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Frequently asked questions#

Note

This section is still under construction. If you have a have a question (about GIMLi) that is not covered here, please open a GitHub issue.

General#

What is the difference between BERT and GIMLi?#

GIMLi is a general library for modelling and inversion in geophysics. BERT builds upon this framework and provides numerous high-level and user-friendly functions and applications specifically tailored for DC resistivity studies.

Installation#

Python 2 or Python 3?#

Short answer: Python 3. Long answer: Currently, pygimli is functionable with all major Python versions from 3.7 on. When compiling from source, it is important that boost_python is build against the same Python version you want to use. However, many (scientific) Python projects recommend to use Python 3 for various reasons. We droped support for Python 2. In most cases you can translate your existing Python 2 scripts to Python 3 by running 2to3.

What do I have to do to use pygimli in Spyder?#

For Linux users it should be sufficient to have proper environment settings:

export PYTHONPATH=$PYTHONPATH:$HOME/src/gimli/gimli/python
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/src/gimli/build/lib
export PATH=$PATH:$HOME/src/gimli/build/bin

Note, these setting will ony affect applications that have been started from the current console. To make these settings permanent, make sure to add them to your .bashrc.

Window users should use the conda/anaconda install which sets all appropriate paths to run pygimli in spyder.

If this does not work, Windows users probably need to tell spyder where your manual pygimli installation can be found by an appropriate setting of the PYTHONPATH in the spyder Menubar:/tools/PYTHONPATH manager.

If you start spyder from Windows startmenu you probably need to set the correct PATH somewhere in your windows personal settings.

You can test you installation within the console via:

python -c 'import pygimli as pg; print(pg.version())'

If there is something wrong with the environment settings you get an error like this:

python: can't open file 'import pygimli as pg; print(pg.version())':
[Errno 2] No such file or directory

Weird findings#

My script called sip.py and nothing works#

Rename your file to something different. One of the prerequisite library (pyQT) import the file sip.py as module for they own and just stuck.

Segfault on import#

Try python -s -c “import pygimli”. The -s option ensures that only system packages are used. This avoids conflicts with local (pip) packages.

CXXABI_1.3.9 not included in libstdc++.so.6#

When installing conda packages on older machines, the above error may occur. If so, check out the suggestion made here.