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

AMBER is available on Ruby, Oakley, and Glenn Clusters. The following versions are currently available at OSC (S means serial executables, P means parallel, and C means CUDA, i.e., GPU enabled):

Version Glenn Oakley ruby notes
9 SP      
10 SP*      
11 SPC SPC   Default version on Oakley prior to 09/15/2015
12 SPC SPC    
14 SP SPC* SPC*  
*: Current default version

You can use module avail 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. 

Usage

Usage on Glenn

Set-up on Glenn

To load the default version of AMBER module, use  module load amber  . To select a particular software version, use   module load amberversion . For example, use  module load amber14   to load AMBER version 14 on Glenn. 

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.:

mpiexec pmemd.MPI

The CUDA Amber programs, which must be run in a batch environment, are recommended due to their computational performance; e.g.:

pmemd.cuda

For supported features of the GPU accelerated version of PMEMD see Amber GPU Support.

In Amber14 the CUDA programs no longer support Glenn's hardware, and thus cannot be installed.

Batch Usage on Glenn

When you log into glenn.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 analysis 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 on Glenn, one can run the following command:
qsub -I -l nodes=1:ppn=8 -l walltime=1:00:00
which gives you 8 cores ( -l nodes=1:ppn=8 ) with 1 hour ( -l walltime=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:

/nfs/10/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
#PBS -N 6pti
#PBS -l nodes=1:ppn=1
#PBS -l walltime=0:20:00
module load amber
# Use TMPDIR for best performance.
cd $TMPDIR
# PBS_O_WORKDIR refers to the directory from which the job was submitted.
cp -p $PBS_O_WORKDIR/6pti.prmtop .
cp -p $PBS_O_WORKDIR/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 $PBS_O_WORKDIR

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

Usage on Oakley

Set-up on Oakley

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/12   to load AMBER version 12 on Oakley. 

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.:

mpiexec pmemd.MPI

The CUDA Amber programs, which must be run in a batch environment, are recommended due to their computational performance; e.g.:

pmemd.cuda

For supported features of the GPU accelerated version of PMEMD see Amber GPU Support.

In Amber14 the CUDA programs no longer support Glenn's hardware, and thus cannot be installed.

Batch Usage on Oakley

When you log into oakley.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 analysis 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 on Oakley, one can run the following command:
qsub -I -l nodes=1:ppn=12 -l walltime=1:00:00
which gives you 12 cores ( -l nodes=1:ppn=12 ) with 1 hour ( -l walltime=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:

/nfs/10/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
#PBS -N 6pti
#PBS -l nodes=1:ppn=1
#PBS -l walltime=0:20:00
module load amber
# Use TMPDIR for best performance.
cd $TMPDIR
# PBS_O_WORKDIR refers to the directory from which the job was submitted.
cp -p $PBS_O_WORKDIR/6pti.prmtop .
cp -p $PBS_O_WORKDIR/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 $PBS_O_WORKDIR

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

Usage on Ruby

Set-up on Ruby

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/14   to load AMBER version 14 on Ruby. 

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.:

mpiexec pmemd.MPI

The CUDA Amber programs, which must be run in a batch environment, are recommended due to their computational performance; e.g.:

pmemd.cuda

For supported features of the GPU accelerated version of PMEMD see Amber GPU Support.

In Amber14 the CUDA programs no longer support Glenn's hardware, and thus cannot be installed.

Batch Usage on Ruby

When you log into ruby.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 analysis 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 on Ruby, one can run the following command:
qsub -I -l nodes=1:ppn=20 -l walltime=1:00:00
which gives you 20 cores ( -l nodes=1:ppn=20 ) with 1 hour ( -l walltime=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:

/nfs/10/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
#PBS -N 6pti
#PBS -l nodes=1:ppn=20
#PBS -l walltime=0:20:00
module load amber
# Use TMPDIR for best performance.
cd $TMPDIR
# PBS_O_WORKDIR refers to the directory from which the job was submitted.
cp -p $PBS_O_WORKDIR/6pti.prmtop .
cp -p $PBS_O_WORKDIR/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 $PBS_O_WORKDIR

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

Further Reading

Supercomputer: 
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