date:20161122

Re: [Paraview] Warning Exporting VRML Files

2016-11-22 Thread Utkarsh Ayachit

Leo,

I can certainly reproduce the issue. I'll try to track it down tomorrow and
get back to you.

Utkarsh

On Tue, Nov 22, 2016 at 3:56 PM, Léo Pessanha 
wrote:

> Hi!
>
> After version 5.0 of paraview for Windows x64 everytime I export a Scene
> in VRML format I get the warning
>
> Warning: In 
> C:\bbd\df0abce0\source-paraview\VTK\Filters\Geometry\vtkDataSetSurfaceFilter.cxx,
>> line 166
>> vtkDataSetSurfaceFilter (01A2CFB3E6E0): Number of cells is zero, no
>> data to process.
>
>
> It happens with any data, even a Box from Source.
>
> The data seems to be exported correctly though.
>
> Is that a bug?
>
> Can anyone help me turning it off? My macros won't work because of that.
>
> Thanks in advance!
>
> Leonardo Pessanha
> COPPE/UFRJ
>
>
>
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Re: [Paraview] RAW (binary) file import issues

2016-11-22 Thread Ken Martin

I believe Visual studio 2010 does not properly handle file seeks/etc beyond
32 bit even on 64 bit builds. If you are using VS 2010 or earlier that is
possibly the issue. I believe it is fixed in VS 2013 and later.

On Tue, Nov 22, 2016 at 5:11 PM, Moreland, Kenneth 
wrote:

> Although we have certainly run into issues with communicating large
> messages, I’m not sure this is the issue with MPI-I/O. File sizes and
> linear offsets use a type MPI_Offset, which according to the specification
> should be large enough to hold the size of any file supported by the file
> system. Although it is true that creating the 3D subarray uses 32-bit
> indices, those are for each of the separate dimensions, and 2000 falls well
> below that limit.
>
>
>
> Besides, it looks like that error happens when checking an ifstream
> object, so it looks like the reader is bypassing the MPI-I/O path anyway.
>
>
>
> I would follow Berk’s suggesting of looking into the filesystem before
> diving into the guts of MPI-I/O.
>
>
>
> -Ken
>
>
>
> *From:* ParaView [mailto:paraview-boun...@paraview.org] *On Behalf Of *Burlen
> Loring
> *Sent:* Tuesday, November 22, 2016 12:55 PM
> *To:* Geveci, Berk (External Contact) ; Keyes
> S.D. 
> *Cc:* paraview@paraview.org
> *Subject:* [EXTERNAL] Re: [Paraview] RAW (binary) file import issues
>
>
>
> I've hit that before. the RAW reader uses MPI-I/O, and MPI uses signed int
> everywhere in its API, so there are limits that you end up hitting. For
> instance to partition the data among processors one must give MPI-I/O the
> starting offset of the data in the file as a signed int, and that is
> limited to 2^31.
>
> Burlen
>
> On 11/22/2016 11:20 AM, Berk Geveci wrote:
>
> Hmmm that happens to be around 4 GB which makes me wonder if there is a
> limit somewhere in that reader... Any chance you can try this on a Linux
> machine?
>
>
>
> On Thu, Nov 17, 2016 at 10:30 AM, Keyes S.D. 
> wrote:
>
> Dear all,
>
> I am encountering issues when trying to import large 8 bit RAW volumes to
> Paraview 5.1.2 (64 bit).
>
> The file I wish to import has xyz dimensions of 2000x2000x1920 voxels
> (Unsigned char), 7.5GB.  I am running a machine with 192 GB RAM and 12 CPU
> cores.
>
> I can import up to a 2000x2000x1000 crop of this file, but I encounter the
> following message when I attempt larger z dimensions:
>
> ERROR: In C:\bbd\df0abce0\source-paraview\VTK\IO\Image\vtkImageReader2.cxx,
> line 592
>
> vtkPVImageReader (07767F90): Initialize: Could not open file
> \\cseg_2\ERC\SLS_201606\Myco_2\CT2PpR3h1_\Hyphalseg_Raw_
> 2000_2000_1920_8bit_SKELETON_FILT_PARAVIEW_TEST.raw
>
>
> I cannot find an obvious memory ceiling within the paraview settings - any
> ideas as to whether there is some effective upper limit to import file size?
>
> Sam
>
> Samuel D Keyes, MEng, PhD
> New Frontiers Fellow
> Bioengineering / μVIS Centre for Computed Tomography
> University of Southampton
> E: s.d.ke...@soton.ac.uk dir.aspx?SURL=dhUg3da8XR77LeItLDzJQwhAwmH0Wx6PHrXeKfxx2tOD3LCr737TCG0AYQBp
> AGwAdABvADoAUwAuAEQALgBLAGUAeQBlAHMAQABzAG8AdABvAG4ALgBhAGMA
> LgB1AGsA=mailto%3aS.D.Keyes%40soton.ac.uk>
> T: 07898720248
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> rce/opensource.html
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> Please keep messages on-topic and check the ParaView Wiki at:
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>
>
>
>
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>
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Re: [Paraview] RAW (binary) file import issues

