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Issues with OpenFOAM in parallel computing

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Old   July 1, 2022, 07:44
Post Issues with OpenFOAM in parallel computing
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Jelle Lagerweij
Join Date: Jul 2022
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Dear cfd friends,
I am a master student that just started his internship. I have used Ansys before and coded my own 2D FVM in python, but my temporary employer wants to use OpenFOAM. So I am learning something new. To make everything work, I created a clean ubuntu install and added Paraview, OpenFOAM and Bender to it. I also executed the following command:


Code:
sudo apt-get -y install openmpi-bin
to make sure that my install would execute multicore applications correctly.


After some single core tutorials, I encountered the depthCharge3D case. I think that I executed all basic commands correctly, in order:



Code:
blockMesh
Code:
decomposePar
Code:
mpirun -np 4 compressibleInterFoam -parallel
I also checked if my core count matches that in the decomposeParDict file,

but I still get the following error message:
Code:
--> FOAM FATAL ERROR: 
bool IPstream::init(int& argc, char**& argv) : attempt to run parallel on 1 processor

    From function static bool Foam::UPstream::init(int&, char**&, bool)
    in file UPstream.C at line 112.

--> FOAM FATAL ERROR: 
bool IPstream::init(int& argc, char**& argv) : attempt to run parallel on 1 processor

    From function static bool Foam::UPstream::init(int&, char**&, bool)
    in file UPstream.C at line 112.

FOAM aborting



--> FOAM FATAL ERROR: 
bool IPstream::init(int& argc, char**& argv) : attempt to run parallel on 1 processor

    From function static bool Foam::UPstream::init(int&, char**&, bool)
    in file UPstream.C at line 112.

FOAM aborting



--> FOAM FATAL ERROR: 
bool IPstream::init(int& argc, char**& argv) : attempt to run parallel on 1 processor

    From function static bool Foam::UPstream::init(int&, char**&, bool)
    in file UPstream.C at line 112.

