Segmentation Fault when running radiation example

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phopfgartner
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Joined: 23 Mar 2018, 17:51
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Segmentation Fault when running radiation example

Post by phopfgartner » 02 Sep 2018, 22:40

OS: Ubuntu Linux 18:04
Elmer Version: from Ubuntu package, Version: 8.3 (Rev: unknown, Compiled: 2018-08-29)

I took the example file from ElmerTutorialsFiles_nonGUI.tar.gz and changed only the output format.

Then I run the following commands, when ElmerSolver crashes:

ElmerGrid 1 2 radiation.grd
gdb ElmerSolver
run radiation.sif

(gdb) run radiation.sif
Starting program: /usr/bin/ElmerSolver radiation.sif
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
[New Thread 0x7fffeec21700 (LWP 4844)]
[New Thread 0x7fffee420700 (LWP 4845)]
[New Thread 0x7fffe9c1f700 (LWP 4846)]
ELMER SOLVER (v 8.3) STARTED AT: 2018/09/02 21:37:26
[Thread 0x7fffe9c1f700 (LWP 4846) exited]
[Thread 0x7fffeec21700 (LWP 4844) exited]
[Thread 0x7fffee420700 (LWP 4845) exited]
[New Thread 0x7fffe9c1f700 (LWP 4852)]
[New Thread 0x7fffee420700 (LWP 4853)]
ParCommInit: Initialize #PEs: 1
MAIN:
MAIN: =============================================================
MAIN: ElmerSolver finite element software, Welcome!
MAIN: This program is free software licensed under (L)GPL
MAIN: Copyright 1st April 1995 - , CSC - IT Center for Science Ltd.
MAIN: Webpage http://www.csc.fi/elmer, Email elmeradm@csc.fi
MAIN: Version: 8.3 (Rev: unknown, Compiled: 2018-08-29)
MAIN: Running one task without MPI parallelization.
MAIN: Running with just one thread per task.
MAIN: HYPRE library linked in.
MAIN: MUMPS library linked in.
MAIN: =============================================================
MAIN:
MAIN:
MAIN: -------------------------------------
MAIN: Reading Model: radiation.sif
LoadInputFile: Scanning input file: radiation.sif
LoadInputFile: Loading input file: radiation.sif
LoadMesh: Starting
ElmerAsciiMesh: Performing step: 1
LoadMesh: Base mesh name: ./radiation
LoadMesh: Reading header info from file: ./radiation/mesh.header
LoadMesh: Number of nodes in mesh: 5206
LoadMesh: Number of bulk elements in mesh: 1231
LoadMesh: Number of boundary elements in mesh: 259
LoadMesh: Initial number of max element nodes: 9
ElmerAsciiMesh: Performing step: 2
LoadMesh: Reading nodes from file: ./radiation/mesh.nodes
LoadMesh: Dimension of model is: 2
LoadMesh: Dimension of mesh is: 2
ElmerAsciiMesh: Performing step: 3
LoadMesh: Reading bulk elements from file: ./radiation/mesh.elements
[New Thread 0x7fffeec21700 (LWP 4854)]
[New Thread 0x7fffd78b4700 (LWP 4855)]
[New Thread 0x7fffd5808700 (LWP 4856)]
ElmerAsciiMesh: Performing step: 4
LoadMesh: Reading boundary elements from file: ./radiation/mesh.boundary
LoadMesh: Performing node mapping
LoadMesh: Skipping remapping of bodies
LoadMesh: Remapping boundaries
LoadMesh: Minimum initial boundary index: 1
LoadMesh: Maximum initial boundary index: 3
ElmerAsciiMesh: Performing step: 5
ElmerAsciiMesh: Performing step: 6
LoadMesh: Loading mesh done
LoadMesh: Elapsed REAL time: 0.0139 (s)
MeshStabParams: Computing stabilization parameters
MeshStabParams: Elapsed REAL time: 0.1322 (s)
MAIN: -------------------------------------
AddVtuOutputSolverHack: Adding ResultOutputSolver to write VTU output in file: radiation
AddVtuOutputSolverHanck: Increasing number of solver to: 2
AddSolvers: Setting up 2 solvers
AddSolvers: Setting up solver 1: heat equation
AddEquationBasics: Setting up keywords internally for legacy solver: heat equation
AddEquationBasics: Using procedure: HeatSolve HeatSolver
AddEquationBasics: Setting up solver: heat equation
Loading user function library: [HeatSolve]...[HeatSolver_Init]
Loading user function library: [HeatSolve]...[HeatSolver_bulk]
Loading user function library: [HeatSolve]...[HeatSolver]
AddEquationBasics: Creating standard variable: temperature
RadiationFactors: ----------------------------------------------------
RadiationFactors: Computing radiation factors for heat transfer
RadiationFactors: ----------------------------------------------------
RadiationFactors: Using sparse matrix for Gebhardt factors
RadiationFactors: Using direct solver for Gebhardt factors
RadiationFactors: Total number of Radiation Surfaces 135 of 259
ViewFactors: error while loading shared libraries: libelmersolver.so: cannot open shared object file: No such file or directory
ERROR:: systemc: Command exit status was 127
ERROR:: systemc: Unable to execute system command
RadiationFactors: Message
RadiationFactors: All done time (s) 1.9070E-03
RadiationFactors: ----------------------------------------------------
OptimizeBandwidth: ---------------------------------------------------------
OptimizeBandwidth: Computing matrix structure for: heat equation...done.
OptimizeBandwidth: Half bandwidth without optimization: 169
OptimizeBandwidth:
OptimizeBandwidth: Bandwidth Optimization ...done.
OptimizeBandwidth: Half bandwidth after optimization: 126
OptimizeBandwidth: ---------------------------------------------------------
AddSolvers: Setting up solver 2: internalvtuoutputsolver
AddEquationBasics: Using procedure: ResultOutputSolve ResultOutputSolver
AddEquationBasics: Setting up solver: internalvtuoutputsolver
Loading user function library: [ResultOutputSolve]...[ResultOutputSolver_Init]
Loading user function library: [ResultOutputSolve]...[ResultOutputSolver_bulk]
Loading user function library: [ResultOutputSolve]...[ResultOutputSolver]
AddMeshCoordinatesAndTime: Setting mesh coordinates and time
SetInitialConditions: Setting up initial conditions (if any)
ListInitElementKeyword: Treating keyword: temperature
ListInitElementKeyword: Initiated handle for: > temperature < of type: 4
MAIN:
MAIN: -------------------------------------
MAIN: Steady state iteration: 1
MAIN: -------------------------------------
MAIN:
SingleSolver: Attempting to call solver
SingleSolver: Solver Equation string is: heat equation
HeatSolver: -------------------------------------------
HeatSolver: Solving the energy equation for temperature
DefaultStart: Starting solver: heat equation
HeatSolve:
HeatSolve:
HeatSolve: -------------------------------------
HeatSolve: TEMPERATURE ITERATION 1
HeatSolve: -------------------------------------
HeatSolve:
HeatSolve: Starting Assembly...
HeatSolve: Assembly:

