On September 22nd, OSC switched to Slurm for job scheduling and resource management on the Pitzer Cluster, along with the deployment of the new Pitzer hardware. We are in the process of updating the example job scripts for each software. If a Slurm example is not yet available, please consult our general Slurm information page or contact OSC help.

AMBER

The Assisted Model Building with Energy Refinement (AMBER) package contains many molecular simulation programs targeted at biomolecular systems. A wide variety of modelling techniques are available. It generally scales well on modest numbers of processors, and the GPU enabled CUDA programs are very efficient.

Availability and Restrictions

Versions

AMBER is available on Owens and Pitzer Clusters. The following versions are currently available at OSC (S means serial executables, P means parallel, C means CUDA, i.e., GPU enabled, and M means MIC, i.e., Xeon Phi enabled):

Version Owens Pitzer Notes
16 SPC   Default version on Owens prior to 09/04/2018
18 SPC SPC  
19 SPC* SPC*  
20 SPC SPC  
* Current default version
*  IMPORTANT NOTE: You need to load correct compiler and MPI modules before you use Amber. In order to find out what modules you need, use module spider amber/{version} .

You can use module spider amber to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access for Academic Users

OSC's Amber is available to not-for-profit OSC users; simply contact OSC Help to request the appropriate form for access.

Access for Commerical Users

For-profit OSC users must obtain their own Amber license. 

Publisher/Vendor/Repository and License Type

University of California, San Francisco, Commercial

Usage

Usage on Owens

Set-up

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. 

Using 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  srun, e.g.:

srun pmemd.MPI

 

Batch Usage

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)

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

Usage on Pitzer

Set-up

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

Using 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

 

Batch Usage

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)

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 .

Troubleshooting

In general, the scientific method should be applied to usage problems.  Users should check all inputs and examine all outputs for the first signs of trouble.  When one cannot find issues with ones inputs, it is often helpful to ask fellow humans, especially labmates, to review the inputs and outputs.  Reproducibility of molecular dynamics simulations is subject to many caveats.  See page 24 of the Amber18 manual for a discussion.

Further Reading

Supercomputer: 
Service: