Dynabench juptyer notebook test error

Atakanzsn / DynaBench

Tool for MD simulation analysis and visualization

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Closed inantu closed 5 months ago

inantu commented 5 months ago

While running on Jupyter notebook, (at step 3), the following error occurs (IndexError: index 0 is out of bounds for axis 0 with size 0).

inantu commented 5 months ago

The same error while running on terminal

Atakanzsn commented 5 months ago

Can you check the .pdb file? Which OS do you use? I do not encounter with this bug in Windows.

inantu commented 5 months ago

3F1P_input.pdb in test folder is empty. By the way I downloaded using git clone. System version is macOS 12.1 (21C52).

Atakanzsn commented 5 months ago

I just re-uploaded the test pdb, which seems 56 MB. So, I'm closing the issue for now. If the bug continues, please open the issue again.

inantu commented 5 months ago

Pdb file can not be downloaded by using git clone. Ps. I can jump the error by downloading externally.

inantu commented 5 months ago

Pdb file can not be downloaded by using git clone. Ps. I can jump the error by downloading externally.

error encountered only MacOs.

Atakanzsn commented 5 months ago

Can you run git lfs install on your shell then try cloning the repo again?

inantu commented 5 months ago

at jupyter notebook step 12, calculation related MDanalysis, the following error showed up.

FileNotFoundError: [Errno 2] No such file or directory: '3F1P_dt05_time_ns_stride10_test/tables/interface_label_perc.csv'

inantu commented 5 months ago

testing ..stride10.ipynb following error encountered.

FileNotFoundError: [Errno 2] No such file or directory: '3F1P_dt05_time_ns_stride10_test/3F1P_input_stride10.pdb'

Atakanzsn commented 5 months ago

can you give the path of pdb file which in the folder '3F1P_dt05_time_ns_stride10_test'?