NONMEM Docker Wrappers

Docker images and thin host scripts for running NONMEM with PsN on macOS, Linux, and Windows. Each NONMEM release has a versioned directory (nm743, nm750, nm760) whose commands invoke docker run with your model folder and license mounted into the container.

License & use
For personal research only. You must supply your own ICON nonmem.lic. Installation media (NONMEM CD / zip) is not included in this repository.

Overview

Concept	Description
Host directory	`nm743/`, `nm750/`, or `nm760/` — templates become runnable scripts after install
Install (Unix)	`./install.sh` → shell scripts (`execute`, `util/nmfeXX`, …)
Install (Windows)	`install.ps1` → PowerShell + `.cmd` launchers (`execute.cmd`, …)
Docker image	Pre-built `kinginsun/nonmem:<version>` — pull with Docker; no local build needed
Model directory	Your working directory; mounted as `/nonmem/models` in the container
License	`license/nonmem.lic` in the host directory, mounted into the container

Host scripts do not install NONMEM on the host OS. They only wrap Docker. Additional PsN tools can be exposed the same way as execute and nmfeXX (see *.dat templates).

Visual flow:

Host:  cd my_project/
       ../nm760/execute mymodel.mod
          │
          ▼
Docker:  mount license + my_project → run NONMEM/PsN inside image
          │
          ▼
Host:  results written in my_project/

Supported versions

NONMEM	Host dir	Image (recommended)	Dockerfile	Base OS	PsN	`nmfe`
7.4.3	`nm743/`	`kinginsun/nonmem:7.4.3`	`Dockerfile.7.4.3`	Ubuntu 16.04	5.7.1	`nmfe74`
7.5.0	`nm750/`	`kinginsun/nonmem:7.5.0`	`Dockerfile.7.5.0`	Ubuntu 18.04	5.7.1	`nmfe75`
7.6.0	`nm760/`	`kinginsun/nonmem:7.6.0`	`Dockerfile.7.6.0`	Ubuntu 22.04	5.7.1	`nmfe76`

7.4.3 alternative (developers): Dockerfile builds a NONMEM-only image without MPI / PsN (not used by host wrappers).

Use Dockerfile.7.4.3 for Pirana, PsN, and parallel runs.

Image size: All Dockerfiles use a multi-stage build and copy only the required CD + PsN-Source (not the whole install/ folder). 7.6.0 is ~1.1–1.3 GB; older single-stage layouts that ADD install/ were ~2.5–3.4 GB.

Prerequisites

Requirement	macOS / Linux	Windows
Docker	Docker Desktop or Engine	Docker Desktop for Windows
Git	Yes	Yes (Git for Windows)
ICON `nonmem.lic`	Yes (your license file)	Same
ICON NONMEM installation media	Only if building images locally	Same
Pirana	Optional (macOS)	Not available (macOS only)
XQuartz + `xterm`	Optional (Pirana terminal)	Not required
PowerShell	—	5.1+ (included in Windows 10/11)

Step-by-step slides (legacy): how to install nonmem.pptx

Quick start

End users: pull a pre-built image — no local build or NONMEM CD required.

git clone https://github.com/kinginsun/nonmem.git
cd nonmem

Pull the Docker image for your NONMEM version:

docker pull kinginsun/nonmem:7.6.0   # or kinginsun/nonmem:7.5.0 / kinginsun/nonmem:7.4.3

Install host wrappers and place your license:

macOS / Linux

cd nm760   # or nm743 / nm750
cp /path/to/your/nonmem.lic license/nonmem.lic
./install.sh

Windows — see Windows installation.

Run from the directory that contains your .mod file:

cd /path/to/your/model_directory
/path/to/nonmem/nm760/execute mymodel.mod

Host scripts (execute, nmfeXX, …) call docker run with the matching kinginsun/nonmem:<version> image. You only need Docker, this repo, and your ICON license file.

Windows installation

On Windows, use Docker Desktop with the Linux container backend (default). Wrappers are generated as *.cmd files (double-click or Command Prompt) backed by *.ps1 scripts.

