user-defined library segmentation fault

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brinkerhoff
Posts: 2
Joined: 24 Feb 2010, 10:25

user-defined library segmentation fault

Post by brinkerhoff »

Hi,
I'm attempting to use the homologous temperature equation solver which is located on the Elmer/Ice wiki. I am able to compile via elmerf90 with no trouble, but when I run a simulation with this (or any solver compiled with elmerf90), I get the following:
ELMER SOLVER (v 5.5.0) STARTED AT: 2010/02/24 00:29:34
MAIN:
MAIN: ==========================================
MAIN: E L M E R S O L V E R S T A R T I N G
MAIN: Library version: 5.5.0 (Rev: )
MAIN: HYPRE library linked in.
MAIN: ==========================================
MAIN:
MAIN:
MAIN: -----------------------
MAIN: Reading Model ...
Model Input: Unlisted keyword: [temp heat conductivity] in section: [material 1]
Model Input: Unlisted keyword: [temp heat capacity] in section: [material 1]
Model Input: Unlisted keyword: [temp upper limit] in section: [material 1]
Model Input: Unlisted keyword: [temp lower limit] in section: [material 1]
Model Input: Unlisted keyword: [temp volume source] in section: [body force 1]
Model Input: Unlisted keyword: [temp] in section: [initial condition 1]
Model Input: Unlisted keyword: [temp] in section: [boundary condition 1]
Model Input: Unlisted keyword: [temp flux bc] in section: [boundary condition 2]
Model Input: Unlisted keyword: [temp heat flux] in section: [boundary condition 2]
Model Input: Unlisted keyword: [temp flux bc] in section: [boundary condition 3]
Model Input: Unlisted keyword: [temp heat flux] in section: [boundary condition 3]
MAIN: Done
MAIN: -----------------------
Loading user function library: [./TemperateIce]...[TemperateIceSolver_Init]
Loading user function library: [./TemperateIce]...[TemperateIceSolver]
OptimizeBandwidth: ---------------------------------------------------------
OptimizeBandwidth: Computing matrix structure for: homologous temperature equation...done.
OptimizeBandwidth: Half bandwidth without optimization: 6385
OptimizeBandwidth:
OptimizeBandwidth: Bandwidth Optimization ...done.
OptimizeBandwidth: Half bandwidth after optimization: 42
OptimizeBandwidth: ---------------------------------------------------------
Loading user function library: [EliminateDirichlet]...[EliminateDirichlet]
MAIN:
MAIN: -------------------------------------
MAIN: Steady state iteration: 1
MAIN: -------------------------------------
MAIN:
Segmentation fault

I'm using an Ubuntu Linux 32-bit system with pre-compiled Elmer binaries from Opennovation. If anyone has any ideas, they would be most appreciated. Also, please let me know if any additional information is necessary.

Cheers,
Doug Brinkerhoff
Dept. of Computer Science
University of Montana
petroo
Posts: 148
Joined: 13 Jan 2010, 19:07
Location: Aachen, Germany

Re: user-defined library segmentation fault

Post by petroo »

Doug,

how recent is your Ubuntu?

I've read somewhere that with recent versions of the GCC compiler suite there has been a change in FORTRAN handling. As I am not the programming guru myself, and especially so not w/r/to FORTRAN, I am not in the state of giving more insightful hints on this.

The problem should not appear on versions of 9.04 or older if I remember correctly.

Kind regards,

Peter
brinkerhoff
Posts: 2
Joined: 24 Feb 2010, 10:25

Re: user-defined library segmentation fault

Post by brinkerhoff »

Thanks for the reply, Peter.
I am indeed using 9.10. Would it be necessary to roll back the whole distro, or do you think that running an earlier version of gcc/gfortran would do it?

Doug Brinkerhoff
Dept. of Computer Science
University of Montana
petroo
Posts: 148
Joined: 13 Jan 2010, 19:07
Location: Aachen, Germany

Re: user-defined library segmentation fault

Post by petroo »

Hello Doug,

as already said: I am not at all familiar with anything FORTRAN'ish so far (and hope I can stay away from that ancient language :mrgreen: ), so I am the wrong person to answer you seriously.

There is an Ubuntu-based distro called CAELinux that is dedicated to scientific computing, with special stress on CFD and neighboring disciplines. It is based on the 8.04 LTS edition, and seems to work quite well with respect to Elmer and its accompanying modules.

If you instead would switch back to other intermediate Ubuntu versions you may be worse of as they haven't been long time support (LTS) ones, and you may not be able to obtain the usual regular (security) updates.

Personally, I never got happy with backrolling just one or a few packages (you mentioned the gcc / gfortran part) as they are frequently interlinked with yet some other packages, making the distribution unstable and unhomogeneous in the long run.

So you may give CAELinux a try and dedicate another 20 GB, scratched from a larger partition to CAELinux as an alternative boot variant? But please mind that there is (to my knowledge) only a 64-bit version of it, so your computer box would need to be capable of swallowing that.

Good luck,

Peter
tzwinger
Site Admin
Posts: 94
Joined: 24 Aug 2009, 12:20
Contact:

Re: user-defined library segmentation fault

Post by tzwinger »

Hi,
hard to tell without debugging info where things go wrong. As a first try I'd take out the "Eliminate Dirichlet". If you have a pathological case, you could send it to me.

Cheers,

Thomas
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