overlayfs fails to run container with a strange file checksum error #10180

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tatsuya6502 opened this Issue Jan 19, 2015 · 76 comments

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@tatsuya6502

I started to use "overlay" driver today and seeing odd behaviors in my containers (CentOS 6).

  1. yum install <pkg> in Dockerfile always fails, but running it again in the same container always succeeds.
  2. tail -f <file> doesn't show appended contents

For 1, this simple Dockerfile always fails at second yum install (for perl)

FROM centos:centos6

RUN yum install -y sudo
RUN yum install -y perl

with this error:

Step 2 : RUN yum install -y perl
 ---> Running in 21669e152088
...
Rpmdb checksum is invalid: dCDPT(pkg checksums): perl-version.x86_64 3:0.77-136.el6_6.1 - u

INFO[0018] The command [/bin/sh -c yum install -y perl] returned a non-zero code: 1

However, running the same command twice in the same container always succeeds.

FROM centos:centos6

RUN yum install -y sudo 
RUN (yum install -y perl || yum install -y perl)
Step 2 : RUN (yum install -y perl || yum install -y perl)
 ---> Running in 5bf1177b4437
...

Rpmdb checksum is invalid: dCDPT(pkg checksums): perl-version.x86_64 3:0.77-136.el6_6.1 - u
  Installing : 4:perl-5.10.1-136.el6_6.1.x86_64                             6/6
Loaded plugins: fastestmirror
Setting up Install Process
Loading mirror speeds from cached hostfile
 * base: mirror.vastspace.net
 * extras: mirror.vastspace.net
 * updates: mirror.vastspace.net
Package 4:perl-5.10.1-136.el6_6.1.x86_64 already installed and latest version
Nothing to do
 ---> 2671034175e9
Removing intermediate container 5bf1177b4437
Successfully built 2671034175e9

Even though I change perl to something else, I get the same behavior.

For 2, I noticed that doing tail -f <application.log> first shows last 10 lines of the log file, then it doesn't show any appended contents. If I press Ctrl+C and redo, it will show the most recent contents.

I have only tried the official centos:centos6 image so far, and the above behavior is 100% reproducible. I didn't try other images.

Docker Host:

CoreOS latest alpha with ext4 root file system and "overlay" driver. I'm running it on EC2, and recreated it once but the problem persists.

core@core-01 ~ $ cat /etc/os-release
NAME=CoreOS
ID=coreos
VERSION=561.0.0
VERSION_ID=561.0.0
BUILD_ID=
PRETTY_NAME="CoreOS 561.0.0"
ANSI_COLOR="1;32"
HOME_URL="https://coreos.com/"
BUG_REPORT_URL="https://github.com/coreos/bugs/issues"

Docker Version and Info:

core@core-01 ~ $ docker --version
Docker version 1.4.1, build 5bc2ff8-dirty

core@core-01 ~ $ docker info
Containers: 1
Images: 4
Storage Driver: overlay
Execution Driver: native-0.2
Kernel Version: 3.18.2
Operating System: CoreOS 561.0.0
CPUs: 1
Total Memory: 3.68 GiB
Name: core-01
ID: TM2L:NIZI:CUGT:EUKX:ACP3:EOFX:YQVR:CTL7:R7L2:ILQF:6E3H:HAHQ

Kernel Config:

core@core-01 ~ $ wget https://raw.githubusercontent.com/docker/docker/master/contrib/check-config.sh
...
2015-01-19 11:09:00 (133 MB/s) - 'check-config.sh' saved [4476/4476]

core@core-01 ~ $ chmod a+x check-config.sh
core@core-01 ~ $ ./check-config.sh
info: reading kernel config from /proc/config.gz ...

