Amber version 7 is installed on redwood at /usr/local/appl/amber7. You should set the AMBERHOME environment variable to /usr/local/appl/amber7. The executables are in /usr/local/appl/amber7/exe, and the examples are in /usr/local/appl/amber7/examples. You may browse this directory and copy example files into your own working directory for execution. You should ensure that the $AMBERHOME/exe/ directory is in your PATH environment variable.

To run a parallel Amber program, use mpirun, and specify the number of CPUs/processes to run on with the -np option to mpirun. For example, to run the Amber "nucgen" program on 4 CPUs, using the sample "nuc.in" input file supplied in the cd $AMBERHOME/tutorial/polyA-polyT directory:

1. Ensure AMBERHOME environment variable is set to /user/local/appl/amber7
2. Ensure PATH environment variable includes $AMBERHOME/exe/
3. Copy the nuc.in file from the $AMBERHOME/tutorial/polyA-polyT directory into your working directory.
4. Type: mpirun -np 4 nucgen -O -i nuc.in -o nuc.out -d $AMBERHOME/dat/leap/parm/nucgen.dat -p nuc.pdb
   Make sure it created a new nuc.out
5. Verify results in view nuc.out
6. For more optimal use of memory, try using the dplace utility:
   Type: mpirun -np $NCPUS dplace -c1-$NCPUS -s1 mpirun -np 4 nucgen -O -i nuc.in -o nuc.out -d $AMBERHOME/dat/leap/parm/nucgen.dat -p nuc.pdb
   where $NCPUS has been defined as the number of CPUs you want to run on.
7. You should use PBS to submit your Amber jobs. Here is a sample script that submits a 4-processors Amber 7 job from the user's /ptmp directory using the dplace utility. The script requests 1000 hours and 3 GB to run.
   #PBS -S /bin/csh
   #PBS -l cput=1000:00:00
   #PBS -l ncpus=4
   #PBS -l mem=3GB
   setenv NCPUS 4
   setenv AMBERHOME /usr/local/appl/amber7
   set path = ( $path $AMBERHOME/exe )
   cd /ptmp/$USER/
   mpirun -np $NCPUS dplace -c1-$NCPUS -s1 nucgen -O -i nuc.in -o nuc.out -d $AMBERHOME/dat/leap/parm/nucgen.dat -p nuc.pdb

At least one MCSR researcher has reported very good performance using Amber 7 on redwood. We would be interested in hearing how your Amber job performs on redwood. In future weeks, MCSR plans to make Amber 8 available on both redwood and mimosa.

For support running Amber on any MCSR system where it is installed, see the FAQ below, or email assist@mcsr.olemiss.edu.