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[foam-extend.org] Problems compiling foam-extend-4.0 + fsiFoam on Ubuntu+WSL

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Old   April 22, 2019, 20:45
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Quick answer: Due to how the foam-extend development group wanted the instructions to look like on the wiki (generic and simple to use), I had to write the custom steps for specific versions on the side pages... in theory it's more "efficient", but in practice it's confusing...

To be 100% certain that everything will work as intended, the following commands must give the respective outputs that I got on my Ubuntu 16.04 installation:
  1. Code:
    gcc --version
    Quote:
    gcc (Ubuntu 5.4.0-6ubuntu1~16.04.11) 5.4.0 20160609
    Copyright (C) 2015 Free Software Foundation, Inc.
    This is free software; see the source for copying conditions. There is NO
    warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
  2. Code:
    g++ --version
    Quote:
    g++ (Ubuntu 5.4.0-6ubuntu1~16.04.11) 5.4.0 20160609
    Copyright (C) 2015 Free Software Foundation, Inc.
    This is free software; see the source for copying conditions. There is NO
    warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
  3. Code:
     flex --version
    Quote:
    flex 2.6.0
  4. Code:
    qmake --version
    Quote:
    QMake version 2.01a
    Using Qt version 4.8.7 in /usr/lib/x86_64-linux-gnu


If I don't make a mistake copy-paste-adapting the steps, here is the intended workflow:
  1. Download the source code and place in the correct location, by running:
    Code:
    cd ~
    mkdir foam
    cd foam
    git clone git://git.code.sf.net/p/foam-extend/foam-extend-4.0 foam-extend-4.0
    cd foam-extend-4.0
  2. Install the necessary packages:
    Code:
    sudo apt-get install git-core build-essential binutils-dev cmake flex \
    zlib1g-dev qt4-dev-tools libqt4-dev libncurses5-dev libiberty-dev \
    libxt-dev rpm mercurial graphviz python python-dev
  3. Apply fixes:
    Quote:
    echo "export WM_THIRD_PARTY_USE_BISON_27=1" >> etc/prefs.sh
    echo "export QT_BIN_DIR=/usr/bin/qmake" >> etc/prefs.sh
  4. edit: Forgot this step, namely to activate the foam-extend shell environment:
    Code:
    source etc/bashrc
  5. edit: And the 3rd party build script has to be run individually as well:
    Code:
    ThirdParty/AllMake.pre > log.make3rd 2>&1
  6. Build by running:
    Code:
    ./Allwmake > log.make 2>&1
    ./Allwmake > log.make_summary 2>&1
    The last two commands will redirect all output into the files "log.make" and "log.make_summary". Hopefully the second file reports a summary of what went wrong or right.
    It will take a considerable amount of time to run, but essentially it will build everything that is intended to be built.
    • If things went wrong, run the following command:
      Code:
      gzip < log.make_summary > log.make_summary.gz
      and attach the file "log.make_summary.gz" to your next post... but if it's too large, then upload it to a file sharing website and provide the link here...
    • If you don't know how to access the file from within WSL, start reading here: https://docs.microsoft.com/en-us/win...-i-do-with-wsl
      Then you can use the knowledge of how the directory paths work between WSL and Ubuntu to copy the file, e.g.:
      Code:
      cp log.make_summary.gz /mnt/c/Temp/
      will place the desired file at "C:\Temp"... assuming that folder already exists before copying it to there...
  7. Finally and this is optional, is building swak4Foam, by running:
    Code:
    export WM_NCOMPPROCS=1
    cd $WM_THIRD_PARTY_DIR
    ./AllMake.post  > log.make.post 2>&1
    and the output is sent to the file "log.make.post".

Last edited by wyldckat; April 25, 2019 at 11:07. Reason: fixing a few mistakes, see "edit:" entries
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Old   April 23, 2019, 17:49
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Hi Wyldckat,

Thank you for these detailed instructions. I am trying it now. The first section all gave the output you have.

Do you intend your step 4 ("./Allwmake > log.make 2>&1...") to be run one at a time, or together? I don't understand how but I am able to copy/paste code in multiple lines seemingly fine, but this one seems like one at a time.

It is currently running "./Allwmake > log.make 2>&1".

A possible concern/point of confusion: I use a file browser called Nautilus, and it is showing that the "foam-extend-4.0" folder only contains an "etc" folder, not all the stuff it had before...is this normal? How did ./Allwmake even run if there is no such file there?
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Old   April 23, 2019, 18:28
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Quick answers:
Quote:
Originally Posted by JBrake View Post
The first section all gave the output you have.
OK, then so far so good...

