialization of matplotlib.

Hope that helps,
Cory

On Thu, Oct 15, 2015 at 4:58 PM, Bill Sherman  wrote:

> Hello all,
>
> Perhaps an odd question -- I'm wondering what important environment
> variables are associated with ParaView, and in some cases what they
> do.
>
> I ask because for an installation of ParaView on an HPC system, I
> am creating a traditional man-page.  And one of the traditional
> sections of man pages for applications is "ENVIRONMENT VARIABLES".
>
> I happened to find that NERSC had previously done a similar thing,
> but based on the command line arguments as well as the environment
> variables it gives no longer in existence, it would seem that this
> is from a rather old version of ParaView, so I'm basically starting
> from scratch.
>
> Searching through the source for "getenv", I found several refernces
> to environment variables, and I'd like to get advice on what should/
> should not be included.
>
> So there are a couple of categories the environment variables can
> be classified as.
>
> 1) ParaView specific variables:
> - PV_ICET_WINDOW_BORDERS
> - PARAVIEW_DATA_ROOT
> - PV_NO_OFFSCREEN_SCREENSHOTS
>
> So I know what the first of those does, and I had an assumption of
> what the second one (PARAVIEW_DATA_ROOT) does -- but I couldn't find
> a way to make it have an effect!  And I can half-guess what the third
> one does -- explanations welcome.
>
>
> 2) VTK related variables:
> - VTK_AUTOLOAD_PATH
> - VTK_RENDERER
>
> And I don't really know what either of them do.
>
>
> 3) Generic environment variables that ParaView accesses:
> - DISPLAY
> - HOME
> - HOSTNAME
> - LOGNAME
> - PATH
> - LD_LIBRARY_PATH
> - PWD (VTK/Utilities/KWSys/vtksys/SystemTools.cxx)
> - PYTHONPATH
> - TCL_LIBRARY (vtkTclUtil.cxx)
> - TK_LIBRARY (vtkTclUtil.cxx)
> - R_HOME (vtkRInterface.cxx)
> - COLUMNS (VTK/Utilities/KWSys/vtksys/SystemTools.cxx)
> - APPDATA -- for MS-Windows only?
> - COMMON_APPDATA -- for MS-Windows only?
>
> So I don't know that I'd need to include those as part of a ParaView
> man-page.
>
>
> 4) Other variables that are probably just for internal testing:
> - PV_DEBUG_LEAKS_VIEW
> - PV_DEBUG_TEST
> - PV_SETTINGS_DEBUG
> - PV_PLUGIN_DEBUG
> - PV_PLUGIN_PATH
> - DASHBOARD_TEST_FROM_CTEST
> - DART_TEST_FROM_DART
> - VERBOSE_TESTING (Exodus)
> - VERY_VERBOSE_TESTING (Exodus)
> - FLIP_CAM_MANIP (Interactor Style Unicam)
> - VTK_MATPLOTLIB_DEBUG (vtkMatplotlibMathTextUtilities.cxx)
> - QT_MAC_NO_NATIVE_MENUBAR
> (ThirdParty/QtTesting/vtkqttesting/pqTestUtility.cxx)
>
> Again, probably wouldn't include these in a man-page, unless they are
> something the end-user could possibly want to affect.
>
>
> Happy to share the man-page when I'm done.
>
> Thanks,
> Bill
>
> --
> Bill Sherman
> Sr. Technology Advisor
> Advanced Visualization Lab
> Pervasive Technology Inst
> Indiana University
> sherm...@indiana.edu
> ___
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>
> Visit other Kitware open-source projects at
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> Search the list

[Paraview] About ParaView catalyst

2015-10-19 Thread Jun Fang

Hello,

Here I have some questions about the in-situ library support. Does anyone
know if the ParaView catalyst is now supported by Intel XL compilers or
not? Based on my recent scaling test on INL Cetus, the XL compilers are
almost twice efficient compared to the GNU compilers for the identical
source codes, compilation flags (-O2), simulation case set-up (16,385
cores) and input parameters. Therefore, it becomes a tough decision for me
to choose either "GNU+in-situ capability" or "XL without in-situ". The
perfect situation is that XL compilers can also support insitu
visualization (i.e. ParaView catalyst), but I am not sure about that.

Thanks a lot,
Jun

-- 
Jun Fang
Department of Nuclear Engineering
North Carolina State University
Phone: (919) 592-2233
___
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Re: [Paraview] Select which fields to load when loading .vtm multi-block

Re: [Paraview] VTK Data File Scalars Analysis

Re: [Paraview] VTK Data File Scalars Analysis

Re: [Paraview] VTK Data File Scalars Analysis

Re: [Paraview] VTK Data File Scalars Analysis

Re: [Paraview] Paraview 4.1.0: Tube filter vary radius by vector or scalar does not work properly

Re: [Paraview] VTK Data File Scalars Analysis

Re: [Paraview] About ParaView catalyst

Re: [Paraview] About ParaView catalyst

Re: [Paraview] About ParaView catalyst

[Paraview] segmentation fault with netCDF when loading state file

Re: [Paraview] ParaView Environment Variables

[Paraview] About ParaView catalyst

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