2016-11-22 Thread Moreland, Kenneth

Although we have certainly run into issues with communicating large messages, 
I’m not sure this is the issue with MPI-I/O. File sizes and linear offsets use 
a type MPI_Offset, which according to the specification should be large enough 
to hold the size of any file supported by the file system. Although it is true 
that creating the 3D subarray uses 32-bit indices, those are for each of the 
separate dimensions, and 2000 falls well below that limit.

Besides, it looks like that error happens when checking an ifstream object, so 
it looks like the reader is bypassing the MPI-I/O path anyway.

I would follow Berk’s suggesting of looking into the filesystem before diving 
into the guts of MPI-I/O.

-Ken

From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Burlen Loring
Sent: Tuesday, November 22, 2016 12:55 PM
To: Geveci, Berk (External Contact) ; Keyes S.D. 

Cc: paraview@paraview.org
Subject: [EXTERNAL] Re: [Paraview] RAW (binary) file import issues

I've hit that before. the RAW reader uses MPI-I/O, and MPI uses signed int 
everywhere in its API, so there are limits that you end up hitting. For 
instance to partition the data among processors one must give MPI-I/O the 
starting offset of the data in the file as a signed int, and that is limited to 
2^31.

Burlen
On 11/22/2016 11:20 AM, Berk Geveci wrote:
Hmmm that happens to be around 4 GB which makes me wonder if there is a limit 
somewhere in that reader... Any chance you can try this on a Linux machine?

On Thu, Nov 17, 2016 at 10:30 AM, Keyes S.D. 
> wrote:
Dear all,

I am encountering issues when trying to import large 8 bit RAW volumes to 
Paraview 5.1.2 (64 bit).

The file I wish to import has xyz dimensions of 2000x2000x1920 voxels (Unsigned 
char), 7.5GB.  I am running a machine with 192 GB RAM and 12 CPU cores.

I can import up to a 2000x2000x1000 crop of this file, but I encounter the 
following message when I attempt larger z dimensions:

ERROR: In C:\bbd\df0abce0\source-paraview\VTK\IO\Image\vtkImageReader2.cxx, 
line 592

vtkPVImageReader (07767F90): Initialize: Could not open file 
\\cseg_2\ERC\SLS_201606\Myco_2\CT2PpR3h1_\Hyphalseg_Raw_2000_2000_1920_8bit_SKELETON_FILT_PARAVIEW_TEST.raw


I cannot find an obvious memory ceiling within the paraview settings - any 
ideas as to whether there is some effective upper limit to import file size?

Sam

Samuel D Keyes, MEng, PhD
New Frontiers Fellow
Bioengineering / μVIS Centre for Computed Tomography
University of Southampton
E: 
s.d.ke...@soton.ac.ukredir.aspx?SURL=dhUg3da8XR77LeItLDzJQwhAwmH0Wx6PHrXeKfxx2tOD3LCr737TCG0AYQBpAGwAdABvADoAUwAuAEQALgBLAGUAeQBlAHMAQABzAG8AdABvAG4ALgBhAGMALgB1AGsA=mailto%3aS.D.Keyes%40soton.ac.uk>
T: 07898720248
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[Paraview] Warning Exporting VRML Files

2016-11-22 Thread Léo Pessanha

Hi!

