How to Run AMBER
Version 9 of AMBER has been installed on lewis and clark.
On lewis, it is installed under /share/apps/amber9.
The executables are under /share/apps/amber9/exe.
On clark, it is installed under /usr/local/amber9.
The executables are under /usr/local/amber9.exe.
There are both serial and parallel versions of the executables.
The parallel versions have a qualifier of ".MPI" on the end, e.g. sander.MPI.
A sample LSF job script on lewis, for the parallel version of sander might look like:
# Set job parametersA sample PBS job script on clark might look like:
#BSUB -a mvapich
#BSUB -J jobname
#BSUB -oo jobname.o%J
#BSUB -eo jobname.e%J
# Set number of CPUs
#BSUB -n 4
# Start AMBER job
mpirun.lsf /share/apps/amber9/exe/sander.MPI -O -i inputfile -o outputfile
#PBS -l ncpus=4,cput=100:00:00,mem=2gb
cd workingdir
mpirun -np 4 /usr/local/amber9/exe/sander.MPI -O -i inputfile -o outputfile