date:20170726

Re: [Paraview] MPI on multiple nodes

2017-07-26 Thread Mariam

Thanks for your reply.

The correct syntax to run on multiple hosts is: mpiexec –hosts N localhost M 
remotehost 1 appName

I tested with hostname and it worked; it printed the expected output.

However, by executing the same command with pvserver, it does not work. I 
ensured the location of paraview/pvserver is the same across both hosts. And I 
am providing the full path of pvserver.

I would like to make sure that I understood the concept correctly:

>From host1, if I executed parallel pvservers with MPI (host1, host2, hostN), 
>the clients should connect to host1. 

Can you please confirm?

From: Patrick Begou 
Date: Tuesday, July 25, 2017 at 5:45 PM
To: Mariam , 
Subject: Re: [Paraview] MPI on multiple nodes

I think the syntax for mpiexec is:

mpiexec -np 8 --host host_one,host_two pvserver

This would launch 4 occurences of pvserver on host_one and 4 on host_two.

1) first check mpi is running:

mpiexec -np 2 --host host_one,host_two hostname

This should print the name of the 2 hosts.

If it does not works check you can ssh from one host to the other without 
password.

2) You need the same paraview/pvserver install on the two hosts in the same 
location (not imposed but it is easier to launch)

3) May be use reverse connection from the parallel pvserver to the paraview 
client when you launch pvserver 

Patrick

Mariam wrote: 

Hi, 

I would like to ask about running pvserver in parallel with MPI on multiple 
hosts. Is that possible?

The following commands were tested successfully:

1)  Running MPI on localhost:

mpiexec –n M localhost pvserver

2)  Running MPI on remotehost:

mpiexec –host remotehost –n M pvserver

But I was not able to run: mpiexec –hosts 2 localhost 1 remotehost 1 pvserver

I run the following to test MPI on multiple hosts and it worked: mpiexec –hosts 
2 localhost 1 remotehost 1 hostname

Is there any pre-configuration that should be done to pvserver? I want the 
clients to connect to the server (master server), and the jobs are distributed 
across multiple nodes.

Regards,

Mariam

___
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

-- 
===
|  Equipe M.O.S.T. |  |
|  Patrick BEGOU   | mailto:patrick.be...@grenoble-inp.fr |
|  LEGI    |  |
|  BP 53 X | Tel 04 76 82 51 35   |
|  38041 GRENOBLE CEDEX    | Fax 04 76 82 52 71   |
===

___
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 Catalyst offscreen rendering

2017-07-26 Thread Andy Bauer

Hi,

It sounds like you didn't properly build with OSMesa. If you share your
CMakeCache.txt from your ParaView build I can see if I can track down the
problem.

Best,
Andy

On Wed, Jul 26, 2017 at 11:20 AM, Lukáš Kresta 
wrote:

> Thank you, but I have ParaView build with OSMesa without X. If I run
> program with Catalyst(genereted script from ParaView, with render views) on
> cluster with mpi, ussually one render view will show, but on anothers
> process it crash with this error: ERROR: In .../ParaView-v5.4.0/VTK/
> Rendering/OpenGL2/vtkOpenGLRenderWindow.cxx, line 819
> vtkXOpenGLRenderWindow (0x3f7cbf0): GLEW could not be initialized. I have
> the same error with pvserver with or without --use-offscreen-rendering or
> without pvserver.
>
> If i run Catalyst with script only for live visualization then the program
> go without problem but i dont get pictures which i want. Is there some
> posibility how fix the error or how to get pictures(with offscreen
> rendering)?
>
> 2017-07-14 16:24 GMT+02:00 Andy Bauer :
>
>> Hi,
>>
>> If you're not memory constrained I suggest just doing a full ParaView
>> build with OSMesa and X11 disabled. There are quite a few discussions on
>> the PV mailing list on how to do that.
>>
>> If you're memory constrained then I would suggest building with all of
>> the Catalyst editions enabled and see if that works for you.
>>
>> Best,
>> Andy
>>
>> On Fri, Jul 14, 2017 at 3:31 AM, Lukáš Kresta 
>> wrote:
>>
>>> Hi,
>>>
>>> I would like to ask, which Paraview Catalyst (python) script use(with
>>> render view or live visualization). If i want save images with offscreen
>>> rendering on HPC.  On cluster is no gpu. And how to properly use it?
>>>
>>> Thank you for your help.
>>>
>>>
>>>
>>>
>>> ___
>>> 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 Catalyst offscreen rendering

