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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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Different results from different version #50

Closed cynthiawqy closed 5 years ago

cynthiawqy commented 5 years ago

Hi When I set this dataset as the input alignment, link I got different loglikelihood from different versions. The model I used: PTHREADS: --msa alignment.phy --model GTR+G+F MPI: --msa alignment.phy --model GTR+G+F --threads 1 In PTHREADS version, the loglikehood is about -14406, while in MPI version, the loglikelihood is about -14018. I have tested several times but got similar results. I am just wondering why this is happening. Thanks in advance.

amkozlov commented 5 years ago

Could you please try using the same random seed (e.g. --seed 1) for both runs and post log files here? Thanks!

cynthiawqy commented 5 years ago

Hi Alexey,

I have tested several times and I found that it is not because different versions. Even if I use same input and parameters in the same version, I can still got different loglikehood.(-14018 and -14407). Is it because the random seed? When I test this alignment on other softwares I can always got same results(about -14018). The attachments are the log file. Both are from the PTHREADS version but got very different loglikehood. Thanks. dna.raxml.log dna1.raxml.log

amkozlov commented 5 years ago

Hi, so I doubled-checked and it's simply an effect of different random seeds (and thus distinct starting trees) - and has nothing to do with PTHREADS vs. MPI version.This is expected behavior, and actually quite common on datasets with relatively few sites and thus weaker signal. It is therefore highly recommended to use multiple starting trees, e.g. --tree pars{10},rand{10}.

Hope this helps, Alexey

cynthiawqy commented 5 years ago

Hi Alexey,

Thanks for your reply!