Overlayfs images permissions investigation

userFeb 2, 02:34:37 AM

assistantFeb 2, 02:34:37 AM

moonshotai/kimi-k2.5 · openrouter$0.0123

The user is asking about overlayfs images in a specific directory (`~/.local/share/containers/storage/overlay`) that have permissions other than the user's. They mention they have podman but want to know about other programs like bwrap that might be creating these. Let me understand what they're asking: 1. What programs might be creating overlayfs images in this directory with wrong permissions? 2. How can they remove/fix these permissions or move them to the correct location? This is a diagnostic/informational question - they're not asking me to make changes yet, just to explain what's happening and how to fix it. Let me think about what could be creating overlayfs mounts in this location: 1. **Podman** - This is the most likely candidate. Podman uses overlayfs for its container storage by default. The path `~/.local/share/containers/storage/overlay` is the default location for podman's rootless container storage. 2. **Buildah** - Buildah also uses containers/storage and could create overlayfs mounts in the same location. 3. **Skopeo** - Can interact with container storage. 4. **bwrap (bubblewrap)** - While bwrap can use overlayfs, it typically doesn't use this specific directory path by default. However, if some application is using bwrap with custom configuration, it could potentially use this location. 5. **Other container tools** - Any tool that uses the containers/storage library (like CRI-O in some configurations, though that's usually system-wide). The permission issues could be caused by: - Running podman/buildah as root (which would create files owned by root) - Running containers with different user namespaces - SELinux or other security contexts - Bugs or interrupted operations Since the user is asking for information and not asking me to make changes, I should: 1. Explain what programs are likely involved 2. Explain why permissions might be wrong 3. Provide guidance on how to diagnose and fix the issue I should NOT make any changes to their system since they haven't asked me to, and this is just an informational question.

The most likely programs creating overlayfs images in that directory are:

Podman - Primary suspect; uses ~/.local/share/containers/storage/overlay as default rootless storage
Buildah - Shares the same storage library and location
Skopeo - Can write to containers/storage
CRI-O (if configured for rootless) - Uses same storage backend

Why permissions differ:

Running podman/buildah with sudo (creates root-owned files)
Interrupted pulls/builds leaving temp files
User namespace mappings creating files as different subuids
SELinux context mismatches

To diagnose:

# See what's in the directory
ls -la ~/.local/share/containers/storage/overlay/

# Check which program owns it
lsof +D ~/.local/share/containers/storage/overlay/ 2>/dev/null | head -20

# Check for root-owned files
find ~/.local/share/containers/storage/overlay/ -user root 2>/dev/null | head -10

To fix:

If files are owned by root:

# Run podman unshare to enter user namespace, then fix
podman unshare chown -R 0:0 ~/.local/share/containers/storage/overlay/

Nuclear option (removes all containers/images):

podman system reset
# Or manually:
rm -rf ~/.local/share/containers/storage/overlay/

If you need to preserve containers:

# Identify and remove only problematic layers
podman images  # see what's being used
podman image prune  # remove dangling images

For bwrap specifically - it usually doesn't use this path unless explicitly configured. Check if any apps are using custom bwrap configs that point here.

Would you like me to help diagnose what's actually in your overlay directory?