Quote:
Originally Posted by JBrake View Post
Do you intend your step 4 ("./Allwmake > log.make 2>&1...") to be run one at a time, or together? I don't understand how but I am able to copy/paste code in multiple lines seemingly fine, but this one seems like one at a time.

It is currently running "./Allwmake > log.make 2>&1".
Can be done one at a time, but given that each one takes a very long time, you wouldn't know if the second command was working or not until the first one had finished.

Quote:
Originally Posted by JBrake View Post
A possible concern/point of confusion: I use a file browser called Nautilus, and it is showing that the "foam-extend-4.0" folder only contains an "etc" folder, not all the stuff it had before...is this normal? How did ./Allwmake even run if there is no such file there?
Uh... soooo... there are two possibilities that come to mind:
  • Nautilus doesn't work all that well via Xming or whichever X-rendering software you are using to thread the windows from WSL to Windows rendering...
  • Or the path you are located at within Nautilus is actually pointing to some other folder elsewhere, hence the weird situation...
After a quick test, Nautilus for me will show on the top bar the path divided into 3 buttons: Home | foam | foam-extend-4.0
Maybe you're seeing something else? You can double-check where you are in each window:
  • On Nautilus, use the Ctrl+L key combination, to see the full path.
  • On the terminal (er, in another terminal window, while it's building), run:
    Code:
    pwd
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Old   April 23, 2019, 18:42
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I think something is wrong because I cannot open another Ubuntu terminal like I usually can, and my Task Manager shows no process for it. However, I think I am using 100% CPU so when I look at what is using it, it shows several instances of "cc1plus" each using up a portion of the CPU (the number of instances and percentages keep fluctuating).
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Old   April 23, 2019, 18:50
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Quote:
Originally Posted by JBrake View Post
it shows several instances of "cc1plus" each using up a portion of the CPU (the number of instances and percentages keep fluctuating).
Yep, it's compiling at the maximum capacity allowed by your machine... I don't know when you launched the command, but it might take anytime from 30 minutes to 3h, depending on how fast is the CPU in your machine.

------

edit: I'm getting myself a bit ahead of time here, but I've been made aware on another thread that the optional line for building swak4Foam will not work all that well with Ubuntu 16.04... the solution is now given in post #7 on this thread: Error on foam-extend build/comilation

Last edited by wyldckat; April 23, 2019 at 19:23. Reason: see "edit:"
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Old   April 24, 2019, 14:54
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Things are finished running and I have attached the log summary. I can't see anything specific that went wrong, but then again I have no idea how to test things.

The tutorial folders are strange in that the ./Allrun files are outside the individual tutorials. What is the proper way to work inside foam-extend?
Attached Files
File Type: gz log.make_summary.gz (6.0 KB, 3 views)
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Old   April 25, 2019, 06:48
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Greetings JBrake,

It's a holiday in Portugal today, so I'm taking a bit more time to look into this.

Funny thing about using "foam-extend-4.0/Allwmake" is that it does not build anything from ThirdParty... so that's sort-of less one headache... because right now you have a mostly-working installation of foam-extend 4.0.

What it's missing is the following:
  1. Metis wasn't built, so it's no wonder the respective decomposition library wasn't built in foam-extend.
  2. Ditto for Scotch...
  3. Ditto for the Mesquite based mesh motion solver...
  4. And MGridGen... on which dbns depends on...
None of these are critical, although having Metis and Scotch would be nice for decomposing the meshes to run cases in parallel... but I'll get to that, once I'm done with the tests I'm conducting now, which hopefully will be done in about 3-5h from now...




As for the tutorial cases, it would have been useful to know to which cases you were referring to, but the convention is mostly the same for most OpenFOAM versions/forks/variants:
  1. If there is an Allrun script in the case folder, use it.
  2. If there isn't, run this command:
    Code:
    foamRunTutorials
    which will essentially:
    1. Run blockMesh.
    2. Run the solver mentioned in the file "system/controlDict".
Best regards,
Bruno


edit: I've finished testing, here are the commands needed to finish up your build:
  1. Go into the foam-extend-4.0 folder by running:
    Code:
    foam
  2. The 3rd party build script must be run:
    Code:
    ThirdParty/AllMake.pre > log.make3rd 2>&1
    ThirdParty/AllMake.pre > log.make3rd_summary 2>&1
    In "log.make3rd_summary" we get the summary...
  3. Then re-run the Allwmake script again, to wrap up the loose parts:
    Code:
    ./Allwmake > log.make 2>&1
    ./Allwmake > log.make_summary 2>&1
    And again, the summary file "log.make_summary" will tell us if everything went well or not.
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Last edited by wyldckat; April 25, 2019 at 11:10.
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Old   April 25, 2019, 15:09
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The process stopped with nothing in the terminal, so I checked log.make3rd and as I expected, it stopped with this:

