Permission issues inside container

LXD
#1

After upgrade of server from 18.04 to 22.04 I have an issue inside a container:

» LANG=C apt update
Hit:1 http://archive.ubuntu.com/ubuntu focal InRelease
Hit:2 http://archive.ubuntu.com/ubuntu focal-updates InRelease
Hit:3 http://archive.ubuntu.com/ubuntu focal-backports InRelease
Hit:4 http://archive.ubuntu.com/ubuntu focal-security InRelease
Reading package lists... Done
W: chown to _apt:root of directory /var/lib/apt/lists/partial failed - SetupAPTPartialDirectory (1: Operation not permitted)
W: chmod 0700 of directory /var/lib/apt/lists/partial failed - SetupAPTPartialDirectory (1: Operation not permitted)
W: chown to _apt:root of directory /var/lib/apt/lists/auxfiles failed - SetupAPTPartialDirectory (1: Operation not permitted)
W: chmod 0700 of directory /var/lib/apt/lists/auxfiles failed - SetupAPTPartialDirectory (1: Operation not permitted)
W: Download is performed unsandboxed as root as file '/var/lib/apt/lists/partial/archive.ubuntu.com_ubuntu_dists_focal_InRelease' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied)
W: Problem unlinking the file /var/lib/apt/lists/partial/archive.ubuntu.com_ubuntu_dists_focal_InRelease - PrepareFiles (13: Permission denied)
W: chmod 0600 of file /var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_focal_InRelease failed - Item::QueueURI (1: Operation not permitted)
W: Problem unlinking the file /var/lib/apt/lists/partial/archive.ubuntu.com_ubuntu_dists_focal-updates_InRelease - PrepareFiles (13: Permission denied)
W: Problem unlinking the file /var/lib/apt/lists/partial/archive.ubuntu.com_ubuntu_dists_focal-backports_InRelease - PrepareFiles (13: Permission denied)
W: Problem unlinking the file /var/lib/apt/lists/partial/archive.ubuntu.com_ubuntu_dists_focal-security_InRelease - PrepareFiles (13: Permission denied)
W: chown to root:root of file /var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_focal_InRelease failed - 201::URIDone (1: Operation not permitted)
W: chmod 0644 of file /var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_focal_InRelease failed - 201::URIDone (1: Operation not permitted)
W: chmod 0600 of file /var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_focal-updates_InRelease failed - Item::QueueURI (1: Operation not permitted)
W: chown to root:root of file /var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_focal-updates_InRelease failed - 201::URIDone (1: Operation not permitted)
W: chmod 0644 of file /var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_focal-updates_InRelease failed - 201::URIDone (1: Operation not permitted)
W: chmod 0600 of file /var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_focal-backports_InRelease failed - Item::QueueURI (1: Operation not permitted)
W: chown to root:root of file /var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_focal-backports_InRelease failed - 201::URIDone (1: Operation not permitted)
W: chmod 0644 of file /var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_focal-backports_InRelease failed - 201::URIDone (1: Operation not permitted)
W: chmod 0600 of file /var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_focal-security_InRelease failed - Item::QueueURI (1: Operation not permitted)
W: chown to root:root of file /var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_focal-security_InRelease failed - 201::URIDone (1: Operation not permitted)
W: chmod 0644 of file /var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_focal-security_InRelease failed - 201::URIDone (1: Operation not permitted)
E: Unable to read /var/lib/apt/lists/partial/ - open (13: Permission denied)

Here is the container config:

# lxc config show duniter
architecture: x86_64
config:
  image.architecture: amd64
  image.description: ubuntu 20.04 LTS amd64 (release) (20210819)
  image.label: release
  image.os: ubuntu
  image.release: focal
  image.serial: "20210819"
  image.type: squashfs
  image.version: "20.04"
  limits.cpu: "4"
  limits.memory: 4GB
  volatile.base_image: 9c939141a94bbdcfd29b0b3be6dc135b9d3e8d73b19235f06de4593898e8b960
  volatile.eth0.host_name: veth59b5d258
  volatile.eth0.hwaddr: 00:16:3e:0c:78:5b
  volatile.idmap.base: "0"
  volatile.idmap.current: '[{"Isuid":true,"Isgid":false,"Hostid":1000000,"Nsid":0,"Maprange":1000000000},{"Isuid":false,"Isgid":true,"Hostid":1000000,"Nsid":0,"Maprange":1000000000}]'
  volatile.idmap.next: '[{"Isuid":true,"Isgid":false,"Hostid":1000000,"Nsid":0,"Maprange":1000000000},{"Isuid":false,"Isgid":true,"Hostid":1000000,"Nsid":0,"Maprange":1000000000}]'
  volatile.last_state.idmap: '[{"Isuid":true,"Isgid":false,"Hostid":1000000,"Nsid":0,"Maprange":1000000000},{"Isuid":false,"Isgid":true,"Hostid":1000000,"Nsid":0,"Maprange":1000000000}]'
  volatile.last_state.power: RUNNING
  volatile.last_state.ready: "false"
  volatile.uuid: 8debd7c2-ff7f-4090-8eac-aaaa8b55a046
devices:
  eth0:
    ipv4.address: 10.2.249.21
    name: eth0
    network: lxdbr0
    type: nic
  root:
    path: /
    pool: pool1
    size: 100GB
    type: disk
ephemeral: false
profiles:
- default
stateful: false
description: ""
#2

