AMPL on Biowulf

AMPL is the Accelerating Therapeutics for Opportunites in Medicine (ATOM) Consortium Modeling PipeLine for drug discovery.


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 input in bold):

[user@biowulf ~]$ sinteractive --gres=lscratch:10 --mem=8g -c4 --tunnel
salloc: Pending job allocation 35296239
salloc: job 35296239 queued and waiting for resources
salloc: job 35296239 has been allocated resources
salloc: Granted job allocation 35296239
salloc: Waiting for resource configuration
salloc: Nodes cn0857 are ready for job
srun: error: x11: no local DISPLAY defined, skipping
error: unable to open file /tmp/slurm-spank-x11.35296239.0
slurmstepd: error: x11: unable to read DISPLAY value

Created 1 generic SSH tunnel(s) from this compute node to
biowulf for your use at port numbers defined
in the $PORTn ($PORT1, ...) environment variables.

Please create a SSH tunnel from your workstation to these ports on biowulf.
On Linux/MacOS, open a terminal and run:

    ssh  -L 36858:localhost:36858

For Windows instructions, see

[user@cn0857 ~]$ module load ampl
[+] Loading ampl  1.3.0  on cn0857

[user@cn0857 ~]$ ipython
Python 3.7.10 (default, Feb 26 2021, 18:47:35)
Type 'copyright', 'credits' or 'license' for more information
IPython 7.16.1 -- An enhanced Interactive Python. Type '?' for help.

In [1]: import atomsci

In [2]: quit()

[user@cn0857 ~]$ cd /lscratch/$SLURM_JOB_ID

[user@cn0857 35296239]$ cp -r ${AMPL_HOME}/ampl .

[user@cn0857 35296239]$ cd ampl/atomsci/ddm/

[user@cn0857 ddm]$ jupyter-notebook --no-browser --port=$PORT1
[I 14:23:09.610 NotebookApp] Serving notebooks from local directory: /lscratch/35296239/ampl/atomsci/ddm
[I 14:23:09.610 NotebookApp] Jupyter Notebook 6.4.10 is running at:
[I 14:23:09.610 NotebookApp] http://localhost:36858/?token=5ebfcff3cfccd637d36250f9a5a8191a22011edd2a262db5
[I 14:23:09.610 NotebookApp]  or
[I 14:23:09.610 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 14:23:09.618 NotebookApp]

    To access the notebook, open this file in a browser:
    Or copy and paste one of these URLs:

Now in a new terminal on your local machine, you should initiate a new ssh session to Biowulf to establish the ssh tunnel. Using the port that was allocated to you during the sinteractive step above:

[user@mymachine ~]$ ssh  -L 36858:localhost:36858

[user@biowulf ~]$

This will allow you to open a local browser and view the Jupyter Notebook session running on the compute node:

AMPL Jupyter Notebook image

When you are finished close the Jupyter Notebook session in original terminal using Ctrl-C and exit the interactive session to conserve system resources.
^C[I 11:48:01.862 NotebookApp] interrupted
Serving notebooks from local directory: /lscratch/1151805/ampl/atomsci/ddm
1 active kernel
The Jupyter Notebook is running at:
Shutdown this notebook server (y/[n])? y
[C 18:43:10.271 NotebookApp] Shutdown confirmed
[I 11:48:03.637 NotebookApp] Shutting down 1 kernel
[I 11:48:03.838 NotebookApp] Kernel shutdown: 1b0c8fe9-a2de-45bc-ab5a-bea16e60dc0f

[user@cn0859 ddm]$ exit
salloc.exe: Relinquishing job allocation 1151805

Batch job
Most jobs should be run as batch jobs.

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

set -e
module load ampl
# command here

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#]
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

Create a swarmfile (e.g. ampl.swarm). For example:


Submit this job using the swarm command.

swarm -f ampl.swarm [-g #] [-t #] --module ampl
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module ampl Loads the ampl module for each subjob in the swarm