FOAM aborting



FOAM aborting

#0  #0  #0  Foam::error::printStack(Foam::Ostream&)#0  Foam::error::printStack(Foam::Ostream&)Foam::error::printStack(Foam::Ostream&)Foam::error::printStack(Foam::Ostream&) at ??:?
 at ??:?
 at ??:?
 at ??:?
#1  #1  Foam::error::abort()Foam::error::abort()#1  #1  Foam::error::abort()Foam::error::abort() at ??:?
#2  Foam::UPstream::init(int&, char**&, bool) at ??:?
#2  Foam::UPstream::init(int&, char**&, bool) at ??:?
#2  Foam::UPstream::init(int&, char**&, bool) at ??:?
#2  Foam::UPstream::init(int&, char**&, bool) at ??:?
 at ??:?
 at ??:?
 at ??:?
#3  Foam::argList::argList(int&, char**&, bool, bool, bool)#3  #3  Foam::argList::argList(int&, char**&, bool, bool, bool)#3  Foam::argList::argList(int&, char**&, bool, bool, bool)Foam::argList::argList(int&, char**&, bool, bool, bool) at ??:?
#4   at ??:?
#4   at ??:?
#4   at ??:?
#4  ???? in  in ""/opt/openfoam9/opt/openfoam9/platform in /platforms/linux64GccDPInt3s/linux64GccDPInt32Opt/bin/2Opt/bin/compressicompressibleInterFoa"/opt/openfoam9/platforms/linux64GccbleInterFoam"
m"
DPInt32Opt/bin/compressibleInterFoam"
 in #5  ?#"/opt/ope5  ?nfoam9/platforms/linu#5  ?x64GccDPInt32Opt/bin/compressibleInterFoam"
#5  ? in "/lib/x86_64-linux-gnu/libc.so.6"
 in "/lib/x86_64-linux-gnu/libc.so.6"
#6  #6  __libc_start_main__libc_start_main in "/lib/x in 86_64-linux-gnu/lib"/lib/x86_64-c.so.6"
linux-gnu/libc.so.6"
#6#6    __libc_start_main__libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6"
#7   in "/lib/x86_6 in "/lib/x86_64-linux-gnu/libc.so.6"
4-linux-gnu/libc.so.6"
#7  #7   in "/lib/x86_64-linux-gnu/libc.so.6"
#7  ???? in "/opt/openfoam9/platforms/linux64GccDPInt32Opt/bin/compressibleInterFoam"
[jelle-IdeaPad-5-Pro-16ACH6:07394] *** Process received signal ***
[jelle-IdeaPad-5-Pro-16ACH6:07394] Signal: Aborted (6)
[jelle-IdeaPad-5-Pro-16ACH6:07394] Signal code:  (-6)
[jelle-IdeaPad-5-Pro-16ACH6:07394] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x7fd627260520]
[jelle-IdeaPad-5-Pro-16ACH6:07394] [ 1] /lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x12c)[0x7fd6272b4a7c]
[jelle-IdeaPad-5-Pro-16ACH6:07394] [ 2]  in "/opt/openfoam9/lib/x86_64-linux-gnu/libc.so.6(raise+0x16)[0x7fd627260476]
[jelle-IdeaPad-5-Pro-16ACH6:07394] [ 3] /platforms/linux64GccDPInt32Opt in /bin/compressibleI"/opt/openfoanterFoam"
m9/platforms/li/lib/x86_64-linux-gnu/libc.so.6(abort+0xd3)[0x7fd6272467f3]
[jelle-IdeaPad-5-Pro-16ACH6:07394] [ 4] nux64GccDPInt32Opt/bin/compressibleInterFoam"
[jelle-IdeaPad-5-Pro-16ACH6:07395] *** Process received signal ***
[jelle-IdeaPad-5-Pro-16ACH6:07395] Signal: Aborted (6)
[jelle-IdeaPad-5-Pro-16ACH6:07395] Signal code:  (-6)
[jelle-IdeaPad-5-Pro-16ACH6:07392] *** Process received signal ***
[jelle-IdeaPad-5-Pro-16ACH6:07392] Signal: Aborted (6)
[jelle-IdeaPad-5-Pro-16ACH6:07392] Signal code:  (-6)
[jelle-IdeaPad-5-Pro-16ACH6:07395] [ 0] [jelle-IdeaPad-5-Pro-16ACH6:07392] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x7f98eb713520]
[jelle-IdeaPad-5-Pro-16ACH6:07395] [ 1] /lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x7f88d7b2e520]
[jelle-IdeaPad-5-Pro-16ACH6:07392] [ 1] /lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x12c)[0x7f98eb767a7c]
[jelle-IdeaPad-5-Pro-16ACH6:07395] [ 2]  in "/opt/openfoam9/pla/lib/x86_64-linux-gnu/libc.so.6(raise+0x16)[0x7f98eb713476]
[jelle-IdeaPad-5-Pro-16ACH6:07395] [ 3] /lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x12c)[0x7f88d7b82a7c]
[jelle-IdeaPad-5-Pro-16ACH6:07392] [ 2] tforms/linux64GccDPInt32Opt/bin/compressibleInt/lib/x86_64-linux-gnu/libc.so.6(abort+0xd3)[0x7f98eb6f97f3]
[jelle-IdeaPad-5-Pro-16ACH6:07395] [ 4] erFoam"
/lib/x86_64-linux-gnu/libc.so.6(raise+0x16)[0x7f88d7b2e476]
[jelle-IdeaPad-5-Pro-16ACH6:07392] [ 3] /lib/x86_64-linux-gnu/libc.so.6(abort+0xd3)[0x7f88d7b147f3]
[jelle-IdeaPad-5-Pro-16ACH6:07392] [ 4] [jelle-IdeaPad-5-Pro-16ACH6:07393] *** Process received signal ***
[jelle-IdeaPad-5-Pro-16ACH6:07393] Signal: Aborted (6)
[jelle-IdeaPad-5-Pro-16ACH6:07393] Signal code:  (-6)
[jelle-IdeaPad-5-Pro-16ACH6:07393] [ 0] /opt/openfoam9/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam5error5abortEv+0x20d)[0x7fd627a5243d]
[jelle-IdeaPad-5-Pro-16ACH6:07394] [ 5] /opt/openfoam9/platforms/linux64GccDPInt32Opt/lib/openmpi-system/libPstream.so(_ZN4Foam8UPstream4initERiRPPcb+0x3e9)[0x7fd627214d19]
[jelle-IdeaPad-5-Pro-16ACH6:07394] [ 6] /lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x7ff84935f520]
[jelle-IdeaPad-5-Pro-16ACH6:07393] [ 1] /lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x12c)[0x7ff8493b3a7c]
[jelle-IdeaPad-5-Pro-16ACH6:07393] [ 2] /lib/x86_64-linux-gnu/libc.so.6(raise+0x16)[0x7ff84935f476]
[jelle-IdeaPad-5-Pro-16ACH6:07393] [ 3] /lib/x86_64-linux-gnu/libc.so.6(abort+0xd3)[0x7ff8493457f3]
[jelle-IdeaPad-5-Pro-16ACH6:07393] [ 4] /opt/openfoam9/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam5error5abortEv+0x20d)[0x7f98ebf0543d]
[jelle-IdeaPad-5-Pro-16ACH6:07395] [ 5] /opt/openfoam9/platforms/linux64GccDPInt32Opt/lib/openmpi-system/libPstream.so(_ZN4Foam8UPstream4initERiRPPcb+0x3e9)[0x7f98eb6c7d19]
[jelle-IdeaPad-5-Pro-16ACH6:07395] [ 6] /opt/openfoam9/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam5error5abortEv+0x20d)[0x7f88d832043d]
[jelle-IdeaPad-5-Pro-16ACH6:07392] [ 5] /opt/openfoam9/platforms/linux64GccDPInt32Opt/lib/openmpi-system/libPstream.so(_ZN4Foam8UPstream4initERiRPPcb+0x3e9)[0x7f88d7ae2d19]
[jelle-IdeaPad-5-Pro-16ACH6:07392] [ 6] /opt/openfoam9/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam7argListC1ERiRPPcbbb+0x7a8)[0x7fd627a6dbf8]
[jelle-IdeaPad-5-Pro-16ACH6:07394] [ 7] compressibleInterFoam(+0x4a744)[0x55bd83793744]
[jelle-IdeaPad-5-Pro-16ACH6:07394] [ 8] /lib/x86_64-linux-gnu/libc.so.6(+0x29d90)[0x7fd627247d90]
[jelle-IdeaPad-5-Pro-16ACH6:07394] [ 9] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80)[0x7fd627247e40]
[jelle-IdeaPad-5-Pro-16ACH6:07394] [10] /opt/openfoam9/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam7argListC1ERiRPPcbbb+0x7a8)[0x7f98ebf20bf8]
[jelle-IdeaPad-5-Pro-16ACH6:07395] [ 7] /opt/openfoam9/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam7argListC1ERiRPPcbbb+0x7a8)[0x7f88d833bbf8]
[jelle-IdeaPad-5-Pro-16ACH6:07392] compressibleInterFoam(+0x5d7e5)[0x55bd837a67e5]
[jelle-IdeaPad-5-Pro-16ACH6:07394] *** End of error message ***
compressibleInterFoam(+0x4a744)[0x557f23976744]
[jelle-IdeaPad-5-Pro-16ACH6:07395] [ 8] [ 7] compressibleInterFoam(+0x4a744)[0x561c01670744]
[jelle-IdeaPad-5-Pro-16ACH6:07392] [ 8] /opt/openfoam9/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam5error5abortEv+0x20d)[0x7ff849b5143d]
[jelle-IdeaPad-5-Pro-16ACH6:07393] [ 5] /opt/openfoam9/platforms/linux64GccDPInt32Opt/lib/openmpi-system/libPstream.so(_ZN4Foam8UPstream4initERiRPPcb+0x3e9)[0x7ff849313d19]
[jelle-IdeaPad-5-Pro-16ACH6:07393] [ 6] /lib/x86_64-linux-gnu/libc.so.6(+0x29d90)[0x7f98eb6fad90]
[jelle-IdeaPad-5-Pro-16ACH6:07395] [ 9] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80)[0x7f98eb6fae40]
[jelle-IdeaPad-5-Pro-16ACH6:07395] [10] /lib/x86_64-linux-gnu/libc.so.6(+0x29d90)[0x7f88d7b15d90]
[jelle-IdeaPad-5-Pro-16ACH6:07392] [ 9] compressibleInterFoam(+0x5d7e5)[0x557f239897e5]
[jelle-IdeaPad-5-Pro-16ACH6:07395] *** End of error message ***
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80)[0x7f88d7b15e40]
[jelle-IdeaPad-5-Pro-16ACH6:07392] [10] compressibleInterFoam(+0x5d7e5)[0x561c016837e5]
[jelle-IdeaPad-5-Pro-16ACH6:07392] *** End of error message ***
/opt/openfoam9/platforms/linux64GccDPInt32Opt/lib/libOpenFOAM.so(_ZN4Foam7argListC1ERiRPPcbbb+0x7a8)[0x7ff849b6cbf8]
[jelle-IdeaPad-5-Pro-16ACH6:07393] [ 7] compressibleInterFoam(+0x4a744)[0x55a3eb964744]
[jelle-IdeaPad-5-Pro-16ACH6:07393] [ 8] /lib/x86_64-linux-gnu/libc.so.6(+0x29d90)[0x7ff849346d90]
[jelle-IdeaPad-5-Pro-16ACH6:07393] [ 9] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80)[0x7ff849346e40]
[jelle-IdeaPad-5-Pro-16ACH6:07393] [10] compressibleInterFoam(+0x5d7e5)[0x55a3eb9777e5]
[jelle-IdeaPad-5-Pro-16ACH6:07393] *** End of error message ***