2017-07-26 Thread Lukáš Kresta

Thank you, but I have ParaView build with OSMesa without X. If I run
program with Catalyst(genereted script from ParaView, with render views) on
cluster with mpi, ussually one render view will show, but on anothers
process it crash with this error: ERROR: In
.../ParaView-v5.4.0/VTK/Rendering/OpenGL2/vtkOpenGLRenderWindow.cxx, line
819
vtkXOpenGLRenderWindow (0x3f7cbf0): GLEW could not be initialized. I have
the same error with pvserver with or without --use-offscreen-rendering or
without pvserver.

If i run Catalyst with script only for live visualization then the program
go without problem but i dont get pictures which i want. Is there some
posibility how fix the error or how to get pictures(with offscreen
rendering)?

2017-07-14 16:24 GMT+02:00 Andy Bauer :

> Hi,
>
> If you're not memory constrained I suggest just doing a full ParaView
> build with OSMesa and X11 disabled. There are quite a few discussions on
> the PV mailing list on how to do that.
>
> If you're memory constrained then I would suggest building with all of the
> Catalyst editions enabled and see if that works for you.
>
> Best,
> Andy
>
> On Fri, Jul 14, 2017 at 3:31 AM, Lukáš Kresta 
> wrote:
>
>> Hi,
>>
>> I would like to ask, which Paraview Catalyst (python) script use(with
>> render view or live visualization). If i want save images with offscreen
>> rendering on HPC.  On cluster is no gpu. And how to properly use it?
>>
>> Thank you for your help.
>>
>>
>>
>>
>> ___
>> 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] Point data to 2d plane data

2017-07-26 Thread Moreland, Kenneth

Teng,

When you saved your data to a csv file, you lost all cell information. If you 
want to look at cells in your data, you will have to recreate them.

The easiest way to create cells is probably to use the Delaunay 2D filter. 
Note, however, that the cells created will not be the same as in your original 
vtk file.

If you want to keep your original cells, you will have to save them in a file 
that supports cell topology. One way to do that is when you save your csv file, 
also save a vtk file of the same data. Then, after you have run Matlab, load 
both the csv file and the vtk file. Do the TableToPoints on the csv data as 
before. Then use append attributes to copy the csv data to the vtk cell data.

-Ken

Sent from my iPad

On Jul 26, 2017, at 12:41 AM, Li, Teng 
mailto:teng...@illinois.edu>> wrote:

Dear Paraview developers,

I have a question about how to convert point data (vtk file) to 2d plane data. 
Actually, originally, I was working with vtk file. Then I use the extract 
selection to select some cells in the original model. In order to process the 
data of the selected cells, I save the data as the csv file. Then I use Matlab 
to do some calculation on the data in the csv file. After that, I open the 
modified csv file by using Paraview directly. And now, I can only see this csv 
file in spreadsheet view. After searching some online information, I use 
TabletoPoint to convert the data to point data. However, I still want to view 
them as the 2d cell. So I use point interpolation to try to convert the points 
data to 2d plane cell data. However, It doesn't work.

So my question is, how to show the data value in the space between different 2d 
points data by using point interpolation? Or is there any way that I can 
process the 2d cell plane data without saving it as the csv file?

Best,
Teng Li


Teng Li

Master Candidate in Structures

Department of Civil and Environmental Engineering

University of Illinois at Urbana-Champaign

205 North Mathews Ave, Urbana, IL. 61801

Phone:(217)8196210, Email: teng...@illinois.edu



___
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] Can I use paraview to visualize molecule dataset?

2017-07-26 Thread 张驭洲


Thank you very much! That's exactly what I want.