Quick start (Windows)

git clone https://github.com/kinginsun/nonmem.git
cd nonmem

Pull the Docker image (PowerShell or cmd in repo root):

docker pull kinginsun/nonmem:7.6.0   # or kinginsun/nonmem:7.5.0 / kinginsun/nonmem:7.4.3

Install host wrappers for your version:

cd nm760
Copy-Item C:\path\to\your\nonmem.lic license\nonmem.lic
powershell -ExecutionPolicy Bypass -File .\install.ps1

Or right-click install.ps1 → Run with PowerShell (if execution policy allows).

Run from the folder that contains your .mod file:

cd C:\projects\my_model
C:\path\to\nonmem\nm760\execute.cmd mymodel.mod
C:\path\to\nonmem\nm760\util\nmfe76.cmd mymodel.mod myoutput

Windows notes

Topic	Guidance
Paths	Install script converts paths to forward slashes for Docker volume mounts. Avoid special characters in project paths if possible.
WSL2	You may use `./install.sh` inside WSL and treat paths like Linux; keep the repo on the WSL filesystem (`~/...`) for best I/O.
Generated files	`install.ps1` creates `execute.cmd`, `execute.ps1`, etc. Do not commit them; re-run install after moving the repo.
Uninstall	`powershell -File uninstall.ps1` removes generated `.cmd` / `.ps1` wrappers.
Skip tests	`install.ps1 -SkipTests` skips the sample `CONTROL5.mod` run.
MPI on Windows	Parafiles in `models/` target Linux paths inside the container; use them via `execute.cmd` the same way as on Unix.

Add to PATH (optional)

Add the version directory (e.g. C:\nonmem\nm760) to your user Path environment variable so you can run execute.cmd from any model folder.

Building images (developers)

For maintainers only. End users should docker pull kinginsun/nonmem:<version> (see Quick start). Building requires ICON NONMEM installation media under install/ (not in git).

Run all docker build commands from the repository root.

Install directory layout

The install/ folder is not committed. Obtain NONMEM from ICON and extract as follows:

Version	Required under `install/`
7.4.3 (MPI + PsN)	`nm743CD/`, `PsN-Source/`
7.4.3 (plain)	`nm743CD/`, `PsN-Source/`
7.5.0	`nm750CD/`, `PsN-Source/`
7.6.0	`nm760CD/` (must contain `SETUP76`), `PsN-Source/` — details in `install/README.7.6.0.md`

Build commands

NONMEM 7.6.0 (recommended layout; smallest image):

docker build -f Dockerfile.7.6.0 -t kinginsun/nonmem:7.6.0 .

NONMEM 7.5.0:

docker build -f Dockerfile.7.5.0 -t kinginsun/nonmem:7.5.0 .

NONMEM 7.4.3:

# MPI + PsN (matches nm743/install.sh)
docker build -f Dockerfile.7.4.3 -t kinginsun/nonmem:7.4.3 .

# NONMEM only (no MPI / PsN; not used by host wrappers)
docker build -f Dockerfile -t nonmem:7.4.3-plain .

Publishing to Docker Hub

Images are published as kinginsun/nonmem:<version> on Docker Hub.

Publish (maintainers)

Log in:
```
docker login
```

Build and push one version or all:

# macOS / Linux
./scripts/publish-docker.sh 7.6.0
./scripts/publish-docker.sh all

# Windows (PowerShell)
.\scripts\publish-docker.ps1 -Version 7.6.0
.\scripts\publish-docker.ps1 -Version all

Push an existing local image without rebuilding:

./scripts/publish-docker.sh 7.6.0 --push-only

Confirm tags on Docker Hub: https://hub.docker.com/r/kinginsun/nonmem/tags

Tag	Dockerfile	Notes
`7.6.0`	`Dockerfile.7.6.0`	Multi-stage, ~1.1 GB
`7.5.0`	`Dockerfile.7.5.0`	Multi-stage; requires `install/nm750CD` + `PsN-Source`
`7.4.3`	`Dockerfile.7.4.3`	Multi-stage; requires `install/nm743CD` + `PsN-Source`

Override the registry name: DOCKER_REGISTRY=myuser/nonmem ./scripts/publish-docker.sh 7.6.0 (default: kinginsun/nonmem)

License note: Images contain NONMEM binaries compiled from ICON installation media. Publishing is for licensed users; end users still mount their own nonmem.lic at run time.

