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Color display problem to view OpenFOAM results.

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Old   May 1, 2013, 18:44
Default Color display problem to view OpenFOAM results.
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Hello everyone,

I am doing OpenFOAM simulations for a microstructure geometry. After getting converged solutions when I used foamToVTK -latestTime. Geometry is not showing different colour distribution after viewing VTK file in paraview. As it can be seen in the attachment that colour bar is showing different colours with respected values but the geometry is showing only one colour everywhere.

Does anyone have any idea why this problem is coming? How can I get rid of this problem?

Best regards,
Sangeeta
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Old   May 2, 2013, 07:06
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Greetings Sangeeta,

There are at least two possibilities:
  1. The values that are different from 0 might be inside the geometry.
  2. ParaView has got representation problems when values are too small or too large.
If it's the second one, apply the filter "Transform" and change the 3 values for "Scale" to 1000 or more. This will increase the geometry by 1000 times, therefore making it easier for ParaView to represent the values.

Best regards,
Bruno
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Old   May 2, 2013, 15:20
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Hi Bruno,

Thank you so much for the reply. Yes, values are too low in my case. As you suggested, I have tried to solve the problem by using Transform filter. But when I am using Transform filter my computer is getting stop. I do not know if there is some problem with paraview or something else with my computer. Similar thing happens when I use slice filter. My computer suddenly stops when I use these filters. Have you encountered this problem? Please let me know if you have any suggestion to get rid of this issue.

Best regards,
Sangeeta
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Old   May 2, 2013, 15:28
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Hi Sangeeta,

It's possible that ParaView is crashing due to a problem with the graphics card drivers. So a few questions:
  1. Which Ubuntu version are you using?
  2. Are you running Ubuntu in a virtual machine or in a real/physical machine?
  3. Which ParaView installation are you using?
    1. More specifically, are you using the ParaView version that comes with Ubuntu or the one that comes with OpenFOAM?
Best regards,
Bruno
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Old   May 2, 2013, 16:11
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Hi Bruno,

Thank you so very much for the quick reply!
1. I am using Ubuntu 10.04 version in my laptop.
2. I have 50-50% partition of Windows and Linux in my machine.
3. I am using paraview381 which which has come with OpenFOAM171 version during installation.

My laptop suddenly stops running specially when I used some filters (as I mentioned in previous message). This problem is going for a long time but I was guessing this might be because of partition in my laptop. I appreciate if you have suggestions to overcome this problem.


Best regards,
Sangeeta
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Old   May 2, 2013, 16:38
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Hi Sangeeta,

OK, try following this tutorial for installing the graphics card drivers: http://www.howtogeek.com/howto/17495...-ubuntu-10.04/ - starting from this paragraph:
Quote:
Alternately, if the tray icon has disappeared, click System, then Administration, and select Hardware Drivers.
In addition, read this post: Segmentation fault when visualizing in ParaView - post #6

Best regards,
Bruno
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Old   May 3, 2013, 13:42
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Hi Bruno,

Thank you for the valuable suggestions. I did click System, then Administration, and select Hardware Drivers and does not show NVidia in my machine (please see in the first attachment).
Then I tried to install this driver through System->Administration->Synaptic Package Manager, here as you could see in the second attachment that it is showing several versions of NVidia. Could you please let me know which version I should install to get rid of the paraview problem?

Thanks,
Sangeeta
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Old   May 3, 2013, 14:09
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First check which NVidia card you've got:
Code:
lspci | grep -i nvidia
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Old   May 3, 2013, 14:29
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Hi Bruno,

As you suggested I have used command in the terminal window.

lspci | grep -i nvidia

It is showing nothing or no information when I entered (please see the attachment).
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Old   May 3, 2013, 14:54
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Hi Sangeeta,

Then it looks like the kernel is not identifying your NVidia card. Try the following commands to see if you have any other major graphics card maker:
Code:
lspci | grep -i ATI
lspci | grep -i Intel
Or better yet, to see which card it's detecting:
Code:
lspci | grep VGA
Best regards,
Bruno

PS: In case it is an NVidia card, see this thread: http://ubuntuforums.org/showthread.p...3#post11307903

Last edited by wyldckat; May 3, 2013 at 14:56. Reason: see "PS:"
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Old   May 3, 2013, 16:50
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Hi Bruno,