-Zhang

> -原始邮件-
> 发件人: "Cory Quammen" 
> 发送时间: 2017年7月26日 星期三
> 收件人: "张驭洲" 
> 抄送: ParaView 
> 主题: Re: [Paraview] Can I use paraview to visualize molecule dataset?
> 
> Zhang,
> 
> Yes, you can visualize molecules in ball-and-stick representation in
> ParaView (see attached). This representation is used whenever you load
> a vtkMolecule data type. If you have a PDB file, for example, it will
> be read in as a vtkMolecule data type and displayed with
> ball-and-stick representation by default. You can also change the
> Molecule "Render Mode" property to "Space Filling" or "Liquorice"
> representation.
> 
> HTH,
> Cory
> 
> 
> 
> On Wed, Jul 26, 2017 at 3:57 AM, 张驭洲  wrote:
> >
> >
> > Hello,
> >
> >   I want to know if I can use paraview to visualize molecule dataset,
> > i.e., using ball-and-stick model to represent molecules? Currently I can
> > only using point gaussian to represent the "ball", but I don't know how to
> > visualize the "stick". I know another visualization tool VMD is designed to
> > do works of this kind, but I've not found similar founctions in ParaView.
> >
> > -Zhang
> >
> >
> >
> >
> >
> > ___
> > 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
> Staff R&D 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 subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/paraview

Re: [Paraview] Can I use paraview to visualize molecule dataset?

2017-07-26 Thread Utkarsh Ayachit

And here's a related blog post:
https://blog.kitware.com/new-features-paraview-chemistry-pettt/

Utkarsh

On Wed, Jul 26, 2017 at 7:25 AM, Cory Quammen 
wrote:

> Zhang,
>
> Yes, you can visualize molecules in ball-and-stick representation in
> ParaView (see attached). This representation is used whenever you load
> a vtkMolecule data type. If you have a PDB file, for example, it will
> be read in as a vtkMolecule data type and displayed with
> ball-and-stick representation by default. You can also change the
> Molecule "Render Mode" property to "Space Filling" or "Liquorice"
> representation.
>
> HTH,
> Cory
>
>
>
> On Wed, Jul 26, 2017 at 3:57 AM, 张驭洲  wrote:
> >
> >
> > Hello,
> >
> >   I want to know if I can use paraview to visualize molecule dataset,
> > i.e., using ball-and-stick model to represent molecules? Currently I can
> > only using point gaussian to represent the "ball", but I don't know how
> to
> > visualize the "stick". I know another visualization tool VMD is designed
> to
> > do works of this kind, but I've not found similar founctions in ParaView.
> >
> > -Zhang
> >
> >
> >
> >
> >
> > ___
> > 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
> Staff R&D 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 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] Can I use paraview to visualize molecule dataset?

2017-07-26 Thread Cory Quammen

Zhang,

Yes, you can visualize molecules in ball-and-stick representation in
ParaView (see attached). This representation is used whenever you load
a vtkMolecule data type. If you have a PDB file, for example, it will
be read in as a vtkMolecule data type and displayed with
ball-and-stick representation by default. You can also change the
Molecule "Render Mode" property to "Space Filling" or "Liquorice"
representation.

HTH,
Cory



On Wed, Jul 26, 2017 at 3:57 AM, 张驭洲  wrote:
>
>
> Hello,
>
>   I want to know if I can use paraview to visualize molecule dataset,
> i.e., using ball-and-stick model to represent molecules? Currently I can
> only using point gaussian to represent the "ball", but I don't know how to
> visualize the "stick". I know another visualization tool VMD is designed to
> do works of this kind, but I've not found similar founctions in ParaView.
>
> -Zhang
>
>
>
>
>
> ___
> 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
Staff R&D 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 subscribe/unsubscribe:
http://public.kitware.com/mailman/listinfo/paraview

[Paraview] Can I use paraview to visualize molecule dataset?

2017-07-26 Thread 张驭洲



Hello,

  I want to know if I can use paraview to visualize molecule dataset, i.e., 
using ball-and-stick model to represent molecules? Currently I can only using 
point gaussian to represent the "ball", but I don't know how to visualize the 
"stick". I know another visualization tool VMD is designed to do works of this 
kind, but I've not found similar founctions in ParaView.

-Zhang



___
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] MPI on multiple nodes

Re: [Paraview] Paraview Catalyst offscreen rendering

Re: [Paraview] Paraview Catalyst offscreen rendering

Re: [Paraview] Point data to 2d plane data

Re: [Paraview] Can I use paraview to visualize molecule dataset?

Re: [Paraview] Can I use paraview to visualize molecule dataset?

Re: [Paraview] Can I use paraview to visualize molecule dataset?

[Paraview] Can I use paraview to visualize molecule dataset?

8 matches

Site Navigation

Mail list logo

Footer information