Problems with executing Elmer/Ice examples

Extension of Elmer in computational glaciology
Post Reply
glebcher
Posts: 6
Joined: 07 Apr 2018, 17:58
Antispam: Yes

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

Code: Select all

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

Code: Select all

 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: 63
Joined: 04 Sep 2009, 16:34
Location: LGGE - Grenoble
Contact:

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 :

Code: Select all

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

Code: Select all

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
Posts: 6
Joined: 07 Apr 2018, 17:58
Antispam: Yes

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

Code: Select all

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

Code: Select all

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

Code: Select all

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: 63
Joined: 04 Sep 2009, 16:34
Location: LGGE - Grenoble
Contact:

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: 6
Joined: 07 Apr 2018, 17:58
Antispam: Yes

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

Code: Select all

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
Site Admin
Posts: 87
Joined: 24 Aug 2009, 12:20
Contact:

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
Posts: 6
Joined: 07 Apr 2018, 17:58
Antispam: Yes

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

glebcher
Posts: 6
Joined: 07 Apr 2018, 17:58
Antispam: Yes

Re: Problems with executing Elmer/Ice examples

Post by glebcher » 11 Nov 2018, 19:46

Thank you everyone for helpful advices. My problem with installing has been solved by the use of virtual machine technology.

Regards,
Gleb Chernyakov

AndaLi
Posts: 6
Joined: 12 Dec 2018, 08:58
Antispam: Yes

Re: Problems with executing Elmer/Ice examples

Post by AndaLi » 19 Dec 2018, 18:36

Hello,
I meet same errors when I install at virtual machine use ubuntu 18.04 by type :

sudo apt-add-repository ppa:elmer-csc-ubuntu/elmer-csc-ppa
sudo apt-get update
sudo apt-get install elmerfem-csc-eg

When I test Elmer/Ice example Toy flow-line model from Elmer/Ice courses
ElmerSolver Stokes_diagnostic.sif

ELMER SOLVER (v 8.3) STARTED AT: 2018/12/19 23:20:24
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: 2018-12-18)
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: 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: [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: [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
MAIN: -------------------------------------
AddVtuOutputSolverHack: Adding ResultOutputSolver to write VTU output in file: Stokes_ELA_400_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 0x7fd9e9a922da in ???
#1 0x7fd9e9a91503 in ???
#2 0x7fd9e96c4f1f in ???
#3 0x7fd9e9eaebda in __lists_MOD_listfind
at /build/elmerfem-csc-eg-vkXKtP/elmerfem-csc-eg-8.3-0ppa0/fem/src/Lists.F90:1901
#4 0x7fd9e9eb16c0 in __lists_MOD_listgetinteger
at /build/elmerfem-csc-eg-vkXKtP/elmerfem-csc-eg-8.3-0ppa0/fem/src/Lists.F90:3026
#5 0x7fd9ea23a1e1 in initcond
at /build/elmerfem-csc-eg-vkXKtP/elmerfem-csc-eg-8.3-0ppa0/fem/src/ElmerSolver.F90:1475
#6 0x7fd9ea23e561 in setinitialconditions
at /build/elmerfem-csc-eg-vkXKtP/elmerfem-csc-eg-8.3-0ppa0/fem/src/ElmerSolver.F90:1198
#7 0x7fd9ea2482ec in elmersolver_
at /build/elmerfem-csc-eg-vkXKtP/elmerfem-csc-eg-8.3-0ppa0/fem/src/ElmerSolver.F90:537
#8 0x555fc7bc617b in solver
at /build/elmerfem-csc-eg-vkXKtP/elmerfem-csc-eg-8.3-0ppa0/fem/src/Solver.F90:69
#9 0x555fc7bc5ece in main
at /build/elmerfem-csc-eg-vkXKtP/elmerfem-csc-eg-8.3-0ppa0/fem/src/Solver.F90:34
Segmentation fault (core dumped)

glebcher
Posts: 6
Joined: 07 Apr 2018, 17:58
Antispam: Yes

Re: Problems with executing Elmer/Ice examples

Post by glebcher » 19 Dec 2018, 22:40

Hallo,

I got a segmentation fault message only while launching Elmer/Ice on pure Ubuntu (not a virtual machine). When I installed a Linux Mint based virtual machine (http://www.nic.funet.fi/pub/sci/physics ... alMachines) on the Windows 10 host according to instruction under the link, I was able to execute with no mistakes different examples from Elmer/Ice courses including Toy flow-line model. I used the version of 21.05.2018. 4 of 51 Elmer/Ice tests failed, but that is not an installing error. Have you tried this way of installing?

Regards,
Gleb

Post Reply