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SLAC provides a pool of login nodes with CVMFS and Grid tools. You can access them by ssh to rhel6-64to centos7.slac.stanford.edu. Assuming your unix shell is /bin/bash, you may use the following as a template of your $HOME/.bashrc file
# setup ATLAS environment
export ALRB_localConfigDir=/gpfs/slac/atlas/fs1/sw/localconfig
export RUCIO_ACCOUNT="change_me" export ATLAS_LOCAL_ROOT_BASE=/cvmfs/atlas.cern.ch/repo/ATLASLocalRootBase
alias setupATLAS='source ${ATLAS$ATLAS_LOCAL_ROOT_BASE}/user/atlasLocalSetup.sh --quiet localSetupRucioClients --quiet '
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upon login, you can run the alias “setupATLAS” to set up CVMFS env, which will print out the available commands such as asetup, rucio, and their usage.
Please refer to Analysis Software Tutorial for more infoType "alias" command to see additional "localSetupXXXX" commands.
Jupyter Notebooks
Please refer to this page for SLAC's new Jupyter resources: https://usatlas.github.io/tier3docs/. The following info are obsoleted.
OLD: Jupyter notebook environment is available at http://jupyter.slac.stanford.edu. Login with your SLAC Unix account, and you can choose any JupyterLab environments (container images) available from that page (some of them will allow access to GPU resources). Only the ATLAS images will mount your GPFS home directory and data directory. The ATLAS images provide PyROOT and JupyROOT (ROOT C++) notebooks with capability to access remote data via the Xroot xroot (root) protocol or webdav (http) protocol. It includes uproot and several Machine Learning software packages. It also allows storing notebooks to Google Drive for portability.
- This is an area that SLAC and the Analysis Computing Facility is constantly looking to improve. Please give us your feed back by sending e-mail to SLAC ACF mailing list atlas-us-slac-acf@cern.ch
- If your home directory is on AFS (which is not visible from the JupyterLab), you can still request a GPFS data directory - send your request to unix-admin@slac.stanford.edu, indicating that "I want a GPFS data directory under /gpfs/slac/atlas/fs1/d/<my_user_name>".
- CVMFS is available in the JupyterLab
- With JupyROOT (ROOT C++) and remote data access (via xroot or webdav/http protocol), it is possible to run ProofLite even inside a JupyROOT notebook
Remote X window access
Please refer to SLAC's FastX page
for detail instructions.
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$ cat myjob.sh #!/bin/sh #BSUB -W180
#BSUB -R 'centos7' pwd echo "hello world" $ bsub < myjob.sh Job <96917> is submitted to default queue <medium>.
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