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| =RAxML=
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| RAxML (Randomized Axelerated Maximum Likelihood) written by [http://wwwkramer.in.tum.de/exelixis/software.html Alexandros Stamatakis and others] is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It has originally been derived from fastDNAml which in turn was derived from Joe Felsentein’s dnaml which is part of the PHYLIP package.
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| == Variations ==
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| {| cellspacing="1" cellpadding="1" border="1" style="width: 954px; height: 138px;"
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| |-
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| | /apps/RAxML/7.3.0/raxmlHPC-PTHREADS-SSE3
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| | OpenMP threaded version
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| |-
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| | /apps/RAxML/7.3.0/raxmlHPC-HYBRID-SSE3
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| | OpemMPI/OpenMP MPI and threaded hybrid version
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| |}
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| == Sample Submission Script for threaded (PTHREADS) version ==
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| #!/bin/sh
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| #PBS -N RAxML
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| #PBS -m bea
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| #PBS -M <e-mail>
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| #PBS -o pbsJobLog
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| #PBS -e pbsJobErr
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| #PBS -l nodes=1:ppn=4
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| #PBS -l pmem=500mb
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| #PBS -l walltime=00:05:00
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| #
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| # This job's working directory
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| echo Working directory is $PBS_O_WORKDIR
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| cd $PBS_O_WORKDIR
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| echo Running on host `hostname`
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| echo Time is `date`
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| echo Directory is `pwd`
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| /apps/RAxML/7.3.0/raxmlHPC-PTHREADS-SSE3 -f a -m GTRGAMMA -s dna.phy -p 12345 -x 12345 -# 100 -n dnaBSML -T 4
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| # Note the -T 4 option specifying the use of 4 cores, matching the nodes=1:ppn=4 in the #PBS -l statement above
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