I would appreciate it if you could help me with the above issue. The main problem I have to solve is how to call E to run for 1000 different .idfs with the same weather file and store the corresponding 1000 output files.

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e.g. a very basic solution:

• copy all 1000x (uniquely named) IDFs in 1x folder
• use preferred scripting language (e.g. Ruby, Python)
• glob all 1000x IDFs in an Array

• loop through Array, with each item replacing "in.idf" below (E+ CLI call):

  energyplus -w weather.epw osms/in.idf

That can take up A LOT of storage depending on output variables/frequencies. Consider (i) extracting required post-simulation results, then (ii) deleting IDF files (at each iteration).