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[foam-extend.org] NEW: Installation guide for foam-extend 4.1 on OpenFoamWiki

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Old   November 26, 2019, 11:03
Default NEW: Installation guide for foam-extend 4.1 on OpenFoamWiki
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Torsten Schenkel
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Hi All,


Since the requirements for foam-extend 4.1 have changed, I have put a new set of instructions on the openfoamwiki.


They have been tested by me (and a colleague and students who are not Linux experts) and should work out-of-the-box. But let me know, if they don't.


Ubuntu version 18.04 LTS and 19.10 is complete. CentOS 7 coming up.


Have fun.
Torsten
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Old   December 4, 2019, 18:02
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I was about to give a like your thread..

..until realising that I have already liked it.

Thanks for your contribution. I really like foam-extend.
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Old   December 8, 2019, 10:53
Default If is it possible to make an instruction of installation on Windows 7 Platform?
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Thank you for your contribution! Recently, I have suffered tortures from compiling the source codes of foam extend on Windows 7 using MinGW, though I followed the instruction in documents of the codes strictly even the version of the dependences. I haven't compiled the scotch in ThirdParty successfull yet so I don't know how many errors I would face during compiling of the main codes. I really expect that an expert can help me
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Old   December 18, 2019, 14:48
Default Centos 7 instructions would be awesome!
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Thank you for posting Ubuntu instructions on the foam wiki. I would love an explanation of how to get things installed on Centos 7 when you have the time. I am currently working on a wing-flapping simulation which some fairly large deformations (90 deg pitching about the x-axis, 30ish about the y and z) and the motion solvers built into Openfoam 7 don't seem to be able to handle that degree of morphing. I am hoping that laplaceFaceDecomposition can do the trick!

Regards,
Anthony
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Old   December 19, 2019, 06:16
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Hi Anthony,


Thanks for the nudge. Instructions for CentOS are online now.



I only have CentOS on the cluster and that is using the Open-HPC environment, but had a quick test in an old VMware image and it seems to work.


Let me know if it does for you.


There may be an issue compiling swak4foam (the last step in the process), so if you get an error referring to BISON and "maintenancescript", let me know.


Best
T
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Old   December 19, 2019, 14:29
Default Centos 7 is working, I think
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Thank you for getting on that so quickly!

I got a weird response when trying to install the first two dependencies (see code below). But strangely enough, things seem to be compiling after typing
Code:
 ./Allwmake.firstInstall
. I have OpenFOAM 6 and 7 already on this server and both were compiled from the source, so I am guessing things will work. I will update when it finishes up (it's been 1.5 hours since running the ./Allwmake so far).

Code:
[al113405@cfd Desktop]$ sudo yum -y groupinstall Development\ Tools
[sudo] password for al113405: 
Sorry, try again.
[sudo] password for al113405: 
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile
 * base: mirror.shastacoe.net
 * centos-sclo-rh: mirrors.cat.pdx.edu
 * centos-sclo-sclo: repo1.sea.innoscale.net
 * epel: d2lzkl7pfhq30w.cloudfront.net
 * extras: mirrors.xmission.com
 * updates: mirror.web-ster.com
Maybe run: yum groups mark install (see man yum)
No packages in any requested group available to install or update
[al113405@cfd Desktop]$ sudo yum -y install wmake
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile
 * base: mirror.shastacoe.net
 * centos-sclo-rh: mirrors.cat.pdx.edu
 * centos-sclo-sclo: repo1.sea.innoscale.net
 * epel: d2lzkl7pfhq30w.cloudfront.net
 * extras: centos.sonn.com
 * updates: mirror.web-ster.com
No package wmake available.
Error: Nothing to do
[al113405@cfd Desktop]$
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Old   December 19, 2019, 17:16
Default Centos 7 working
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Everything seems to work! I don't know if swak4foam ended up installing. I forgot to log the Allmake.

Strangely enough, it seems that laplaceFaceDecomposition is gone from foam-extend. I'll have to do some searching to see if I can find it.

Thank you,
Anthony
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Old   December 28, 2019, 17:20
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Quote:
Originally Posted by tschenkel View Post
Hi Anthony,


Thanks for the nudge. Instructions for CentOS are online now.



I only have CentOS on the cluster and that is using the Open-HPC environment, but had a quick test in an old VMware image and it seems to work.


Let me know if it does for you.


There may be an issue compiling swak4foam (the last step in the process), so if you get an error referring to BISON and "maintenancescript", let me know.


Best
T
Do the issues compiling swak4foam manifest as tar.hh files not found as in the attached log? Are there recommendations how to correct for a successful installation? Iím experiencing trouble installing swak4foam in a ubuntu (openfoam 5) and centOS (openfoam v1906) with the same errors. Attempts have been made to install after compileRequirements.sh and also a clean install with WmakeAll. These from the mercurial download from the swak4foam twitter feed.

Apologies if there is a better thread into which to ask this question. I havenít found a related solution (or install symptoms) in other threads.

