mongodb error in docker with xfs file system

prabowosakti · January 13, 2025, 9:58am

ello, I want to ask, why does docker use extf when installing mongodb? not xfs, so it raises an error like the one below:

025-01-11T14:37:14.247+00:00: Using the XFS filesystem is strongly recommended with the WiredTiger storage engine. See http://dochub.mongodb.org/core/prodnotes-filesystem
2025-01-11T14:37:15.917+00:00: Access control is not enabled for the database. Read and write access to data and configuration is unrestricted
2025-01-11T14:37:15.917+00:00: /sys/kernel/mm/transparent_hugepage/enabled is ‘always’. We suggest setting it to ‘never’ in this binary version
2025-01-11T14:37:15.917+00:00: vm.max_map_count is too low

“I have already used Ubuntu with the XFS file system and typef=1, but Docker still detects that I am not using XFS.”

bluepuma77 · January 14, 2025, 7:28am

Share your Docker compose file.

meyay · January 14, 2025, 8:44pm

That’s what the xfs needs to work with the overlay2 storage driver:

OverlayFS is the recommended storage driver, and supported if you meet the following prerequisites:

Version 4.0 or higher of the Linux kernel, or RHEL or CentOS using version 3.10.0-514 of the kernel or higher.

The overlay2 driver is supported on xfs backing filesystems, but only with d_type=true enabled.Use xfs_info to verify that the ftype option is set to 1. To format an xfs filesystem correctly, use the flag -n ftype=1.

Changing the storage driver makes existing containers and images inaccessible on the local system. Use docker save to save any images you have built or push them to Docker Hub or a private registry before changing the storage driver, so that you don’t need to re-create them later.

Source: https://docs.docker.com/engine/storage/drivers/overlayfs-driver/#prerequisites

prabowosakti · January 16, 2025, 12:53am

It’s still showing an error when I apply Overlay2.

Here is my Docker Compose file:


version: "3.8"


services:
  database:
    container_name: whispering-database
    image: mongo:7.0
    ports:

      - "27017:27017"

    volumes:
      - db-storage:/data/db

volumes:
  db-storage:

prabowosakti · January 16, 2025, 12:53am


version: "3.8"


services:
  database:
    container_name: whispering-database
    image: mongo:7.0
    ports:

      - "27017:27017"

    volumes:
      - db-storage:/data/db

volumes:
  db-storage:

prabowosakti · January 16, 2025, 12:54am

prabowosakti · January 16, 2025, 1:01am

meyay · January 16, 2025, 7:55am

Please do not share text output as screenshots. I don’t look at them, and might miss information shared in them.

Last time I missed the most relevant part: you must have docker root on a different filesystem than xfs.
The docu link I shared last is about the requirement of xfs as backing filesystem for the overlay2 storage driver.

Please share the output of docker info and mount without filtering anything with grep.

bluepuma77 · January 16, 2025, 8:08pm

Have you tried to use a simple Docker bind mount instead of a pure Docker volume?

prabowosakti · January 18, 2025, 11:46pm

docker info

prabowosakti@prabowo-sakti-ubuntu-gigabyte:~$ docker info
Client: Docker Engine - Community
 Version:    27.4.1
 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: 3
  Running: 1
  Paused: 0
  Stopped: 2
 Images: 4
 Server Version: 27.4.0
 Storage Driver: overlay2
  Backing Filesystem: extfs
  Supports d_type: true
  Using metacopy: false
  Native Overlay Diff: true
  userxattr: false
 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: runc io.containerd.runc.v2
 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: 4
 Total Memory: 3.717GiB
 Name: docker-desktop
 ID: 94d3261a-365e-4269-9ee8-2125560d2702
 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/prabowosakti/.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

