Biowulf High Performance Computing at the NIH
Acemd on Biowulf

HTMD is a molecular-specific programmable environment to prepare, handle, simulate, visualize and analyse molecular systems. HTMD includes the Acemd software.

HTMD/Acemd is produced by Acellera. [Acellera website]
Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --constraint=gpuk80 --gres=gpu:k80:1 --license=acemd
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load acemd
[+] Loading acemd  3.5  ...

[user@cn3144 ~]$  cd mydir

[user@cn3144 ~]$ cp -r  $(dirname $(which acemd3))/../share/acemd3/dhfr_charmm .

[user@cn3144 ~]$ acemd3 input
#
# ACEMD version 3.5
#
# Copyright (C) 2017-2019 Acellera (www.acellera.com)
#
# When publishing, please cite:
#   ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale
#   M. J. Harvey, G. Giupponi and G. De Fabritiis,
#   J Chem. Theory. Comput. 2009 5(6), pp1632-1639
#   DOI: 10.1021/ct9000685
#
# Looking for node-locked license in [/opt/acellera/license.dat]
# Looking for node-locked license in [/opt/acellera/.acellera/license.dat]
# Looking for node-locked license in [/opt/acellera/.htmd/license.dat]
# Looking for node-locked license in [/home/user/license.dat]
# Looking for node-locked license in [/home/user/.acellera/license.dat]
# Looking for node-locked license in [/home/user/.htmd/license.dat]
# Looking for floating-locked license in [11111@xxxxx.cit.nih.gov]
 - found
# Read input file: input
# Parse input file
[...]
# Step       Time         Bond         Angle        Urey-Bradley Dihedral     Improper     CMAP         Non-bonded   Implicit
 External     Potential    Kinetic      Total        Temperature  Volume
#            [ps]         [kcal/mol]   [kcal/mol]   [kcal/mol]   [kcal/mol]   [kcal/mol]   [kcal/mol]   [kcal/mol]   [kcal/mol]
 [kcal/mol]   [kcal/mol]   [kcal/mol]   [kcal/mol]   [K]          [A^3]
       25000       100.00     537.7867    1281.4603     155.2703    1634.3376      95.5368     -66.3912  -74851.6306       0.0000
       0.0000  -71213.6300   14366.8914  -56846.7386      298.867    240990.21
# Speed: average  204.99 ns/day, current  204.99 ns/day
# Progress: 0.4%, remaining time: 3:15:59, ETA: Thu May  7 18:03:31 2020
[...]
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. Acemd.sh). For example:

#!/bin/bash
set -e
cd /data/$USER/somedir
module load acemd
acemd3 input

Submit this job using the Slurm sbatch command.

sbatch --partition=gpu --gres=gpu:k80:1  jobscript

Benchmarks

Please see the Acemd benchmarks page.