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[OpenFOAM.org] OpenFoam installation V6 on opensuse leap 15

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Old   September 7, 2018, 14:35
Default OpenFoam installation V6 on opensuse leap 15
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Stanley John
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Hi All,

I am trying to install openfoam v6 in opensuse leap 15.0 using the steps mentioned in the openfoam.org website

https://openfoam.org/download/6-linux/

Steps that worked are
uname -r
sudo zypper -n in docker
sudo systemctl start docker
sudo systemctl enable docker
sudo usr/bin/usermod -aG docker $(username)
sudo sh -c "wget http://dl.openfoam.org/docker/openfoam6-linux -O /usr/bin/openfoam6-linux"
sudo chmod 755 /usr/bin/openfoam6-linux

mkdir -p $HOME/OpenFOAM/${username}-6
cd $HOME/OpenFOAM/${username}-6

Everything is fine till now

when I run

openfoam6-linux



Launching /usr/bin/openfoam6-linux
User: "username" (ID ****, group ID **)
Welcome to the OpenFOAM v6 Docker Image

Provides bash terminal with OpenFOAM 6 and ParaView 5.4.0

Produced and maintained by CFD Direct (https://cfd.direct), on behalf of the
OpenFOAM Foundation (https://openfoam.org), the owner and distributor of
OpenFOAM as free, open source software under the General Public Licence v3.

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OpenFOAM-6(1)



The system hangs up at this stage

There is no error message or anything

Can you advise what is happening in the background? what must be the issue?


Thanks
Stanley

Last edited by sjohn2; September 10, 2018 at 09:39.
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Old   September 11, 2018, 10:01
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Anyone has any idea of this?
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Old   September 14, 2018, 07:38
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Bruno Santos
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Quick answer: Please try running with the '-x' option, to see if it helps:
Code:
openfoam6-linux -x
If it doesn't work, I'll have to look into this more closely, to try and diagnose the issue.
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Old   November 22, 2018, 11:17
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Nopes it does not work
Stuck at the same step

When I install the source code too, I get an error
mpicc command not found
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Old   December 27, 2018, 16:19
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Greetings Stanley,

I've finally managed to test building OpenFOAM 6 on openSUSE 15.0 and I've written the instructions here: https://openfoamwiki.net/index.php/I...SUSE_Leap_15.0

The reason why you got the "mpicc" message was because Open-MPI is not ready to be used as soon as it's installed. You either have to log-out then log back in or have to source the script files that will load Open-MPI into the shell environment. This is instructed on the aforementioned wiki page

Best regards,
Bruno
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Old   January 1, 2019, 21:13
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I am just starting my PhD at university of Alberta, Canada and we are trying to install openfoam from source code from few months now. I tried your steps and it worked ! I also noted that if I do
su instead of su -s to login as root, again I get the error that mpicc command not found.

After compiling openfoam, I was able to run a cavity tutorial and everything went well. However while post processing, I found that I am not able to use paraFoam, getting the following error. I have done the process of installinf paraview too mentioned in the wiki page. I am doing a remote login to do all this.


Created temporary 'cavity.OpenFOAM'
************************************************** ********
ParaView failed to open using available graphics hardware.
Trying fallback to software rendering using MESA.
************************************************** ********
/root/OpenFOAM/ThirdParty-6/platforms/linux64Gcc/ParaView-5.4.0/lib/paraview-5.4/paraview: symbol lookup error: /usr/lib64/libQtSql.so.4: undefined symbol: _ZN14QObjectPrivate15checkWindowRoleEv



Any idea?
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Old   January 2, 2019, 19:25
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Quick answer: My guess is that the big problem here is that you are running OpenFOAM and ParaView as root, which you should not be doing!!

Right there in step #3, it instructs to exit from root mode!! This is likely why things aren't working as intended
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Old   January 2, 2019, 23:52
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Yes I did forget to do it.
So I recompiled openfoam and third party software's the code locally, exiting root mode.

running
source /etc/profile.d/mpi-selector.sh
and of6 is the key here for me, otherwise I get the same error mpicc command not found

Able to run, icoFoam etc
but get the same error with interaction with paraview and graphics card
I also updated the driver for the graphics card to the latest nvidia graphics card
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Old   January 3, 2019, 06:18
Default Not SUSE but...
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Paul Johnston
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When building on Centos I modified my .bashrc to load the open-mpi module adding


mpi/openmpi-x86_64
source /home/paulj/OpenFOAM/OpenFOAM-6/etc/bashrc

I loaded the module before building then kept it there.


