Existing traj integration

markovmodel / adaptivemd

A python framework to run adaptive Markov state model (MSM) simulation on HPC resources

GNU Lesser General Public License v2.1

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Existing traj integration #45

Open thempel opened 7 years ago

thempel commented 7 years ago

This is the documentation on how to add existing trajectories. It includes a few fixes that were necessary:

For multiple engines in a pyemma analysis, file names have to be adjusted accordingly. This fix is a bit hacky.
Paths with prefix shared://are now taken as absolute paths and have to be entered as such. @jhprinz is this compatible with what you were thinking of when introducing shared://?

jhprinz commented 7 years ago

Instead of using worker:// you could also add a new prefix like root:// which does exactly what you wanted. Just that in theory, all you can ever use is the shared folder and upwards. All other folders are not accessible from all nodes (at least that is the assumption for shared)

thempel commented 7 years ago

You are absolutely right. Paths are now directly passed with file names from PyEMMAAnalysis to _remote. So far, it seems to work fine.