Host wrappers

Each nmXXX/ directory contains *.dat templates for Unix. On Windows, install.ps1 generates PowerShell and CMD wrappers via scripts/install-windows.ps1.

Unix: ./install.sh · Windows: powershell -File install.ps1

Script	7.4.3	7.5.0	7.6.0
`execute`	✓	✓	✓
`util/nmfeXX`	`nmfe74`	`nmfe75`	`nmfe76`
`vpc`, `bootstrap`	partial	✓	✓
`scm`, `util/ddexpand`	—	✓	✓
`nmshell`	✓	✓	✓

Example after install in nm760:

# macOS / Linux
cd nm760/models && ../execute CONTROL5.mod

REM Windows
cd nm760\models
..\execute.cmd CONTROL5.mod

Uninstall: ./uninstall.sh (Unix) or powershell -File uninstall.ps1 (Windows).

Running models

Via host wrappers (typical)

cd /path/to/your/model_directory
/path/to/nonmem/nm750/execute CONTROL5.mod
/path/to/nonmem/nm750/util/nmfe75 CONTROL5.mod OUTPUT5

Output files are created in the current directory.

Direct `docker run` (no `install.sh`)

Adjust NM_ROOT, image tag, and in-container paths for your version (nm750 / nmfe75 shown):

NM_ROOT=/path/to/nonmem/nm750
TAG=kinginsun/nonmem:7.5.0
MODEL_DIR=$(pwd)

docker run --rm \
  --workdir /nonmem/models \
  -v "${NM_ROOT}/license:/nonmem/nm750/license" \
  -v "${MODEL_DIR}:/nonmem/models" \
  "${TAG}" execute CONTROL5.mod

docker run --rm \
  --workdir /nonmem/nm750/util \
  -v "${NM_ROOT}/license:/nonmem/nm750/license" \
  -v "${MODEL_DIR}:/nonmem/models" \
  "${TAG}" nmfe75 CONTROL5.mod OUTPUT5 -rundir=/nonmem/models

For 7.4.3 / 7.6.0, replace nm750 and nmfe75 with nm743/nmfe74 or nm760/nmfe76.

Pirana integration

PsN executables location — point to the version directory (e.g. .../nonmem/nm760).
NONMEM — same path; add a named installation (e.g. nm76) and let Pirana discover binaries.
When running via nmfeXX, enable Copy back results to main folder so outputs appear in Pirana.
Ensure /usr/local/bin is on the PATH Pirana uses (see Troubleshooting).

Downloads

Pirana 2.9.9 (newer macOS): https://s3.amazonaws.com/certara-pirana/pirana_2.9.9_MacOSX.dmg
Pirana 2.9.8 (legacy link): https://www.evernote.com/l/ABkzIX34qFxOB6aqA1Sxk3pFat5VLDC0f9E
Academic license: contact Certara

Parallel runs (MPI)

Use a parafile with execute or nmfeXX. Each version ships models/pirana_auto_mpi.pnm for Linux/Docker:

cd nm750/models
../execute -parafile=pirana_auto_mpi.pnm CONTROL5.mod -nodes=4
../util/nmfe75 CONTROL5.mod OUTPUT5 "-parafile=pirana_auto_mpi.pnm" "[nodes]=4"

Reference parafile (Linux, in-container paths):

$DEFAULTS
[nodes]=4

$GENERAL
NODES=[nodes] PARSE_TYPE=2 TIMEOUTI=20 TIMEOUT=500 PARAPRINT=1 TRANSFER_TYPE=1

$COMMANDS
1:mpirun -wdir "$PWD" -n 1 ./nonmem  $*
2-[nodes]:-wdir "$PWD/worker{#-1}" -n 1 ./nonmem

$DIRECTORIES
1:NONE
2-[nodes]:worker{#-1}

7.4.3 host MPI notes (non-Docker): The NONMEM 7.4.3 CD includes mpich2. Replace nm743/mpi/mpi_ling/libmpich.a with the 64-bit library from your mpich2 build; configure mpd.conf (mode 600). Docker images already bundle MPI. Auto-FPI across multiple hosts is not documented here.

