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NBISweden / MrBayes

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:
http://NBISweden.github.io/MrBayes/
GNU General Public License v3.0
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Error in function: ConfirmAbortRun at line: 15511 in file: mcmc.c Mcmc run continued ... #260

Closed zzzygolden closed 2 years ago

zzzygolden commented 2 years ago

I use morphology and DNA combined data as an input, set mcmcp ngen=10000000 and submit my task in Linux. When MrBayes ran in insufficient generations it stopped. And its log output is:

        Average standard deviation of split frequencies: 0.005470
        623000 -- (-164520.244) (-164508.877) [-164114.194] (-164149.176) * [-164125.771] (-164508.524) (-164124.362) (-164140.780) -- 81:38:43
        624000 -- (-164529.369) (-164508.715) [-164106.839] (-164135.822) * (-164122.630) (-164512.593) [-164122.009] (-164150.927) -- 81:30:35
        634000 -- (-164526.318) (-164518.163) (-164127.091) [-164138.676] * (-164148.822) (-164535.934) (-164145.491) [-164115.804] -- 80:09:48
        636000 -- (-164517.073) (-164523.789) (-164122.106) [-164113.277] * [-164140.386] (-164536.369) (-164150.913) (-164112.990) -- 79:55:07
   Ctrl-C detected
   Do you really want to stop the run (y/n)?Error in function: ConfirmAbortRun at line: 15511 in file: mcmc.c   Mcmc run continued ...
   Ctrl-C detected
   Do you really want to stop the run (y/n)?Error in function: ConfirmAbortRun at line: 15511 in file: mcmc.c   Mcmc run continued ...
   Ctrl-C detected
   Do you really want to stop the run (y/n)?Error in function: ConfirmAbortRun at line: 15511 in file: mcmc.c   Mcmc run continued ...
   Ctrl-C detected
   Do you really want to stop the run (y/n)?Error in function: ConfirmAbortRun at line: 15511 in file: mcmc.c   Mcmc run continued ...

I cannot find the file mcmc.c and resubmit my task with code mpirun -np 8 mb combined-mydata.nex -mcmcdiagn no -mcmcappend yes, it stopped with different and insufficient generations everytime.

I use MrBayes 3.2.7 x86_64.

Maybe someone knows how to solve this problem and thank you very much!

kusalananda commented 2 years ago

Hi @zzzygolden

It looks as if you are running mb with MPI, and it seems like the mb that you are trying to run with MPI was not compiled to be run with MPI.

What does the interactive Version command output if you give it in mb?

The reason that I think you are trying to run an mb without MPI support is that the error message that is displayed can only be displayed when a non-MPI variant of the software receives a Ctrl+C key-press (or an interrupt signal). That piece of code is disabled in the mb with MPI support.

zzzygolden commented 2 years ago

Hi @kusalananda

Thanks for your reply.

I used conda install MyBayes to download and install MrBayes and also saw the mb-mpi file in my mrbayes directory. So I thinked MPI was useful. I tried MPI previously and it succeeded in running the whole generations. But the result is not converged and I reset parameters but it never ran sufficient generations again.

I'll try mb and my data is a little bit big so it may spend some time. I'll reply you in time when I get my output.

kusalananda commented 2 years ago

@zzzygolden

If you have an mb-mpi executable, then this is probably what you want to use with MPI (maybe something like mpirun -np 8 mb-mpi combined-mydata.nex -mcmcdiagn no -mcmcappend yes, looking at your initial message here). I know about the existence of Conda, but I never use it myself, so I can't say much about that.

zzzygolden commented 2 years ago

Hi @kusalananda

mpirun -np 8 mb-mpi combined-mydata.nex -mcmcdiagn no -mcmcappend yes runs well now. I think this is the problem!

Sorry to have taken up your time. Thank you very much!!!

kusalananda commented 2 years ago

@zzzygolden

I'm just happy we resolved fairly easily.

Take care!