Docker Configuration

Docker can be configured in a wide-varietry of ways based on hardware resources available. Parameters such as CPU cores, RAM and storage can be assigned to Docker for running NeuroDock.

For validations purposes, the NeuroDock image was tested to work as intended on the following three systems:

Part	Machine A	Machine B	Machine C
Build	Apple iMac Pro	Custom	Custom
OS	Mac OS X Mojave	Ubuntu 18.04	Microsoft Windows 10 Pro
CPU	Intel Xeon W [8C/16T]	AMD Ryzen R9 2700X [8C/16T]	AMD Ryzen R9 2700X [8C/16T]
Memory	64 GB	16 GB	16 GB
Video	Raden Pro Vega 56 8 GB	Nvidia GTX 1080 8 GB	Nvidia GTX 1080 8 GB

We found identical results across the three operating systes on all these configurations.

Docker Preferences

Based on Docker’s system requirements, we recommend assigning the following sysem resources to Docker:

Parameter	Value
CPUs	8
Memory	16.00 GB
Disk image size	32.00 GB

By default, Docker assigns itself half the number of available CPU cores and 2 GB of memory. Considering that the entire NeuroDock image is ~14.5 GB, we recommend at least double in disk image size. You may configure your Docker Engine to run on this configuration, or input your own values based on your processing needs. The following sections detail how to set these parameters.

Linux

CPU and memory access to Docker containers on Linux machines is manipulated via CFGS scheduler flags at run time. These flags are:

Flag	Description
--cpus=<value>	specify how many CPU cores to use
-m or --memory	specify the maximum amount of memory available to containers

For a more comprehensive list of manupulable system parameters for for Linux, please visit the Runtime options with Memory, CPUs, and GPUs page on Docker documentation.

Mac OS

Manipulating these three variables is very simple on Mac OS because these parameters are located in the GUI.

1. On the Docker icon in the status bar, right-click on the Docker icon, then Preferences.

2. Click on the Resources tab on the left

Docker Mac preferences GUI; click on resources

3. The Resourcs menu will show you the configuration, please change them to desired valus. You may leave “Swap” at default.

Docker Mac resources configuration

Windows

Similar to the Mac, the same sequence of steps apply for the Windows platform.

1. Right-click on the Dpcker icon in the taskbar, then click on Preferences.

2. Clock on the Resources tab on the left.

Docker Windows preferences GUI; configure as desired

3. The Resourcs menu will show you the configuration, please change them to desired valus. You may leave “Swap” at default.

Setting the correct configuration will force Docker to not exceed these constraints. By splitting up CPU and memory loads, researchers can process multiple DWIs simultaneously.

GPU Support

At this time, there is no CUDA or ROCm GPU support. These feature are planned for a later release. Please use the non-Docker, native Linux configuration to utilize GPU for eddy and EPI correction.