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Installed container missing parent layers

The POC involves building the enclosed pyhelloworld container, based on Fedora 30. One would need a Fedora 30 RPM installed as a dependency to install the pyhelloworld container. Thus a common base image RPM could provide the common layers for any other containers that share that base image, keeping RPM sizes minimal.

This is achieved by some fuckery. The present approach exports a container image using skopeo into a dir: and modifies the exported artifacts - the base image layers are removed from the manifest and deleted from the export. The configuration JSON file is not altered.

Once converted to RPMs and installed, the metadata for the pyhelloworld container looks correct; it includes the references to the image layers for the base OS image. But when instantiated into a container and run, those layers are not present.

Demonstration

[root@localhost ~]# rpm -ql fedora-ubi
/var/cosplay/fedora-30
/var/cosplay/fedora-30/4650c04b851c62897e9c02c6041a0e3127f8253fafa3a09642552a8e77c044c8
/var/cosplay/fedora-30/9754ce14641df7f1f3751d21e14b3037dce7dca2472cf4cdff38d96891703453
/var/cosplay/fedora-30/manifest.json
/var/cosplay/fedora-30/version
[root@localhost ~]# rpm -ql pyhelloworld
/usr/lib/systemd/system/pyhelloworld.service
/var/cosplay/pyhelloworld-1
/var/cosplay/pyhelloworld-1/245fd514e05713512bfac35a81527dbf308d95e78a42e30bcf9530c4199723c8
/var/cosplay/pyhelloworld-1/74b4c93c7a86e966ea2176cb764a6527556347f722b5c69e71f48dc093593c75
/var/cosplay/pyhelloworld-1/7720c1d3f2384b664b1d2e2161dfb98bdbd1ea3252478d607673281a2561a15a
/var/cosplay/pyhelloworld-1/9d9b8a4743a397399adf8ac389750541b39bb38be4bbb000910998ec6ee6f780
/var/cosplay/pyhelloworld-1/manifest.json
/var/cosplay/pyhelloworld-1/version

The Fedora 30 package contains the layer beginning with 4650c0.

[root@localhost ~]# podman inspect fedora:30
[
    {
        "Id": "9754ce14641df7f1f3751d21e14b3037dce7dca2472cf4cdff38d96891703453",
        "Digest": "sha256:c61a5c483e454a4c5585e57304be3cb4ee25302a7336e83cde00c51aef142a27",
        "RepoTags": [
            "docker.io/library/fedora:30"
        ],
        "RepoDigests": [
            "docker.io/library/fedora@sha256:c61a5c483e454a4c5585e57304be3cb4ee25302a7336e83cde00c51aef142a27"
        ],
        "Parent": "",
        "Comment": "",
        "Created": "2019-04-24T21:20:42.215534802Z",
        "Config": {
            "Env": [
                "PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin",
                "DISTTAG=f30container",
                "FGC=f30",
                "FBR=f30"
            ],
            "Cmd": [
                "/bin/bash"
            ],
            "Labels": {
                "maintainer": "Clement Verna <[email protected]>"
            }
        },
        "Version": "18.06.1-ce",
        "Author": "",
        "Architecture": "amd64",
        "Os": "linux",
        "Size": 311479633,
        "VirtualSize": 311479633,
        "GraphDriver": {
            "Name": "overlay",
            "Data": {
                "MergedDir": "/var/lib/containers/storage/overlay/4650c04b851c62897e9c02c6041a0e3127f8253fafa3a09642552a8e77c044c8/merged",
                "UpperDir": "/var/lib/containers/storage/overlay/4650c04b851c62897e9c02c6041a0e3127f8253fafa3a09642552a8e77c044c8/diff",
                "WorkDir": "/var/lib/containers/storage/overlay/4650c04b851c62897e9c02c6041a0e3127f8253fafa3a09642552a8e77c044c8/work"
            }
        },
        "RootFS": {
            "Type": "layers",
            "Layers": [
                "sha256:4650c04b851c62897e9c02c6041a0e3127f8253fafa3a09642552a8e77c044c8"
            ]
        },
        "Labels": {
            "maintainer": "Clement Verna <[email protected]>"
        },
        "Annotations": {},
        "ManifestType": "application/vnd.docker.distribution.manifest.v2+json",
        "User": "",
        "History": [
            {
                "created": "2019-01-16T21:21:55.569693599Z",
                "created_by": "/bin/sh -c #(nop)  LABEL maintainer=Clement Verna <[email protected]>",
                "empty_layer": true
            },
            {
                "created": "2019-01-16T21:21:55.720736034Z",
                "created_by": "/bin/sh -c #(nop)  ENV DISTTAG=f30container FGC=f30 FBR=f30",
                "empty_layer": true
            },
            {
                "created": "2019-04-24T21:20:41.816382191Z",
                "created_by": "/bin/sh -c #(nop) ADD file:8fc6644a6befc976a9195c1535d32a79c61dc66fb75efa6f10b7aa8eaf4b8eee in / "
            },
            {
                "created": "2019-04-24T21:20:42.215534802Z",
                "created_by": "/bin/sh -c #(nop)  CMD [\"/bin/bash\"]",
                "empty_layer": true
            }
        ]
    }
]