After version 5.0 of paraview for Windows x64 everytime I export a Scene in
VRML format I get the warning

Warning: In
> C:\bbd\df0abce0\source-paraview\VTK\Filters\Geometry\vtkDataSetSurfaceFilter.cxx,
> line 166
> vtkDataSetSurfaceFilter (01A2CFB3E6E0): Number of cells is zero, no
> data to process.


It happens with any data, even a Box from Source.

The data seems to be exported correctly though.

Is that a bug?

Can anyone help me turning it off? My macros won't work because of that.

Thanks in advance!

Leonardo Pessanha
COPPE/UFRJ
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Re: [Paraview] RAW (binary) file import issues

2016-11-22 Thread Burlen Loring

I've hit that before. the RAW reader uses MPI-I/O, and MPI uses signed 
int everywhere in its API, so there are limits that you end up hitting. 
For instance to partition the data among processors one must give 
MPI-I/O the starting offset of the data in the file as a signed int, and 
that is limited to 2^31.


Burlen

On 11/22/2016 11:20 AM, Berk Geveci wrote:
Hmmm that happens to be around 4 GB which makes me wonder if there is 
a limit somewhere in that reader... Any chance you can try this on a 
Linux machine?


On Thu, Nov 17, 2016 at 10:30 AM, Keyes S.D. > wrote:


Dear all,

I am encountering issues when trying to import large 8 bit RAW
volumes to Paraview 5.1.2 (64 bit).

The file I wish to import has xyz dimensions of 2000x2000x1920
voxels (Unsigned char), 7.5GB.  I am running a machine with 192 GB
RAM and 12 CPU cores.

I can import up to a 2000x2000x1000 crop of this file, but I
encounter the following message when I attempt larger z dimensions:

ERROR: In
C:\bbd\df0abce0\source-paraview\VTK\IO\Image\vtkImageReader2.cxx,
line 592

vtkPVImageReader (07767F90): Initialize: Could not open
file

\\cseg_2\ERC\SLS_201606\Myco_2\CT2PpR3h1_\Hyphalseg_Raw_2000_2000_1920_8bit_SKELETON_FILT_PARAVIEW_TEST.raw


I cannot find an obvious memory ceiling within the paraview
settings - any ideas as to whether there is some effective upper
limit to import file size?

Sam

Samuel D Keyes, MEng, PhD
New Frontiers Fellow
Bioengineering / μVIS Centre for Computed Tomography
University of Southampton
E: s.d.ke...@soton.ac.uk

>
T: 07898720248
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Re: [Paraview] RAW (binary) file import issues

2016-11-22 Thread Berk Geveci

Hmmm that happens to be around 4 GB which makes me wonder if there is a
limit somewhere in that reader... Any chance you can try this on a Linux
machine?

On Thu, Nov 17, 2016 at 10:30 AM, Keyes S.D.  wrote:

