Docker engine crashing randomly from running fmriprep

[Joshnneal]

Description

Run fmriprep on a significant set of data through docker (see instructions below). Will run dataset for some period of time, then quit randomly, without an error message. Restart docker and reenter the command, but following a period of time the crash occurs again. Have tried multiple times to adjust memory/thread limits to prevent crashing, but still occurs.

Reproduce

Entered the following command:
fmriprep-docker /media/josh/andlab_ext11/datalad/KKI
/media/josh/andlab_ext11/datalad/KKI/Derivatives
participant
--fs-license-file /home/josh/license.txt
--fs-no-reconall
--output-spaces MNI152NLin6Asym:res-02
--nprocs 16 --mem 24000
-w /home/josh/tmp
--low-mem
-v
Which runs as:
docker run --rm -e DOCKER_VERSION_8395080871=27.4.0 -it -v /home/josh/license.txt:/opt/freesurfer/license.txt:ro -v /media/josh/andlab_ext11/datalad/KKI:/data:ro -v /media/josh/andlab_ext11/datalad/KKI/Derivatives:/out -v /home/josh/tmp:/scratch nipreps/fmriprep:24.1.1 /data /out participant --fs-no-reconall --nprocs 16 --mem 24000 --low-mem -v -w /scratch --output-spaces MNI152NLin6Asym:res-02

Expected behavior

Fmriprep should run to completion, with whatever effects being due to the underlying data and/or pipeline.

docker version

Client: Docker Engine - Community
 Version:           28.0.1
 API version:       1.47 (downgraded from 1.48)
 Go version:        go1.23.6
 Git commit:        068a01e
 Built:             Wed Feb 26 10:41:19 2025
 OS/Arch:           linux/amd64
 Context:           desktop-linux

Server: Docker Desktop 4.37.1 (178610)
 Engine:
  Version:          27.4.0
  API version:      1.47 (minimum version 1.24)
  Go version:       go1.22.10
  Git commit:       92a8393
  Built:            Sat Dec  7 10:38:57 2024
  OS/Arch:          linux/amd64
  Experimental:     false
 containerd:
  Version:          1.7.21
  GitCommit:        472731909fa34bd7bc9c087e4c27943f9835f111
 runc:
  Version:          1.1.13
  GitCommit:        v1.1.13-0-g58aa920
 docker-init:
  Version:          0.19.0
  GitCommit:        de40ad0

docker info

Client: Docker Engine - Community
 Version:    28.0.1
 Context:    desktop-linux
 Debug Mode: false
 Plugins:
  ai: Ask Gordon - Docker Agent (Docker Inc.)
    Version:  v0.5.1
    Path:     /usr/lib/docker/cli-plugins/docker-ai
  buildx: Docker Buildx (Docker Inc.)
    Version:  v0.19.2-desktop.1
    Path:     /usr/lib/docker/cli-plugins/docker-buildx
  compose: Docker Compose (Docker Inc.)
    Version:  v2.31.0-desktop.2
    Path:     /usr/lib/docker/cli-plugins/docker-compose
  debug: Get a shell into any image or container (Docker Inc.)
    Version:  0.0.37
    Path:     /usr/lib/docker/cli-plugins/docker-debug
  desktop: Docker Desktop commands (Beta) (Docker Inc.)
    Version:  v0.1.0
    Path:     /usr/lib/docker/cli-plugins/docker-desktop
  dev: Docker Dev Environments (Docker Inc.)
    Version:  v0.1.2
    Path:     /usr/lib/docker/cli-plugins/docker-dev
  extension: Manages Docker extensions (Docker Inc.)
    Version:  v0.2.27
    Path:     /usr/lib/docker/cli-plugins/docker-extension
  feedback: Provide feedback, right in your terminal! (Docker Inc.)
    Version:  v1.0.5
    Path:     /usr/lib/docker/cli-plugins/docker-feedback
  init: Creates Docker-related starter files for your project (Docker Inc.)
    Version:  v1.4.0
    Path:     /usr/lib/docker/cli-plugins/docker-init
  sbom: View the packaged-based Software Bill Of Materials (SBOM) for an image (Anchore Inc.)
    Version:  0.6.0
    Path:     /usr/lib/docker/cli-plugins/docker-sbom
  scout: Docker Scout (Docker Inc.)
    Version:  v1.15.1
    Path:     /usr/lib/docker/cli-plugins/docker-scout

Server:
 Containers: 0
  Running: 0
  Paused: 0
  Stopped: 0
 Images: 1
 Server Version: 27.4.0
 Storage Driver: overlayfs
  driver-type: io.containerd.snapshotter.v1
 Logging Driver: json-file
 Cgroup Driver: cgroupfs
 Cgroup Version: 2
 Plugins:
  Volume: local
  Network: bridge host ipvlan macvlan null overlay
  Log: awslogs fluentd gcplogs gelf journald json-file local splunk syslog
 CDI spec directories:
  /etc/cdi
  /var/run/cdi
 Swarm: inactive
 Runtimes: io.containerd.runc.v2 runc
 Default Runtime: runc
 Init Binary: docker-init
 containerd version: 472731909fa34bd7bc9c087e4c27943f9835f111
 runc version: v1.1.13-0-g58aa920
 init version: de40ad0
 Security Options:
  seccomp
   Profile: unconfined
  cgroupns
 Kernel Version: 6.10.14-linuxkit
 Operating System: Docker Desktop
 OSType: linux
 Architecture: x86_64
 CPUs: 16
 Total Memory: 23.47GiB
 Name: docker-desktop
 ID: b72bc175-de31-4531-95be-53b114689251
 Docker Root Dir: /var/lib/docker
 Debug Mode: false
 HTTP Proxy: http.docker.internal:3128
 HTTPS Proxy: http.docker.internal:3128
 No Proxy: hubproxy.docker.internal
 Labels:
  com.docker.desktop.address=unix:///home/josh/.docker/desktop/docker-cli.sock
 Experimental: false
 Insecure Registries:
  hubproxy.docker.internal:5555
  127.0.0.0/8
 Live Restore Enabled: false

WARNING: daemon is not using the default seccomp profile

Diagnostics ID

73BCC800-B9D9-4462-9AA2-F10F54626B83/20250318181945

Additional Info

No response