Following information is coming when I am using the commands you suggested:

sangeeta@sangeeta-laptop:~$ lspci | grep -i ATI
00:00.0 Host bridge: Intel Corporation Core Processor DRAM Controller (rev 02)
00:02.0 VGA compatible controller: Intel Corporation Core Processor Integrated Graphics Controller (rev 02)
00:16.0 Communication controller: Intel Corporation 5 Series/3400 Series Chipset HECI Controller (rev 06)
00:19.0 Ethernet controller: Intel Corporation 82577LC Gigabit Network Connection (rev 06)
00:1a.0 USB Controller: Intel Corporation 5 Series/3400 Series Chipset USB2 Enhanced Host Controller (rev 06)
00:1b.0 Audio device: Intel Corporation 5 Series/3400 Series Chipset High Definition Audio (rev 06)
00:1c.0 PCI bridge: Intel Corporation 5 Series/3400 Series Chipset PCI Express Root Port 1 (rev 06)
00:1c.1 PCI bridge: Intel Corporation 5 Series/3400 Series Chipset PCI Express Root Port 2 (rev 06)
00:1c.2 PCI bridge: Intel Corporation 5 Series/3400 Series Chipset PCI Express Root Port 3 (rev 06)
00:1c.3 PCI bridge: Intel Corporation 5 Series/3400 Series Chipset PCI Express Root Port 4 (rev 06)
00:1d.0 USB Controller: Intel Corporation 5 Series/3400 Series Chipset USB2 Enhanced Host Controller (rev 06)
00:1e.0 PCI bridge: Intel Corporation 82801 Mobile PCI Bridge (rev a6)
00:1f.0 ISA bridge: Intel Corporation Mobile 5 Series Chipset LPC Interface Controller (rev 06)
00:1f.2 SATA controller: Intel Corporation 5 Series/3400 Series Chipset 4 port SATA AHCI Controller (rev 06)
00:1f.6 Signal processing controller: Intel Corporation 5 Series/3400 Series Chipset Thermal Subsystem (rev 06)
02:00.0 Network controller: Broadcom Corporation Device 4727 (rev 01)
ff:00.0 Host bridge: Intel Corporation Core Processor QuickPath Architecture Generic Non-core Registers (rev 02)
ff:00.1 Host bridge: Intel Corporation Core Processor QuickPath Architecture System Address Decoder (rev 02)
ff:02.0 Host bridge: Intel Corporation Core Processor QPI Link 0 (rev 02)
ff:02.1 Host bridge: Intel Corporation Core Processor QPI Physical 0 (rev 02)
ff:02.2 Host bridge: Intel Corporation Core Processor Reserved (rev 02)
ff:02.3 Host bridge: Intel Corporation Core Processor Reserved (rev 02)



sangeeta@sangeeta-laptop:~$ lspci | grep -i Intel
00:00.0 Host bridge: Intel Corporation Core Processor DRAM Controller (rev 02)
00:02.0 VGA compatible controller: Intel Corporation Core Processor Integrated Graphics Controller (rev 02)
00:16.0 Communication controller: Intel Corporation 5 Series/3400 Series Chipset HECI Controller (rev 06)
00:19.0 Ethernet controller: Intel Corporation 82577LC Gigabit Network Connection (rev 06)
00:1a.0 USB Controller: Intel Corporation 5 Series/3400 Series Chipset USB2 Enhanced Host Controller (rev 06)
00:1b.0 Audio device: Intel Corporation 5 Series/3400 Series Chipset High Definition Audio (rev 06)
00:1c.0 PCI bridge: Intel Corporation 5 Series/3400 Series Chipset PCI Express Root Port 1 (rev 06)
00:1c.1 PCI bridge: Intel Corporation 5 Series/3400 Series Chipset PCI Express Root Port 2 (rev 06)
00:1c.2 PCI bridge: Intel Corporation 5 Series/3400 Series Chipset PCI Express Root Port 3 (rev 06)
00:1c.3 PCI bridge: Intel Corporation 5 Series/3400 Series Chipset PCI Express Root Port 4 (rev 06)
00:1d.0 USB Controller: Intel Corporation 5 Series/3400 Series Chipset USB2 Enhanced Host Controller (rev 06)
00:1e.0 PCI bridge: Intel Corporation 82801 Mobile PCI Bridge (rev a6)
00:1f.0 ISA bridge: Intel Corporation Mobile 5 Series Chipset LPC Interface Controller (rev 06)
00:1f.2 SATA controller: Intel Corporation 5 Series/3400 Series Chipset 4 port SATA AHCI Controller (rev 06)
00:1f.6 Signal processing controller: Intel Corporation 5 Series/3400 Series Chipset Thermal Subsystem (rev 06)
ff:00.0 Host bridge: Intel Corporation Core Processor QuickPath Architecture Generic Non-core Registers (rev 02)
ff:00.1 Host bridge: Intel Corporation Core Processor QuickPath Architecture System Address Decoder (rev 02)
ff:02.0 Host bridge: Intel Corporation Core Processor QPI Link 0 (rev 02)
ff:02.1 Host bridge: Intel Corporation Core Processor QPI Physical 0 (rev 02)
ff:02.2 Host bridge: Intel Corporation Core Processor Reserved (rev 02)
ff:02.3 Host bridge: Intel Corporation Core Processor Reserved (rev 02)


sangeeta@sangeeta-laptop:~$ lspci | grep VGA
00:02.0 VGA compatible controller: Intel Corporation Core Processor Integrated Graphics Controller (rev 02)
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Old   May 3, 2013, 17:23
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Hi Sangeeta,

