AMBER

To load the default version of AMBER module, use  module load amber . To select a particular software version, use  module load amber/version . For example, use  module load amber/16  to load AMBER version 16. 

A serial Amber program in a short duration run can be executed interactively on the command line, e.g.:

tleap

Parallel Amber programs must be run in a batch environment with  srun, e.g.:

srun pmemd.MPI

 

When you log into owens.osc.edu you are actually logged into a linux box referred to as the login node. To gain access to the mutiple processors in the computing environment, you must submit your AMBER simulation to the batch system for execution. Batch jobs can request mutiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations and Batch Limit Rules for more info. 

Interactive Batch Session

For an interactive batch session, one can run the following command:

sinteractive -A <project-account> -N 1 -n 28 -t 1:00:00

which gives you one node with 28 cores ( -N 1 -n 28 ), with 1 hour ( -t 1:00:00 ). You may adjust the numbers per your need.

Non-interactive Batch Job (Serial Run)

A batch script can be created and submitted for a serial or parallel run. You can create the batch script using any text editor you like in a working directory on the system of your choice. Sample batch scripts and Amber input files are available here:

~srb/workshops/compchem/amber/

Below is the example batch script ( job.txt ) for a serial run:

# AMBER Example Batch Script for the Basic Tutorial in the Amber manual
#!/bin/bash
#SBATCH --job-name 6pti
#SBATCH --nodes=1 --ntasks-per-node=28
#SBATCH --time=0:20:00
#SBATCH --account=<project-account>

module load amber
# Use TMPDIR for best performance.
cd $TMPDIR
# SLURM_SUBMIT_DIR refers to the directory from which the job was submitted.
cp -p $SLURM_SUBMIT_DIR/6pti.prmtop .
cp -p $SLURM_SUBMIT_DIR/6pti.prmcrd .
# Running minimization for BPTI
cat << eof > min.in
# 200 steps of minimization, generalized Born solvent model
&cntrl
maxcyc=200, imin=1, cut=12.0, igb=1, ntb=0, ntpr=10,
/
eof
sander -i min.in -o 6pti.min1.out -p 6pti.prmtop -c 6pti.prmcrd -r 6pti.min1.xyz
cp -p min.in 6pti.min1.out 6pti.min1.xyz $SLURM_SUBMIT_DIR

In order to run it via the batch system, submit the  job.txt  file with the command:  sbatch job.txt . 

To load the default version of AMBER module, use  module load amber. 

A serial Amber program in a short duration run can be executed interactively on the command line, e.g.:

tleap

Parallel Amber programs must be run in a batch environment with mpiexec, e.g.:

srun pmemd.MPI

 

When you log into owens.osc.edu you are actually logged into a linux box referred to as the login node. To gain access to the mutiple processors in the computing environment, you must submit your AMBER simulation to the batch system for execution. Batch jobs can request mutiple nodes/cores and compute time up to the limits of the OSC systems. Refer to Queues and Reservations and Batch Limit Rules for more info. 

Interactive Batch Session

For an interactive batch session, one can run the following command:

sinteractive -A <project-account> -N 1 -n 48 -t 1:00:00

which gives you one node with 48 cores ( -N 1 -n 48) with 1 hour ( -t 1:00:00). You may adjust the numbers per your need.

Non-interactive Batch Job (Serial Run)

A batch script can be created and submitted for a serial or parallel run. You can create the batch script using any text editor you like in a working directory on the system of your choice. Sample batch scripts and Amber input files are available here:

~srb/workshops/compchem/amber/

Below is the example batch script ( job.txt ) for a serial run:

# AMBER Example Batch Script for the Basic Tutorial in the Amber manual 
#!/bin/bash
#SBATCH --job-name 6pti #
SBATCH --nodes=1 --ntasks-per-node=48 
SBATCH --time=0:20:00
#SBATCH --account=<project-account>

module load amber
# Use TMPDIR for best performance.
cd $TMPDIR
# SLURM_SUBMIT_DIR refers to the directory from which the job was submitted.
cp -p $SLURM_SUBMIT_DIR/6pti.prmtop .
cp -p $SLURM_SUBMIT_DIR/6pti.prmcrd .
# Running minimization for BPTI
cat << eof > min.in
# 200 steps of minimization, generalized Born solvent model
&cntrl
maxcyc=200, imin=1, cut=12.0, igb=1, ntb=0, ntpr=10,
/
eof
sander -i min.in -o 6pti.min1.out -p 6pti.prmtop -c 6pti.prmcrd -r 6pti.min1.xyz
cp -p min.in 6pti.min1.out 6pti.min1.xyz $SLURM_SUBMIT_DIR

In order to run it via the batch system, submit the  job.txt  file with the command:  sbatch job.txt .