Week 1 Action items - Githubissues

radical-collaboration / MDFF-EnTK

MDFF-EnTK: Scalable Adaptive Protein Ensemble Refinement Integrating Flexible Fitting

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Week 1 Action items #23

Closed lee212 closed 3 years ago

lee212 commented 3 years ago

[x] setup environment on $WORLDWORK/bip115/conda/rct
[x] introduce simple_mdff_vds.py, branching simple_mdff.py
[x] create a wrapper script for debugging/testing submit_debug.sh
[x] complete 8 replicas
- [x] cfg/workflow_cfg.yml has ensemble_size count to represent number of replicas
- [x] cfg/workflow_cfg.yml has total_iter to represent number of iterations

lee212 commented 3 years ago

notes on the recent changes:

task name is mandatory to locate files by data staging, e.g.: https://github.com/radical-collaboration/MDFF-EnTK/blob/374a0df10f7eb60b9ee2445b49e434aaac95d609/simple_mdff_vds.py#L171
ensemble_size represents a number of replicas: https://github.com/radical-collaboration/MDFF-EnTK/blob/ff1b0d9ef4c5e9cf11cb91f48d56cae0e36e03b5/cfg/workflow_cfg.yml#L2
total_iters represents number of iterations: https://github.com/radical-collaboration/MDFF-EnTK/blob/ff1b0d9ef4c5e9cf11cb91f48d56cae0e36e03b5/cfg/workflow_cfg.yml#L4
submt_debug*.sh wrapper script is not pushed to github remote but stored on $WORLDWORK/bip115/git/MDFF-EnTK, local repository as it contains auth info.

lee212 commented 3 years ago

Early result of 8 replicas with 3iterations for 1.8A: https://github.com/radical-collaboration/MDFF-EnTK/tree/master/experiments/summit/simple_mdff_vds_8_replicas_1.8_restart_devel