Thank you,
Jeff
Attached Files
File Type: txt log.AllwmakeAll.txt (52.7 KB, 11 views)
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Old   January 21, 2020, 07:10
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Hi Torsten,

Thanks a lot for updating the Wiki for foam-extend-4.1! I just used your instructions to install foam-extend-4.1 from source, under Ubuntu-18.04 LTS (clean install). I was surprised to notice that apparently Ubuntu-18.04 LTS comes without OpenMPI; I had to install libopenmpi-dev and openmpi-bin manually. The Allwmake script is still running, so I'm not sure yet whether my install will be successful, but at least I wanted to let you know that perhaps you should add libopenmpi-dev and openmpi-bin to the list of packages to install.

Cheers,
Sita
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Old   January 21, 2020, 07:38
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Hi Sita,


most FOAM installation ship their own MPI to avoid incompatibilities with the system wide installation of openMPI.

You can force the installation to use a system MPI, but if you followed the instructions, it will compile a local version of openMPI which will be installed in the foam directory and FOAM will ignore the systemwide installation.



That said, if you need openMPI for other things, then the system-installation and the FOAM installation should be happy to cohabit on the same system (i have a system MPI, but use the FOAM openMPI for convenience and to not have to troubleshoot students' systems).
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Old   January 21, 2020, 07:44
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No, the problems would only be the make system asking you to go and run the maintanancescript (to install local versions of Bison and LUA). Your problems seem to start quite a lot earlier (on line 49).



Quote:
Originally Posted by stewaj5 View Post
Do the issues compiling swak4foam manifest as tar.hh files not found as in the attached log? Are there recommendations how to correct for a successful installation? Iím experiencing trouble installing swak4foam in a ubuntu (openfoam 5) and centOS (openfoam v1906) with the same errors. Attempts have been made to install after compileRequirements.sh and also a clean install with WmakeAll. These from the mercurial download from the swak4foam twitter feed.

Apologies if there is a better thread into which to ask this question. I havenít found a related solution (or install symptoms) in other threads.

Thank you,
Jeff
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Old   January 21, 2020, 09:05
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Hi Torsten,

Ah, right, I must have missed something in the instructions then; my install somehow uses the system MPI.

By the way, the build finished successfully. I got a few errors (metisDecomp, MGridGenGAMGAgglomerate, mgMeshLevel, dbnsFoam, dbnsTurbFoam, compressible), but as long as I don't touch any of these, everything works fine so far, so thanks again for those instructions!

Sita


P.S. Something goes wrong with the ParaView install too. According to the log file, the system installed QT was used, but QT_BIN_DIR is not set, so the installation of ParaView was skipped altogether. My foam-extend (git clone) doesn't have a prefs.sh, only prefs.sh-EXAMPLE and prefs.sh.mingw, am I supposed to create this manually, using the example?


Quote:
Originally Posted by tschenkel View Post
Hi Sita,


most FOAM installation ship their own MPI to avoid incompatibilities with the system wide installation of openMPI.

You can force the installation to use a system MPI, but if you followed the instructions, it will compile a local version of openMPI which will be installed in the foam directory and FOAM will ignore the systemwide installation.



That said, if you need openMPI for other things, then the system-installation and the FOAM installation should be happy to cohabit on the same system (i have a system MPI, but use the FOAM openMPI for convenience and to not have to troubleshoot students' systems).

Last edited by sita; January 21, 2020 at 11:02.
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Old   January 22, 2020, 07:12
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Nearly there now, just can't seem to get paraFoam to work completely. With the Third Party ParaView, I kept getting errors (latest one: "gcc: error: ARGS: no such file or directory", like also reported in this thread - without solutions unfortunately). So I decided to install ParaView separately, and go with this system install instead.Now at least ParaView works, but upon entering paraFoam, I got this warning:

Code:
Cannot use ParaView reader module library (PVFoamReader)
The PV_PLUGIN_PATH environment value is not set

Continuing with builtin reader:  paraFoam -vtk

Created temporary 'cavity.foam'
So I manually set the PV_PLUGIN_PATH, and then got:

Code:
Cannot use ParaView reader module library (PVFoamReader) - not built?
Consider building the reader module
    cd $WM_PROJECT_DIR/applications/utilities/postProcessing/graphics/PVReaders
    ./Allwclean
    ./Allwmake

Continuing with builtin reader:  paraFoam -vtk

Created temporary 'cavity.foam'
(Re-)building the reader module didn't do anything, as far as I can see now.

The built-in vtk reader works alright, it just gives some warnings every time, but still, I'd like to have everything working as it should. Does anyone have any tips on how best to fix this?

Many thanks,
Sita


P.S. In the end I did create a prefs.sh file manually, using the example file. This got me rid of the errors I mentioned earlier, but clearly it didn't fix quite everyting
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Old   January 29, 2020, 10:28
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Hi all,

I'm having a terribly hard time getting ParaView installed properly under foam-extend-4.1. As I explained in my previous post, with the system installed ParaView the PVFoamReader won't work. If I try to build the ThirdParty version of ParaView, I get a CMake error about not being able to find some Qt5 files. However, in my prefs.sh I explicitly specify

Code:
export WM_THIRD_PARTY_USE_QT_486=1
I even switched to the ThirdParty Qt, but that didn't help either. How can I tell CMake to use Qt4?