What is the output of lxc storage show pool1?

#3

Are newly created instances OK?

#4 
config:
  source: pool1/lxd
  volatile.initial_source: pool1/lxd
  zfs.pool_name: pool1/lxd
description: ""
name: pool1
driver: zfs
used_by:
- /1.0/instances/backup
- /1.0/instances/coturn
- /1.0/instances/duniter
- /1.0/instances/front
- /1.0/instances/prepa
- /1.0/instances/stats
- /1.0/instances/texto
- /1.0/instances/mariadb
- /1.0/instances/vm31
- /1.0/instances/vm32
- /1.0/profiles/default
- /1.0/profiles/vm-pool1
status: Created
locations:
- none

Good catch, and no, I get this:

E: Could not open file /var/lib/apt/lists/security.ubuntu.com_ubuntu_dists_jammy-security_main_cnf_Commands-amd64 - open (2: No such file or directory)
Traceback (most recent call last):
  File "/usr/lib/cnf-update-db", line 32, in <module>
    col.create(db)
  File "/usr/lib/python3/dist-packages/CommandNotFound/db/creator.py", line 95, in create
    self._fill_commands(con)
  File "/usr/lib/python3/dist-packages/CommandNotFound/db/creator.py", line 144, in _fill_commands
    raise subprocess.CalledProcessError(returncode=sub.returncode,
subprocess.CalledProcessError: Command '/usr/lib/apt/apt-helper cat-file /var/lib/apt/lists/security.ubuntu.com_ubuntu_dists_jammy-security_main_cnf_Commands-amd64' returned non-zero exit status 100.
Reading package lists... Done
E: Problem executing scripts APT::Update::Post-Invoke-Success 'if /usr/bin/test -w /var/lib/command-not-found/ -a -e /usr/lib/cnf-update-db; then /usr/lib/cnf-update-db > /dev/null; fi'
E: Sub-process returned an error code
#5

Please can you show lxc info, lxc storage show <pool>

#6

Here you go @tomp :

