Trouble Storing auxdata in h5

[shelby case]

Hello WESTPA users, 

I am having trouble storing my aux data in my h5 file. I believe my pcoord.py, west.cfg, and runseg.sh files are updated to run and calculate aux data, but I must have missed something to store the data correctly. I've attached my pcoord.py, west.cfg, runseg.sh, and west.h5 files.  

If anyone has experience dealing with a similar issue, I would greatly appreciate any suggestions or feedback on aux data collection. 

Thank you!

Shelby Case 

[Jeremy Leung]

Hi Shelby,

Looking at your files, nothing seems glaringly wrong. That is, assuming your `auxdata.txt` is correctly formatted and that `$WEST_AUX_RETURN` is correctly returning a tmp path. What are you getting in the `west.h5` file? Specifically does `west.h5[f'iterations/iter_{1:>08}/auxdata/aux']` exist? Are there any related errors in `seg_logs`?

Also, given the size of your dataset (10 columns at a minimum?), I'd use the `npy_data_loader` or just mv/cp the whole text file over to `$WEST_AUX_RETURN`. The former will involve:

- saving your hstacked array with `numpy.save('FILE_NAME.npy', hstacked _array)` in `pcoord.py` 

- running `cp FILE_NAME.npy $WEST_AUX_RETURN` instead of `cat ...` in `runseg.sh`

- specifying the `loader: npy_data_loader` under line 30 of `west.cfg`

More info on the data loaders here: https://github.com/westpa/westpa/wiki/Configuration-File#propagator-executable.

Best,

Jeremy L.

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

[Jeremy Leung]

Hi all,

Just a small update on the situation for future reference. Shelby was able to identify the following line in her `seg_logs` (`runseg.sh: line 68: $WEST_AUX_RETURN: ambiguous redirect`), which suggests that the temp path for `$WEST_AUX_RETURN` was not set up properly. We identified that she was not using the latest versions of westpa (2022.09 or later), so she needed to enable the dataset in `west.cfg` under executable/datasets. See here:

https://github.com/westpa/westpa/pull/408

https://github.com/westpa/westpa/wiki/Configuration-File#propagator-executable

Best,

Jeremy L.