To list available local software, do

Locally installed packages

1. module avail
2. module load moduleName

To get the description of a particular module

1. module help moduleName

OSG/CERN/FERMILAB software libraries

1. source /cvmfs/oasis.opensciencegrid.org/osg/modules/lmod/5.6.2/init/bash
2. module avail
3. module load moduleName

These libraries are mounted as /opt/osg, /opt/cms and /opt/atlas.

Python modules

• pip3 install pkgName
  • A python package from the pip3 predefined repository will be placed in the user's home directory ~/.local/lib/python3.6/site-packages under user ownership. All dependencies will be checked/resolved.
• pip3 install git+git://github.com/xxxx/pkgName.git
  • same as above but using the exact address for a package

Jupyter notebook

• Install local jupyter notebook
  • pip3 install jupyter
• Launch the notebook using the port number of your choice (12345 in the example below)
  • jupyter notebook --no-browser --port=12345 --ip=0.0.0.0

~]$ jupyter notebook --no-browser --port=12345 --ip=0.0.0.0 
[I 23:26:55.768 NotebookApp] Serving notebooks from local directory: /home/username
[I 23:26:55.768 NotebookApp] Jupyter Notebook 6.4.10 is running at:
[I 23:26:55.768 NotebookApp] http://t3int0.nicadd.niu.edu:12345/?token=f7586e3b06bddb86f130f762860dfc4af4ce70223a8b8e77
[I 23:26:55.769 NotebookApp]  or http://127.0.0.1:12345/?token=f7586e3b06bddb86f130f762860dfc4af4ce70223a8b8e77
[I 23:26:55.769 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 23:26:55.790 NotebookApp]
......

• At the beginning of the above output, look for the URL to copy/past in your local browser; in this example
• http://127.0.0.1:12345/?token=f7586e3b06bddb86f130f762860dfc4af4ce70223a8b8e77

• Create the ssh tunnel for the chosen port from your computer to the jupyter notebook server
  • ssh -f username@t3int0.nicadd.niu.edu -L 12345:t3int0.nicadd.niu.edu:12345 -N
• Open a browser on your local computer and copy/paste the access URL
• Detailed tutorial: https://thedatafrog.com/en/articles/remote-jupyter-notebooks/

ATLAS packages

Add to .bashrc

• export ATLAS_LOCAL_ROOT_BASE='/cvmfs/atlas.cern.ch/repo/ATLASLocalRootBase'
• alias setupATLAS='source ${ATLAS_LOCAL_ROOT_BASE}/user/atlasLocalSetup.sh'

Open a new terminal, do

• [@t3int0 ~] setupATLAS

More details can be found here.

Packages for personal use

Create /bdata/$USER/contrib area; download a package source; build it.

Anything else

Please send a request to system@nicadd.niu.edu