Setup

Before start
Suppose you already have access to BIH cluster, read the BIH HPC Docs and tried to log into the cluster successfully.
To be able to run applications with graphic user interface on the cluster, check in your terminal if echo $DISPLAY returns empty. If so, add this line export DISPLAY=:0 to the end of your shell rc file (.bashrc or .zshrc depending on which one you use).
For macOS, run brew install xquartz in your terminal to enable X11 forwarding.
Log into the cluster
ssh -Y [email protected]
Log into a compute node
srun -I60 --pty --cpus-per-task=8 --mem=32G --part=medium --time=1-0 bash
Everything below should be done in a compute node.
Create folders and soft links
ln -sfn /fast/work/groups/ag_horn group
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mkdir -p $HOME/work/home/.cache
mkdir -p $HOME/work/home/.ccache
mkdir -p $HOME/work/home/.conda
mkdir -p $HOME/work/home/.config
mkdir -p $HOME/work/home/.local
mkdir -p $HOME/work/home/.singularity
​
ln -sfn $(realpath $HOME/work/home/.cache) $HOME/.cache
ln -sfn $(realpath $HOME/work/home/.ccache) $HOME/.ccache
ln -sfn $(realpath $HOME/work/home/.conda) $HOME/.conda
ln -sfn $(realpath $HOME/work/home/.config) $HOME/.config
ln -sfn $(realpath $HOME/work/home/.local) $HOME/.local
ln -sfn $(realpath $HOME/work/home/.singularity) $HOME/.singularity
Copy preset files
cp -rT $HOME/group/setup/config $HOME
Things included:
.bash_profile, .bashrc, .zshrc
.tmux.conf
.condarc
ys-cluster.zsh-theme
startup.m (MATLAB startup script)
Setup Mambaforge
curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh"
sh Mambaforge-Linux-x86_64.sh -b -p $HOME/work/mambaforge
rm Mambaforge-Linux-x86_64.sh
Install and configure zsh and .oh-my-zsh
mamba install zsh -y
ZSH="$HOME/work/home/.oh-my-zsh" sh -c "$(curl -fsSL https://raw.githubusercontent.com/ohmyzsh/ohmyzsh/master/tools/install.sh)"
mv $HOME/.zshrc.pre-oh-my-zsh $HOME/.zshrc
mv $HOME/ys-cluster.zsh-theme $HOME/work/home/.oh-my-zsh/custom/themes/
Initialize conda for bash and zsh
conda init bash zsh
Now open another terminal and try to log into the cluster
ssh -Y [email protected]
If you see error during login, fix it in the terminal in which you already logged into the cluster.
If everything works, you should see that you are using zsh now. From now on, you can log into a compute node and start a interactive session using:
srun -I60 --x11 --pty --cpus-per-task=8 --mem=32G --part=medium --time=1-0 --nodelist=hpc-cpu-50 zsh
where --x11, --cpus-per-task, --mem and --nodelist are optional parameters. Check out BIH HPC Docs for details.
You can also check out the BIH HPC Docs on how to use GPU nodes (for example, run CUDA version of eddy from FSL). eddy available in $FSLDIR/bin uses CUDA 11 by default. OpenMPI version is also available via eddy_openmp.
Copy MATLAB Singularity image
mkdir -p $HOME/work/container
cp $HOME/group/setup/container/matlab-ossdbs.sif $HOME/work/container
Set up Lead-DBS
getspm -P $HOME/work/MATLAB/toolbox
unzip $HOME/work/MATLAB/toolbox/spm12.zip
unzip -d $HOME/work/MATLAB/toolbox $HOME/work/MATLAB/toolbox/spm12.zip
rm $HOME/work/MATLAB/toolbox/spm12.zip
git clone https://github.com/netstim/leaddbs.git $HOME/work/MATLAB/toolbox/leaddbs
git -C $HOME/work/MATLAB/toolbox/leaddbs checkout classic
cp -r $HOME/group/setup/lead_data/* $HOME/work/MATLAB/toolbox/leaddbs
Use MATLAB
Log into a compute node with X11 forwarding enabled (--x11)
actmatlab # This activates MATLAB on the compute node
runmatlab # This starts MATLAB without GUI
runmatlabx # This starts MATLAB with GUI
After you start LeadDBS, edit the preference file from the menu and set the two keys below:
prefs.lc.datadir = [ea_gethome, 'group', filesep, 'connectomes', filesep];
prefs.env.dev = 1;

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Last modified 7mo ago