Problems with executing Elmer/Ice examples

Extension of Elmer in computational glaciology
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glebcher
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Problems with executing Elmer/Ice examples

Post by glebcher » 14 Apr 2018, 22:07

Hello,

I am a new Elmer/Ice user. The program (Elmer with Elmer/Ice) was just installed on my computer (OS Ubuntu 16.04 LTS), so I have never used it before. The tests for Elmer/Ice were started from command line with

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ctest -L elmerice
and were passed almost completely (41 of 42, except Contact test). The first question is whether this installation error is crucial and I would not be able to use the system effectively with it?

The second problem arose when I tried to execute my first Elmer/Ice example Toy flow-line model from Elmer/Ice courses. First, I put the directory TestGlacier with data and code to elmerice directory (the full path is home/home/elmerfem-release-8.3/elmerice/examples/TestGlacier). Then I perform in command line consequently

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 gmsh -2 testglacier.geo  
ElmerGrid 14 2 testglacier.msh\ –autoclean –order 0.1 1.0 0.01 
emacs Stokes_diagnostic.sif  
ElmerSolver Stokes_diagnostic.sif
I got two error messages (see attachments). The files testglacier.msh and Stokes_diagnostic.sif do exist.
Their full paths are
home/home/elmerfem-release-8.3/elmerice/examples/TestGlacier/SolutionFiles/testglacier.msh,
home/home/elmerfem-release-8.3/elmerice/examples/TestGlacier/Stokes_diagnostic.sif.
So I don't have any output and don't understand what is wrong. I would be very grateful for any help or advise.

Regards,
Gleb
Attachments
2.png
Reply to ElmerSolver Stokes_diagnostic.sif
(134.93 KiB) Not downloaded yet
1.png
Reply to ElmerGrid 14 2 testglacier.msh\ –autoclean –order 0.1 1.0 0.01
(110.06 KiB) Not downloaded yet

gagliar
Posts: 55
Joined: 04 Sep 2009, 16:34
Location: LGGE - Grenoble
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Re: Problems with executing Elmer/Ice examples

Post by gagliar » 24 Apr 2018, 16:43

Hi Gleb,

The problem with the Contact test is not an issue and the fact that 41 of the 42 tests have passed indicates that you have a working Elmer/Ice program.

For the TestGlacier, when you untar the archive from the wiki (http://elmerice.elmerfem.org/wiki/lib/e ... 017.tar.gz), you should get a directory TestGlacier which contains at least the two files Stokes_diagnostic.sif and testglacier.geo

To create the mesh :

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gmsh -1 -2 testglacier.geo 
should create testglacier.msh (if not, what is the error message?). Then,

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ElmerGrid 14 2 testglacier.msh –autoclean 
should create the Elmer mesh (a directory named testglacier with 4 files mesh.* inside).
It seems that you have added a "\" after testglacier.msh that might have created a problem?

Then, if you don't have the Elmer mesh, the execution of ElmerSolver will not work. So, the second error is due to the first one.

Hope it helps,
Olivier

glebcher
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Re: Problems with executing Elmer/Ice examples

Post by glebcher » 25 Apr 2018, 20:12

Dear Oliver,

thank you very much for your reply and advice. I have tried what you suggested. Nevertheless, I didn't succeed in solving my problem. In fact, directory TestGlacier already includes file testglacier.msh and directory testglacier, and when I perform

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gmsh -1 -2 testglacier.geo
it creates one more testglacier.msh file, but it contains no nodes and elements. The second command

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ElmerGrid 14 2 testglacier.msh –autoclean
doesn't create directory testglacier besides already existing one (you were right about odd symbol "\"). Finally,

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ElmerSolver Stokes_diagnostic.sif
can't find Stokes_diagnostic.sif. I attach a screenshot of all the commands and messages.

Regards,
Gleb
Attachments
3.png
(210.45 KiB) Not downloaded yet

gagliar
Posts: 55
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Location: LGGE - Grenoble
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Re: Problems with executing Elmer/Ice examples

Post by gagliar » 25 Apr 2018, 20:41

Are you executing the commands in the directory that contains the files testglacier.geo and Stokes_diagnostic.sif, i.e. in the directory TestGlacier? If not, you should first move in this directory (e.g. cd home/home/elmerfem-release-8.3/elmerice/examples/TestGlacier/) and then execute the different commands.
Olivier

glebcher
Posts: 4
Joined: 07 Apr 2018, 17:58
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Re: Problems with executing Elmer/Ice examples

Post by glebcher » 28 Apr 2018, 00:32

Dear Oliver,

thank you once more for continuing helping me. Sorry for disturbing you again. I have moved in the TestGlacier directory as you suggested and it helped. The system is now able to find file Stokes_diagnostic.sif. But unfortunately a new error message appeared and the file stokes_ela400_diagnostic0001.vtu was not produced. I learned that segmentation fault error is very widespread and can have diverse reasons. Actually, I don't understand whether the problem is in some Elmer settings or in my Ubuntu OS? The error message is given below. Sory for long code.

