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[OpenFOAM.com] Openfoam solvers and snappyHexMesh stopped working in parallel after update

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Old   December 17, 2020, 20:24
Default Openfoam solvers and snappyHexMesh stopped working in parallel after update
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KTG
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Hi everyone,


I recently updated to Fedora 33, and no suddenly I get this error whenever I run snappy or an openFoam solver in parallel:


Quote:
--> FOAM FATAL IO ERROR:
[4] error in IOstream "IOstream" for operation Foam::Istream& Foam:perator>>(Foam::Istream&, Foam::List<T>&) [with T = Foam::Vector<double>]
[4]
[4] file: IOstream at line 0.
[4]
[4] From bool Foam::IOstream::fatalCheck(const char*) const
[4] in file db/IOstreams/IOstreams/IOstream.C at line 63.


I have no idea what this means, or why it is happening. simpleFoam and snappyHexMesh produce the same error! Things still work in serial for some reason. I have tried updating, restarting, running various tutorial files, and keep getting the same behavior. I am not even 100% sure this is an installation issue. I removed the OF binary with dnf, and reinstalled it. Could this be a bug? If it is, it probably can't be reproduced off my computer.



Any help would be much appreciated.


Thanks
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Old   December 17, 2020, 22:04
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I should clarify what I mean by "suddenly". The programs start ok, and then crash after a short time. For example, snappyHexMesh gets to Feature refinement iteration 2 before it throws the error, which is very strange.
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Old   December 18, 2020, 18:43
Angry
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This is so insanely frustrating! I tried on a smaller casefile to see what would happen, and get a slightly different IO error!




Code:
[4] --> FOAM FATAL IO ERROR:  
[4] incorrect first token, expected '(', found on line 0: punctuation '[' 
[4]  
[4] file: IOstream at line 0. 
[4]  
[4]     From Foam::Istream& Foam::operator>>(Foam::Istream&, Foam::List<T>&) [with T = Foam::Pair<int>] 
[4]     in file lnInclude/ListIO.C at line 153. 
[4]  
FOAM parallel run exiting

Here, snappy got further along than before, I think because the mesh is smaller. Its as if something is getting overloaded, causing the crash, and then it sends out and unrelated error from whatever part of the code was currently running.


It gives different behavior every time I run it! I just ran it again and snappy made it all the way through, again, and it crashes during castellated, then again and it crashes during the snap! What could possibly cause this?!
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Old   December 19, 2020, 10:26
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Could be mpi-related.
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Old   December 19, 2020, 21:51
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I had that thought, and did the brainless thing of just reinstalling it - no change. I am not an expert on MPI, so if anyone has an ideas of how to diagnose, let me know!



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Old   January 23, 2021, 23:18
Default I am having the same issue but on Fedora 34
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Quote:
Originally Posted by KTG View Post
I had that thought, and did the brainless thing of just reinstalling it - no change. I am not an expert on MPI, so if anyone has an ideas of how to diagnose, let me know!
Thanks
It definitely seems like an mpi issue with the mpi version in fedora 33/34. Best bet is to try to purge and reinstall openmpi and then rerun Allwmake to see if it works. Or go into prefs file to tell Allwmake to use the openmpi given with the third party folder.
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Old   January 25, 2021, 14:53
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Thanks for the info. I ended up tearing everything down and switching to CentOS to appease IT. Hopefully it is helpful to other Fedora people out there...
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Old   January 25, 2021, 23:52
Default Seems like openmpi in F33 has bugs
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Quote:
Originally Posted by KTG View Post
Thanks for the info. I ended up tearing everything down and switching to CentOS to appease IT. Hopefully it is helpful to other Fedora people out there...
Okay I just build myself the latest OpenMPI (v4.1.0) and it works fine with all openfoam I have (namely 7,8, 1912 and 2012). I think the OpenMPI v 4.04 is bugged
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Old   January 26, 2021, 14:02
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Quote:
Originally Posted by EternalSeekerX View Post
I think the OpenMPI v 4.04 is bugged
Thanks for the heads up.
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Old   February 14, 2021, 02:14
Default An update
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Quote:
Originally Posted by olesen View Post
Thanks for the heads up.
It seems the update to OpenMPI v4.0.5 fixed the issue, either that or me compiling OF8 inside a Fedora 32 container and then transferring it to f34 did the trick?

Edit: Seems like a F33 issue, works flawlessly inside F32 docker I created.
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