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Using the images you have built on the jupyter-lab and on the worker nodes

On the Hub

From the gitlab.cern.ch container registry copy the path of the relevant image.

imageselect

Paste it in the Jupyter Hub startup page and wait for the server to start.

hub_privateimage

Job submission script (an example)

Please find here a complete submission script that was succesfully used on the testbed, based on the Latinos framework discussed earlier. 

Requirements = HasSingularity
transfer_input_files    = proxy
executable = ./mkShapes__ggH2018_v7_11_11__ALL/qqH_hww.1/mkShapes__ggH2018_v7_11_11__ALL__qqH_hww.1.sh
universe = vanilla
output = ./mkShapes__ggH2018_v7_11_11__ALL/qqH_hww.1/mkShapes__ggH2018_v7_11_11__ALL__qqH_hww.1.out
error = ./mkShapes__ggH2018_v7_11_11__ALL/qqH_hww.1/mkShapes__ggH2018_v7_11_11__ALL__qqH_hww.1.err
log = ./mkShapes__ggH2018_v7_11_11__ALL/qqH_hww.1/mkShapes__ggH2018_v7_11_11__ALL__qqH_hww.1.log
request_cpus = 1
+SingularityImage = "/cvmfs/unpacked.cern.ch/gitlab-registry.cern.ch/lenzip/latinoanalysis:0b855edd/"
Requirements   = (SiteName == "T2_LNL_PD")
queue
Note that:

  • the singularity image that is loaded is the same one we used to start the server, except it is taken from /cvmfs, instead of the gitlab.cern.ch container registry directly.

The exectutable script looks like this:

#!/bin/bash
export VO_CMS_SW_DIR=/cvmfs/cms.cern.ch
export X509_USER_PROXY=$PWD/proxy
#voms-proxy-info
export SCRAM_ARCH=slc7_amd64_gcc900
export VO_CMS_SW_DIR=/cvmfs/cms.cern.ch
source $VO_CMS_SW_DIR/cmsset_default.sh
cd /opt/CMSSW_11_2_5
eval `scramv1 ru -sh`
ulimit -c 0 -s unlimited
cd -
set -e
python ./mkShapes__ggH2018_v7_11_11__ALL/qqH_hww.1/mkShapes__ggH2018_v7_11_11__ALL__qqH_hww.1.py
[ $? -eq 0 ] && mv ./mkShapes__ggH2018_v7_11_11__ALL/qqH_hww.1/mkShapes__ggH2018_v7_11_11__ALL__qqH_hww.1.jid ./mkShapes__ggH2018_v7_11_11__ALL/qqH_hww.1/mkShapes__ggH2018_v7_11_11__ALL__qqH_hww.1.done

Note that:

  • The job points to the voms proxy that was transferred to the worker
  • Since the job lands in a singularity shell based on the docker image we have created, it does cd /opt/CMSSW_11_2_5 and then cmsenv to source the environment.

Output retrieval

Options are:

  • Stage-out on a SE with xrdcp or davix-put
  • use condor_trasfer_data, which will return all files that have been created in the working directory.
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