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]
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
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 openmpi 1.10.7  for GCC 4.8.5
[+] Loading acemd  latest  ...
[+] Loading acemd  latest
HTMD startup directory /home/$USER/.htmd  exists

[user@cn3144 ~]$ acemd input
# ACEMD Molecular Dynamics Version [2017.11.30] (git [476b168])
# (c) 2009-2017 Acellera Ltd.
# See License Agreement for terms and conditions of use
# or write to
# Licensed by Acellera Ltd (
# No node-locked license available.
# Checked out one floating license for ACEMD 2.00
# Ensemble execution available
# Running on host [cn4242]
# Undefined TCL function [calcforces_terminate]
# Time per step (avg over 50000 steps): 6.075 ms
# Nanoseconds per day: 56.889
# JOBINFO: Terminated  [Tue, 27  Feb  2018  18:58:08  +0000 UT]

[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. For example:

set -e
cd /data/$USER/somedir
module load acemd
acemd input

Submit this job using the Slurm sbatch command.

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