13,450in / 848out / 544reasoning$0.0123

userFeb 2, 02:40:39 AM

podman image rm --all
WARN[0002] Unexpected error on reading Additional Layer Store pointer open /home/jm/.local/share/containers/storage/overlay/1cd07cece13fb8b129105331406c8566baf91b5c1f4679cdd17aee739f97f026/additionallayer: permission denied
Untagged: docker.io/oven/bun:1.1-alpine
Untagged: docker.io/jaegertracing/all-in-one:latest
Untagged: docker.io/tabbyml/tabby:latest
Untagged: docker.io/library/node:22.12-alpine
Untagged: us-docker.pkg.dev/gemini-code-dev/gemini-cli/sandbox:0.11.0
Untagged: docker.io/library/node:lts-alpine
Untagged: docker.io/library/neo4j:2025.03.0-enterprise
Untagged: docker.io/library/golang:1.25.4-alpine
Untagged: gcr.io/distroless/base-debian12:latest
Untagged: ghcr.io/github/github-mcp-server:latest
Untagged: docker.io/library/node:16-buster-slim
Untagged: docker.io/library/node:18-alpine
Untagged: docker.io/library/python:3.12-slim
Untagged: localhost/a2a-inspector:latest
Untagged: docker.io/library/alpine:latest
Untagged: localhost/opencode-alpine:latest
Untagged: docker.io/ollama/ollama:0.13.5-rocm
Untagged: docker.io/ollama/ollama:rocm
Untagged: docker.io/oven/bun:1.3.5-slim
Untagged: docker.io/cloudflare/sandbox:0.6.7
Untagged: localhost/opencode:latest
Untagged: docker.io/library/node:20-slim
Untagged: docker.io/oven/bun:1
Untagged: docker.io/library/ubuntu:22.04
Untagged: localhost/cloudflare/sandbox-test:0.6.7
Untagged: localhost/cloudflare/sandbox-test:0.6.7-python
Untagged: localhost/cloudflare/sandbox-test:0.6.7-opencode
Untagged: localhost/cloudflare/sandbox-test:0.6.7-standalone
Untagged: docker.io/maximhq/bifrost:latest
Untagged: docker.io/neosmemo/memos:stable
Untagged: docker.io/tabbyml/tabby-rocm:latest
Deleted: 3e0fe5990183701de280ae85311dd90fa5e44dde32d8e94b63f12422faa18982
Deleted: 326d6a869faa4fa7e8eaff9dd7c11aa9c414181beb3f6a698ce87049bb607cdb
Deleted: 3448d7ddbc59370198cd7d48b99562f4391042088e1aa33bd4b9c0f0401121d2
Deleted: e4624811c664a4734f942fb39f96363a3fa5ace762a7c5ebbbeb7c89b43d37b2
Deleted: e4a821e4027215700f8fd1dfd8097b2850da80a229c24d4f7e4fb0015f04bdd8
Deleted: e9d53facffecbdda4ca252f617b9d6bc240af5ed62136d5e3da8b9d23208eac4
Deleted: f86e735e7a39c546c1f105f637c63efcf44f4d6d285f9d8f524c1c62d9125377
Deleted: 314086290b80a3ab8662632326377779100649fff4a1a530f8354f8f97d8aefd
Deleted: 3c3c08e396e2b6dacce68bec356782ccc05be65041ef2878c766657e8894db86
Deleted: eb8b8b8a361056a1107428997a0c13a18c013ad612f24e54cb6990e60bfed3ec
Deleted: ee77c6cd7c1886ecc802ad6cedef3a8ec1ea27d1fb96162bf03dd3710839b8da
Deleted: 86da76f5177a8c9e4c31e87de34514595640c6080b9c2a708d71671485e2c160
Deleted: 378630ad609cbd394f360bc09368dd8dc5e39ef9910790e1e8d11b981f6d8e79
Deleted: dbfa6f98470eaeb811e3e18683719a3ed318694723d1d45fb389f0bce10c0aff
Deleted: 26ba52df8f27a83e64d6ec840d295e00401bcd477c17efc9b75348560258be06
Deleted: c40769eb2637e353ce65c2374db5c8f9d4b6e27a880f0f4683f279ad032615ee
Deleted: f02bf476ca5717e1e07f15481a8c9abe9b7266d62ab656d5687ac4e341a7e1b1
Deleted: d76db0ce3312a66957d958516955cf1f5f4900dcf22e6fe3129f9c58fbfe862f
Deleted: 763a9af5a518a5c842dbb6a8eb8dec6cc2815a749ea6195addfecaa71f6e9108
Deleted: 57cddd3f33135d0f89d137657126bc0062cffe0ba943aefb44b5a313d61198bb
Deleted: 76cabbea88111a0ed4ce4e4f7a5ff880bb307773568d5eadf86fe61121520798
Deleted: b9b85d057858df42c423837e30701707a076f54a93f52ddfeeb2edcc266de619
Deleted: a43066533fa2217376967967b893491cfa67ad9b9d840a9bf401c2c6d97677f8
Deleted: 3c318b9b9d6f8c86c46b696802a38341da6bea2309161691b0d05980652d69de

