AMBER is a Molecular Dynamics Package written by various institutions including The Scripps Research Institute, University of California, Irvine among many others. We currently have both AMBER 8 and AMBER 9 installed.

In order to run AMBER 8 or 9 you will need to set up your environment correctly. Run the following commands in your shell and submit scripts for AMBER 8:

module load compilers/pathscale-3.2 blas/acml-4.1.0-pathscale mpi/openmpi-1.2.6-pathscale-3.2 md/amber-8-pathscale

Use the following for AMBER 9:

module load compilers/pathscale-3.2 \
            blas/acml-4.1.0-pathscale \
            mpi/openmpi-1.2.6-pathscale-3.2 \
            md/amber-9-pathscale

After those commands you will have sander and sander.MPI in your environment.

$ which sander
/share/apps/amber-8/pathscale/exe/sander
$ which sander.MPI
/share/apps/amber-8/pathscale/exe/sander.MPI

Note: Do not use the full path to these executables because they will change in the future.

Here is a sample submit script for MPI-enabled sander:

#!/bin/sh
#$ -cwd
#$ -j y
#$ -S /bin/bash
#$ -N AMBER8
#$ -m b
#$ -m e
#$ -e e.err
#$ -o sge.out
#$ -pe mpi 4
 
cd $SGE_O_WORKDIR
 
# Load the required modules
module load compilers/pathscale-3.2 \
    blas/acml-4.1.0-pathscale \
    mpi/openmpi-1.2.6-pathscale-3.2 \
    md/amber-8-pathscale
# Use: md/amber-9-pathscale if you want to try AMBER 9
 
mpirun -v sander.MPI -O \
        -i $SGE_O_WORKDIR/parm/min.conf \
        -o $SGE_O_WORKDIR/output/min.out \
        -r $SGE_O_WORKDIR/output/DSTP.min.rstcrd \
        -p $SGE_O_WORKDIR/parm/DSTP.prmtop \
        -c $SGE_O_WORKDIR/parm/DSTP.prmcrd \
        -ref $SGE_O_WORKDIR/parm/DSTP.prmcrd \
        -v $SGE_O_WORKDIR/output/DSTP.min.mdvel \
        -x $SGE_O_WORKDIR/output/DSTP.min.mdcrd \
        -e $SGE_O_WORKDIR/output/DSTP.min.mden \
        -inf $SGE_O_WORKDIR/output/DSTP.min.mdinfo   < /dev/null

If you want to use xleap please make sure you ssh to the cluster using: ssh -X user@tribe and that your caps lock and num lock is not active.

AMBER has currently been built for the OpenMPI 1.2.6 using the Pathscale compiler.

There are some quirks to building AMBER 8. First you must make sure the latest bugfixes have been installed. Our installation has up to and including bugfix#64. Amber 8 was compiled using the following process:

ACML_DIR=/share/apps/acml-4.1.0/pathscale64/lib
AMBERHOME=/share/apps/amber-8
NETCDF_HOME=/share/apps/netcdf-3.6.3
MPI_HOME=/share/apps/openmpi-1.2.6/pathscale-3.2
./configure pathscale
make serial
make install
make clean
./configure -openmpi pathscale
make parallel
make install

Note: You will probably have to compile parser.y using bison -y. You should also rename the parallel sander to sander.MPI and sander.LES to sander.LES.MPI

There are also some quirks to building AMBER 9. First you must make sure the latest bugfixes have been installed. Our installation has up to and including bugfix#40. Amber 9 was compiled using the following process:

ACML_DIR=/share/apps/acml-4.1.0/pathscale64/lib
AMBERHOME=/share/apps/amber-9
NETCDF_HOME=/share/apps/netcdf-3.6.3
MPI_HOME=/share/apps/openmpi-1.2.6/pathscale-3.2
./configure pathscale
make serial
make install
make clean
./configure -openmpi pathscale
make parallel
make install

Note: You will probably have to compile parser.y using bison -y.