Troubleshooting

Common symptoms and fixes. See also Installation, Batch Processing Tab, and COR Management.

GUI / launch

ModuleNotFoundError: No module named 'tomogui'

The editable install did not register, or a stale site-packages copy is shadowing it. From the repo root:

pip uninstall tomogui -y
rm -rf $(python -c "import site; print(site.getsitepackages()[0])")/tomogui*
pip install -e . --config-settings editable_mode=compat
Qt platform plugin could not be initialized
export QT_QPA_PLATFORM_PLUGIN_PATH=""
export QT_QPA_PLATFORM=xcb       # or wayland / offscreen
Changes to source do not take effect

Check that the running tomogui is from the tree you edited. On shared beamline accounts, multiple clones often exist:

python -c "import tomogui, inspect; print(inspect.getfile(tomogui))"

Reconstruction

Try works, Full OOMs

Decrease nsino-per-chunk on the Recon tab, or increase binning.

“Invalid COR” in batch mode

The row’s COR is empty and the top-bar fallback is also empty / invalid. Fix the row, set the top-bar, or use Fix COR Outliers to fill missing CORs from the series mean.

Mass invalid CORs after AI Reco

Check:

  • AI model path is valid on the reconstruction host

  • nvidia-smi shows GPU activity during Phase B

  • log lines start with [infer-worker]

If center_of_rotation.txt exists but the GUI isn’t picking it up, verify read permissions on the try_center/ folder.

AI Reco

Only one GPU in use during Phase B

  • Number of GPUs in Advanced Config must be > 1

  • all GPUs must be visible to nvidia-smi

  • CUDA_VISIBLE_DEVICES must not be pre-set in the parent shell

Inference worker stuck (0 % GPU, no progress)

The worker is hung before inference starts — usually on an NFS read or a CUDA init. Kill it with kill <pid>; the queue continues on the other GPUs. If it happens repeatedly, grab a py-spy dump --pid <pid> stack trace before killing.

Worker prints FAIL <file>

Look at the traceback immediately above the FAIL line. Common causes: wrong model path, torch / CUDA version mismatch, missing try_center TIFFs for that file.

TomoLog

Flat or saturated PDFs

Leave Min / Max blank on the TomoLog panel → 5 – 95 % percentile auto-contrast per file.

Phase D upload skipped

Tick the → TomoLog checkbox next to Batch AI Reco before starting. Files whose Full failed are skipped automatically.