assistantFeb 2, 02:40:39 AM

moonshotai/kimi-k2.5 · openrouter$0.0116

The user is showing me output from `podman image rm --all` which shows warnings about permission denied errors when reading additional layer store pointers. This is exactly the issue they mentioned earlier - files with incorrect permissions in the overlay storage directory. The warning shows: ``` WARN[0002] Unexpected error on reading Additional Layer Store pointer open /home/jm/.local/share/containers/storage/overlay/1cd07cece13fb8b129105331406c8566baf91b5c1f4679cdd17aee739f97f026/additionallayer: permission denied ``` This indicates that there are files in the overlay directory that the current user doesn't have permission to read. The images were untagged and some were deleted, but there are permission issues preventing complete cleanup. Since I'm in Plan Mode (READ-ONLY), I should: 1. Help diagnose what's happening 2. Explain the permission issue 3. Provide a plan to fix it without making changes yet The user wants to know how to fix these permission issues. I should explain what's happening and provide a plan for resolution.

The permission errors indicate files owned by a different UID (likely from running podman with sudo or a different user namespace). Here's what's happening and how to fix it:

The Problem

The additionallayer files have wrong ownership - probably created when:

You ran sudo podman at some point
A tool ran podman in a different user namespace
Previous UID mapping conflicts

Solutions (choose one)

Option 1: Fix permissions with podman unshare (recommended)

# Enter the user namespace and fix ownership
podman unshare chown -R 0:0 ~/.local/share/containers/storage/overlay/

# Then clean up properly
podman system prune -a

Option 2: Nuclear reset (loses all containers/images)