# lxc info
config: {}
api_extensions:
- storage_zfs_remove_snapshots
- container_host_shutdown_timeout
- container_stop_priority
- container_syscall_filtering
- auth_pki
- container_last_used_at
- etag
- patch
- usb_devices
- https_allowed_credentials
- image_compression_algorithm
- directory_manipulation
- container_cpu_time
- storage_zfs_use_refquota
- storage_lvm_mount_options
- network
- profile_usedby
- container_push
- container_exec_recording
- certificate_update
- container_exec_signal_handling
- gpu_devices
- container_image_properties
- migration_progress
- id_map
- network_firewall_filtering
- network_routes
- storage
- file_delete
- file_append
- network_dhcp_expiry
- storage_lvm_vg_rename
- storage_lvm_thinpool_rename
- network_vlan
- image_create_aliases
- container_stateless_copy
- container_only_migration
- storage_zfs_clone_copy
- unix_device_rename
- storage_lvm_use_thinpool
- storage_rsync_bwlimit
- network_vxlan_interface
- storage_btrfs_mount_options
- entity_description
- image_force_refresh
- storage_lvm_lv_resizing
- id_map_base
- file_symlinks
- container_push_target
- network_vlan_physical
- storage_images_delete
- container_edit_metadata
- container_snapshot_stateful_migration
- storage_driver_ceph
- storage_ceph_user_name
- resource_limits
- storage_volatile_initial_source
- storage_ceph_force_osd_reuse
- storage_block_filesystem_btrfs
- resources
- kernel_limits
- storage_api_volume_rename
- macaroon_authentication
- network_sriov
- console
- restrict_devlxd
- migration_pre_copy
- infiniband
- maas_network
- devlxd_events
- proxy
- network_dhcp_gateway
- file_get_symlink
- network_leases
- unix_device_hotplug
- storage_api_local_volume_handling
- operation_description
- clustering
- event_lifecycle
- storage_api_remote_volume_handling
- nvidia_runtime
- container_mount_propagation
- container_backup
- devlxd_images
- container_local_cross_pool_handling
- proxy_unix
- proxy_udp
- clustering_join
- proxy_tcp_udp_multi_port_handling
- network_state
- proxy_unix_dac_properties
- container_protection_delete
- unix_priv_drop
- pprof_http
- proxy_haproxy_protocol
- network_hwaddr
- proxy_nat
- network_nat_order
- container_full
- candid_authentication
- backup_compression
- candid_config
- nvidia_runtime_config
- storage_api_volume_snapshots
- storage_unmapped
- projects
- candid_config_key
- network_vxlan_ttl
- container_incremental_copy
- usb_optional_vendorid
- snapshot_scheduling
- snapshot_schedule_aliases
- container_copy_project
- clustering_server_address
- clustering_image_replication
- container_protection_shift
- snapshot_expiry
- container_backup_override_pool
- snapshot_expiry_creation
- network_leases_location
- resources_cpu_socket
- resources_gpu
- resources_numa
- kernel_features
- id_map_current
- event_location
- storage_api_remote_volume_snapshots
- network_nat_address
- container_nic_routes
- rbac
- cluster_internal_copy
- seccomp_notify
- lxc_features
- container_nic_ipvlan
- network_vlan_sriov
- storage_cephfs
- container_nic_ipfilter
- resources_v2
- container_exec_user_group_cwd
- container_syscall_intercept
- container_disk_shift
- storage_shifted
- resources_infiniband
- daemon_storage
- instances
- image_types
- resources_disk_sata
- clustering_roles
- images_expiry
- resources_network_firmware
- backup_compression_algorithm
- ceph_data_pool_name
- container_syscall_intercept_mount
- compression_squashfs
- container_raw_mount
- container_nic_routed
- container_syscall_intercept_mount_fuse
- container_disk_ceph
- virtual-machines
- image_profiles
- clustering_architecture
- resources_disk_id
- storage_lvm_stripes
- vm_boot_priority
- unix_hotplug_devices
- api_filtering
- instance_nic_network
- clustering_sizing
- firewall_driver
- projects_limits
- container_syscall_intercept_hugetlbfs
- limits_hugepages
- container_nic_routed_gateway
- projects_restrictions
- custom_volume_snapshot_expiry
- volume_snapshot_scheduling
- trust_ca_certificates
- snapshot_disk_usage
- clustering_edit_roles
- container_nic_routed_host_address
- container_nic_ipvlan_gateway
- resources_usb_pci
- resources_cpu_threads_numa
- resources_cpu_core_die
- api_os
- container_nic_routed_host_table
- container_nic_ipvlan_host_table
- container_nic_ipvlan_mode
- resources_system
- images_push_relay
- network_dns_search
- container_nic_routed_limits
- instance_nic_bridged_vlan
- network_state_bond_bridge
- usedby_consistency
- custom_block_volumes
- clustering_failure_domains
- resources_gpu_mdev
- console_vga_type
- projects_limits_disk
- network_type_macvlan
- network_type_sriov
- container_syscall_intercept_bpf_devices
- network_type_ovn
- projects_networks
- projects_networks_restricted_uplinks
- custom_volume_backup
- backup_override_name
- storage_rsync_compression
- network_type_physical
- network_ovn_external_subnets
- network_ovn_nat
- network_ovn_external_routes_remove