> Dear all,
>
> I am encountering issues when trying to import large 8 bit RAW volumes to
> Paraview 5.1.2 (64 bit).
>
> The file I wish to import has xyz dimensions of 2000x2000x1920 voxels
> (Unsigned char), 7.5GB.  I am running a machine with 192 GB RAM and 12 CPU
> cores.
>
> I can import up to a 2000x2000x1000 crop of this file, but I encounter the
> following message when I attempt larger z dimensions:
>
> ERROR: In C:\bbd\df0abce0\source-paraview\VTK\IO\Image\vtkImageReader2.cxx,
> line 592
>
> vtkPVImageReader (07767F90): Initialize: Could not open file
> \\cseg_2\ERC\SLS_201606\Myco_2\CT2PpR3h1_\Hyphalseg_Raw_
> 2000_2000_1920_8bit_SKELETON_FILT_PARAVIEW_TEST.raw
>
>
> I cannot find an obvious memory ceiling within the paraview settings - any
> ideas as to whether there is some effective upper limit to import file size?
>
> Sam
>
> Samuel D Keyes, MEng, PhD
> New Frontiers Fellow
> Bioengineering / μVIS Centre for Computed Tomography
> University of Southampton
> E: s.d.ke...@soton.ac.uk redir.aspx?SURL=dhUg3da8XR77LeItLDzJQwhAwmH0Wx
> 6PHrXeKfxx2tOD3LCr737TCG0AYQBpAGwAdABvADoAUwAuAEQALgBLAGUAeQ
> BlAHMAQABzAG8AdABvAG4ALgBhAGMALgB1AGsA=mailto%3aS.D.
> Keyes%40soton.ac.uk>
> T: 07898720248
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Re: [Paraview] Automatic connect to Catalyst

2016-11-22 Thread Utkarsh Ayachit

Thanks for reporting, Arno.

On Tue, Nov 22, 2016 at 9:47 AM, Arno Mayrhofer
 wrote:
> Utkarsh,
>
> thanks for your reply. As you suggested I opened the following issue on your
> gitlab page:
>
> https://gitlab.kitware.com/paraview/paraview/issues/17037
>
> Unfortunately I do not have time to devote to resolving this issue myself
> currently. Whether or not that will change is unclear at the moment.
>
> Thanks,
> Arno
>
>
>
>>> I tried to generate a PV Python script using the trace option, but it did
>>> not show me any output related to connecting to the Catalyst simulation.
>>> Is
>>> it at all possible to do this via a Python script?
>>
>> Not currently, I am afraid. The connect-to-live functionality is
>> currently not exposed to Python and hence not scriptable or accessible
>> via Python API alone.
>>
>>> I also have not found any command line options that would allow me to
>>> connect to a certain Catalyst port, did I miss something here?
>>
>> Correct, they don't exist either. Feel free to add a feature request
>> for the case or put together a merge-request to add support for this.
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Re: [Paraview] Automatic connect to Catalyst

2016-11-22 Thread Arno Mayrhofer


Utkarsh,

thanks for your reply. As you suggested I opened the following issue on 
your gitlab page:


https://gitlab.kitware.com/paraview/paraview/issues/17037

Unfortunately I do not have time to devote to resolving this issue 
myself currently. Whether or not that will change is unclear at the moment.


Thanks,
Arno



I tried to generate a PV Python script using the trace option, but it did
not show me any output related to connecting to the Catalyst simulation. Is
it at all possible to do this via a Python script?

Not currently, I am afraid. The connect-to-live functionality is
currently not exposed to Python and hence not scriptable or accessible
via Python API alone.


I also have not found any command line options that would allow me to
connect to a certain Catalyst port, did I miss something here?

Correct, they don't exist either. Feel free to add a feature request
for the case or put together a merge-request to add support for this.

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Re: [Paraview] Migration from Paraview 4.4 to 5.2

2016-11-22 Thread Lodron, Gerald

thanks

-Ursprüngliche Nachricht-
Von: Utkarsh Ayachit [mailto:utkarsh.ayac...@kitware.com] 
Gesendet: Dienstag, 22. November 2016 14:17
An: Lodron, Gerald
Cc: Paraview Developer (paraview-develop...@paraview.org); Paraview User 
(paraview@paraview.org)
Betreff: Re: [Paraview] Migration from Paraview 4.4 to 5.2

Gerald,

The pqObjectPanel/pqNamedObjectPanel have been long deprecated -- ~4.0. This 
page covers the new design:
http://www.paraview.org/Wiki/ParaView/Properties_Panel

This covers the changes to the plugins:
http://www.paraview.org/Wiki/Plugin_HowTo#Adding_Customizations_for_Properties_Panel

