Amber version 9 is installed at /share/apps/amber9 (also pointed by $AMBERHOME environment variable). Please note that, Amber is NOT a free software so you need to be authorized user to use this software. If you want to use Amber, please contact us at support@thaigrid.or.th and send us your license information.

NOTE: Amber is being compiled against MPICH2. This usage is basically following MPICH manual.

• Use the following job script to run your Amber job. (copy and paste)

  #!/bin/bash
  #$ -cwd
  #$ -S /bin/bash
  #$ -j y
  export MPICH_HOME=/share/apps/mpich/intel
  export MPICH_BIN=$MPICH_HOME/bin
  export AMBERHOME=/share/apps/amber9
  APP=/share/apps/amber9/exe/sander.MPI
  ARG="-O -i md2.in -o md2.out -p ABD28181.top -c ABD28181_md1.rst -x ABD28181_md2.mdcrd -r ABD28181_md2.rst -ref ABD28181_md1.rst -inf md2.info"
  if [ "$#" -ge 1 ]; then
          ARG=$@
  fi
  $MPICH_BIN/mpirun -machinefile $TMPDIR/machines -np $NSLOTS -nolocal $APP $ARG

• Now submit the script to SGE. Since this application is the parallel application, user need to indicate parallel environment (highlighted in green) and a number of processors (in orange) with option -pe. Note that, you can specify queue name other than default queue by using -q option. You can find more instruction on SGE here.

  [user@tera mpich2]$ qsub -pe mpich 4 amber_job_script.job

• To view your job status

[user@tera mpich]$ qstat

• The output and error from MPI application are created in directory where user submitted jobs.