Hey everyone,
I’m having trouble running OpenFOAM in parallel. Specifically, I cannot run, in parallel, any cases with the RBF mapping option. I get a segmentation violation error before it even communicates with partner (e.g. CalculiX) and starts the calculation. The following log is from the perpendicular flap tutorial; the same happens with the Turek-Hron FSI3 tutorial or any case I set up which involves RBF mapping. Serial seems to work fine. Parallel in cases where other mappings are used (nearest-projection, for example) also seems to work fine.
*---------------------------------------------------------------------------*\
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration | Website: https://openfoam.org
\\ / A nd | Version: 7
\\/ M anipulation |
\*---------------------------------------------------------------------------*/
Build : 7-3bcbaf946ae9
Exec : pimpleFoam -parallel
Date : Nov 03 2021
Time : 11:13:22
Host : "andres-linux"
PID : 24224
I/O : uncollated
Case : /home/andres/OpenFOAM/andres-7/preCICE-adapter/tutorials/perpendicular-flap/fluid-openfoam
nProcs : 4
Slaves :
3
(
"andres-linux.24225"
"andres-linux.24226"
"andres-linux.24227"
)
Pstream initialized with:
floatTransfer : 0
nProcsSimpleSum : 0
commsType : nonBlocking
polling iterations : 0
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster (fileModificationSkew 10)
allowSystemOperations : Allowing user-supplied system call operations
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time
Create mesh for time = 0
Selecting dynamicFvMesh dynamicMotionSolverFvMesh
Selecting motion solver: displacementLaplacian
Selecting motion diffusion: quadratic
Selecting motion diffusion: inverseDistance
PIMPLE: No convergence criteria found
PIMPLE: Operating solver in transient mode with 1 outer corrector
PIMPLE: Operating solver in PISO mode
Reading field p
Reading field U
Reading/calculating face flux field phi
Selecting incompressible transport model Newtonian
Selecting turbulence model type laminar
Selecting laminar stress model Stokes
No MRF models present
No finite volume options present
Constructing face velocity Uf
Courant Number mean: 0 max: 0
Starting time loop
---[preciceAdapter] Loaded the OpenFOAM-preCICE adapter v1.0.0.
---[preciceAdapter] Reading preciceDict...
---[precice] This is preCICE version 2.3.0
---[precice] Revision info: v2.3.0
---[precice] Configuration: Release (Debug and Trace log unavailable)
---[precice] Configuring preCICE with configuration "../precice-config.xml"
---[precice] I am participant "Fluid"
[2]PETSC ERROR: ------------------------------------------------------------------------
[2]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[2]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[2]PETSC ERROR: or see https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[2]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
[2]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[2]PETSC ERROR: to get more information on the crash.
[2]PETSC ERROR: User provided function() line 0 in unknown file
---[precice] Connecting Master to 3 Slaves
[3]PETSC ERROR: ------------------------------------------------------------------------
[3]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[3]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[3]PETSC ERROR: or see https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[3]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
[3]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[3]PETSC ERROR: to get more information on the crash.
[3]PETSC ERROR: User provided function() line 0 in unknown file
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 2 in communicator MPI_COMM_WORLD
with errorcode 59.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
---[precice] Setting up master communication to coupling partner/s
[1]PETSC ERROR: ------------------------------------------------------------------------
[1]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the batch system) has told this process to end
[1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[1]PETSC ERROR: or see https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[1]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
[1]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[1]PETSC ERROR: to get more information on the crash.
[1]PETSC ERROR: User provided function() line 0 in unknown file
[2]PETSC ERROR: ------------------------------------------------------------------------
[2]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the batch system) has told this process to end
[2]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[2]PETSC ERROR: or see https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[2]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
[2]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[2]PETSC ERROR: to get more information on the crash.
[2]PETSC ERROR: User provided function() line 0 in unknown file
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the batch system) has told this process to end
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: User provided function() line 0 in unknown file
[andres-linux:24219] 4 more processes have sent help message help-mpi-api.txt / mpi-abort
My system and installation details are:
- Ubuntu 20.04 Focal, fresh install (though the same happens on 18.04 Bionic).
- preCICE 2.3.0 installed from .deb package (same issue with 2.2.1).
- OpenFOAM v7, installed from .deb package.
- preCICE Adapter for OF v7, succesfully compiled with ./Allwmake
- mpirun --version output:
mpirun (Open MPI) 4.0.3
Report bugs to http://www.open-mpi.org/community/help/
- sudo update-alternatives --list mpi output:
/usr/bin/mpicc.openmpi
- PETSC 3.12 (installed by preCICE’s .deb)
How should I proceed?
Best regards,
Andrés