Common Problems and Questions #

Docker #

I cannot start or run Docker on Linux #

On Linux, non-sudo users may encounter permission denied or Cannot connect to the Docker daemon. Is the docker daemon running on this host? errors. By default, only sudo users may run Docker commands on Linux (by adding sudo to the start of the command). To allow other users to run commands, a sudo user must created a new group called docker and add users to it:

sudo groupadd docker             # Create new group
sudo usermod -aG docker $USER    # Add USER to group

Exercise caution with the usermod command; incorrect use may result in privileges being removed from users. Users may need to log out and then log back in for changes to take effect. Users belonging to the docker group should now be able to run Docker without the sudo command.

In addition, sudo users can control the Docker daemon using the following commands:

sudo systemctl start docker      # Start daemon
sudo systemctl stop docker       # Stop daemon
sudo systemctl restart docker    # Restart daemon
sudo systemctl status docker     # Check status of daemon

Installing dependencies #

I don’t know how to check if a package is already installed #

Before installing a dependency it is important to check if it is already present on your system, as multiple different installs of dependencies can cause issues during the build process. This can be done using the whereis $PACKAGE_NAME command which searches your system for the package’s binary, source, or manual files. Additionally, the version number of many packages can be checked using $PACKAGE_NAME --version.

I don’t know how to install packages #

In general, on Linux there are three main ways to install software packages:

Via a package manager: There are a variety of Linux package managers, for example apt is used on Debian systems and dnf is used on RHEL/Fedora. Common packages can be installed and managed using these package managers, for example:

sudo apt install $PACKAGE_NAME    # On Debian
sudo dnf install $PACKAGE_NAME    # On RHEL/Fedora

This can only be carried out by a user with sudo privileges, and also installs packages system-wide.

By downloading a binary: If a package is not available via a package manager, or if you do not have sudo privileges, then pre-built binaries might be available. Binaries are files which have been build from the source code of the package, and are operating-system specific. These can be downloaded to your system and require no further installation. This can be useful for keeping installed packages in one folder and not installing system-wide.

You can download files using a web browser, or if you have a link to the download (which may be a compressed folder) you can use:

wget $DOWNLOAD_LINK            # Download folder
tar -xvf $COMPRESSED_FOLDER    # Extract (if folder is tarball)
unzip $COMPRESSED_FOLDER       # Extract (if folder is zip file)

By building from source: If the package is not available via package managers or as a binary, then you may have to build the package from source. Often there will be detailed instructions on how to do this on the package’s website. Alternatively, the source code may include an INSTALL file (similar to a README file) which provides installation instructions. For example, GSL 2.7.1 can be fully installed from source using the following commands:

wget https://mirror.ibcp.fr/pub/gnu/gsl/gsl-latest.tar.gz
tar -xvf gsl-latest.tar.gz
cd gsl-2.7.1
./configure
make
make install

Some packages are header-only; this means that the package does not need to be built and consists simply of header files.

I can’t or don’t want to install dependencies system-wide #

For users on a shared cluster, it may not be possible (or desirable) to install dependencies system-wide. Instead, dependencies should be installed in a folder specified by the user.

In general, package managers do not support installing packages to arbitrary directories. To install a package in a specific folder, you will need to either download a binary to that folder or build the package from source.

See I don’t know how to install packages for an example of building GSL from source. The make install command will attempt to install the package system-wide in the /usr or /usr/local directories, and if you do not have sudo privileges this will result in a permission denied error. To change the install directory, change the prefix flag of the ./configure command:

./configure --prefix=$INSTALL_DIRECTORY

When installing Python packages using pip, it is good practice to use a virtual environment. Python virtual environments allow Python packages to be installed in a specific folder, separate from the other packages already installed on the system. Provided that you already have Python installed, a folder containing virtual environments can be created like so:

python -m venv $FOLDER_PATH    # Create virtual environment
cd $FOLDER_PATH                # Navigate to folder
source bin/activate            # Run activation script
pip install $PACKAGE           # Install package in virtual environment

Note that every terminal session you will need to re-run the activation script to work in the virtual environment.

My system cannot find an installed package #

If you have installed a package but $PACKAGE_NAME --version or similar cannot detect any installed versions, then you may need to take extra steps so that your system can find the package.

The PATH variable contains a list of directories which are searched when the system is trying to find a package. This list can be viewed with the command echo $PATH. If a package is not in any of these directories then it will not be found by the system; this can be fixed by adding the folder containing the package to the PATH variable using:

export PATH=$PATH:$FOLDER_PATH

This will temporarily add a folder to the PATH variable. To make it permanent, you must add this command to your .bashrc file located in the /home directory.