... which matches the RootFS layer with the same hash, 4650c0. 311MB is the correct size.

[root@localhost ~]# podman inspect pyhelloworld:1
[
    {
        "Id": "9d9b8a4743a397399adf8ac389750541b39bb38be4bbb000910998ec6ee6f780",
        "Digest": "sha256:d6855a6bf6acd92322e44bae75e8a0f26e9b36dd3c2889e5d5bd5e66429105f9",
        "RepoTags": [
            "docker.io/library/pyhelloworld:1"
        ],
        "RepoDigests": [
            "docker.io/library/pyhelloworld@sha256:d6855a6bf6acd92322e44bae75e8a0f26e9b36dd3c2889e5d5bd5e66429105f9"
        ],
        "Parent": "",
        "Comment": "",
        "Created": "2019-06-03T03:19:55.079003215Z",
        "Config": {
            "ExposedPorts": {
                "8080/tcp": {}
            },
            "Env": [
                "PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin",
                "DISTTAG=f30container",
                "FGC=f30",
                "FBR=f30"
            ],
            "Cmd": [
                "/usr/bin/python3",
                "/src/index.py"
            ],
            "Labels": {
                "maintainer": "Clement Verna <[email protected]>"
            }
        },
        "Version": "",
        "Author": "",
        "Architecture": "amd64",
        "Os": "linux",
        "Size": 6800015,
        "VirtualSize": 6800015,
        "GraphDriver": {
            "Name": "overlay",
            "Data": {
                "LowerDir": "/var/lib/containers/storage/overlay/65f110ce9db37a3439692752c1a35b2ade7bfb0f9efb20a30c049949c8064dea/diff:/var/lib/containers/storage/overlay/74b4c93c7a86e966ea2176cb764a6527556347f722b5c69e71f48dc093593c75/diff",
                "MergedDir": "/var/lib/containers/storage/overlay/1bc65ae24f89b417eef5ed9dc565d4d58d0453d98d8fc132b1614243daf985f4/merged",
                "UpperDir": "/var/lib/containers/storage/overlay/1bc65ae24f89b417eef5ed9dc565d4d58d0453d98d8fc132b1614243daf985f4/diff",
                "WorkDir": "/var/lib/containers/storage/overlay/1bc65ae24f89b417eef5ed9dc565d4d58d0453d98d8fc132b1614243daf985f4/work"
            }
        },
        "RootFS": {
            "Type": "layers",
            "Layers": [
                "sha256:4650c04b851c62897e9c02c6041a0e3127f8253fafa3a09642552a8e77c044c8",
                "sha256:74b4c93c7a86e966ea2176cb764a6527556347f722b5c69e71f48dc093593c75",
                "sha256:7720c1d3f2384b664b1d2e2161dfb98bdbd1ea3252478d607673281a2561a15a",
                "sha256:245fd514e05713512bfac35a81527dbf308d95e78a42e30bcf9530c4199723c8"
            ]
        },
        "Labels": {
            "maintainer": "Clement Verna <[email protected]>"
        },
        "Annotations": {},
        "ManifestType": "application/vnd.oci.image.manifest.v1+json",
        "User": "",
        "History": [
            {
                "created": "2019-01-16T21:21:55.569693599Z",
                "created_by": "/bin/sh -c #(nop)  LABEL maintainer=Clement Verna <[email protected]>",
                "empty_layer": true
            },
            {
                "created": "2019-01-16T21:21:55.720736034Z",
                "created_by": "/bin/sh -c #(nop)  ENV DISTTAG=f30container FGC=f30 FBR=f30",
                "empty_layer": true
            },
            {
                "created": "2019-04-24T21:20:41.816382191Z",
                "created_by": "/bin/sh -c #(nop) ADD file:8fc6644a6befc976a9195c1535d32a79c61dc66fb75efa6f10b7aa8eaf4b8eee in / "
            },
            {
                "created": "2019-04-24T21:20:42.215534802Z",
                "created_by": "/bin/sh -c #(nop)  CMD [\"/bin/bash\"]",
                "empty_layer": true
            },
            {
                "created": "2019-06-03T03:19:50.166665037Z",
                "created_by": "/bin/sh -c dnf -y install python3-pip && dnf clean all"
            },
            {
                "created": "2019-06-03T03:19:51.343040228Z",
                "created_by": "/bin/sh -c #(nop) ADD . /src"
            },
            {
                "created": "2019-06-03T03:19:53.295833398Z",
                "created_by": "/bin/sh -c cd /src; pip3 install -r requirements.txt"
            },
            {
                "created": "2019-06-03T03:19:54.238291689Z",
                "created_by": "/bin/sh -c #(nop) EXPOSE 8080",
                "empty_layer": true
            },
            {
                "created": "2019-06-03T03:19:55.079003215Z",
                "created_by": "/bin/sh -c #(nop) CMD [\"/usr/bin/python3\", \"/src/index.py\"]",
                "empty_layer": true
            }
        ]
    }
]