podman system reset

Option 3: Manual cleanup of specific directories

# Check which directories have wrong permissions
find ~/.local/share/containers/storage/overlay/ -not

14,756in / 645out / 273reasoning$0.0116

userFeb 2, 02:40:59 AM

Error: 17 errors occurred:
* failed to add to stage directory: rename /home/jm/.local/share/containers/storage/overlay/1cd07cece13fb8b129105331406c8566baf91b5c1f4679cdd17aee739f97f026 /home/jm/.local/share/containers/storage/overlay/tempdirs/temp-dir-2464438722/0-1cd07cece13fb8b129105331406c8566baf91b5c1f4679cdd17aee739f97f026: permission denied
* removing temp dir failed: openfdat /home/jm/.local/share/containers/storage/overlay/tempdirs/temp-dir-3096898138/1-d9801a419fc8933114b600e6a4d9e23deb145398cde3b01caec1ecc3b87ba167/diff1/home/ubuntu: permission denied
removing temp dir failed: unlinkat /home/jm/.local/share/containers/storage/overlay/tempdirs/temp-dir-3774160775/1-879f683f65011a8c2f496b102fffa5f1fbd071b8d296e3655e4fe06e9f883dc8/diff/run/systemd/netif/links: permission denied
removing temp dir failed: openfdat /home/jm/.local/share/containers/storage/overlay/tempdirs/temp-dir-3688576825/1-073ec47a8c22dcaa4d6e5758799ccefe2f9bde943685830b1bf6fd2395f5eabc/diff/home/ubuntu: permission denied
* image used by b229077a45ba19ab7500cd34e20e7ead9c4b7d3fc06f87d170aab8237150a2f8: image is in use by a container: consider listing external containers and force-removing image
* image used by 1640fe0a1a40450c04d14b52a095864728f40c83858030e53cd91cecb360d250: image is in use by a container: consider listing external containers and force-removing image
* image used by 8f5f0df502de00a1a34da9a0b2492f7f2791aa0098bdada575f7174b3cbf5f8c: image is in use by a container: consider listing external containers and force-removing image
* image used by 76ad96f9dbbec923ecf19ee5e5a98c167f6ea9b3e333f428376cda8b01954433: image is in use by a container: consider listing external containers and force-removing image
* image used by ea76acf246de4d984427538df47c6c116350e070e7cbcc00e41ff8732a46aa8d: image is in use by a container: consider listing external containers and force-removing image
* image used by 262d4203aee58c4330553b7c8dc7199677c40481bdd988536702289d99db776c: image is in use by a container: consider listing external containers and force-removing image
* image used by eef6629580900c4d45c24b26f64ed4272684255b40298ff6b5d176158edd0e70: image is in use by a container: consider listing external containers and force-removing image
* image used by 8e3ea6bad72c9d0df9ace29dea4fab429c072857a9afcfbe2107220248e78796: image is in use by a container: consider listing external containers and force-removing image
* image used by b09fd681440e305aa8fc3ab10783ce4f0e329b88e7d7143f06e3dd73c898a966: image is in use by a container: consider listing external containers and force-removing image
* image used by f2a3c8854e3ce9926fe72ba810df8ede7f3c234bc0f6e683580f5b36a889c6be: image is in use by a container: consider listing external containers and force-removing image
* image used by efba71aecca0e8aa220271865f6851adbee39e054a6f0b570862380078a83121: image is in use by a container: consider listing external containers and force-removing image
* image used by 6f54d7194750cd0a831d6ec0ca7c3cda5fa97d1e40bf5c10d70da49d8650fc74: image is in use by a container: consider listing external containers and force-removing image
* image used by b2bba7e9fdc8be78a33575d2c696123d0d0e18163a5f8b3b2422d95df1b06eb0: image is in use by a container: consider listing external containers and force-removing image
* image used by b2bba7e9fdc8be78a33575d2c696123d0d0e18163a5f8b3b2422d95df1b06eb0: image is in use by a container: consider listing external containers and force-removing image
* removing temp dir failed: openfdat /home/jm/.local/share/containers/storage/overlay/tempdirs/temp-dir-1575801902/1-ea6dee290f9b82dc66194c01097bf97d5d3b0c8fbeac1310ae3dd5c7b8a160c6/diff/home/rocm: permission denied

assistantFeb 2, 02:41:36 AM

moonshotai/kimi-k2.5 · openrouter$0.0044

The user is getting more errors from podman. The errors show: 1. Permission denied errors when trying to rename/remove directories in the overlay storage 2. Multiple "image is in use by a container" errors 3. Issues with temp directories having wrong permissions This is a mess of permission issues and containers still using images. Let me provide a comprehensive fix approach. Since we're in plan mode (read-only), I should provide a plan to fix this but not execute anything yet.

The errors show two problems: permission issues (wrong ownership in overlay storage) and containers still running that reference those images.

Plan to Fix This

Since we're in plan mode, here's the comprehensive approach:

Step 1: Stop All Containers

podman stop -a
podman rm -a
# Or force remove: podman rm -af

Step 2: Fix Permissions (choose one approach)

Approach A - Podman unshare (safest):

podman unshare chown -R 0:0 ~/.local/share/containers/storage/overlay/

Approach B - Direct chown if you know the UIDs:

sudo chown -R $USER:$USER ~/.local/share

2,126in / 421out / 128reasoning$0.0044

userFeb 2, 02:47:35 AM

Quickly, how can I list all dirs/files with ownership properties other than 1000:1000

assistantFeb 2, 02:47:35 AM

moonshotai/kimi-k2.5 · openrouter$0.0111

The user wants to find all directories/files with ownership other than 1000:1000 (which is likely their user's UID/GID). This is a read-only query, so I can execute this. I'll provide a find command to list all files/dirs with ownership other than 1000:1000.

find ~/.local/share/containers/storage/overlay/ \( -not -uid 1000 -o -not -gid 1000 \) -ls

Or more concise:

find ~/.local/share/containers/storage/overlay/ ! -user 1000 -o ! -group 1000 -ls 2>/dev/null | head -50

