I think I have found part of the problem, I tried it on a single processor last
night and didn't get past the second molecule. The script hangs on this
molecule.
>>> from rdkit import Chem
>>> from rdkit.Chem import Recap
>>> mol =
>>> Chem.MolFromSmiles('CC[C@H](C)[C@H](NC(=O)[C@H](CC(C)C)NC(=O)[C@@H](NC(=O)[C@@H](N)CCSC)[C@@H](C)O)C(=O)NCC(=O)N[C@@H](C)C(=O)N[C@@H](C)C(=O)N[C@@H](Cc1c[nH]cn1)C(=O)N[C@@H](CC(=O)N)C(=O)NCC(=O)N[C@@H](C)C(=O)N[C@@H](C)C(=O)N[C@@H](CCC(=O)N)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](CCCN=C(N)N)C(=O)N[C@@H](CCC(=O)N)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](CCCN=C(N)N)C(=O)NCC(=O)N[C@@H](CCC(=O)N)C(=O)N[C@@H](CC(C)C)C(=O)NCC(=O)N2CCC[C@H]2C(=O)N3CCC[C@H]3C(=O)NCC(=O)N[C@@H](CO)C(=O)N[C@@H](CCCN=C(N)N)C(=O)N')
>>> hierarch = Recap.RecapDecompose(mol)
>>> ks = hierarch.GetLeaves().keys()
I imagined it would be slow for this molecule, but 8 hours might be an issue
rather than a feature!
Best,
Nick
Nicholas C. Firth | PhD Student | Cancer Therapeutics
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On 10 Jun 2014, at 20:53, Dimitri Maziuk
<[email protected]<mailto:[email protected]>> wrote:
On 06/10/2014 01:48 PM, Nicholas Firth wrote:
I still have plenty of CPU's and memory available though, so this
seems odd. Some of the processes have done nothing and the others seem
to have frozen at different times.
Yeah. Parallel processing is often not quite that straightforward.
For instance, since you say they're writing to files, how's your disk i/o?
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