The pyhelloworld image has the same layer as its first in the RootFS section. That's good. However, when we try to run the pyhelloworld image, it fails:

[root@localhost ~]# podman run -it --rm=true pyhelloworld:1
Error: container create failed: time="2019-06-04T10:48:23-04:00" level=error msg="container_linux.go:346: starting container process caused \"exec: \\\"/usr/bin/python3\\\": stat /usr/bin/python3: no such file or directory\"\n"
container_linux.go:346: starting container process caused "exec: \"/usr/bin/python3\": stat /usr/bin/python3: no such file or directory"
: internal libpod error

And if we unpack the image using buildah, we find that the base Fedora layer doesn't appear to be a part of what ultimately exists.

[root@localhost ~]$ buildah mount 28
/var/lib/containers/storage/overlay/e652966800a6ed036e92bd93162269c355ddc00edd2398cabab2d9f1a9e8576f/merged
[root@localhost ~]# cd /var/lib/containers/storage/overlay/e652966800a6ed036e92bd93162269c355ddc00edd2398cabab2d9f1a9e8576f/merged
[root@localhost merged]# ls -la
total 0
drwxr-xr-x. 1 root root  62 Jun  2 23:23 .
drwx------. 5 root root  69 Jun  2 23:23 ..
drwxr-xr-x. 2 root root   6 Jun  2 23:23 dev
drwxr-xr-x. 2 root root  54 Jun  2 23:23 etc
drwxr-xr-x. 2 root root   6 Jun  2 23:23 proc
dr-xr-x---. 3 root root  20 Jun  2 23:19 root
drwxr-xr-x. 1 root root  27 Jun  2 23:23 run
drwxr-xr-x. 3 root root 101 Jun  2 23:19 src
drwxr-xr-x. 2 root root   6 Jun  2 23:23 sys
drwxrwxrwt. 1 root root   6 Jun  2 23:19 tmp
drwxr-xr-x. 5 root root  41 Apr 22 15:48 var
[root@localhost merged]# ls usr
ls: cannot access 'usr': No such file or directory
[root@localhost merged]# find .
.
./run
./run/secrets
./run/.containerenv
./tmp
./var
./var/cache
./var/cache/dnf
./var/cache/dnf/.gpgkeyschecked.yum
./var/cache/dnf/expired_repos.json
./var/cache/dnf/fedora-a924e206df91842b
./var/cache/dnf/fedora-a924e206df91842b/repodata
./var/cache/dnf/fedora-modular-ad2f02cac192e3ec
./var/cache/dnf/fedora-modular-ad2f02cac192e3ec/repodata
./var/cache/dnf/fedora-modular-ad2f02cac192e3ec/repodata/2dc47974b6a0fa76e1dc78c7b091b34b5d6dc986519824642401b6cf341446eb-modules.yaml.gz
