Troubleshooting

Ubuntu linux installing

The imported target "CGAL::CGAL_Qt5" references the file "/usr/lib/x86_64-linux-gnu/libCGAL_Qt5.so.11.0.1" but this file does not exist...

If you ran into this error when typing cmake .. -Wno-dev then this might help.

Some Ubuntu versions have a failed CMakeLists.txt. This line should fix it:

sudo apt-get install libcgal-qt5-dev

target_compile_features specified unknown feature "cxx_std_17" for target "ANA2"

If you ran into this error when typing cmake .. -Wno-dev then this might help.

This shows up if you have a very old gcc compiler. ANA is written in C++17 and C++17 features are available since GCC 5, which came out in 2015.

To update your gcc in a Ubuntu system add the ppa repository and update the APT database:

sudo add-apt-repository ppa:ubuntu-toolchain-r/test
sudo apt-get update

Then install the desired GCC and G++ versions. As of this day, gcc-11 is the latest version:

sudo apt-get install gcc g++ gcc-11 g++-11

Now the new compiler version is available in the system by using a different command name (that is, gcc-11), but the default version, the one that is executed with the command gcc, will still be the previous one. To change the default version executed with the gcc command we have to configure the alternatives in the system.

First lets remove any previous configuration with:

sudo update-alternatives --remove-all gcc

Each alternative has a priority associated with it. When a link group is in automatic mode, the alternatives pointed to by members of the group will be those which have the highest priority.

sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-11 10 --slave /usr/bin/g++ g++ /usr/bin/g++-11

Once the different alternatives for the gcc package have been created then it can be configured with:

sudo update-alternatives --config gcc

And a menu will appear, from which you can choose the gcc version. Then test the version executed with the gcc command:

g++ -v

Discarding vectors from Amber file format

If you computed more Amber vectors than you want to use, you have to change the header line to let ANA know your intentions.

For example, if you want to discard most vectors from this file and only preserve the first 10, there's no need to cut the original file, just modify the original header from this:

 Eigenvector file: MWCOVAR nmodes 330 width 11

to this:

 Eigenvector file: MWCOVAR nmodes 10 width 11

So now ANA knows it has to read only 10 vectors.