Generally Necessary:
- cgroup hierarchy: properly mounted [/sys/fs/cgroup]
- CONFIG_NAMESPACES: enabled
- CONFIG_NET_NS: enabled
- CONFIG_PID_NS: enabled
- CONFIG_IPC_NS: enabled
- CONFIG_UTS_NS: enabled
- CONFIG_DEVPTS_MULTIPLE_INSTANCES: enabled
- CONFIG_CGROUPS: enabled
- CONFIG_CGROUP_CPUACCT: enabled
- CONFIG_CGROUP_DEVICE: enabled
- CONFIG_CGROUP_FREEZER: enabled
- CONFIG_CGROUP_SCHED: enabled
- CONFIG_MACVLAN: enabled
- CONFIG_VETH: enabled
- CONFIG_BRIDGE: enabled
- CONFIG_NF_NAT_IPV4: enabled
- CONFIG_IP_NF_FILTER: enabled
- CONFIG_IP_NF_TARGET_MASQUERADE: enabled
- CONFIG_NETFILTER_XT_MATCH_ADDRTYPE: enabled
- CONFIG_NETFILTER_XT_MATCH_CONNTRACK: enabled
- CONFIG_NF_NAT: enabled
- CONFIG_NF_NAT_NEEDED: enabled
- CONFIG_POSIX_MQUEUE: enabled

Optional Features:
- CONFIG_MEMCG_SWAP: enabled
- CONFIG_RESOURCE_COUNTERS: enabled
- CONFIG_CGROUP_PERF: enabled
- Storage Drivers:
  - "aufs":
    - CONFIG_AUFS_FS: missing
    - CONFIG_EXT4_FS_POSIX_ACL: enabled
    - CONFIG_EXT4_FS_SECURITY: enabled
  - "btrfs":
    - CONFIG_BTRFS_FS: enabled
  - "devicemapper":
    - CONFIG_BLK_DEV_DM: enabled
    - CONFIG_DM_THIN_PROVISIONING: enabled
    - CONFIG_EXT4_FS: enabled
    - CONFIG_EXT4_FS_POSIX_ACL: enabled
    - CONFIG_EXT4_FS_SECURITY: enabled
  - "overlay":
    - CONFIG_OVERLAY_FS: enabled
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jessfraz Jan 19, 2015

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I was under the impression coreos used btrfs as the backing filesystem.

On Mon, Jan 19, 2015 at 3:16 AM, Tatsuya Kawano notifications@github.com
wrote:

I started to use "overlay" driver today and seeing odd behaviors in my
containers (CentOS 6).

  1. yum install in Dockerfile always fails, but running it again in the
    same container always succeeds.
  2. tail -f doesn't show appended contents

For 1, this simple Dockerfile always fails at second yum install (for
perl)

FROM centos:centos6

RUN yum install -y sudo
RUN yum install -y perl

with this error:

Step 2 : RUN yum install -y perl
---> Running in 21669e152088
...
Rpmdb checksum is invalid: dCDPT(pkg checksums): perl-version.x86_64 3:0.77-136.el6_6.1 - u

INFO[0018] The command [/bin/sh -c yum install -y perl] returned a non-zero code: 1

However, running the same command twice in the same container always
succeeds.

FROM centos:centos6

RUN yum install -y sudo
RUN (yum install -y perl || yum install -y perl)

Step 2 : RUN (yum install -y perl || yum install -y perl)
---> Running in 5bf1177b4437
...

Rpmdb checksum is invalid: dCDPT(pkg checksums): perl-version.x86_64 3:0.77-136.el6_6.1 - u
Installing : 4:perl-5.10.1-136.el6_6.1.x86_64 6/6
Loaded plugins: fastestmirror
Setting up Install Process
Loading mirror speeds from cached hostfile

  • base: mirror.vastspace.net
  • extras: mirror.vastspace.net
  • updates: mirror.vastspace.net
    Package 4:perl-5.10.1-136.el6_6.1.x86_64 already installed and latest version
    Nothing to do
    ---> 2671034175e9
    Removing intermediate container 5bf1177b4437
    Successfully built 2671034175e9

Even though I change perl to something else, I get the same behavior.

