lower threshold for using workdir on node

rinikerlab / reeds

This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration free energies or ligand binding free energies.

https://rinikerlab.github.io/reeds/

MIT License

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lower threshold for using workdir on node #48

Closed SalomeRonja closed 3 years ago

SalomeRonja commented 3 years ago

fixes issue #49

candidechamp commented 3 years ago

@epbarros @SchroederB @SalomeRonja

I haven't run many RE-EDS simulations lately so I haven't come across these issues but your fix seems good to me.

I would suggest two things:

ask for the same number of s-values which determines where the calculation is run in the sopt and production submission scripts.
rename the local directory where the calculation will be run from 'scratch' to 'localscratch' (or something else) to avoid any confusion between the real scratch (on the node) and the directory we are creating.

Finally, I know there have been quite a few changes on the Euler side where the reinstalled things so I'm surprised we still have this issue. Did anyone try contacting the Euler cluster support more recently with this problem?

RiesBen commented 3 years ago

@SalomeRonja I like the changes! :+1: I'm experiencing the same issues at the moment... and I wonder what the problem with euler is there...

@candidechamp:

Maybe we really should ask the cluster, if they know whats the issue.
I don't understand your first point in your list, could you please clearify? :relaxed: (ask for the same number of s-values which determines where the calculation is run in the sopt and production submission scripts.)

candidechamp commented 3 years ago

@SchroederB

My comment was about using the same number (e.g. 15) to determine the threshold at which we shift from running the calculation on scratch or locally, in all parts of the pipeline (sopt and production). This is similar to your code comment above.

RiesBen commented 3 years ago

@SchroederB

My comment was about using the same number (e.g. 15) to determine the threshold at which we shift from running the calculation on scratch or locally, in all parts of the pipeline (sopt and production). This is similar to your code comment above.

Ah I see! :) yah that is a fair point (I also pointed it out ;) )

SalomeRonja commented 3 years ago

Hey everyone, thanks a lot for the feedback, I implemented your suggestions, so since everyone seems to be happy with the changes, I'll do the merge now.