Thread 1 "ElmerSolver" received signal SIGSEGV, Segmentation fault.
0x00007ffff78aa6a0 in radiation::computeradiationload (model=...,
mesh=0x5555559c18f0, element=..., temperature=..., reorder=...,
emissivity=0.59999999999999998, anglefraction=4.6355706435560276e-310)
at /build/elmerfem-csc-eg-pvnOZf/elmerfem-csc-eg-8.3-0ppa0/fem/src/Radiation.F90:77
77 /build/elmerfem-csc-eg-pvnOZf/elmerfem-csc-eg-8.3-0ppa0/fem/src/Radiation.F90: No such file or directory.
(gdb) bt
#0 0x00007ffff78aa6a0 in radiation::computeradiationload (model=...,
mesh=0x5555559c18f0, element=..., temperature=..., reorder=...,
emissivity=0.59999999999999998, anglefraction=4.6355706435560276e-310)
at /build/elmerfem-csc-eg-pvnOZf/elmerfem-csc-eg-8.3-0ppa0/fem/src/Radiation.F90:77
#1 0x00007fffd2df5e2f in diffusegrayradiation (text=6.9533558062836382e-310,
anglefraction=6.9533558062832429e-310, forcevector=..., tempperm=...,
temperature=..., element=0x7fffffff86e8, solver=..., model=...)
at /build/elmerfem-csc-eg-pvnOZf/elmerfem-csc-eg-8.3-0ppa0/fem/src/modules/HeatSolve.F90:1522
#2 addheatfluxbc ()
at /build/elmerfem-csc-eg-pvnOZf/elmerfem-csc-eg-8.3-0ppa0/fem/src/modules/HeatSolve.F90:1326
#3 0x00007fffd2df971b in heatsolver (timestep=<optimized out>)
at /build/elmerfem-csc-eg-pvnOZf/elmerfem-csc-eg-8.3-0ppa0/fem/src/modules/HeatSolve.F90:1053
#4 0x00007ffff792b26e in mainutils::singlesolver (model=...,
solver=0x55555575c2f0, dt=1, transientsimulation=.FALSE.)
at /build/elmerfem-csc-eg-pvnOZf/elmerfem-csc-eg-8.3-0ppa0/fem/src/MainUtils.F90:5044
#5 0x00007ffff793de89 in mainutils::solveractivate (model=...,
solver=0x55555575c2f0, dt=1, transientsimulation=.FALSE.)
at /build/elmerfem-csc-eg-pvnOZf/elmerfem-csc-eg-8.3-0ppa0/fem/src/MainUtils


Regards, Peter
Attachments
radiation.sif
(1.63 KiB) Downloaded 19 times
radiation.grd
(890 Bytes) Downloaded 11 times

raback
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Re: Segmentation Fault when running radiation example

Post by raback » 03 Sep 2018, 22:35

Hi

The problem is

Code: Select all

ViewFactors: error while loading shared libraries: libelmersolver.so: cannot open shared object file: No such file or directory
ERROR:: systemc: Command exit status was 127
ERROR:: systemc: Unable to execute system command[
Possibly the ViewFactors executable is not in the path to be found.

The bug is really that it continuous after this.

-Peter

phopfgartner
Posts: 2
Joined: 23 Mar 2018, 17:51
Antispam: Yes

Re: Segmentation Fault when running radiation example

Post by phopfgartner » 04 Sep 2018, 21:51

That was the right hint. I had an old version of ViewFactor in /usr/local/bin from a incompletely removed Elmer installation.

Thank you very much,
Peter

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