Many thanks,
Sita
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Old   January 29, 2020, 11:52
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Quote:
Originally Posted by sita View Post
My foam-extend (git clone) doesn't have a prefs.sh, only prefs.sh-EXAMPLE and prefs.sh.mingw, am I supposed to create this manually, using the example?
Hi, yes, the commands as they are will create a new prefs.sh file.
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Old   January 29, 2020, 11:55
Default Paraview problems
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Not sure what causes the paraview problems - I cannot reproduce them on my system (following instructions based on a bare-metal installation). I have paraview 5.7 installed from the tar-ball download on all my systems which works fine with the built-in reader.

It should work out of the box (fe41 creates a $CASENAME.foam file when paraFoam is called, and then starts paraview $CASENAME.foam).

If it doesnt, you could try:

a) Either create a file $CASENAME.foam
b) or use the --native-reader option of paraFoam
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Old   January 29, 2020, 13:50
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Hi Torsten,

Thanks, I'll give that a try.

Cheers,
Sita
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Old   February 1, 2020, 06:12
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For those who (unfortunately) runs WSL, the easiest (ok not the easiest, but this way you skip paraview that brigs along a lot of useless stuff under wsl) way to install foam-extend-4.1 is the following:

1. Download .deb package in $HOME and create a temp working directory (like mkdir ~/fe41)
2. Unpack the package with
Code:
sudo dpkg-deb -R foam-extend-4.1_blablalba.deb ~/fe41/
3. Move, change ownership, cleanup
Code:
sudo mv ~/fe41/foam /opt/
sudo chown -r $USER /opt/foam
sudo rm -rf ~/fe41
4. Install minimal deps
Code:
sudo apt install build-essentials m4 bison flex libopenmpi-dev
5. Create alias or source /opt/foam/foam-extend-4.1/etc/bashrc and make usual post-install stuff (mkdir -p {$FOAM_RUN, $FOAM_USER_APPBIN, $FOAM_USER_LIBBIN}, etc etc)

Should run under clean ubuntu 18.04, if it doesn't just fix any missing dep. Custom solver compilation works as expected and all the tutorials ran fine. If you have any issue try to ask but it should go flawlessly.

Obviously forget about paraFoam, as usual postprocessing is made with standard paraview.

bye
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Old   February 2, 2020, 13:43
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Quote:
Originally Posted by time- View Post
For those who (unfortunately) runs WSL, the easiest (ok not the easiest, but this way you skip paraview that brigs along a lot of useless stuff under wsl) way to install foam-extend-4.1 is the following:

1. Download .deb package in $HOME and create a temp working directory (like mkdir ~/fe41)
2. Unpack the package with
Code:
sudo dpkg-deb -R foam-extend-4.1_blablalba.deb ~/fe41/
3. Move, change ownership, cleanup
Code:
sudo mv ~/fe41/foam /opt/
sudo chown -r $USER /opt/foam
sudo rm -rf ~/fe41
4. Install minimal deps
Code:
sudo apt install build-essentials m4 bison flex libopenmpi-dev
5. Create alias or source /opt/foam/foam-extend-4.1/etc/bashrc and make usual post-install stuff (mkdir -p {$FOAM_RUN, $FOAM_USER_APPBIN, $FOAM_USER_LIBBIN}, etc etc)

Should run under clean ubuntu 18.04, if it doesn't just fix any missing dep. Custom solver compilation works as expected and all the tutorials ran fine. If you have any issue try to ask but it should go flawlessly.

Obviously forget about paraFoam, as usual postprocessing is made with standard paraview.

bye
Just in case you want to run parallel cases:

The debian package does not have the bugfix that allows to use the GAMG solver for the pressure equation in parallel runs.
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Old   February 3, 2020, 09:40
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Hi Torsten,

In the end I decided to delete everything and start from scratch (Ubuntu 18-04). Unfortunately I'm running into the exact same errors again (foam-extend can't find OpenMPI, paraFoam not working, etc.). So, when you wrote

Quote:
Originally Posted by tschenkel View Post
Hi, yes, the commands as they are will create a new prefs.sh file.
did you mean that, when following the instructions in the Wiki, prefs.sh will be created? In my case it wasn't, I'm afraid. I'll start over once more, with a manually created prefs.sh this time, hopefully that'll improve things.

If you have any ideas as to what I'm doing wrong, please let me know.

Thanks,
Sita


EDIT: just to be sure, I set export QT_THIRD_PARTY=1. In that case, the QT ThirdParty scripts are supposed to take care of setting QT_DIR and QT_BIN_DIR, but still I got the message: QT_BIN_DIR not set ..... Proceed without compiling ParaView? What's happening here?
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