Quote:
Making package metis-5.1.0 using RPM.
Building package metis-5.1.0 using SPEC file : metis-5.1.0.spec. Optional args:
Something about my system cannot install things this way. It always gets stuck on this part, no matter the program.

Edit: By stop, I mean it gets stuck. There is no prompt in the terminal, as if it were still running, but it's using no CPU.

Last edited by JBrake; April 25, 2019 at 16:51.
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Old   April 25, 2019, 18:56
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I have some good news about it getting stuck... this isn't a new issue and there is sort-of a fix: https://github.com/Microsoft/WSL/issues/3233

I was able to reproduce the issue with Ubuntu 16.04 on WSL (I was using a VM until now) and the issue is that the RPM database becomes corrupted due to a weird bug under WSL... the fix is to run the following command for repairing the RPM database:
Code:
rpm --rebuilddb --dbpath $HOME/foam/foam-extend-4.0/ThirdParty/rpmBuild/rpmDB
Uh... well, apparently it's not enough. We have to simultaneously always repair the issue whenever rpmbuild is used, as well as manually unpack the generated tarballs...

So, the steps needed for building the ThirdParty packages and wrap up foam-extend with success, should be as follows:
  1. Run these commands:
    Code:
    foam
    sed -i -e 's=\(  ${RPM_CMD}\)=rpm --rebuilddb --dbpath $buildBase/rpmDB;\1=' -e 's=\(  rpmbuild\)=rpm --rebuilddb --dbpath $buildBase/rpmDB;\1=' ThirdParty/tools/makeThirdPartyFunctionsForRPM
  2. Then try running the build script again:
    Code:
    ThirdParty/AllMake.pre > log.make3rd 2>&1
    ThirdParty/AllMake.pre > log.make3rd_summary 2>&1
    Hopefully it doesn't lock up this time around...
  3. Then we need to unpack the built packages manually:
    Code:
    cd ThirdParty
    for a in rpmBuild/TGZS/*/*.tgz; do tar -xf $a; done
    du -sh packages/
    cd ..
    It may take a few seconds to unpack, but it luck it doesn't take more than a minute. The du command should tell you that the unpackaged 'packages' folder is occupying around 41 MB.
  4. And finally, wrap up the foam-extend build:
    Code:
    ./Allwmake > log.make 2>&1
    ./Allwmake > log.make_summary 2>&1
Hopefully this finally sorts things out...
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Old   April 26, 2019, 13:52
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I think things finished with no errors, but I won't have time to test it today. Here is my log.make_summary from the second run.

Thank you so much for all the help and detailed instructions. I have a feeling working with foam-extend itself will present plenty of challenges and that I will be back on the forum in the near future.
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Old   April 26, 2019, 13:59
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Finally, it seems to have built properly without problems, since the summary seems all OK.

It's missing ParaView, but after so much trouble to get to this point and given that you're working with WSL, you might as well use ParaView on Windows natively or use another OpenFOAM installation to give you ParaView from within WSL...
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Old   April 29, 2019, 15:53
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Thanks again wyldckat!

The main reason I am needing foam-extend in the first place is to try fsiFoam. After installing I get the same bug that other users using fe4.0 have, and there is a thread about how to fix it here:

https://www.cfd-online.com/Forums/op...tutorials.html

Should I just trust this kind of thread and follow it in hopes that things work? Why haven't the installation instructions simply been updated and/or fixed to incorporate the necessary changes?
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Old   April 29, 2019, 20:11
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Quick answer:
Quote:
Originally Posted by JBrake View Post
Should I just trust this kind of thread and follow it in hopes that things work? Why haven't the installation instructions simply been updated and/or fixed to incorporate the necessary changes?
Each FSI toolkit version has had a single release for each foam-extend version, but foam-extend keeps changing in the meantime.

