VilleneuveLab Documentation

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Access neuroimaging softwares

When you are logged into the lab cluster, you can use the module function to easily access softwares already installed.

How to use module : Compute Canada documentation

Loading the default modules on beluga

Each time you connect to the server, type these lines to load the VilleneuveLab module. This module contain a bundle of default softwares install in the quarantine

export VL_QUARANTINE_DIR="/project/ctb-villens/quarantine"
module use ${VL_QUARANTINE_DIR}/modulefiles
module load VilleneuveLab

News with beluga

  • afni is already installed by Compute Canada. See module spider afni/20180404 for instructions
  • freesurfer/6.0.0 is loaded by default by the VilleneuveLab module to be able to use freeview from VNC
  • freesurfer/5.3.0 is still the default with vl_lancer_recon-all
  • fsleyes is not available by default from the VilleneuLab module. Load the python environment with source ${VL_QUARANTINE_DIR}/python_virtualenv/fsleyes/bin/activate, deactivate to unload it
  • vl_vncserver setup change, see vl_vncserver -h for instructions
  • If stuck with the lock screen with VNC, type killall -9 .mate-screensav from the worker node
  • minc-toolkit is already installed by Compute Canada. See module spider minc-toolkit/1.9.16 for instructions.
  • python3 virtualenv for the lab available with source ${VL_QUARANTINE_DIR}/python_virtualenv/villeneuve/bin/activate. deactivate to unload the virtualenv.

Loading the default modules on guillimin

Each time you connect to the server, type these lines to load the VilleneuveLab module. This module contain a bundle of default softwares.

source /software/soft.computecanada.ca.sh
export VL_QUARANTINE_DIR="/sf1/project/yai-974-aa/quarantine"
module use ${VL_QUARANTINE_DIR}/modulefiles
module load VilleneuveLab

Optional

To automatically load the default softwares, it is possible to add the following lines at the end of your ~/.bashrc file. This file is loaded each time you connect to guillimin.

if [ -z "$BASHRC_READ" ]; then
   export BASHRC_READ=1
   # Place the previous commands here
fi

For a better default to check your running jobs, you could add this alias at the end of your ~/.bashrc file.

alias showme='squeue -u $USER -o "%i %j %T %M %l %R %Z" | column -t'

Note

Due to an issue within /software/soft.computecanada.ca.sh this will break the loading if you use tmux or the VNC server. Just comment the line export BASHRC_READ=1 if you are in this case. This will be fixed when beluga comes online

Python3 environment

A multi purpose python3 environment exists on the server for running scripts interactively. You can use it with module load PythonenvVilleneuve.

It should not be used to run within jobs. For that, create your own environment to control your modules version. See Compute Canada documentation for more information.

Loading the default modules the old way

Deprecated

This way is deprecated and will be deactivate when beluga comes online

Each time you connect to the server, type these lines:

module use /sf1/project/yai-974-aa/local/modulefiles
module load VilleneuveLab