This problem is observed with Anaconda Python platform and is related to the required GLIBCXX version (GLIBCXX_3.4.30).
Scan libstdc++ of the conda environment for the list of the compatible libc versions to see if GLIBCXX_3.4.30 is included:
$ conda_env_path=<path to conda>/envs/<conda env name>
$ strings $conda_env_path/lib/libstdc++.so.6 | grep GLIBCXX_3.4.30
If this reveals that GLIBCXX_3.4.30 is not included in the list of the compatible libc version, then find the libstdc++ of the system via
$ ldconfig -p | grep libstdc++.so
and scan the system libstdc++ for the list of the compatible libc versions to see if GLIBCXX_3.4.30 is included:
$ strings /usr/lib/x86_64-linux-gnu/libstdc++.so.6 | grep GLIBCXX_3.4.30
If GLIBCXX_3.4.30 is included in the list of compatible versions, then set LD_LIBRARY_PATH environment variable to use the libstdc++ of the system when running the BornAgain GUI:
$ export LD_LIBRARY_PATH=/lib/x86_64-linux-gnu/:$conda_env_path/lib:
$ bin/bornagain
On some Windows machines, you might get the message “The program can’t start because api-ms-win-crt-runtime-l1-1-0.dll is missing from your computer”. You then have to install the Visual C++ Redistributable for Visual Studio 2015. See for example the discussion at stackoverflow.
Before installing the Visual C++ Redistributable, install all Windows updates. Then download and install the Visual C++ Redistributable from Microsoft.
When Mantid is installed on the system, BornAgain might conflict with its libraries if the path to Mantid is specified in the DYLD_LIBRARY_PATH and/or PYTHONPATH environment variables. This conflict can occur while running any of the BornAgain Python examples or just during the import of BornAgain into Python, with an error message similar to:
$ python -c "import bornagain"
Incompatible library version: libBornAgainSim.so requires
version 18.0.0 or later, but libgsl.0.dylib provides version 16.0.0
Make sure that the path to the Mantid folders is not defined in your DYLD_LIBRARY_PATH and/or PYTHONPATH variables by running the commands echo $DYLD_LIBRARY_PATH and echo $PYTHONPATH. If this is the case, unset the given variables to prevent the MacOS loader from loading Mantid
$ unset DYLD_LIBRARY_PATH; unset $PYTHONPATH
This should resolve the issue.
To see which libraries get loaded by the MacOS loader during the import of BornAgain, use
$ export DYLD_PRINT_LIBRARIES=1
$ python -c "import bornagain"
To accelerate the build process, cmake maintains a cache. The downside is that this cache can cause false positives (erroneous error reports) and false negatives (cmake overlooking missing dependencies). Unless cmake has been run for the first the time in a fresh build directory, troubleshooting should start by removing the cache
$ rm CMakeCache.txt
and running cmake anew. If that does not help, then empty the build directory completely, and run cmake yet again.
Next, carefully read the error message, which will have the following form:
CMake Error at [cmake module]:[line number] (message):
[specific error message]
Call Stack (most recent call first):
[cmake module]:[line] ([command])
...
-- Configuring incomplete, errors occurred!
See also "[build_dir]/CMakeFiles/CMakeOutput.log".
See also "[build_dir]/CMakeFiles/CMakeError.log".
The most frequent error is a missing dependence because a third party library not installed on the system, or not found by cmake.
If you require our support, then please rerun cmake in an empty build directory and provide a full copy of its output, most easily generated by output redirection
$ cmake [<options>] <source_dir> >& my_cmake.log
Besides the so obtained my_cmake.log also send us three other log files produced by cmake in the build directory:
CMakeCache.txt
CMakeFiles/CMakeOutput.log
CMakeFiles/CMakeError.log
In the case of a complex system setup, with libraries of different versions scattered across multiple places, cmake might fail in identifying the correct paths to the libraries or include directories. This might lead at some point to a compilation failure. This might happen, for example, during the compilation of the BornAgain graphical user interface if the system has both Qt5 and Qt6 libraries installed. Please send us the build log generated by running the following make command
$ make VERBOSE=1 >& my_build.log
BornAgain installed on the system. Make sure the LD_LIBRARY_PATH and PYTHONPATH variables do not contain the older installation location and run ctest again.If ctest fails, then rerun it without the multi-core option -j[N]. This yields clearer, sorted output, and allows to rule out errors due to thread-safety violations.
Error messages from ctest have the form
The following tests FAILED:
53 - CoreSuite/HexParacrystal (Failed)
123 - PySuite/HexParacrystal (Failed)
For details, see the log files in Testing/Temporary/
More info at ...
Errors while running CTest
To analyse these errors one by one, it is convenient to run ctest on a single test:
$ ctest -V -R PySuite/HexParacrystal
Then analyse the output in Testing/Temporary/LastTest.log. Alternatively, set the environment variable CTEST_OUTPUT_ON_FAILURE=1 to get full terminal output from the failed tests. Yet another alternative would be to run the test binary directly from <build_dir>/bin.
When reporting errors to us, please run just the plain ctest without options -j or -R, and submit Testing/Temporary/LastTest.log.
This error shows up when a Python module tries to use a Python library that is different than the one the interpreter uses. This might happen if the user’s system contains several Python installations.
For example, BornAgain was compiled against /usr/lib64/libpython3.10.so and then used by mistake with a Python interpreter from another installation. This interpreter might depend on his own version of libpython3.10.so located, for example, at /usr/local. Importing of the bornagain module into this interpreter will cause the loading of two different libpython3.10.so libraries: one will be loaded by the bornagain module, the other will be loaded by the interpreter itself. This will cause the given fatal Python error. Make sure you are running the correct Python interpreter and that your PYTHONPATH and DYLD_LIBRARY_PATH doesn’t contain the old BornAgain installation.