./var/cache/dnf/updates-d6521d96a82a4d6a
./var/cache/dnf/updates-d6521d96a82a4d6a/repodata
./var/cache/dnf/updates-modular-783da5de2e38c644
./var/cache/dnf/updates-modular-783da5de2e38c644/repodata
./var/cache/dnf/updates-modular-783da5de2e38c644/repodata/5c8855cb9efca1165c075208af7c6d4b8f97fd63f3f31dcdd2f48522310a31ca-modules.yaml.gz
./var/lib
./var/lib/dnf
./var/lib/dnf/history.sqlite
./var/lib/dnf/history.sqlite-shm
./var/lib/dnf/history.sqlite-wal
./var/lib/rpm
./var/lib/rpm/.dbenv.lock
./var/lib/rpm/Group
./var/lib/rpm/Installtid
./var/lib/rpm/Name
./var/lib/rpm/Providename
./var/lib/rpm/Sha1header
./var/lib/rpm/__db.001
./var/lib/rpm/__db.002
./var/lib/rpm/__db.003
./var/log
./var/log/dnf.librepo.log
./var/log/dnf.log
./var/log/dnf.rpm.log
./var/log/hawkey.log
./proc
./dev
./sys
./etc
./etc/hostname
./etc/resolv.conf
./etc/hosts
./root
./root/.cache
./root/.cache/pip
./root/.cache/pip/http
./root/.cache/pip/http/a
./root/.cache/pip/http/a/1
./root/.cache/pip/http/a/1/9
./root/.cache/pip/http/a/1/9/5
./root/.cache/pip/http/a/1/9/5/3
./root/.cache/pip/http/a/1/9/5/3/a19537d3cf37c122db841d6fe4cd322bc10d1a558bb00d146b85cb9a
./root/.cache/pip/selfcheck.json
./src
./src/Dockerfile
./src/index.py
./src/pyhelloworld.spec
./src/requirements.txt

How to reproduce

All of the below commands should be run as root.

  1. Pull the latest fedora:30 image.
  2. Build the fedora-ubi package using: python3 cosplay.py --base scratch --no-service docker.io/library/fedora:30
  3. Build the pyhelloworld container using podman build --tag pyhelloworld:1 . from the pyhelloworld/ directory.
  4. Build the pyhelloworld package using python3 cosplay.py --base docker.io/library/fedora:30 --ports 8080 localhost/pyhelloworld:1
  5. Either copy the RPMs from /root/rpmbuild/RPMS/x86_64 to a fresh system or remove the fedora:30 and pyhelloworld:1 images using podman rmi.
  6. Install the fedora-ubi RPM and then the pyhelloworld RPM.

You now can reproduce the steps above.

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