Cheers Paul J
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Old   January 3, 2019, 10:27
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Thanks I added the two lines of step 4 in my bashrc file and all I do is source my bashrc file to run anything with openfoam

I tried 2 different ways of installing paraview locally

1) ./makeParaView -python -mpi -python-lib /usr/lib64/libpython2.7.so.1.0 > log.makePV 2>&1

on running paraFoam
error :
Created temporary 'cavity.OpenFOAM'
************************************************** ********
ParaView failed to open using available graphics hardware.
Trying fallback to software rendering using MESA.
************************************************** ********
/root/OpenFOAM/ThirdParty-6/platforms/linux64Gcc/ParaView-5.4.0/lib/paraview-5.4/paraview: symbol lookup error: /usr/lib64/libQtSql.so.4: undefined symbol: _ZN14QObjectPrivate15checkWindowRoleEv


2) ./makeParaView > log.makePV2 2>&1


on running paraFoam

Created temporary 'cavity.OpenFOAM'
I/O : uncollated

paraFoam works fine!

Also I tried to run paraview by unzipping a rpm file available at opensuse website and running the executable, it works fine.

I think there a bug/ or some more steps are required while compiling paraview in third party.

Please find attached both log files.

Stanley
Attached Files
File Type: gz logs.tar.gz (125.6 KB, 1 views)
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Old   January 4, 2019, 18:48
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Quick answers:

@paulj:
Quote:
Originally Posted by paulj View Post
When building on Centos I modified my .bashrc to load the open-mpi module adding

mpi/openmpi-x86_64
source /home/paulj/OpenFOAM/OpenFOAM-6/etc/bashrc

I loaded the module before building then kept it there.
I hope the first line is:
Code:
module load mpi/openmpi-x86_64
otherwise it's not going to work.

With openSUSE, it shouldn't be necessary to source "mpi-selector.sh" after logging out or at least after rebooting. It's a weird limitation that they have, for it to not propagate properly the functionality by simply allowing us to start a new terminal and having it work straight away.

----------

@sjohn2:
Quote:
Originally Posted by sjohn2 View Post
I tried 2 different ways of installing paraview locally

1) ./makeParaView -python -mpi -python-lib /usr/lib64/libpython2.7.so.1.0 > log.makePV 2>&1

on running paraFoam
error :
Created temporary 'cavity.OpenFOAM'
************************************************** ********
ParaView failed to open using available graphics hardware.
Trying fallback to software rendering using MESA.
************************************************** ********
/root/OpenFOAM/ThirdParty-6/platforms/linux64Gcc/ParaView-5.4.0/lib/paraview-5.4/paraview: symbol lookup error: /usr/lib64/libQtSql.so.4: undefined symbol: _ZN14QObjectPrivate15checkWindowRoleEv
I'm suspecting that the instructions are not being followed to the letter ... because:
  1. The message in your latest post is still referring to being run as "root".
  2. The file "log.makePV" in the attached file has nothing to do with ParaView, given that it's referring to the output from running "ThirdParty-6/Allwmake".


Quote:
Originally Posted by sjohn2 View Post
2) ./makeParaView > log.makePV2 2>&1

on running paraFoam

Created temporary 'cavity.OpenFOAM'
I/O : uncollated

paraFoam works fine!
I'm glad it's finally working fine, even though it doesn't have Python and MPI working.

After some Googling for the other error, it seems possible that "libQtSql4.so" was installed from another repository and therefore be a mix of 2 different versions of Qt4, which lead to the original crash by ParaView... but it's weird, because it works in one build mode but not the other...

The instructions given in the page I found to diagnose the issue with Qt4 was as follows:
Quote:
Please provide the output of:
Code:
rpm -qa libqt4*
Are you using additional repos?
Code:
zypper lr -d
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Old   January 7, 2019, 11:10
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I think I posted the wrong error text before. I had re installed Third Party software as local user and this the error I get. It is the same except without the root directory:

~/OpenFOAM/OpenFOAM-6/tutorials/incompressible/icoFoam/cavity/cavity> paraFoam
Created temporary 'cavity.OpenFOAM'
************************************************** ********
ParaView failed to open using available graphics hardware.
Trying fallback to software rendering using MESA.
************************************************** ********
/home/sjohn2/OpenFOAM/ThirdParty-6/platforms/linux64Gcc/ParaView-5.4.0/lib/paraview-5.4/paraview: symbol lookup error: /usr/lib64/libQtSql.so.4: undefined symbol: _ZN14QObjectPrivate15checkWindowRoleEv


