HPC Amber FAQ

Supercomputer documentation is always a work in progress! Please email questions, corrections, or suggestions to the HPC support team at help-hpc@uky.edu as usual. Thanks!

For help getting started with Amber, see the Amber README page.

Frequently Asked Questions

1. How do I submit a Amber job?

Build a job script to load the Amber and OpenMPI modules and use mpiexec to run amber across one or more nodes. For more information about job scripts, see Getting Started - Job Scripts. Here is a sample job script:

#!/bin/bash
#SBATCH -n16
#SBATCH -t 24:00:00
module load amber/openmpi/12p12 mpi/openmpi/intel/1.6.3
cd ~/amberjob1/
time mpirun pmemd.MPI -O -i mdin -o mdout -p prmtop -c inpcrd

This script requests 16 processors (one node) and 24 hours of run time. The modules shown in the module load command are examples. Use the module avail command to see which versions of Amber and OpenMPI are available and choose the ones you need.

Use the sbatch command to submit your job. If the job script file were named amber1.sh, then you could use the command sbatch amber1.sh to submit it. You can specify sbatch options in the job script or on the sbatch command itself. If an option is specified in both places, then the value on the sbatch command will be used.

2. How do I run Amber on GPUs?

Build a job script to load the Amber and OpenMPI modules and use mpiexec to run amber across one or more nodes. For more information about job scripts, see Getting Started - Job Scripts. See also Running Amber on GPUs. Here is a sample job script:

#!/bin/bash
# One CPU and one GPU on one node.
#SBATCH -p GPU
#SBATCH -t 1:00:00
#SBATCH -n1
#SBATCH --tasks-per-node=1
module load amber/openmpi/12p12 mpi/openmpi/intel/1.6.3
cd ~/amberjob1/
time mpirun pmemd.MPI -O -i mdin -o mdout -p prmtop -c inpcrd

This script requests 1 processor and one hour of run time on a GPU node. The modules shown in the module load command are examples. Use the module avail command to see which versions of Amber and OpenMPI are available and choose the ones you need.

Use the sbatch command to submit your job. If the job script file were named amber1.sh, then you could use the command sbatch amber01.sh to submit it. You can specify sbatch options in the job script or on the sbatch command itself. If an option is specified in both places, then the value on the sbatch command will be used.

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