MUSCLE 3.8.1551

Basic information

Tested on (Requirements)

  • OS base: CentOS (x86_64) \(\boldsymbol{\ge}\) 6.6 (Rocks 6.2)
  • Dependencies:
    • g++ >= 4.9.4

Installation

  1. Download the desired version of the software (Source code - tar.gz)

    cd /home/mgomezzul/apps/muscle/gcc
http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_src.tar.gz
tar -zxvf muscle3.8.31_src.tar.gz

  2. Do the following changes in the Makefile inside the unpacked directory:

    cd muscle3.8.31/src/
emacs mk
...
# mateo
g++ $ENV_GCC_OPTS -c -O3 -march=native -mfpmath=sse -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 $CPPName.cpp -o $CPPName.o  >> muscle.make.stdout.txt 2>> muscle.make.stderr.txt
...

  3. Compilation:

    module load gcc/4.9.4
make

  4. Install MUSCLE:

    sudo mkdir -p /share/apps/muscle/gcc/4.9.4/bin
sudo cp  muscle /share/apps/muscle/gcc/4.9.4/bin

Module

#%Module1.0#####################################################################
##
## module muscle/3.8.31_gcc-4.9.4
##
## /share/apps/modules/muscle/3.8.31_gcc-4.9.4     Written by Mateo Gomez-Zuluaga
##

proc ModulesHelp { } {
    puts stderr "\tmuscle/3.8.31_gcc-4.9.4 - sets the Environment for MUSCLE 3.8.31 in \
    \n\tthe share directory /share/apps/muscle/3.8.31/gcc/4.9.4\n"
}

module-whatis "\n\n\tSets the environment for using MUSCLE 3.8.31 \
            \n\tbuilded with GNU GCC 4.9.4\n"

# for Tcl script use only
set       topdir     /share/apps/muscle/3.8.31/gcc/4.9.4
set       version    3.8.31
set       sys        x86_64-redhat-linux

module load gcc/4.9.4

prepend-path PATH    $topdir/bin

Use

Slurm template

#!/bin/bash
#SBATCH --partition=longjobs
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=32
#SBATCH --time=1:00:00
#SBATCH --job-name=muscle
#SBATCH -o result_%N_%j.out
#SBATCH -e result_%N_%j.err

export SBATCH_EXPORT=NONE
export OMP_NUM_THREADS=1

module load muscle/3.8.31

muscle xxx

Author

  • Mateo Gómez Zuluaga