Best regards,
Gleb

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home@home-HP-ZBook-15u-G3:~/elmerfem-release-8.3/elmerice/examples/TestGlacier$ ElmerSolver Stokes_diagnostic.sif
ELMER SOLVER (v 8.3) STARTED AT: 2018/04/27 22:59:56
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: 2018-03-22)
MAIN: =============================================================
MAIN: 
MAIN: 
MAIN: -------------------------------------
MAIN: Reading Model: Stokes_diagnostic.sif
LoadInputFile: Scanning input file: Stokes_diagnostic.sif
LoadInputFile: Loading input file: Stokes_diagnostic.sif
Model Input:  Unlisted keyword: [depth] in section: [initial condition 1]
Model Input:  Unlisted keyword: [mesh velocity first zero] in section: [solver 1]
Model Input:  Unlisted keyword: [gradient] in section: [solver 2]
Model Input:  Unlisted keyword: [calc free surface] in section: [solver 2]
Model Input:  Unlisted keyword: [freesurf name] in section: [solver 2]
Model Input:  Unlisted keyword: [rate factor 1] in section: [material 1]
Model Input:  Unlisted keyword: [rate factor 2] in section: [material 1]
Model Input:  Unlisted keyword: [activation energy 1] in section: [material 1]
Model Input:  Unlisted keyword: [activation energy 2] in section: [material 1]
Model Input:  Unlisted keyword: [limit temperature] in section: [material 1]
Model Input:  Unlisted keyword: [constant temperature] in section: [material 1]
Model Input:  Unlisted keyword: [conpute normals] in section: [boundary condition 1]
Model Input:  Unlisted keyword: [depth] in section: [boundary condition 3]
Loading user function library: [StructuredMeshMapper]...[StructuredMeshMapper_Init0]
Loading user function library: [ElmerIceSolvers]...[FlowDepthSolver_Init0]
LoadMesh: Base mesh name: ./testglacier
WARNING:: CheckTimer: Requesting time from non-existing timer: LoadMesh
WARNING:: CheckTimer: Requesting time from non-existing timer: MeshStabParams
MAIN: -------------------------------------
AddVtuOutputSolverHack: Adding ResultOutputSolver to write VTU output in file: Stokes_ELA400_diagnostic
Loading user function library: [StructuredMeshMapper]...[StructuredMeshMapper_Init]
Loading user function library: [StructuredMeshMapper]...[StructuredMeshMapper_bulk]
Loading user function library: [StructuredMeshMapper]...[StructuredMeshMapper]
Loading user function library: [ElmerIceSolvers]...[FlowDepthSolver_Init]
Loading user function library: [ElmerIceSolvers]...[FlowDepthSolver_bulk]
Loading user function library: [ElmerIceSolvers]...[FlowDepthSolver]
Loading user function library: [FlowSolve]...[FlowSolver_Init]
Loading user function library: [FlowSolve]...[FlowSolver_bulk]
Loading user function library: [FlowSolve]...[FlowSolver]
Loading user function library: [ResultOutputSolve]...[ResultOutputSolver_Init]
Loading user function library: [ResultOutputSolve]...[ResultOutputSolver_bulk]
Loading user function library: [ResultOutputSolve]...[ResultOutputSolver]

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

Backtrace for this error:
#0  0x7FA8ECFACE08
#1  0x7FA8ECFABF90
#2  0x7FA8ECBFC4AF
#3  0x7FA8ED305AB1
#4  0x7FA8ED3084E0
#5  0x7FA8ED653B59
#6  0x7FA8ED655E67
#7  0x7FA8ED65B036
#8  0x401075
#9  0x400DDE
#10  0x7FA8ECBE782F
#11  0x400E18
#12  0xFFFFFFFFFFFFFFFF
home@home-HP-ZBook-15u-G3:~/elmerfem-release-8.3/elmerice/examples/TestGlacier$ 

tzwinger
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Re: Problems with executing Elmer/Ice examples

Post by tzwinger » 01 Jun 2018, 09:17

Hi,
one question: I assume you compiled Elmer yourself. If so, what branch did you pull from?

Regards,
Thomas

glebcher
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Re: Problems with executing Elmer/Ice examples

Post by glebcher » 06 Jun 2018, 22:07

Hi, Thomas!

May be I did not understand your question, but I got Ubuntu OS and then Elmer with Elmer/Ice installed by other people. So I am not sure about branch. Thank you for your reply and I will be very grateful for any advice.

Regards,
Gleb

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