MrBayes 3.2.6

Dependencies

  • Beagle (CUDA or CPU version)
  • Intel compiler (C y C++)
  • Intel MPI (C y C++)

Installation

  1. First download the tar from the main page
wget https://downloads.sourceforge.net/project/mrbayes/mrbayes/3.2.6/mrbayes-3.2.6.tar.gz?r=http%3A%2F%2Fmrbayes.sourceforge.net%2Fdownload.php&ts=1486584181&use_mirror=superb-dca2
tar -zxvf mrbayes-3.2.6.tar.gz
  1. Makefile config
cd mrbayes-3.2.6
module load beagle-lib/2.1.2_cuda-7.0_intel-2017_update-1
module load impi/2017_update-1
./configure --prefix=/share/apps/mrbayes/3.2.6/cuda/7.0/intel_impi/2017_update-1 --enable-mpi --enable-sse --with-beagle=/share/apps/beagle-lib/2.1.2/cuda/7.0/intel/2017_update-1 2>&1 | tee mrbayes-conf.log
make 2>&1 | tee mrbayes-make.log

then

sudo mkdir -p /share/apps/mrbayes/3.2.6/cuda/7.0/intel_impi/2017_update-1
make install 2>&1 | tee mrbayes-make-install.log
  1. CUDA SUPPORT
cd /home/mgomezzul/apps/garli/intel
wget https://downloads.sourceforge.net/project/mrbayes/mrbayes/3.2.6/mrbayes-3.2.6.tar.gz?r=http%3A%2F%2Fmrbayes.sourceforge.net%2Fdownload.php&ts=1486584181&use_mirror=superb-dca2
tar -zxvf mrbayes-3.2.6.tar.gz
  1. edit makefile
cd mrbayes-3.2.6
module load beagle-lib/2.1.2_intel-2017_update-1
module load impi/2017_update-1
./configure --prefix=/share/apps/mrbayes/3.2.6/intel_impi/2017_update-1 --enable-mpi --enable-sse --with-beagle=/share/apps/beagle-lib/2.1.2/intel/2017_update-1 2>&1 | tee mrbayes-conf.log
make 2>&1 | tee mrbayes-make.log

Module

CUDA

#%Module1.0#####################################################################
##
## module mrbayes/3.2.6_cuda-7.0_intel-2017_update-1
##
## /share/apps/modules/mrbayes/3.2.6_cuda-7.0_intel-2017_update-1     Written by Mateo Gomez-Zuluaga
##

proc ModulesHelp { } {
    puts stderr "\tzlib/1.2.11 - sets the Environment for MrBayes 3.2.6 in \
    \n\tthe share directory /share/apps/mrbayes/3.2.6/cuda/7.0/intel/2017_update-1\n"
}

module-whatis "\n\n\tSets the environment for using MrBayes 3.2.6 \
               \n\tbuilded with Intel Parallel Studio XE 2017 and CUDA 7.0\n"

# for Tcl script use only
set       topdir     /share/apps/mrbayes/3.2.6/cuda/7.0/intel_impi/2017_update-1
set       version    3.2.6
set       sys        x86_64-redhat-linux

module load beagle-lib/2.1.2_cuda-7.0_intel-2017_update-1
module load impi/2017_update-1

prepend-path PATH    $topdir/bin

CPU

#%Module1.0#####################################################################
##
## module mrbayes/3.2.6_intel-2017_update-1
##
## /share/apps/modules/mrbayes/3.2.6_intel-2017_update-1     Written by Mateo Gomez-Zuluaga
##

proc ModulesHelp { } {
    puts stderr "\tmrbayes/3.2.6_intel-2017_update-1 - sets the Environment for MrBayes in \
    \n\tthe share directory /share/apps/mrbayes/3.2.6/intel/2017_update-1\n"
}

module-whatis "\n\n\tSets the environment for using MrBayes 3.2.6 \
               \n\tbuilded with Intel Parallel Studio XE 2017\n"

# for Tcl script use only
set       topdir     /share/apps/mrbayes/3.2.6/cuda/7.0/intel_impi/2017_update-1
set       version    3.2.6
set       sys        x86_64-redhat-linux

module load beagle-lib/2.1.2_intel-2017_update-1
module load impi/2017_update-1

prepend-path PATH    $topdir/bin

usage mode

CUDA

#!/bin/bash
#SBATCH --partition=accel
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --gres=gpu:2
#SBATCH --time=1:00:00
#SBATCH --job-name=mrbayes_gpu
#SBATCH -o result_%N_%j.out
#SBATCH -e result_%N_%j.err

export SBATCH_EXPORT=NONE
export OMP_NUM_THREADS=1

module load mrbayes/3.2.6_cuda-7.0_intel_impi-2017_update-1

mb concat_prot_corrected.nexus

CPU

#!/bin/bash
#SBATCH --partition=bigmem
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=24
#SBATCH --time=1:00:00
#SBATCH --job-name=mrbayes_cpu
#SBATCH -o result_%N_%j.out
#SBATCH -e result_%N_%j.err

export SBATCH_EXPORT=NONE
export OMP_NUM_THREADS=1

module load garli/2.01_intel_impi-2017_update-1

srun -n $SLURM_NTASKS mb concat_prot_corrected.nexus

References

  • manual

Author

  • Mateo Gómez Zuluaga