Utkarsh

On Tue, Nov 22, 2016 at 3:10 AM, Lodron, Gerald  
wrote:
> Hi
>
> I currently updated my paraview and saw that my custom filter object panels 
> which are inherited from pqObjectPanel and pqNamedObjectPanel seems to be 
> deprecated.. I googled but could not find a migration guide. Can you give me 
> a hint where to look?
>
> thanks
> --
> --
> Gerald Lodron
>
> Researcher of Machine Vision Applications Group DIGITAL - Institute 
> for Information and Communication Technologies
>
> JOANNEUM RESEARCH Forschungsgesellschaft mbH Steyrergasse 17, 8010 
> Graz, AUSTRIA
>
> phone:   +43-316-876-1751
> general fax: +43-316-876-1751
> web: http://www.joanneum.at/digital
> e-mail: gerald.lod...@joanneum.at
>
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Re: [Paraview] Automatic connect to Catalyst

2016-11-22 Thread Utkarsh Ayachit

Arno,

> I tried to generate a PV Python script using the trace option, but it did
> not show me any output related to connecting to the Catalyst simulation. Is
> it at all possible to do this via a Python script?

Not currently, I am afraid. The connect-to-live functionality is
currently not exposed to Python and hence not scriptable or accessible
via Python API alone.

> I also have not found any command line options that would allow me to
> connect to a certain Catalyst port, did I miss something here?

Correct, they don't exist either. Feel free to add a feature request
for the case or put together a merge-request to add support for this.

> And finally if none of the above works, would a custom plug-in that is auto
> loaded allow me to perform this small piece of magic? Or any other ways of
> doing this?

Yes, that may be possible. Follow the code path starting with
pqCatalystConnectReaction::connect()[1]. That will tell you how
ParaView connects to insitu. You can mimic parts of that in your
plugin's auto-start method.

Utkarsh

[1] 
https://gitlab.kitware.com/paraview/paraview/blob/master/Qt/ApplicationComponents/pqCatalystConnectReaction.cxx#L61-72
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Re: [Paraview] Migration from Paraview 4.4 to 5.2

2016-11-22 Thread Utkarsh Ayachit

Gerald,

The pqObjectPanel/pqNamedObjectPanel have been long deprecated --
~4.0. This page covers the new design:
http://www.paraview.org/Wiki/ParaView/Properties_Panel

This covers the changes to the plugins:
http://www.paraview.org/Wiki/Plugin_HowTo#Adding_Customizations_for_Properties_Panel

Utkarsh

On Tue, Nov 22, 2016 at 3:10 AM, Lodron, Gerald
 wrote:
> Hi
>
> I currently updated my paraview and saw that my custom filter object panels 
> which are inherited from pqObjectPanel and pqNamedObjectPanel seems to be 
> deprecated.. I googled but could not find a migration guide. Can you give me 
> a hint where to look?
>
> thanks
> 
> Gerald Lodron
>
> Researcher of Machine Vision Applications Group
> DIGITAL - Institute for Information and Communication Technologies
>
> JOANNEUM RESEARCH Forschungsgesellschaft mbH
> Steyrergasse 17, 8010 Graz, AUSTRIA
>
> phone:   +43-316-876-1751
> general fax: +43-316-876-1751
> web: http://www.joanneum.at/digital
> e-mail: gerald.lod...@joanneum.at
>
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>
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[Paraview] Migration from Paraview 4.4 to 5.2

2016-11-22 Thread Lodron, Gerald

Hi

I currently updated my paraview and saw that my custom filter object panels 
which are inherited from pqObjectPanel and pqNamedObjectPanel seems to be 
deprecated.. I googled but could not find a migration guide. Can you give me a 
hint where to look?

thanks

Gerald Lodron
 
Researcher of Machine Vision Applications Group
DIGITAL - Institute for Information and Communication Technologies
 
JOANNEUM RESEARCH Forschungsgesellschaft mbH
Steyrergasse 17, 8010 Graz, AUSTRIA
 
phone:   +43-316-876-1751   
general fax: +43-316-876-1751
web: http://www.joanneum.at/digital
e-mail: gerald.lod...@joanneum.at

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Visit other Kitware open-source projects at 
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