Restarting corrupt segment

[Bryan Gworek]

Dear WESTPA users,

I will admit that I am still new to this, so I could be missing something.

However, I tried to restart a "corrupt" segment (seg fault due to lincs) using what was stated in the Wiki. It states to delete all residual files associated with the iteration you do not wish to keep and use w_truncate to get rid of the iteration. so for my example, I ran the following:

rm -r traj_segs/000075

rm -r seg_logs/000075*

w_truncate -W west.h5 -n 75

Unfortunately, I then get the following after starting an iteration at 75

Thu Nov  6 15:26:58 2025
Iteration 75 (2000 requested)
Beginning iteration 75
50 segments remain in iteration 75 (50 total)
10 of 20 (50.000000%) active bins are populated
per-bin minimum non-zero probability:       2.24526e-05
per-bin maximum probability:                0.469195
per-bin probability dynamic range (kT):     9.94737
per-segment minimum non-zero probability:   4.49052e-06
per-segment maximum non-zero probability:   0.13662
per-segment probability dynamic range (kT): 10.323
norm = 1, error in norm = 0 (0*epsilon)
Waiting for segments to complete...
exception caught; shutting down
-- ERROR    [w_run] -- error message: group ``/log/75_1`` already has a child node named ``data``

Did I miss anything else that I should have also deleted? I tried exploring this further and I see the west.h5 file does not have the iteration in the west.h5 file (image 3 is before truncation, image 4 is after truncation). I'm unclear as to what /log/75_1 is referring too. Any help is appreciated! Thanks in advance.

[Leung, Jeremy]

Hi Bryan,

I assume you're also using the HDF5 Framework? You'll need to delete per-iter HDF5 file, `iter_000075.h5`, inside traj_segs. 

Best,

Jeremy L.

---
Jeremy M. G. Leung, PhD
Research Assistant Professor, Chemistry (Chong Lab)
University of Pittsburgh | 219 Parkman Avenue, Pittsburgh, PA 15260
jml...@pitt.edu | [He, Him, His]

On Nov 6, 2025, at 5:06 PM, Bryan Gworek <bgwo...@illinois.edu> wrote:

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[Bryan Gworek]

Jeremy,

Yes! This was my problem. Thank you for pointing it out, I figured I was missing something. After deleting, it works well restarting. Thanks!

Best,

Bryan