To see just the unique owners:

find ~/.local/share/containers/storage/overlay/ -printf "%u:%g %p\n" 2>/dev/null | grep -v "^1000:1000" | sort | uniq -c | head -20

17,108in / 203out / 67reasoning$0.0111

userFeb 2, 02:49:35 AM

100999 100999
and
11000 11000

are the 2 main ids. What do you suggest? They are old and I can just remove if rm them will not break anything

assistantFeb 2, 02:49:35 AM

moonshotai/kimi-k2.5 · openrouter$0.0122

The user has identified that the files are owned by UID 100999 and 11000. These are likely subordinate UIDs (subuids) used by rootless podman for user namespace mapping. In rootless podman: - The user's UID (1000) is mapped to root (0) inside the container - Other UIDs are mapped to subuids starting from the user's base subuid UID 100999 and 11000 are likely subuids allocated to this user for container processes. Since the user says these are old and can be removed, I should explain: 1. What these UIDs represent (subuids for rootless containers) 2. That it's safe to remove them if the containers/images are no longer needed 3. How to properly clean them up Since we're in plan mode, I should not execute anything, just provide the plan.

Those are subordinate UIDs (subuids) used by rootless Podman for user namespace mapping. UID 100999 and 11000 are mapped users from inside containers.

Safe Removal Options

Option 1: Podman system reset (cleanest)

podman system reset

Destroys everything but guarantees clean state.

Option 2: Manual cleanup of orphaned layers

# Remove just the problematic directories
rm -rf ~/.local/share/containers/storage/overlay/1cd07cece13fb8b129105331406c8566baf91b5c1f4679cdd17aee739f97f026/
rm -rf ~/.local/share/containers/storage/overlay/tempdirs/

Option 3: Fix ownership via user namespace

podman unshare rm -rf ~/.local/share/containers/storage/overlay/tempdirs/
podman unshare chown -R 0:0 ~/.local/share/containers/storage/overlay/

Since these are orphaned overlay layers (not referenced by running containers), removing them is safe. The tempdirs are definitely safe to delete.

Which approach do you prefer? The podman system reset is the nuclear option that fixes everything but destroys all images/containers. The surgical removal of specific directories preserves your working containers.

17,042in / 461out / 197reasoning$0.0122

userFeb 2, 02:50:54 AM

ERRO[0016] 13 errors occurred:
* error removing stale temp dir: openfdat /home/jm/.local/share/containers/storage/overlay/tempdirs/temp-dir-3096898138/1-d9801a419fc8933114b600e6a4d9e23deb145398cde3b01caec1ecc3b87ba167/diff1/home/ubuntu: permission denied
error removing stale temp dir: openfdat /home/jm/.local/share/containers/storage/overlay/tempdirs/temp-dir-3688576825/1-073ec47a8c22dcaa4d6e5758799ccefe2f9bde943685830b1bf6fd2395f5eabc/diff/home/ubuntu: permission denied
error removing stale temp dir: unlinkat /home/jm/.local/share/containers/storage/overlay/tempdirs/temp-dir-3774160775/1-879f683f65011a8c2f496b102fffa5f1fbd071b8d296e3655e4fe06e9f883dc8/diff/run/systemd/netif/links: permission denied
error removing stale temp dir: openfdat /home/jm/.local/share/containers/storage/overlay/tempdirs/temp-dir-1575801902/1-ea6dee290f9b82dc66194c01097bf97d5d3b0c8fbeac1310ae3dd5c7b8a160c6/diff/home/rocm: permission denied
all similar errors

assistantFeb 2, 02:50:54 AM

moonshotai/kimi-k2.5 · openrouter$0.0040

The user is still getting permission errors when trying to clean up. These are stale temp directories with wrong ownership (100999 and 11000). Since we're in plan mode, I need to provide a solution that will work. The issue is that even `podman system reset` is failing because it can't clean up these temp dirs due to permission issues. The user needs to either: 1. Use sudo to remove them 2. Use podman unshare to enter the user namespace and remove them 3. Manually identify and remove with elevated permissions Since the user said these are old and can be removed, and the errors are all about tempdirs, the simplest solution is to use sudo or podman unshare to remove the tempdirs directory entirely.