Quoting myself from a recent post:
Quote:
Originally Posted by wyldckat View Post
Note: The solids4Foam toolkit merges and extends the FSI toolkit with the solidMechanics toolkit.
  • It's currently (mid-April 2019) still in development, so access is restricted to those who ask for access to the repository. Send a Private Message to the forum member bigphil with your email address and a statement as to why you want access to it; it will require you to create an account at bitbucket.org.
So unless you reaaaally need to use the old FSI toolkit version, it's best that you switch to using the solids4Foam toolkit.

By the way, there is a new sub-forum for these FSI toolkits and FSI simulations here: https://www.cfd-online.com/Forums/op...e-interaction/
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Old   April 30, 2019, 14:14
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Quote:
Originally Posted by wyldckat View Post
So unless you reaaaally need to use the old FSI toolkit version, it's best that you switch to using the solids4Foam toolkit.
I might do that, but for now I need to learn the basics of fsiFoam and determine if it will work for my research. I think going to the fsi part of the forum you shared will be very helpful.

I noticed that typing "paraFoam" works as before when I used OpenFoam (not extend), but it has reverted to some older version of paraview? How do I update paraview and make sure I'm using that version with my new foam-extend environment, or do I have to use this older verion (4.4)?
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Old   April 30, 2019, 19:28
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Quote:
Originally Posted by JBrake View Post
How do I update paraview and make sure I'm using that version with my new foam-extend environment, or do I have to use this older verion (4.4)?
The simplest trick is to use 2 terminal windows or tabs:
  1. In the first terminal you use foam-extend.
  2. In the second terminal you use OpenFOAM.
This way you don't need to go around messing with foam-extend's installation any further.

You can easily activate a shell environment per terminal by following the instructions given here: https://openfoamwiki.net/index.php/I...nFOAM_versions

I actually didn't expect for ParaView 4.4 to have built successfully with foam-extend, so I was going to give the same exact solution if it hadn't been built.
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Last edited by wyldckat; April 30, 2019 at 19:59. Reason: removed excess line breaks
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Old   June 20, 2019, 15:18
Default Similar fix on 18.04?
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Hi Wyldkat,

Do you know if there is a similar fix (editing the rpmbuild files, etc...) for Ubunutu 18.04? I have tried the solution for 16.04, and like expected, it did not work on 18.04.

I did download 16.04 and try this fix on that version, and it works! Thank you very much!

Thanks.
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Old   July 23, 2019, 19:53
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Quote:
Originally Posted by russel60 View Post
Do you know if there is a similar fix (editing the rpmbuild files, etc...) for Ubunutu 18.04? I have tried the solution for 16.04, and like expected, it did not work on 18.04.
Quick question, although somewhat late: Did you first do the steps provided here: https://openfoamwiki.net/index.php/I...u#Ubuntu_18.04 ? Because a fix that is first needed for Ubuntu 18.04 is provided there. Only then perhaps the trick above for working around RPM issues on WSL may or may not work.
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Old   July 24, 2019, 08:20
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Quote:
Originally Posted by wyldckat View Post
Quick question, although somewhat late: Did you first do the steps provided here: https://openfoamwiki.net/index.php/I...u#Ubuntu_18.04 ? Because a fix that is first needed for Ubuntu 18.04 is provided there. Only then perhaps the trick above for working around RPM issues on WSL may or may not work.
Yes, I tried those steps again this morning and it did not work. Seems to be getting stuck between the new version and the old version. See the log file attached.

It crossed my mind that it might be worth trying to completely wipe FE4 and try again from scratch, but at this point I have work that I can't risk losing in my working (ish) version of Foam-Extend. Is there a way to get a clean install while maintaining the data and custom solvers I have in my current version?
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Old   July 25, 2019, 18:45
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Quote:
Originally Posted by russel60 View Post
Is there a way to get a clean install while maintaining the data and custom solvers I have in my current version?
There is one somewhat crazy way to do it... create a new user in your Windows 10 machine and install Ubuntu 18.04 via Microsoft Store on that new user's account. Technically it should install separately from your own user account. It's the only way to ensure it is completely separate.

But I'll have to take a look into this myself. WSL is a pain in the neck with these limitations... although it should be possible to compile foam-extend directly on Windows, so that's another way to do it cleanly.
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Old   August 21, 2019, 01:39
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Hi all,

Thanks to Wyldckat for the helpful answers. I followed the steps given on this forum, but facing errors in the final build using ./Allwmake runs. My .gz files is attached. Also, du -sh packages/ showed me 39 MB.

Can someone please guide me on where I got it wrong?
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File Type: gz log.make_summary.gz (10.1 KB, 1 views)
File Type: gz log.make3rd_summary.gz (11.4 KB, 1 views)
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