ML search aborted from core dump

[Conor Meehan]

Hi,

I am running a very large SNP dataset through raxml (35,795 site patterns, 942 sequences) with the following command:

raxmlHPC-PTHREADS-AVX -T 12 -f a -m ASC_GTRCAT -V -s SNPonly_hbNames.fasta -p 413287 -x 71653 -N 100 --asc-corr=stamatakis -q partition.txt -n hsnp

It runs the bootstrap analysis fine and the slow ML optimization. However it exits as such:

Slow ML search Time: 11448.317007 seconds

Aborted (core dumped)

And does not create the best tree or bipartitions file. Any idea why this is and how to get around it?

Thanks in advance,

Conor

[Alexandros Stamatakis]

could it be that you don't have enough memory for inferences under GAMMA?

In the end the code will siwtch to GTR+GAMMA by default unfortunately

I'd try running it on a machine with more RAM,

alexis

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Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org

[Conor Meehan]

The machine I am using has 64gb of ram available. How much more do you estimate would be needed for such an analysis?

Con

[Alexandros Stamatakis]

you can calculate the mem reqs on-line at:

http://sco.h-its.org/exelixis/web/software/raxml/index.html

alexis

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>
> --
> Alexandros (Alexis) Stamatakis
>
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
> Adjunct Professor, Dept. of Ecology and Evolutionary Biology,
> University
> of Arizona at Tucson
>

> www.exelixis-lab.org <http://www.exelixis-lab.org>

[Alexey Kozlov]

Dear Conor,

you could also use "-F" switch to disable final optimization under GAMMA (and thus reduce the memory footprint).

Alexey

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>
> --
> Alexandros (Alexis) Stamatakis
>
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
> Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
> of Arizona at Tucson
>

> www.exelixis-lab.org <http://www.exelixis-lab.org>

[Conor Meehan]

Ok great, thanks for the info. I don't need a gamma optimisation for what I am doing so I will leave that off.

Thanks again,

Conor