Alternatively, if you do not want to change the PATH variable then you can use full paths. For example, Docker commands can be run by replacing docker with the full path /usr/bin/docker. If you are using full paths frequently, you may wish to create a shortcut using the alias command, for example:

alias $SHORT_COMMAND=$LONG_COMMAND

This allows long commands (possible including full paths) to be invoked using a short, user-defined command. This effect only lasts until the end of the terminal session; to make it permanent it will also need to be added to the .bashrc file.

Building GAMBIT #

CMake is finding Python backends in a different place to the interpreter #

You may encounter the message:

NOTE: You are using different Python versions for the interpreter and the libraries!

The best way to make sure that CMake finds the right versions of Python is to specify the following flags:

• -DPYTHON_EXECUTABLE: This should point to a Python interpreter. If you are using a virtual environment then this should point towards the interpreter present in the virtual environment (this makes sure that the Python libraries installed in the virtual environment are detected).
• -DPYTHON_INCLUDE_DIR: This should point to the include directory for the system’s Python, not the include directory in the virtual environment!
• -DPYTHON_LIBRARY: This should point to the system’s Python library file, which should be of the form libpython.so or libpython3.so.

If this still is not working, or if CMake cannot determine the version number of the libraries that it finds, it may be that you need to install the Python Development Package. This can be found on major package managers with the name python-dev or python-devel or some numbered variation.

CMake cannot find the LAPACK libraries #

If CMake cannot find LAPACK then you should specify the -DLAPACK_LIBRARIES flag. This should point to the shared library file liblapack.so. Unfortunately, when built from source, LAPACK by default includes the static library file liblapack.a rather than the shared library file liblapack.so. This static library file will result in a CMake error.

To fix this, try to find a LAPACK distribution which includes the shared library file. For example, for RHEL/Fedora systems a version of LAPACK can be obtained via dnf which contains the shared library file.

Changing CMake flags does not change the output #

On every run, CMake caches flags and values in the build directory. If you do not delete the build directory each time you run CMake then the cached values will be used and the new flags will be ignored.

It may also be the case that you have spelled a flag incorrectly, or forgotten to add the -D prefix. If you have used a flag that CMake does not recognise then you will receive the message:

CMake Warning:
  Manually-specified variables were not used by the project:
  $INCORRECT_FLAGS

If you are frequently re-running CMake while trying to debug the output, it may be useful to use a bash script. For example:

#!/bin/bash

rm -r build          # Delete previous run   
mkdir build          # Make build directory
cd build
cmake $YOUR_FLAGS    # Run cmake

GAMBIT builds extremely slowly #

If the final make gambit command takes a long time (or fails), then you may want to consider using the -Ditch flag with the first cmake command. This flag allows you to specify Bits and components of GAMBIT to “ditch” from the build process, allowing GAMBIT to build faster.

For example, if you wish to ditch all Bits apart from ColliderBit, add the flag:

-Ditch="CosmoBit;FlavBit;NeutrinoBit;DarkBit;DecayBit;FlavBit;ObjectivesBit;PrecisionBit;ScannerBit;SpecBit"

Python header files are not found #

During the make gambit command you may encounter the message:

fatal error: Python.h: No such file or directory

If these header files cannot be found, it may be because you have not installed the Python Development Package. This package provides extra header files and libraries for Python development. You can find it on major package managers with the name python-dev or python-devel or some numbered variation.

Running GAMBIT #

When I try to run a scan, I get a GAMBIT error which says Inifile entry _____ does not specify a valid _____! #

First of all, check that everything is spelled correctly. If everything is spelled correctly, then the YAML entry may be referencing a backend or dependency which has not been installed. For example, trying to set printer: hdf5 without installing the hdf5 backend will result in the following error:

 FATAL ERROR

GAMBIT has exited with fatal exception: GAMBIT error
ERROR: A problem has occurred in the printer utilities.
Inifile entry 'printer:"hdf5"' does not specify a valid printer!

In this case, HDF5 would have to be installed and GAMBIT rebuilt for the YAML file to work as-is. Alternatively, you could specify a different printer.

Running pippi gives me the error undefined symbol: rb_safe_level error #

This error results from having the wrong version of Ruby installed. rb_safe_level was removed in ruby 3.0, so using any versions after this will result in this error - it is recommended that you use ruby 2.7.6.

The easiest way to install and use different versions of Ruby is via the Ruby Version Manager ⧉.

Miscellaneous Questions #