Executing packaged app locally¶

The MONAI Application Runner (MAR) is a command-line utility that allows users to run and test their MONAI Application Package (MAP) locally. MAR is developed to make the running and testing of MAPs locally an easy process for developers and scientists by abstracting away the need to understand the internal details of the MAP. MAR allows the users to specify input and output paths on the local file system which it maps to the input and output of MAP during execution.

Setting up¶

MONAI Application Runner comes as a part of the MONAI Deploy CLI and can be accessed as a run subcommand to the CLI. You can see the help message for MAR using the following command:

monai-deploy run --help

Output:

usage: monai-deploy run [-h] [-l {DEBUG,INFO,WARN,ERROR,CRITICAL}] [-q] <map-image[:tag]> <input> <output>

positional arguments:
  <map-image[:tag]>     MAP image name
  <input>               Input data path
  <output>              Output data directory path

optional arguments:
  -h, --help            show this help message and exit
  -l {DEBUG,INFO,WARN,ERROR,CRITICAL}, --log-level {DEBUG,INFO,WARN,ERROR,CRITICAL}
                        Set the logging level (default: INFO)
  -q, --quiet           Suppress the STDOUT and print only STDERR from the application (default: False)

Syntax¶

monai-deploy run <container-image-name>[:tag] <input> <output> [-q|--quiet]

Arguments¶

Positional arguments¶

Name	Format	Description
MAP	`container-image-name[:tag]`	MAP container image name with or without image tag.
input	file or directory path	Local file or folder that contains input dataset for the MAP.
output	path	Local path to store output from the executing MAP.

Optional arguments¶

Name	Shorthand	Default	Description
quiet	-q	False	Suppress the STDOUT and print only STDERR from the application

Example¶

After you have written your application using MONAI Application SDK and have packaged the application, let’s try running it on your workstation using the MONAI Application Runner.

Example MAP and input¶

Given the following information.

MAP name and tag : monaispleen:latest
Input folder : ./spleen_input
Output folder : ./spleen_output

Launching the application¶

monai-deploy run monaispleen:latest spleen_input spleen_output

Output:

Checking dependencies...
--> Verifying if "docker" is installed...

--> Verifying if "monaispleen:latest" is available...

Checking for MAP "monaispleen:latest" locally
"monaispleen:latest" found.

Reading MONAI App Package manifest...
INFO:__main__:Operator started: 2021-09-10 21:53:25.363
INFO:__main__:Input path: /input
INFO:__main__:Output path: /output
...
...
continued...

Launching the application in quiet mode¶

If you only want to run your application such that the STDOUT is suppressed and only STDERR from the application is printed, try using --quiet flag.

monai-deploy run --quiet monaispleen:latest spleen_input spleen_output

Note

Currently MAR does not validate all resources specified in the MAP manifest.
If gpu is specified (>0), it executes nvidia-docker instead of docker internally to make sure that GPU is available inside the container.

Packaging app Deploying to the remote server (coming soon)