Elmer Command-Line Workflow -> Program received signal SIGSEGV

Numerical methods and mathematical models of Elmer
FFF
Posts: 15
Joined: 11 Jun 2021, 11:00
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Elmer Command-Line Workflow -> Program received signal SIGSEGV

Post by FFF »

Dear Elmer community,

I installed Elmer on the virtual machine following the steps of this document.
https://www.nic.funet.fi/index/elmer/do ... dElmer.pdf
Afterwards I tried to conduct the steps described in the video of Elmer Command-Line Workflow (see the link below).
https://www.youtube.com/watch?v=S6OjQGh-iB4
Unfortunately, I fail to run the simulation described at min 4.58.

I get the Solver output depicted below.

Code: Select all

ELMER SOLVER (v 9.0) STARTED AT: 2021/09/23 16:03:40
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: 9.0 (Rev: unknown, Compiled: 2021-09-22)
MAIN:  Running one task without MPI parallelization.
MAIN:  Running with just one thread per task.
MAIN:  MUMPS library linked in.
MAIN:  Lua interpreter linked in.
MAIN: =============================================================
LoadInputFile: Trying to read "Run Control" section only
MAIN: 
MAIN: 
MAIN: -------------------------------------
MAIN: Reading Model: hinge.sif
LoadInputFile: Scanning input file: hinge.sif
LoadInputFile: Scanning only size info
LoadInputFile: First time visiting
LoadInputFile: Reading base load of sif file
LoadInputFile: Loading input file: hinge.sif
LoadInputFile: Reading base load of sif file
CheckKeyword:  Unlisted keyword: [extruded mesh max coordinate] in section: [simulation]
LoadInputFile: Number of BCs: 7
LoadInputFile: Number of Body Forces: 0
LoadInputFile: Number of Initial Conditions: 0
LoadInputFile: Number of Materials: 1
LoadInputFile: Number of Equations: 1
LoadInputFile: Number of Solvers: 1
LoadInputFile: Number of Bodies: 1
ElmerAsciiMesh: Base mesh name: ./hinge
LoadMesh: Elapsed REAL time:     0.0015 (s)
UnitSegmentDivision: Creating linear division
MAIN: -------------------------------------
AddVtuOutputSolverHack: Adding ResultOutputSolver to write VTU output in file: hinge
StressSolve_init: --------------------------------------------------
StressSolve_init: Solving displacements from linear elasticity model
StressSolve_init: --------------------------------------------------
OptimizeBandwidth: ---------------------------------------------------------
OptimizeBandwidth: Computing matrix structure for: displacement analysis...done.
OptimizeBandwidth: Half bandwidth without optimization: 1242
OptimizeBandwidth: 
OptimizeBandwidth: Bandwidth Optimization ...done.
OptimizeBandwidth: Half bandwidth after optimization: 116
OptimizeBandwidth: ---------------------------------------------------------
ElmerSolver: Number of timesteps to be saved: 1
MAIN: 
MAIN: -------------------------------------
MAIN:  Steady state iteration:            1
MAIN: -------------------------------------
MAIN: 
StressSolve: 
StressSolve: --------------------------------------------------
StressSolve: Solving displacements from linear elasticity model
StressSolve: --------------------------------------------------
StressSolve: Starting assembly...
StressSolve: Assembly:
      10 0.6049E-03 0.6049E-03
      17 0.5379E-08 0.5379E-08
ComputeChange: NS (ITER=1) (NRM,RELC): ( 0.13631543      2.0000000     ) :: displacement analysis
StressSolver: ------------------------------------------
StressSolver: Starting Stress Computation
OptimizeBandwidth: ---------------------------------------------------------
OptimizeBandwidth: Computing matrix structure for: displacement analysis...done.
OptimizeBandwidth: Half bandwidth without optimization: 1242
OptimizeBandwidth: 
OptimizeBandwidth: Bandwidth Optimization ...done.
OptimizeBandwidth: Half bandwidth after optimization: 116
OptimizeBandwidth: ---------------------------------------------------------

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0  0x7fb4ce37bd21 in ???
#1  0x7fb4ce37aef5 in ???
#2  0x7fb4ce1af20f in ???
#3  0x7fb4ce5d5569 in ???
#4  0x7fb4ce5d55eb in ???
#5  0x7fb4ce6bf8e5 in __lists_MOD_variableaddvector
	at /build/elmerfem-csc-v6J0ht/elmerfem-csc-8.4-0ppa0/fem/src/Lists.F90:1089
#6  0x7fb4c525507d in computestress
	at /home/elmeruser/elmerfem/fem/src/modules/StressSolve.F90:1727
#7  0x7fb4c5264099 in stresssolver_
	at /home/elmeruser/elmerfem/fem/src/modules/StressSolve.F90:952
#8  0x7fb4ce8db335 in __mainutils_MOD_singlesolver
	at /build/elmerfem-csc-v6J0ht/elmerfem-csc-8.4-0ppa0/fem/src/MainUtils.F90:5257
#9  0x7fb4ce8f0a8b in __mainutils_MOD_solveractivate
	at /build/elmerfem-csc-v6J0ht/elmerfem-csc-8.4-0ppa0/fem/src/MainUtils.F90:5498
#10  0x7fb4ce8f223f in solvecoupled
	at /build/elmerfem-csc-v6J0ht/elmerfem-csc-8.4-0ppa0/fem/src/MainUtils.F90:3208
#11  0x7fb4ce8f355c in __mainutils_MOD_solveequations
	at /build/elmerfem-csc-v6J0ht/elmerfem-csc-8.4-0ppa0/fem/src/MainUtils.F90:2908
#12  0x7fb4ceb1b4bf in execsimulation
	at /build/elmerfem-csc-v6J0ht/elmerfem-csc-8.4-0ppa0/fem/src/ElmerSolver.F90:2840
#13  0x7fb4ceb1b4bf in elmersolver_
	at /build/elmerfem-csc-v6J0ht/elmerfem-csc-8.4-0ppa0/fem/src/ElmerSolver.F90:543
#14  0x5569ed9a33cd in solver
	at /build/elmerfem-csc-v6J0ht/elmerfem-csc-8.4-0ppa0/fem/src/Solver.F90:57
#15  0x5569ed9a313e in main
	at /build/elmerfem-csc-v6J0ht/elmerfem-csc-8.4-0ppa0/fem/src/Solver.F90:34
Segmentation fault (core dumped)
How can I fix this issue?
Any help would be highly appreciated!

