Draft: Time out feature

Problem: GSAM and particularly the code calling RDT remained blocked because of some reactions resulting in several days of computing without any results.

Solution: I modified ComputeGSAM.java to add a timeout.

To do so I created a void called "perform_aam" that performs the atom mapping step. This void is converted to a callable task and called for each entry of rxnSmilesMap. If the executor cannot get the results from the thread before a defined time (default = 6hours) set by the user with the parameter -t, the task is killed and the failed reaction is displayed in the log.

This is a quick and dirty solution. I think the optimal solution would be to define timers directly in RDT and for each algorithm.

Cheers,

Louison

requested review from @clement.frainay

assigned to @clement.frainay

changed target branch from master to develop

added 1 commit

• 55b3ce83 - add executor.shutdown()

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• 9269b96c - replace hard coded timeout by parameter's value

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added 1 commit

• cdcbd7df - update TimeOut default value

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• f693abca - update TimeOut executors (declare and shutdown inside the loop)

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added 1 commit

• c9e81722 - shorten task, only aam is subject to timeout

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collateral timeout problem: when one reaction AAM exceed allowed time, few following runs also fail due to timeout, while their expected computation time should be below threshold. Issue seems to be related with thread locks.

marked this merge request as draft