mount

prabowosakti@prabowo-sakti-ubuntu-gigabyte:~$ mount
sysfs on /sys type sysfs (rw,nosuid,nodev,noexec,relatime)
proc on /proc type proc (rw,nosuid,nodev,noexec,relatime)
udev on /dev type devtmpfs (rw,nosuid,relatime,size=8133124k,nr_inodes=2033281,mode=755,inode64)
devpts on /dev/pts type devpts (rw,nosuid,noexec,relatime,gid=5,mode=620,ptmxmode=000)
tmpfs on /run type tmpfs (rw,nosuid,nodev,noexec,relatime,size=1633828k,mode=755,inode64)
/dev/sdb4 on / type xfs (rw,relatime,attr2,inode64,logbufs=8,logbsize=32k,noquota)
securityfs on /sys/kernel/security type securityfs (rw,nosuid,nodev,noexec,relatime)
tmpfs on /dev/shm type tmpfs (rw,nosuid,nodev,inode64)
tmpfs on /run/lock type tmpfs (rw,nosuid,nodev,noexec,relatime,size=5120k,inode64)
cgroup2 on /sys/fs/cgroup type cgroup2 (rw,nosuid,nodev,noexec,relatime,nsdelegate,memory_recursiveprot)
pstore on /sys/fs/pstore type pstore (rw,nosuid,nodev,noexec,relatime)
efivarfs on /sys/firmware/efi/efivars type efivarfs (rw,nosuid,nodev,noexec,relatime)
bpf on /sys/fs/bpf type bpf (rw,nosuid,nodev,noexec,relatime,mode=700)
systemd-1 on /proc/sys/fs/binfmt_misc type autofs (rw,relatime,fd=32,pgrp=1,timeout=0,minproto=5,maxproto=5,direct,pipe_ino=5277)
debugfs on /sys/kernel/debug type debugfs (rw,nosuid,nodev,noexec,relatime)
mqueue on /dev/mqueue type mqueue (rw,nosuid,nodev,noexec,relatime)
hugetlbfs on /dev/hugepages type hugetlbfs (rw,nosuid,nodev,relatime,pagesize=2M)
tracefs on /sys/kernel/tracing type tracefs (rw,nosuid,nodev,noexec,relatime)
fusectl on /sys/fs/fuse/connections type fusectl (rw,nosuid,nodev,noexec,relatime)
configfs on /sys/kernel/config type configfs (rw,nosuid,nodev,noexec,relatime)
/var/lib/snapd/snaps/bare_5.snap on /snap/bare/5 type squashfs (ro,nodev,relatime,errors=continue,threads=single,x-gdu.hide,x-gvfs-hide)
/var/lib/snapd/snaps/canonical-livepatch_286.snap on /snap/canonical-livepatch/286 type squashfs (ro,nodev,relatime,errors=continue,threads=single,x-gdu.hide,x-gvfs-hide)
/var/lib/snapd/snaps/core22_1564.snap on /snap/core22/1564 type squashfs (ro,nodev,relatime,errors=continue,threads=single,x-gdu.hide,x-gvfs-hide)
/var/lib/snapd/snaps/fbreader_30.snap on /snap/fbreader/30 type squashfs (ro,nodev,relatime,errors=continue,threads=single,x-gdu.hide,x-gvfs-hide)
/var/lib/snapd/snaps/core22_1722.snap on /snap/core22/1722 type squashfs (ro,nodev,relatime,errors=continue,threads=single,x-gdu.hide,x-gvfs-hide)
/var/lib/snapd/snaps/core18_2846.snap on /snap/core18/2846 type squashfs (ro,nodev,relatime,errors=continue,threads=single,x-gdu.hide,x-gvfs-hide)
/var/lib/snapd/snaps/core24_609.snap on /snap/core24/609 type squashfs (ro,nodev,relatime,errors=continue,threads=single,x-gdu.hide,x-gvfs-hide)
/var/lib/snapd/snaps/firefox_5561.snap on /snap/firefox/5561 type squashfs (ro,nodev,relatime,errors=continue,threads=single,x-gdu.hide,x-gvfs-hide)
/var/lib/snapd/snaps/firmware-updater_127.snap on /snap/firmware-updater/127 type squashfs (ro,nodev,relatime,errors=continue,threads=single,x-gdu.hide,x-gvfs-hide)
/var/lib/snapd/snaps/firmware-updater_147.snap on /snap/firmware-updater/147 type squashfs (ro,nodev,relatime,errors=continue,threads=single,x-gdu.hide,x-gvfs-hide)
/var/lib/snapd/snaps/firefox_5600.snap on /snap/firefox/5600 type squashfs (ro,nodev,relatime,errors=continue,threads=single,x-gdu.hide,x-gvfs-hide)
