clearmap-nmr 0.3.0

A package for ClearMap project

ClearMap (NMR - G. Fenton customized version)

To learn about ClearMap read the Documentation.

To use ClearMap in SOMA cluster follow these steps:

Setup

1. Clone this repository in soma login nodes (using your soma account):

git clone https://github.com/mpinb/clearmap-nmr.git

2. Change into the cloned repository folder and create the container using the ilastik-nmr definition file (ilastik-nmr.def)

cd ~/clearmap-nmr
module load apptainer
apptainer build ilastik-nmr.sif ilastik-nmr.def

3. Create conda environment using the environment definition file in this repository

module load anaconda3/2022.10
source activate
cd ~/clearmap-nmr
CONDA_OVERRIDE_CUDA="11.8" conda env create -n clearmap-nmr -f clearmap-nmr-env.yml

4. Activate the environment, add scripts that setup the environment variables and create an ipython kernel to use the environment inside Jupyter Notebook.

conda activate clearmap-nmr
cp env_vars.sh $CONDA_PREFIX/etc/conda/activate.d
cp reset_env_vars.sh $CONDA_PREFIX/etc/conda/deactivate.d
python -m ipykernel install --user --name clearmap-nmr --display-name 'clearmap-nmr'

pip install clearmap-nmr (NEW: 26.08.2025)

We now recommend to pip install the package to avoid recompilation of the Cython extensions in soma cluster.

python -m pip install clearmap-nmr

Running clearmap-nmr

Allocate a compute node from soma GPU partition (large memory nodes).

srun -p GPU -t 8:00:00 --mem 720G --cpus-per-task=48 --nodes=1 --pty bash

If there are no GPU nodes available, allocate a node from the CPU partition instead.

srun -p GPU -t 8:00:00 --mem 350G --cpus-per-task=48 --nodes=1 --pty bash

Start a shell using the apptainer container image and then inside the container load anaconda3 and launch jupyter lab

Note: The environment modules script is used to load anaconda.

module load apptainer
apptainer shell --bind /gpfs:/gpfs ilastik-nmr.sif
# another alternative is using the ilastik-nmr.sif image in /gpfs/soma_fs/scratch/containers
# apptainer shell --bind /gpfs:/gpfs /gpfs/soma_fs/scratch/containers/ilastik-nmr.sif
source /gpfs/soma_fs/soft/CentOS_7/packages/x86_64/environment-modules/5.1.1/init/bash
module load anaconda3/2022.10
source activate
conda activate clearmap-nmr

# OPTION 1: Use jupyter-lab 
cd ** CLEARMAP-NMR REPOSITORY CLONE DIRECTORY **
jupyter-lab --port 2020 --no-browser

# OPTION 2: Run a python script
python PYTHON-SCRIPT.py

From your workstation open an ssh-tunnel connection to the compute node where the jupyter server instance is running.

ssh -fN -L 2020:localhost:2020 somacpu0XX

Open your browser and enter the jupyter-lab link from the previous step to start a Jupyter Lab session and run the ClearMap NMR notebooks. Remember to switch the ipython kernel to use the one created above.