Since podman system reset is failing on the tempdirs, you need to force remove those directories first using elevated permissions, then run the reset.

Plan

Step 1: Force remove the problematic tempdirs

sudo rm -rf ~/.local/share/containers/storage/overlay/tempdirs/

Step 2: Then run podman system reset

podman system reset

Alternative (if you don't want to use sudo)

Use podman unshare to enter the user namespace where those UIDs are mapped:

# Enter user namespace and remove tempdirs
podman unshare rm -rf ~/.local/share/containers/storage/overlay/tempdirs/

# Then reset
podman system reset

The tempdirs are just temporary extraction directories - they're safe to delete. The issue is they're owned by the container's internal UID mappings (100999, 11000) which your normal user can't access without entering the user namespace.

Which approach do you prefer? The sudo method is most reliable. The podman unshare method is cleaner but sometimes has edge cases with deeply nested permissions.

973in / 400out / 183reasoning$0.0040

userFeb 2, 03:00:50 AM

When running podman on a debian system, with the intention to run rootless containers with limited network permissions (usually localhost, but also the ability to expose ports on localhost and access the wider network through a bridge), what systemd services should I have running, on both the system slice, and on the user systemd slice.

Do I need libvirtd services nessecarily?

assistantFeb 2, 03:00:50 AM

moonshotai/kimi-k2.5 · openrouter$0.0143

The user is asking about the systemd services needed for rootless Podman on Debian, specifically for networking (localhost, port exposure, bridge access). They also ask if libvirtd is necessary. Key points to address: 1. System-level systemd services needed 2. User-level systemd services needed 3. Networking setup for rootless containers 4. Whether libvirtd is required Let me think about this: - Rootless Podman uses slirp4netns or pasta for networking by default - For rootless containers with port binding, you need the user systemd services - System-level: podman.socket (for API), maybe aardvark-dns if using custom networks - User-level: podman.service, podman.socket - libvirtd is NOT needed for Podman - that's for KVM/QEMU virtualization - For bridge networking in rootless mode, you might need pasta or slirp4netns configured I should provide a comprehensive answer about what services are needed and why libvirtd isn't necessary.

For rootless Podman with the networking setup you described, here's what you need:

System-Level Services (system slice)

Required:

podman.socket - Enables Podman API for rootless users (activated on demand)
dbus - Required for systemd user session integration

Optional/Conditional:

systemd-networkd or NetworkManager - For system networking (if not already running)
aardvark-dns - Only if using custom networks with DNS (usually auto-started)

NOT needed:

libvirtd - This is for KVM/QEMU virtualization, completely separate from Podman

User-Level Services (user slice)

Required for your use case:

# Enable these as your user (not sudo)
systemctl --user enable podman.socket
systemctl --user enable podman.service

Why these matter:

podman.socket - Allows podman run -p 8080:80 to work (API for port binding)
podman.service - Keeps containers running after logout (if needed)

Networking for Rootless

By default, rootless Podman uses:

slirp4netns or pasta (newer default) - Provides NAT + localhost port binding
Containers can access external network through this
Port exposure on localhost works with -p 127.0.0.1:8080:80

For bridge networking (if you need custom bridges):

Rootless containers can't create real bridges without privileges
Use podman network create which creates a bridge via pasta/slirp4netns
Or use --network=slirp4netns:port_handler=slirp4netns for specific behaviors

Quick Setup Commands

# As your user (1000), enable the socket
systemctl --user enable --now podman.socket

# Verify it's working
systemctl --user status podman.socket

# Test networking
podman run --rm -p 8080:80 nginx:alpine

Summary

No libvirtd needed - that's for virtual machines, not containers
Main requirement: podman.socket in your user session
Bridge access: Works out-of-the-box with pasta/slirp4netns, no extra services needed
Port exposure on localhost: Works with standard -p flag when socket is enabled

Is there a specific networking scenario you're trying to achieve that isn't working?

18,857in / 750out / 249reasoning$0.0143