AMBER-Sapelo2

Category

Chemistry

Program On

Sapelo2

Version

18, 22

Author / Distributor

Please see http://ambermd.org/#developers

When citing Amber22 or AmberTools22 please use the following: D.A. Case, H.M. Aktulga, K. Belfon, I.Y. Ben-Shalom, J.T. Berryman, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, G.A. Cisneros, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, G. Giambasu, M.K. Gilson, H. Gohlke, A.W. Goetz, R. Harris, S. Izadi, S.A. Izmailov, K. Kasavajhala, M.C. Kaymak, E. King, A. Kovalenko, T. Kurtzman, T.S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, M. Machado, V. Man, M. Manathunga, K.M. Merz, Y. Miao, O. Mikhailovskii, G. Monard, H. Nguyen, K.A. O'Hearn, A. Onufriev, F. Pan, S. Pantano, R. Qi, A. Rahnamoun, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, A. Shajan, J. Shen, C.L. Simmerling, N.R. Skrynnikov, J. Smith, J. Swails, R.C. Walker, J Wang, J. Wang, H. Wei, R.M. Wolf, X. Wu, Y. Xiong, Y. Xue, D.M. York, S. Zhao, and P.A. Kollman (2022), Amber 2022, University of California, San Francisco.

Description

From http://ambermd.org/: " "Amber" refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos."

Running Program

Also refer to Running Jobs on Sapelo2.

For more information on Environment Modules on Sapelo2 please see the Lmod page.

AMBER18 and AmberTools 18

AMBER18 and AmberTools 18 were compiled with the fosscuda-2018b toolchain (GNU 7.3.0 compiler suite, OpenMPI 3.1.1, and CUDA 9.2.88). This version includes serial binaries, and binaries with CUDA and MPI support.

To use this version of AMBER, first load the Amber/18-fosscuda-2018b-AmberTools-18-patchlevel-10-8 module with

ml Amber/18-fosscuda-2018b-AmberTools-18-patchlevel-10-8

This module will automatically load its dependencies. Note: Some of the CUDA-enabled programs, such as antechamber, are not compatible with the K20 and K40 GPU devices.

AMBER22 and AmberTools 22

AMBER22 and AmberTools 22 were compiled with the foss-2019b toolchain (GNU 8.3.0 compiler suite, OpenMPI 3.1.4), and CUDA 11.1.1. This version includes serial binaries, and binaries with CUDA and MPI support.

To use this version of AMBER, first load the Amber/22-foss-2019b-CUDA-11.1.1-AmberTools-22 module with

ml Amber/22-foss-2019b-CUDA-11.1.1-AmberTools-22

This module will automatically load its dependencies. The testsuite for the cuda serial version passed on the K20, K40, P100, V100, and A100 GPU devices.

1. Running the MPI version:

In the example below the name of the input file is prod.in.

Example of shell script (submpi.sh) to run Amber18 in the batch queue, using 96 processes:

#!/bin/bash
#SBATCH --job-name=amber             # Job name
#SBATCH --partition=batch            # Partition (queue) name      
#SBATCH --ntasks=96                  # Run a single task	
#SBATCH --cpus-per-task=1            # Number of CPU cores per task
#SBATCH --mem-per-cpu=2gb            # Job memory per MPI process request
#SBATCH --time=10:00:00              # Time limit hrs:min:sec
cd $SLURM_SUBMIT_DIR

export OMP_NUM_THREADS=1
ml Amber/18-fosscuda-2018b-AmberTools-18-patchlevel-10-8
source ${AMBERHOME}/amber.sh
srun $AMBERHOME/bin/pmemd.MPI -O -i prod.in -o prod_${SLURM_JOB_ID}.out  -p prod.prmtop -c restart.rst -r prod.rst -x prod.mdcrd

Note: Here the input parameter file is called prod.in and the files prod.prmtop and restart.rst are also needed. The parameters of the job, such as the maximum wall clock time, the memory per MPI process, the number of ntasks, and the job name need to be modified appropriately as well.

Sample job submission command:

sbatch submpi.sh

2. Running the CUDA version:

In the example below the name of the input file is prod.in.

Example of shell script (subcuda.sh) to run AMBER18 in the GPU queue (gpu_q), using one GPU card:

#!/bin/bash
#SBATCH --job-name=amber             # Job name
#SBATCH --partition=gpu_p            # Partition (queue) name     
#SBATCH --gres=gpu:P100:1 
#SBATCH --ntasks=24                  # Run a single task	
#SBATCH --cpus-per-task=1            # Number of CPU cores per task
#SBATCH --mem-per-cpu=2gb            # Job memory per MPI process request
#SBATCH --time=10:00:00              # Time limit hrs:min:sec
cd $SLURM_SUBMIT_DIR

ml Amber/18-fosscuda-2018b-AmberTools-18-patchlevel-10-8

source ${AMBERHOME}/amber.sh

$AMBERHOME/bin/pmemd.cuda -O -i prod.in -o prod_${SLURM_JOB_ID}.out -p prod.prmtop -c restart.rst -r prod.rst -x prod.mdcrd

Note: Here the input parameter file is called prod.in and the files prod.prmtop and restart.rst are also needed. The parameters of the job, such as the maximum wall clock time, the memory per MPI process, the number of ntasks, and the job name need to be modified appropriately as well.

Note: Some of the CUDA-enabled programs, such as antechamber, in Amber/18-fosscuda-2018b-AmberTools-18-patchlevel-10-8 are not compatible with the K20 and K40 GPU devices.

Sample job submission command:

sbatch subcuda.sh

Documentation

Please see http://ambermd.org/

Installation

• Amber 18: Source code compiled with the fosscuda-2018b toolchain (GNU 7.3.0 compiler suite, OpenMPI 3.1.1, and CUDA 9.2.88).

• Amber 22: Source code compiled with the foss-2019b toolchain (GNU 8.3.0 compiler suite, OpenMPI 3.1.4), and CUDA 11.1.1.

System

64-bit Linux