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   PID 7392 RUNNING AT jelle-IdeaPad-5-Pro-16ACH6
=   EXIT CODE: 134
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Aborted (signal 6)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions
After this, I checked my mpi install again, and
Code:
mpirun --help
seems to work. I tried to find some sugestions online, but I couldn't find a solution. Does someone here have an idea what I do wrong?
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Old   July 1, 2022, 08:12
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Jelle Lagerweij
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I did notice that my problem is probably the same as Problems with running in parallel, but sadly, that thread only states that a solution is reached, not how.
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Old   September 7, 2023, 13:52
Default Remove anaconda
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Yousuf Ali
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Hi..
I had this problem. I removed anaconda. Then it was working. I dont know how but they are connected.

Maybe you have installed anaconda in ubuntu also for python. If that is the case. Try removing it
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Old   January 21, 2024, 12:45
Default Reinstalling openmpi
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Hi Jelle,

I had the same issue after updating Ubuntu on my computer. I found the solution to my problem at the end of the Installation wiki of openfoam.com:

https://develop.openfoam.com/Develop...am-environment

Apparently this error is documented, and the following commands solved my problem:

$ sudo dpkg --remove --force-all libopenmpi-dev
$ sudo apt install libopenmpi-dev

Sorry for the late reply, but maybe it can be helpful for someone else.

Best regards,

Pablo
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