I have attached the results of the 2 commands you had listed
Attached Files
File Type: gz logzypper.tar.gz (1.6 KB, 1 views)
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Old   January 8, 2019, 18:54
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Quote:
Originally Posted by sjohn2 View Post
/home/sjohn2/OpenFOAM/ThirdParty-6/platforms/linux64Gcc/ParaView-5.4.0/lib/paraview-5.4/paraview: symbol lookup error: /usr/lib64/libQtSql.so.4: undefined symbol: _ZN14QObjectPrivate15checkWindowRoleEv

I have attached the results of the 2 commands you had listed
Quick answers:
  1. There are no clear signs of there being slightly different versions of "libQtSql.so.4" installed, given that the package versions indicated by the rpm command, are identical to the ones on my clean VM installation.
  2. I can't spot any inconsistencies with the repositories you are using in Zypper, at least no clear reason for Qt4 packages to be pulled from the wrong repository.
  3. I'm unable to deduce why this command:
    Code:
    ./makeParaView -python -mpi -python-lib /usr/lib64/libpython2.7.so.1.0 > log.makePV 2>&1
    failed to provide a working build of ParaView, while without Python and MPI worked just fine, namely:
    Code:
    ./makeParaView > log.makePV 2>&1
    • My best guess is that somehow the Python 2.7 or the MPI installations were somehow also using another Qt4 version for whatever weird reason...
  4. If I had access to the actual "log.makePV" that was created from this command:
    Code:
    ./makeParaView -python -mpi -python-lib /usr/lib64/libpython2.7.so.1.0 > log.makePV 2>&1
    when built as normal user, I could then compare to the one on my build and with some luck be able to find a discrepancy on the build process... but without it, I'm just not seeing the breaking point
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Old   January 9, 2019, 10:07
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The file is over 195 Kb limit after compressing using tar. I used 7z but apparently I cannot attach the particular format here. Any ideas how to upload it?

Last edited by sjohn2; January 9, 2019 at 20:02.
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Old   January 9, 2019, 17:19
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Quick answer: You can simply change the file extension and upload it here. As long as you tell us what's the real format, you can pretend it's a ".zip".
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Old   January 10, 2019, 10:22
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Here's the google drive link, let me know if does not work for any reason

https://drive.google.com/file/d/1-JP...ew?usp=sharing
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Old   January 10, 2019, 16:16
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Greetings Stanley,

Ah HA! It's ANSYS fault
At around line 2200 of the log file we can see this:

Code:
CMake Warning at VTK/CMake/vtkModuleMacros.cmake:548 (add_library):
  Cannot generate a safe runtime search path for target
  vtkPVVTKExtensionsRendering because files in some directories may conflict
  with libraries in implicit directories:

    runtime library [libQtGui.so.4] in /usr/lib64 may be hidden by files in:
      /ansys_inc/v191/Framework/bin/Linux64
    runtime library [libQtCore.so.4] in /usr/lib64 may be hidden by files in:
      /ansys_inc/v191/Framework/bin/Linux64
and only stops complaining about it at around line 3069.

Then near the end of the log are lines like this one:
Code:
-- Set runtime path of "/home/sjohn2/OpenFOAM/ThirdParty-6/platforms/linux64Gcc/ParaView-5.4.0/lib/paraview-5.4/paraview" to "/usr/lib64/mpi/gcc/openmpi/lib64:/ansys_inc/v191/Framework/bin/Linux64"
So this is the real problem and why ParaView is not working properly. It has used the local system's Qt4 include files, but then it links to the Qt4 libraries in ANSYS, but even then it tries running ParaView with the system's Qt4 version... so yeah, this was the problem.


OK, so how to solve this... the simplest solution would be to depends on how the ANSYS v19.1 paths are being loaded into the shell variables "PATH" and "LD_LIBRARY_PATH" and deactivate that from being loaded into the shell environment, at least while you are building ParaView.

But if you don't know where that was defined to comment it out and then start a new terminal, then we will have to go the other way around and remove those paths from "PATH" and "LD_LIBRARY_PATH"... OK, if I'm not mistaken, run the following commands before running makeParaView:
Code:
export PATH=$(foamCleanPath "$PATH" "/ansys_inc/v191")
export LD_LIBRARY_PATH=$(foamCleanPath "$LD_LIBRARY_PATH" "/ansys_inc/v191")
These commands will use OpenFOAM's path cleaning script and therefore remove anything that starts with said main path for ANSYS v191.

If all goes well, after you've rebuilt ParaView, it should work as intended. Oh, then don't forget to run the commands for rebuilding the OpenFOAM readers for ParaView, in the same terminal where you build ParaView:
Code:
wmRefresh
cd $FOAM_UTILITIES/postProcessing/graphics/PVReaders 
./Allwclean
./Allwmake
Best regards,
Bruno
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Old   January 10, 2019, 18:33
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Cheers mate! ParsFoam works fine!

Many Thanks
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