- tpm_device_type
- storage_zfs_clone_copy_rebase
- gpu_mdev
- resources_pci_iommu
- resources_network_usb
- resources_disk_address
- network_physical_ovn_ingress_mode
- network_ovn_dhcp
- network_physical_routes_anycast
- projects_limits_instances
- network_state_vlan
- instance_nic_bridged_port_isolation
- instance_bulk_state_change
- network_gvrp
- instance_pool_move
- gpu_sriov
- pci_device_type
- storage_volume_state
- network_acl
- migration_stateful
- disk_state_quota
- storage_ceph_features
- projects_compression
- projects_images_remote_cache_expiry
- certificate_project
- network_ovn_acl
- projects_images_auto_update
- projects_restricted_cluster_target
- images_default_architecture
- network_ovn_acl_defaults
- gpu_mig
- project_usage
- network_bridge_acl
- warnings
- projects_restricted_backups_and_snapshots
- clustering_join_token
- clustering_description
- server_trusted_proxy
- clustering_update_cert
- storage_api_project
- server_instance_driver_operational
- server_supported_storage_drivers
- event_lifecycle_requestor_address
- resources_gpu_usb
- clustering_evacuation
- network_ovn_nat_address
- network_bgp
- network_forward
- custom_volume_refresh
- network_counters_errors_dropped
- metrics
- image_source_project
- clustering_config
- network_peer
- linux_sysctl
- network_dns
- ovn_nic_acceleration
- certificate_self_renewal
- instance_project_move
- storage_volume_project_move
- cloud_init
- network_dns_nat
- database_leader
- instance_all_projects
- clustering_groups
- ceph_rbd_du
- instance_get_full
- qemu_metrics
- gpu_mig_uuid
- event_project
- clustering_evacuation_live
- instance_allow_inconsistent_copy
- network_state_ovn
- storage_volume_api_filtering
- image_restrictions
- storage_zfs_export
- network_dns_records
- storage_zfs_reserve_space
- network_acl_log
- storage_zfs_blocksize
- metrics_cpu_seconds
- instance_snapshot_never
- certificate_token
- instance_nic_routed_neighbor_probe
- event_hub
- agent_nic_config
- projects_restricted_intercept
- metrics_authentication
- images_target_project
- cluster_migration_inconsistent_copy
- cluster_ovn_chassis
- container_syscall_intercept_sched_setscheduler
- storage_lvm_thinpool_metadata_size
- storage_volume_state_total
- instance_file_head
- instances_nic_host_name
- image_copy_profile
- container_syscall_intercept_sysinfo
- clustering_evacuation_mode
- resources_pci_vpd
- qemu_raw_conf
- storage_cephfs_fscache
- network_load_balancer
- vsock_api
- instance_ready_state
- network_bgp_holdtime
- storage_volumes_all_projects
- metrics_memory_oom_total
- storage_buckets
- storage_buckets_create_credentials
- metrics_cpu_effective_total
- projects_networks_restricted_access
- storage_buckets_local
- loki
- acme
- internal_metrics
- cluster_join_token_expiry
- remote_token_expiry
- init_preseed
api_status: stable
api_version: "1.0"
auth: trusted
public: false
auth_methods:
- tls
environment:
  addresses: []
  architectures:
  - x86_64
  - i686
  certificate: |
    -----BEGIN CERTIFICATE-----
    [redacted]
    -----END CERTIFICATE-----
  certificate_fingerprint: [redacted]
  driver: qemu | lxc
  driver_version: 7.1.0 | 5.0.1
  firewall: xtables
  kernel: Linux
  kernel_architecture: x86_64
  kernel_features:
    idmapped_mounts: "true"
    netnsid_getifaddrs: "true"
    seccomp_listener: "true"
    seccomp_listener_continue: "true"
    shiftfs: "false"
    uevent_injection: "true"
    unpriv_fscaps: "true"
  kernel_version: 5.15.0-52-generic
  lxc_features:
    cgroup2: "true"
    core_scheduling: "true"
    devpts_fd: "true"
    idmapped_mounts_v2: "true"
    mount_injection_file: "true"
    network_gateway_device_route: "true"
    network_ipvlan: "true"
    network_l2proxy: "true"
    network_phys_macvlan_mtu: "true"
    network_veth_router: "true"
    pidfd: "true"
    seccomp_allow_deny_syntax: "true"
    seccomp_notify: "true"
    seccomp_proxy_send_notify_fd: "true"
  os_name: Ubuntu
  os_version: "20.04"
  project: default
  server: lxd
  server_clustered: false
  server_event_mode: full-mesh
  server_name: server
  server_pid: 3172010
  server_version: "5.7"
  storage: zfs
  storage_version: 2.1.4-0ubuntu0.1
  storage_supported_drivers:
  - name: cephobject
    version: 15.2.16
    remote: true
  - name: dir
    version: "1"
    remote: false
  - name: lvm
    version: 2.03.07(2) (2019-11-30) / 1.02.167 (2019-11-30) / 4.45.0
    remote: false
  - name: zfs
    version: 2.1.4-0ubuntu0.1
    remote: false
  - name: btrfs
    version: 5.4.1
    remote: false
  - name: ceph
    version: 15.2.16
    remote: true
  - name: cephfs
    version: 15.2.16
    remote: true
#7

@tomp please help …

#8

As you’re running 22.04, you’re kernel will be 5.15, and you’re running on ZFS, meaning idmapped mounts are not available, which means you’re likely using shiftfs and could be being affected by:

Can you try this: