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The programs scp and rsync can be used to move files to and from Stampede. Keep files in $WORK or $HOME on Stampede.
Running Pythia and Delphes
Pythia and Delphes 3 are part of the Madgraph installation. They will be automatically run as part of bin/generate_events if the cards pythia_card.dat and delphes_card.dat exist in the Cards directory. A Delphes card for 140-pileup ATLAS is part of the template so will be in your Cards directory; you can copy it to delphes_card.dat. However this will not handle pileup.
Making a gridpack
It's great to have Stampede, but we may need to run the generated Madgraph code in other environments. In particular it appears that the Snowmass effort is trying to collect Madgraph codes for various processes. One way to make a distributable version of a Madgraph run is to create a "gridpack." These are frozen versions of the code (no parameter changes allowed, integration grids already fixed) which can be easily run on Grid sites.
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