ICHEC Software

Information about software packages installed on the ICHEC systems.

Amber

Versions Installed

Stokes: 10 / 11

Stoney: 11

Description

Amber (Assisted Model Building with Energy Refinement), is a general purpose molecular mechanics/dynamics suite which uses analytic potential energy functions, derived from experimental and ab initio data, to refine macromolecular conformations.

License

ICHEC has acquired a site license for the Amber 10 and 11 (AmberTools 1.5) packages. Users should express their interest to the Helpdesk to gain access to the executables.

Benchmarks

The Amber Benchmarks from Mike Wu and Ross Walker were run on the Stoney cluster. The benchmark was downloaded from here.

Implicit Solvent Simulations Using PMEMD

The implicit solvent GB nucleosome simulations using pmemd run across nodes for both the CPU-only and the CPU/GPU version. Where possible the gpu version of the code should be used as he number of ns/day of a single node with two M2090s is 1.34 compared to 0.78 from 24 nodes each with 8 cores.

Explicit Solvent Simulations Using PMEMD

The explicit solvent simulations don't scale across nodes on Stoney, most likely due to the ConnectX Infiniband (DDR) interconnect. Users should submit jobs to run on a single node with two M2090s as shown below.

Additional Notes

To use a version of Amber load the relevant environment module:

module load amber/11

Job Submission Example on Stokes

#!/bin/bash
#PBS -l nodes=2:ppn=12
#
#PBS -l walltime=30:00:00
#PBS -N MyJobName
#PBS -A MyProjectName

#Load the Amber module
module load amber/11

cd $PBS_O_WORKDIR

mpiexec -machinefile $PBS_NODEFILE -np 24 $AMBERHOME/exe/pmemd.MPI -O \
-i mdin -p prmtop -c inpcrd -ref inpcrd -suffix outSuffix

Job Submission Example on Stoney

#!/bin/bash
#PBS -l nodes=2:ppn=8
#
#PBS -l walltime=30:00:00
#PBS -N MyJobName
#PBS -A MyProjectName

#Load the Amber module
module load amber/11

cd $PBS_O_WORKDIR

mpiexec.hydra -n 16 -rmk pbs $AMBERHOME/exe/pmemd.MPI -O -i mdin \
-p prmtop -c inpcrd -ref inpcrd -suffix outSuffix

Job Submission Example on Stoney using a single GPGPU

The following script will run on a single node but only use one NVIDIA M2090 card.

#!/bin/bash
#PBS -l nodes=1:ppn=8
#
#PBS -l walltime=30:00:00
#PBS -N MyJobName
#PBS -A MyProjectName

#Load the Amber module
module load amber/11

cd $PBS_O_WORKDIR

$AMBERHOME/exe/pmemd.cuda -O -i mdin -p prmtop -c inpcrd \
-ref inpcrd -suffix outSuffix -gpu 1

Job Submission Example on Stoney using Multiple GPGPUs

The following script will run on a single node but use two NVIDIA M2090 cards.

#!/bin/bash
#PBS -l nodes=1:ppn=8
#
#PBS -l walltime=30:00:00
#PBS -N MyJobName
#PBS -A MyProjectName

#Load the Amber module
module load amber/11

cd $PBS_O_WORKDIR

# Create hosts file
for i in {1..1}; do cat $PBS_NODEFILE | uniq >> hosts.1.2; done;

mpiexec.hydra -machine hosts.1.2 -n 2 -rmk pbs $AMBERHOME/bin/pmemd.cuda.MPI \
-O -i mdin -p prmtop -c inpcrd -ref inpcrd -suffix outSuffix

Job Submission Example on Stoney using Multiple Nodes/GPGPUs

The following script will run on two nodes and use four NVIDIA M2090 cards.

#!/bin/bash
#PBS -l nodes=2:ppn=8
#
#PBS -l walltime=30:00:00
#PBS -N MyJobName
#PBS -A MyProjectName

#Load the Amber module
module load amber/11

cd $PBS_O_WORKDIR

# Create hosts file
for i in {1..2}; do cat $PBS_NODEFILE | uniq >> hosts.2.4; done;

mpiexec.hydra -machine hosts.2.4 -n 4 -rmk pbs $AMBERHOME/bin/pmemd.cuda.MPI \
-O -i mdin -p prmtop -c inpcrd -ref inpcrd -suffix outSuffix

Assuming that this PBS script is saved as amber.pbs, the job can be submitted to the queue by running the following command in the same directory:

qsub amber.pbs

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