/var/lib/snapd/snaps/snap-store_1173.snap on /snap/snap-store/1173 type squashfs (ro,nodev,relatime,errors=continue,threads=single,x-gdu.hide,x-gvfs-hide)
/var/lib/snapd/snaps/gtk-common-themes_1535.snap on /snap/gtk-common-themes/1535 type squashfs (ro,nodev,relatime,errors=continue,threads=single,x-gdu.hide,x-gvfs-hide)
/var/lib/snapd/snaps/snapd-desktop-integration_178.snap on /snap/snapd-desktop-integration/178 type squashfs (ro,nodev,relatime,errors=continue,threads=single,x-gdu.hide,x-gvfs-hide)
/var/lib/snapd/snaps/gnome-42-2204_176.snap on /snap/gnome-42-2204/176 type squashfs (ro,nodev,relatime,errors=continue,threads=single,x-gdu.hide,x-gvfs-hide)
/var/lib/snapd/snaps/snapd-desktop-integration_253.snap on /snap/snapd-desktop-integration/253 type squashfs (ro,nodev,relatime,errors=continue,threads=single,x-gdu.hide,x-gvfs-hide)
/var/lib/snapd/snaps/telegram-desktop_6474.snap on /snap/telegram-desktop/6474 type squashfs (ro,nodev,relatime,errors=continue,threads=single,x-gdu.hide,x-gvfs-hide)
/var/lib/snapd/snaps/snap-store_1248.snap on /snap/snap-store/1248 type squashfs (ro,nodev,relatime,errors=continue,threads=single,x-gdu.hide,x-gvfs-hide)
/var/lib/snapd/snaps/snapd_21759.snap on /snap/snapd/21759 type squashfs (ro,nodev,relatime,errors=continue,threads=single,x-gdu.hide,x-gvfs-hide)
/var/lib/snapd/snaps/snapd_23545.snap on /snap/snapd/23545 type squashfs (ro,nodev,relatime,errors=continue,threads=single,x-gdu.hide,x-gvfs-hide)
tmpfs on /run/qemu type tmpfs (rw,nosuid,nodev,relatime,mode=755,inode64)
/dev/sdb5 on /boot/efi type vfat (rw,relatime,fmask=0022,dmask=0022,codepage=437,iocharset=iso8859-1,shortname=mixed,errors=remount-ro)
/dev/sdb6 on /home type xfs (rw,relatime,attr2,inode64,logbufs=8,logbsize=32k,noquota)
binfmt_misc on /proc/sys/fs/binfmt_misc type binfmt_misc (rw,nosuid,nodev,noexec,relatime)
tmpfs on /run/snapd/ns type tmpfs (rw,nosuid,nodev,noexec,relatime,size=1633828k,mode=755,inode64)
nsfs on /run/snapd/ns/canonical-livepatch.mnt type nsfs (rw)
nsfs on /run/snapd/ns/snapd-desktop-integration.mnt type nsfs (rw)
tmpfs on /run/user/1000 type tmpfs (rw,nosuid,nodev,relatime,size=1633824k,nr_inodes=408456,mode=700,uid=1000,gid=1000,inode64)
portal on /run/user/1000/doc type fuse.portal (rw,nosuid,nodev,relatime,user_id=1000,group_id=1000)
gvfsd-fuse on /run/user/1000/gvfs type fuse.gvfsd-fuse (rw,nosuid,nodev,relatime,user_id=1000,group_id=1000)
nsfs on /run/snapd/ns/telegram-desktop.mnt type nsfs (rw)
nsfs on /run/snapd/ns/snap-store.mnt type nsfs (rw)

I don’t see anything related to Docker when I run the mount command.

prabowosakti · January 18, 2025, 11:54pm

Hold on, let me try, and I’ll tell you when I’m done.

meyay · January 19, 2025, 12:16pm

Docker Desktop always uses a utility vm to run the docker engine. Thus, it doesn’t matter what filesystem your host uses, as it is not the one being used by the vm. I doubt there is a way to modify the filesystem of the utility vm.

I doubt that a bind in Docker Desktop will actually bind the host folder into the utility vm and from there into the container. I wouldn’t be surprised if it uses a protocol like p9 to access the host folders.

If you used docker-ce, instead of Docker Desktop, your host’s filesystem would be used, and docker-ce would actually detect your xfs filesystem.

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