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ngsxfem trouble

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3 years 8 months ago #3027 by JSR
ngsxfem trouble was created by JSR
I've been trying to migrate my code over to our high-performance cluster, but I'm having difficulty getting ngsxfem to work. When I run my code, I get the following error:
Code:
Traceback (most recent call last): File "filename.py", line 7, in <module> from xfem import * File "/usr/lib/python3/dist-packages/xfem/__init__.py", line 15, in <module> from xfem.ngsxfem_xfem_py import * ImportError: /usr/lib/python3/dist-packages/xfem/../../../netgen/libngsxfem_utils.so: undefined symbol: _ZTIN5ngstd9ExceptionE

Apparently this is supposed to come from the libodb library, but installing it didn't fix the issue.

If it's relevant, I'm not trying to do anything in paralell yet, and my batch script uses "python3 filename.py", which works without errors on my home computer.

Any insight into what might be going wrong?
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3 years 8 months ago #3028 by schruste
Replied by schruste on topic ngsxfem trouble
Hi JSR,

Can you give me a bit more information? Is a similar ngsolve script running? Which NGSolve-Version are you using? Are you installing ngsxfem with or without included ngsolve-build?

Perhaps you can post the version of ngsolve and ngsxfem as well as the installation directories and the build-flags of ngsxfem here to help us get a picture of your situation?

Best,
Christoph
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3 years 7 months ago - 3 years 7 months ago #3029 by JSR
Replied by JSR on topic ngsxfem trouble
Hi Christoph,

I didn't do the installation myself, but the administrator who did it sent me the following description of how they installed it:
Code:
singularity build --sandbox ubuntu-18.04.4-bionic-ngsolve-ngsxfem docker://ubuntu:bionic sudo singularity shell --writable ubuntu-18.04.4-bionic-ngsolve-ngsxfem apt-get update apt-get -y install software-properties-common apt-get -y install python3 python3-dev python3-tk libpython3-dev libxmu-dev tk-dev tcl-dev cmake git g++ libglu1-mesa-dev liblapacke-dev apt-add-repository universe add-apt-repository ppa:ngsolve/ngsolve apt-get update apt-get install ngsolve add-apt-repository ppa:mhochsteger/ngsxfem apt-get update apt-get install ngsxfem exit # build image sudo singularity build ubuntu-18.04.4-bionic-ngsolve-ngsxfem.sif ubuntu-18.04.4-bionic-ngsolve-ngsxfem

This was done on June 22nd, so I assume everything is in its most current version.

I'll try running a simple ngsolve example (without ngsxfem) to confirm that ngsxfem is the problem.

update: ngsolve works fine by itself. It's just ngsxfem that's the problem.
Last edit: 3 years 7 months ago by JSR.
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3 years 7 months ago #3044 by schruste
Replied by schruste on topic ngsxfem trouble
Dear JSR,

Sorry for the late reply. The problem is with the debian package of ngsxfem. At the moment we do not have regular ngsxfem debian packages, i.e. in your case you will get a very old ngsxfem combined with a recent ngsolve. Please build ngsxfem from scratch. You can also try out "pip install ngsxfem" if you want to use pip.

Best,
Christoph
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3 years 7 months ago #3045 by JSR
Replied by JSR on topic ngsxfem trouble
Thanks for the help. I'll try that.
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