Best regards,

Felix
kevinarden
Posts: 2237
Joined: 25 Jan 2019, 01:28
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Re: Elmer Command-Line Workflow -> Program received signal SIGSEGV

Post by kevinarden »

Segmentation faults are difficult to debug
If you can post the problem so testing could be done.

Have you tried running on of the test models?

https://github.com/ElmerCSC/elmerfem/tr ... /fem/tests
FFF
Posts: 15
Joined: 11 Jun 2021, 11:00
Antispam: Yes

Re: Elmer Command-Line Workflow -> Program received signal SIGSEGV

Post by FFF »

Hi kevin,

Thank you for the reply!
Below you find the data of the Elastic beam.
ElasticBeamHinged3D.zip
(45.7 KiB) Downloaded 130 times
I tried the subsequent tests:
heateq_steady_start.zip
(10.55 KiB) Downloaded 127 times
mgdyn_harmonic_wire.zip
(162.28 KiB) Downloaded 128 times
The test of the heateq passed, but the harmonic wire showed the same behavior (see my first post) as the elastic beam.

What can be the cause of Segmentation faults?

Best regards,

Felix
FFF
Posts: 15
Joined: 11 Jun 2021, 11:00
Antispam: Yes

Re: Elmer Command-Line Workflow -> Program received signal SIGSEGV

Post by FFF »

Hi,

I don't know if it does help for further investigation, but i did the same tests as describe in my last post on windows.

I could obtain results with the heateq and the harmonic wire.

The elastic beam could converge but the obtained results (vonmisis or displacement) have a magnitude of 1.2e-38.
ElasticBeamHinged3D_SolvedOnWindows.zip
(123.71 KiB) Downloaded 129 times
If anything else is needed to solve this issue please let me know!

Best,

Felix
Rich_B
Posts: 421
Joined: 24 Aug 2009, 20:18

Re: Elmer Command-Line Workflow -> Program received signal SIGSEGV

Post by Rich_B »

Hi,

For your fourth case 'solved on windows', try creating the four elmer mesh files with the command 'elmergrid 14 2 hinge -autoclean'.

Let us know what happens.

Thanks, Rich.
kevinarden
Posts: 2237
Joined: 25 Jan 2019, 01:28
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Re: Elmer Command-Line Workflow -> Program received signal SIGSEGV

Post by kevinarden »

Felix,
I downloaded your file and ran them as is with no changes no problems. The issue must be in the system setup you have. You said you were running in a virtual machine, what parameters did you use for the virtual machine, RAM, disc space, etc.?

Also Elmer is available in windows

https://www.nic.funet.fi/pub/sci/physic ... dElmer.pdf
kevinarden
Posts: 2237
Joined: 25 Jan 2019, 01:28
Antispam: Yes

Re: Elmer Command-Line Workflow -> Program received signal SIGSEGV

Post by kevinarden »

I download your solved on windows file, and had the same results, the sif files are the same, however the mesh files are different between the two cases.

The first set of files worked fine on my machine.

The solved on windows files did not, but the mesh files are different.
Rich_B
Posts: 421
Joined: 24 Aug 2009, 20:18

Re: Elmer Command-Line Workflow -> Program received signal SIGSEGV

Post by Rich_B »

Hi Kevin,

I had the same results as you did on windows. The first three cases ran fine, without changes. The fourth case ran after recreating the mesh files with '-autoclean', which removed (12) point elements. I did not try any of the cases using the Elmer virtual machine.

Rich.
FFF
Posts: 15
Joined: 11 Jun 2021, 11:00
Antispam: Yes

Re: Elmer Command-Line Workflow -> Program received signal SIGSEGV

Post by FFF »

Thank you very much for your fast replies!

I conducted the test of the Elastic beam in windows agian and it works fine!
The crutial piont is to do the mesh conversation as decribed above (elmergrid 14 2 hinge -autoclean) by Rich!
I fogot to include the "-autoclean" in my previous mesh transformation.

As for the simulation on my linux virtual machine:
I have the settings as depicted in the figure below:
SettingsVirtualMachine.PNG
(55.32 KiB) Not downloaded yet
What parameters would you suggest fot the virtual machine?
As I am new with the usage of virtual machines and linux, I apprechiate any further hints how to procced.

Best regards,

Felix
kevinarden
Posts: 2237
Joined: 25 Jan 2019, 01:28
Antispam: Yes

Re: Elmer Command-Line Workflow -> Program received signal SIGSEGV

Post by kevinarden »

I do not see any issues with the system, however if you used the Elmer Virtual Machine as is, you may consider updating the the Elmer software, I believe the Elmer Supplied virtual machine may not be updated as the Elmer Software is. However, if you made an UBUNTU virtual machine and then installed Elmer it should have worked.
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