⚠️ This guide became official!Please check the SPARCED repository for updates, as this version wil no longer be maintained.
Hi! 🌄
If you are new to SPARCED and wish to get a working environment setup on Ubuntu, then you are at the right place! This is a document I wrote as a summer intern at the Birtwistle lab to make the process easier for newcomers like me 🙂
I am running an Ubuntu 22.04 LTS virtual machine on VirtualBox. This guide should work even if you are using another hypervisor than VirtualBox or that you are running Ubuntu directly on your computer. With a few arrangements, the described steps should also work for other versions of Ubuntu or any Debian-based Linux distribution.
Before starting, open a terminal and run the following commands to make sure everything is up to date:
sudo apt-get update
sudo apt-get upgrade🪙 Tip: Ubuntu's terminal has autocompletion, so if you don't know the end of the name of a file (for example because of version numbers) while entering a command in your terminal, just press [tab] and see if it fills in correctly.
If you are not using VirtualBox, skip this section.
In the menu at the top of the virtual machine you are running, go to Devices>Insert Guest Additions CD image, then in your terminal run:
sudo apt install build-essential dkms linux-headers-generic # Necessary if you chose the minimal installation of Ubuntu
lsblk | grep "rom"
cd /media/{username}/VBox_GAs_{version number} # with {username} being your username and {version number} the version number
sudo ./VBoxLinuxAdditions.runYou will need to restart the VM after that. Don't forget to eject the CD! 😉
If you are not going to use parallel computation on your computer, skip this section.
If you want to run some parallel code on your computer (for example to debug on your own machine some code intented to run parallely on Palmetto), then you will need to install OpenMPI.
🪙 Tip: Starting with the OpenMPI installation will prevent you from starting everything from scratch again in case of failure (as it happened to me).
First, download the latest stable version of OpenMPI from the openmpi.org website. You want the .tar.gz extension.
Then run the following commands in your terminal (some can take a few minutes and be very verbose, so get a ☕):
mkdir openmpi
cd openmpi
cp ~/Downloads/openmpi-{version number}.tar.gz . # with {version number} being the version number
tar -xzvf openmpi-{version number}.tar.gz # with {version number} being the version number
cd openmpi-{version number} # with {version number} being the version number
./configure --prefix=$HOME/openmpi # do not add any flag related to C++ (cxx) as they are no longer supported
make install
export PATH=$HOME/openmpi/bin:$PATH
export LD_LIBRARY_PATH=$HOME/openmpi/lib:$LD_LIBRARY_PATHYou can check if the installation process worked using:
mpirun --versionIf you get an error involving Fortran during this process and you find a way to fix it without having to reinstall everything, please notify me! 🙏
sudo apt install git-allYou can use the following commands to set your username and your user's email.
git config --global user.name {username}
git config --global user.email {email}I assume that you already have an account on GitHub.
ssh-keygen -t ed25519 -C "{email}" # with {email} being your email for GitHub
eval "$(ssh-agent -s)"
ssh-add ~/.ssh/id_ed25519🪙 Tip: Just press [enter] to use the default file in which to save the key.
Print your SSH key in the terminal using:
cat ~/.ssh/id_ed25519.pubCopy it. The in your GitHub settings, create a new SSH key and paste it.
Run the following command to test your SSH connexion:
ssh -T git@github.comDownload the Anaconda installer for Linux, then run the following commands in your terminal:
sudo apt-get install libgl1-mesa-glx libegl1-mesa libxrandr2 libxrandr2 libxss1 libxcursor1 libxcomposite1 libasound2 libxi6 libxtst6
bash ~/Downloads/Anaconda3-{version-number}-Linux-x86_64.sh # with {version-number} being your version numberThen follow the instructions of the installer. Make sure it initializes Anaconda3 by running conda init (type "yes" when asked for).
Once the installation is over, you need to restart your terminal (close and reopen it or type source ~/.bashrc).
Conda will automatically activate your base environment when launching the terminal. If you want to disable this behavior, enter:
conda config --set auto_activate_base False # set it according to your preferencesFinally, verify your installation using:
conda listTo make sure Anaconda is up to date, run:
conda update -allCreate a new Anaconda environment using the following commands:
conda create -n sparced # Creates an environment named "sparced"
source activate sparced # Activates the "sparced" environmentUnless you decide to set it otherwise, you will have to manually activate the "sparced" environment each time you reopen your terminal.
conda install matplotlib pandas scipy
pip install python-libsbml
pip install -Iv antimony==2.12.0.1 # WARNING: antimony >= 2.13.0 doesn't work with SPARCEDsudo apt install libatlas-base-dev swig
pip install amiciYou might get an error about the CBLAS library (this happens mostly on Palmetto), to fix it run:
conda install -c conda-forge openblas
export BLAS_LIBS=-lopenblasIf you are not going to use parallel computation, skip this section.
conda remove compilers # if the compilers package is missing then don't install it!
conda install -c forge mpi4py # if you encounter any dependency version failure, try downgrading to Python 3.11 by typing 'conda install python=3.11'
conda install -c conda-forge compilers
python -m pip install gmx_MMPBSAIf you are not going to run SPARCED inside the official Jupyter Notebook container, skip this section.
This is only a setup suggestion:
cd ~/Documents
mkdir birtwistle-lab ; cd birtwistle-lab
git clone --recursive ssh://git@github.com/birtwistlelab/SPARCED.git # The official SPARCED repository
cd ..
git clone --recursive ssh://git@github.com/{username}/SPARCED.git # with {username} being your username on GitHub, assuming that you already forked SPARCED
git clone --recursive ssh://git@github.com/ChocolateCharlie/sparced-personal-utilities.git # My code, feel free to improve it :)Remove all unused packages that were installed by dependencies during the setup:
sudo apt-get autoremoveCongratulations! You now have a full setup of SPARCED! 🦠