Troubleshooting

Windows: Docker volume or path errors

Enable File sharing for your drive in Docker Desktop → Settings → Resources → File sharing.
Prefer paths under your user profile (e.g. C:\Users\you\projects) rather than network drives.
Re-run install.ps1 after moving the repository so embedded paths stay correct.

Windows: script execution disabled

Set-ExecutionPolicy -Scope CurrentUser RemoteSigned
# or invoke once:
powershell -ExecutionPolicy Bypass -File .\install.ps1

Pirana does not open a terminal (macOS)

After macOS upgrades, /usr/bin/xterm may be missing. Terminal runs of execute / PsN work, but Pirana fails to spawn a window.

which xterm
sudo ln -sf /opt/X11/bin/xterm /usr/local/bin/xterm

In Pirana: Settings → Software integration → Other Terminal, and add /usr/local/bin to the PATH (Environment variables → Add to PATH by Pirana).

Pirana does not show run results

Enable Copy back results to main folder when using nmfe74, nmfe75, or nmfe76.

Docker build fails on PsN / `psn.conf` (7.6.0)

Use the current Dockerfile.7.6.0. PsN installs under /usr/local/share/perl/<version>/PsN_5_7_1/, not Debian’s archlib path.

Image still large (7.6.0)

Rebuild with the multi-stage Dockerfile.7.6.0 (selective COPY, not ADD install/). Do not keep old layers tagged as 7.6.0 without rebuilding.

Related projects

kinginsun/nonmem — this repository
Pharmacometrics-Docker — alternative NONMEM Docker builds

Navigation Menu

Repository files navigation

NONMEM Docker Wrappers

Table of contents

Overview

Supported versions

Prerequisites

Quick start

Windows installation

Quick start (Windows)

Windows notes

Add to PATH (optional)

Building images (developers)

Install directory layout

Build commands

Publishing to Docker Hub

Publish (maintainers)

Host wrappers

Running models

Via host wrappers (typical)

Direct `docker run` (no `install.sh`)

Pirana integration

Parallel runs (MPI)

Troubleshooting

Windows: Docker volume or path errors

Windows: script execution disabled

Pirana does not open a terminal (macOS)

Pirana does not show run results

Docker build fails on PsN / `psn.conf` (7.6.0)

Image still large (7.6.0)

Related projects

Acknowledgments

About

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Name		Name	Last commit message	Last commit date
nm743		nm743
nm750		nm750
nm760		nm760
scripts		scripts
.dockerignore		.dockerignore
.gitignore		.gitignore
Dockerfile		Dockerfile
Dockerfile.7.4.3		Dockerfile.7.4.3
Dockerfile.7.5.0		Dockerfile.7.5.0
Dockerfile.7.6.0		Dockerfile.7.6.0
README.md		README.md
deploy.sh		deploy.sh
docker_hub_overview.md		docker_hub_overview.md
how to install nonmem.pptx		how to install nonmem.pptx
pirana.lic		pirana.lic

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NONMEM Docker Wrappers

Table of contents

Overview

Supported versions

Prerequisites

Quick start

Windows installation

Quick start (Windows)

Windows notes

Add to PATH (optional)

Building images (developers)

Install directory layout

Build commands

Publishing to Docker Hub

Publish (maintainers)

Host wrappers

Running models

Via host wrappers (typical)

Direct docker run (no install.sh)

Pirana integration

Parallel runs (MPI)

Troubleshooting

Windows: Docker volume or path errors

Windows: script execution disabled

Pirana does not open a terminal (macOS)

Pirana does not show run results

Docker build fails on PsN / psn.conf (7.6.0)

Image still large (7.6.0)

Related projects

Acknowledgments

About

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Direct `docker run` (no `install.sh`)

Docker build fails on PsN / `psn.conf` (7.6.0)