MrBayes 3.2.7

Dependencies

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

Installation

  1. First download the tar from the main page
mkdir mrbayes
cd /home/blopezp/Desktop/mrbayes
wget https://github.com/NBISweden/MrBayes/releases/download/v3.2.7/mrbayes-3.2.7.tar.gz
tar -xzvf mrbayes-3.2.7.tar.gz
cd mrbayes-3.2.7
  1. Makefile config and CUDA support
mkdir build
cd build
module load openmpi/3.1.5_intel-19.0.4
module load beagle-lib/2.1.2_cuda-7.0_intel-2017_update-1
module load gcc/7.4.0
../configure --prefix=/share/apps/mrbayes/3.2.7/cuda/7.0/gcc/7.4.0 --with-mpi=/share/apps/openmpi/3.1.5/intel-19.0.4 --enable-sse --with-beagle=/share/apps/beagle-lib/2.1.2/cuda/7.0/intel2017_update-1 2>&1 | tee mrbayes-conf.log
make 2>&1 | tee mrbayes-make.log
sudo make install
  1. Makefile config and CUDA no support
module unload beagle-lib/2.1.2_cuda-7.0_intel-2017_update-1
module unload gcc/7.4.0

module load openmpi/3.1.5_intel-19.0.4
module load beagle-lib/2.1.2_intel-2017_update-1
module load gcc/7.4.0
../configure --prefix=/share/apps/mrbayes/3.2.7/gcc/7.4.0 --with-mpi=/share/apps/openmpi/3.1.5/intel-19.0.4 --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
sudo make install

Module

CUDA

#%Module1.0#####################################################################
##
## module mrbayes/3.2.7_cuda-7.0_gcc-7.4.0
##
## /share/apps/modules/mrbayes/3.2.7_cuda-7.0_gcc-7.4.0    Written by Bryan López Parra
##

proc ModulesHelp { } {
    puts stderr "\tzlib/1.2.11 - sets the Environment for MrBayes 3.2.7 in \
    \n\tthe share directory /share/apps/mrbayes/3.2.7_cuda-7.0_gcc-7.4.0\n"
}

module-whatis "\n\n\tSets the environment for using MrBayes 3.2.7 \
                \n\tbuilded with CUDA 7.0 AND gcc-7.4.0\n"

# for Tcl script use only
set       topdir     /share/apps/mrbayes/3.2.7_cuda-7.0_gcc-7.4.0
set       version    3.2.7
set       sys        x86_64-redhat-linux

module load beagle-lib/2.1.2_cuda-7.0_intel-2017_update-1
module load openmpi/3.1.5_intel-19.0.4

prepend-path PATH    $topdir/bin

CPU

#%Module1.0#####################################################################
##
## module mrbayes/3.2.7_gcc-7.4.0
##
## /share/apps/modules/mrbayes/3.2.7_gcc-7.4.0    Written by Bryan López Parra
##

proc ModulesHelp { } {
    puts stderr "\tmrbayes/3.2.7_gcc-7.4.0 - sets the Eviroment for MrBayes in \
    \n\tthe share directory /share/apps/mrbayes/3.2.7_gcc-7.4.0\n"
}

module-whatis "\n\n\tSets the environment for using MrBayes 3.2.7 \
               \n\tbuilded with gcc-7.4.0\n"

# for Tcl script use only
set       topdir     /share/apps/mrbayes/3.2.7_gcc-7.4.0
set       version    3.2.7
set       sys        x86_64-redhat-linux

module load beagle-lib/2.1.2_intel-2017_update-1
module load openmpi/3.1.5_intel-19.0.4

prepend-path PATH    $topdir/bin

Slurm template

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/3.2.7_cuda-7.0_gcc-7.4.0

mpirun -np 1 mb primates-gtr-gamma.nex

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 mrbayes/3.2.7_gcc-7.4.0

mpirun -np $SLURM_NTASKS mb primates-gtr-gamma.nex