aizynthfinder process is killed after loading config.yml

[ZHZihangHuang]

Hi,

I am trying to run Retrosynthesis on a small sample of Building Blocks. From the published paper "AiZynthFinder: a fast, robust and flexible open-source software for retrosynthetic planning".

I got 2 hdf5 for policy configuration and 1 hdf5 for zinc stock from the reference: https://figshare.com/articles/dataset/AiZynthFinder_a_fast_robust_and_flexible_open-source_software_for_retrosynthetic_planning/12334577/1

My config file is shown as follows:

config.yml starts here

properties:
exclude_target_from_stock: False
iteration_limit: 100
time_limit: 10
cutoff_cumulative: 0.995
cutoff_number: 50
max_transforms: 5
policy:
files:
uspto:
- ~/repos/full_uspto_03_05_19_rollout_policy.hdf5
- ~/repos/full_uspto_03_05_19_unique_templates.hdf5
stock:
files:
zinc: ~/repos/zinc_stock_17_04_20.hdf5

config.yml ends here

After loading the config.yml, the aizynthfinder process is unexpectedly killed without any error message. Here is the log:

log starts here

(aizynth-env) [user1@c0308a-s25 Lib-INVENT]$ aizynthcli --smiles ../sample_output/AC_SMILES_split_0.smi --config ../sample_run/config.yml --output ../sample_output/aizynthfinder_output_AC.hdf5
Setting exclude target from stock to False
Setting iteration limit to 10000000
Setting time limit to 100
Setting cutoff cumulative to 0.9
Setting cutoff number to 25
Setting max transforms to 4
Loading template-based expansion policy model from ~/repos/full_uspto_03_05_19_rollout_policy.hdf5 to uspto
Loading templates from ~/repos/full_uspto_03_05_19_unique_templates.hdf5 to uspto
Loading stock from ~/repos/zinc_stock_17_04_20.hdf5 to zinc
Killed
(aizynth-env) [user1@c0308a-s25 Lib-INVENT]$

log ends here

I have tried adjusting the time limit and all other variables in my config.yml, but it will always be killed within 20 seconds. I wonder what is the cause and how I can fix it.

Thank you!

[ZHZihangHuang]

Hi, I figured that if I use the stockfile.hdf5 file from "https://github.com/SeemonJ/combinatorial-library-design-dpp/tree/main/publication_example", aizynthfinder will work.

[SGenheden]

Hello. Thanks for your respons.

My initial thought is that you ran out of memory when trying to load the rather large ZINC stock.

Looking at your input file, it appears that you are running on old version of aizynthfinder with old model files. I would recommend upgrading to the latest version and downloading the models files anew with "download_public_data" script.