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amkozlov / raxml-ng

RAxML Next Generation: faster, easier-to-use and more flexible
GNU Affero General Public License v3.0
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Suggestion - don't search for starting tree when restarting from checkpoint #94

Closed davipatti closed 4 years ago

davipatti commented 4 years ago

Hello - I just wanted to leave this here as a suggestion.

I have been using raxml on a largish dataset where the starting parsimony tree takes ~4 hours to find. I had to restart the run from a checkpoint, but before continuing from the checkpoint raxml-ng began to look for the starting tree (again).

(It's easily hacked by passing a starting tree with --tree which raxml-ng then presumably ignores, and continues using the topology and parameters in the .ckp file.)

It seems that raxml-ng should not search for the starting tree again when restarting from a checkpoint.

David

amkozlov commented 4 years ago

this is actually how raxml-ng should work now, could you please post your log file?

davipatti commented 4 years ago

FLU.raxml.log

amkozlov commented 4 years ago

Thanks! I tested with the same version (0.9.0git released on 26.11.2019), but cannot reproduce this behavior. Could it be that you copied .ckp file to a different machine? raxml-ng will try to reload existing starting trees from .raxml.startTree file, but if this file is not present, it will automatically re-generate them from scratch. I suspect this is what happened in your case.

davipatti commented 4 years ago

Thanks - you are right!