OK, it's an Intel GPU you've got there. I've helped someone sometime ago on how to install the latest drivers for Intel:
Quote:
Originally Posted by wyldckat View Post
As for installing the Intel GPU drivers... I don't have a machine to test this, but a bit of googling tells me that this should work (source: http://askubuntu.com/a/215967 ):
  1. Run:
    Code:
    sudo apt-add-repository ppa:ubuntu-x-swat/x-updates
    sudo apt-get update && sudo apt-get upgrade
  2. Then reboot.
If by any chance you have a laptop that says on the outside that it has got NVidia, then the problem you're having is due to a missing driver that helps switch between Intel and NVidia cards. Problem is that last time I checked, said driver still actually does not exist and this system only works on Windows... Unless you install a software hack on Linux for being able to switch between the two cards, but that doesn't always work and not all card pairs work.

Best regards,
Bruno
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Old   May 3, 2013, 21:56
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Hi Bruno,

I used run the two commands in terminal as you mentioned your message.

  1. Run:
    Code:
    sudo apt-add-repository ppa:ubuntu-x-swat/x-updates sudo apt-get update && sudo apt-get upgrade
  2. Then reboot.
After rebooting I opened paraview and used slice filter but again my laptop stopped running (full black screen comes). Actually it did not shut down, screen becomes black and I needed to shut it down manually by using external keys (otherwise it didn't shut down automatically).


Does it happening because I installed paraview381 with OpenFOAM171? What do you think?


Best regards,
Sangeeta
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Old   May 4, 2013, 06:47
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Hi Sangeeta,

This problem also use to happen to some people back when OpenFOAM 1.7.1 was released, as I had pointed out in a previous thread link.

OK, let's try this:
  1. Uninstall "paraview381":
    Code:
    sudo apt-get remove paraviewopenfoam381
  2. Then try following these instructions: Using the official pre-built ParaView 3.10.1 version with OpenFOAM - Keep in mind to adapt the version "3.10.1" to the latest "3.98.1".
Best regards,
Bruno
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Old   May 7, 2013, 11:39
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Hi Bruno,

I am sorry for the late reply. I have removed paraview3.8.1 from my machine and was trying to install it again as you mentioned in the Using the official pre-built ParaView 3.10.1 version with OpenFOAM - post. When I was using step 3 mentioned in the above post

Now run: Code:
cd $HOME/OpenFOAM mkdir -p $ParaView_DIR
following information is coming in my machine:

mkdir: cannot create directory `/opt/paraviewopenfoam381': Permission denied

I have run step 4 successfully and untar the paraview3.8.1 folder. but when I used paraview command in my machine it says:

The program 'paraview' is currently not installed. You can install it by typing:
sudo apt-get install paraview

Do I need to reinstall OpenFOAM in my machine?

Best regards,
Sangeeta
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Old   May 7, 2013, 17:28
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Hi Sangeeta,

Sorry, I should have provided an easier set of instructions to follow. The ones I gave you were under the assumption that you had some more experience with Linux.

And there is no need to re-install OpenFOAM

OK, here are some much easier instructions:
  1. Download the ParaView 3.98.1 package from here: http://www.paraview.org/paraview/resources/software.php - In the "Operating System" line, choose "Linux 32-bit" or "Linux 64-bit" according to the outcome of this command:
    Code:
    uname -m
    • If it says "i686", choose 32-bit.
    • If it says "x86_64", choose 64-bit.
  2. Unpack the downloaded file inside the "~/Downloads" folder, or some other folder if you prefer.
  3. Then there is this quote from another post I made 5 days ago:
    Quote:
    Originally Posted by wyldckat View Post
    you can create an alias command that works as ... an alias Add to the end of the file "$HOME/.bashrc" the following command (adapt accordingly):
    Code:
    alias paraview3981="$HOME/Downloads/ParaView-3.98.1/bin/paraview"
    Then whenever you need to run this version of ParaView from the command line, simply run:
    Code:
    paraview3981
You can also add the following line to "$HOME/.bashrc", if you want to use paraFoam as a valid command:
Code:
alias paraFoam='touch case.foam && paraview3981 --data=case.foam'
Best regards,
Bruno
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Old   May 11, 2013, 00:10
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Hi Bruno,

Thanks a lot for your suggestions! I have tried all the ways as you suggested. Latter I found that I can be able to make slice for simple geometries (e.s. solid cube) in my machine but not with complicated geometries (e.g. two phase structure). I think this is some other problem related to the memory of my machine. I checked mesh of complicated geometry and it is fine even I can able to do slicing of complicated geometry from another machine.

I would like to thank you once again for your help!


Best regards,
Sangeeta
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