Comments (3)
You wouldn't have a minimal example for us to reproduce this segmentation fault?
If the error is really random, then one workaround for you could be to continuously save the atom-mapped reactions, rerun the script after the segmentation fault on the remaining reactions until you have the atom-mapping for all of them.
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Thank you for your advice, but it seems to be that catching C++ segfaults is impossible in python interpreter.
However, we managed to run mapping in Linux environment on our cluster and it helped, but atom-mapping speed reduced by several times, presumably, because of lack of GPU acceleration.
from rxnmapper.
Yes, without GPU the atom-mapping speed is reduced by a factor of ~7.
The best would probably be a Linux environment with an Nvidia GPU.
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Related Issues (20)
- If a low confidence score means that the obtained mapped_rxn is invalid and can not use it? HOT 2
- atom mapping for some reaction is error, how to fix this probrom HOT 4
- AttributeError: 'SmilesTokenizer' object has no attribute 'max_l HOT 4
- Request: All source code to reproduce will be contained in this repository? HOT 1
- False atom mapping result. HOT 2
- Script to finetune model? HOT 1
- ValueError when processing reaction smiles HOT 2
- Cannot run on M1 Mac
- Training dataset of rxnmapper? HOT 1
- rxn module not present in 0.2.0 release -- ModuleNotFoundError HOT 3
- Imbalanced Stoichiometry/ Missing Atom Mapping HOT 2
- Can not reproduce the result of Fig 4. HOT 2
- Can you share the code to reproduce the figure 4(A)? HOT 2
- pip error with python 3.11 HOT 13
- Error while generating Atom-atom mapping HOT 1
- Could you share the script to train the model? HOT 1
- if the atom mapping is invalid, should we remove this reaction when trainning model? HOT 2
- use get_attention_guided_atom_maps on generic compound HOT 1
- Dubious mapping case HOT 2
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