For 2, I noticed that doing tail -f <application.log> first shows last 10
lines of the log file, then it doesn't show any appended contents. If I
press Ctrl+C and redo, it will show the most recent contents.

I have only tried the official centos:centos6 image so far, and the above
behavior is 100% reproducible. I didn't try other images.

Docker Host:

CoreOS latest alpha with ext4 root file system and "overlay" driver. I'm
running it on EC2, and recreated it once but the problem persists.

core@core-01 ~ $ cat /etc/os-release
NAME=CoreOS
ID=coreos
VERSION=561.0.0
VERSION_ID=561.0.0
BUILD_ID=
PRETTY_NAME="CoreOS 561.0.0"
ANSI_COLOR="1;32"
HOME_URL="https://coreos.com/"
BUG_REPORT_URL="https://github.com/coreos/bugs/issues"

Docker Version and Info:

core@core-01 ~ $ docker --version
Docker version 1.4.1, build 5bc2ff8-dirty

core@core-01 ~ $ docker info
Containers: 1
Images: 4
Storage Driver: overlay
Execution Driver: native-0.2
Kernel Version: 3.18.2
Operating System: CoreOS 561.0.0
CPUs: 1
Total Memory: 3.68 GiB
Name: core-01
ID: TM2L:NIZI:CUGT:EUKX:ACP3:EOFX:YQVR:CTL7:R7L2:ILQF:6E3H:HAHQ

Kernel Config:

core@core-01 ~ $ wget https://raw.githubusercontent.com/docker/docker/master/contrib/check-config.sh
...
2015-01-19 11:09:00 (133 MB/s) - 'check-config.sh' saved [4476/4476]

core@core-01 ~ $ chmod a+x check-config.sh
core@core-01 ~ $ ./check-config.sh
info: reading kernel config from /proc/config.gz ...

Generally Necessary:

  • cgroup hierarchy: properly mounted [/sys/fs/cgroup]
  • CONFIG_NAMESPACES: enabled
  • CONFIG_NET_NS: enabled
  • CONFIG_PID_NS: enabled
  • CONFIG_IPC_NS: enabled
  • CONFIG_UTS_NS: enabled
  • CONFIG_DEVPTS_MULTIPLE_INSTANCES: enabled
  • CONFIG_CGROUPS: enabled
  • CONFIG_CGROUP_CPUACCT: enabled
  • CONFIG_CGROUP_DEVICE: enabled
  • CONFIG_CGROUP_FREEZER: enabled
  • CONFIG_CGROUP_SCHED: enabled
  • CONFIG_MACVLAN: enabled
  • CONFIG_VETH: enabled
  • CONFIG_BRIDGE: enabled
  • CONFIG_NF_NAT_IPV4: enabled
  • CONFIG_IP_NF_FILTER: enabled
  • CONFIG_IP_NF_TARGET_MASQUERADE: enabled
  • CONFIG_NETFILTER_XT_MATCH_ADDRTYPE: enabled
  • CONFIG_NETFILTER_XT_MATCH_CONNTRACK: enabled
  • CONFIG_NF_NAT: enabled
  • CONFIG_NF_NAT_NEEDED: enabled
  • CONFIG_POSIX_MQUEUE: enabled

Optional Features:

  • CONFIG_MEMCG_SWAP: enabled
  • CONFIG_RESOURCE_COUNTERS: enabled
  • CONFIG_CGROUP_PERF: enabled
  • Storage Drivers:
    • "aufs":
      • CONFIG_AUFS_FS: missing
      • CONFIG_EXT4_FS_POSIX_ACL: enabled
      • CONFIG_EXT4_FS_SECURITY: enabled
    • "btrfs":
      • CONFIG_BTRFS_FS: enabled
    • "devicemapper":
      • CONFIG_BLK_DEV_DM: enabled
      • CONFIG_DM_THIN_PROVISIONING: enabled
      • CONFIG_EXT4_FS: enabled
      • CONFIG_EXT4_FS_POSIX_ACL: enabled
      • CONFIG_EXT4_FS_SECURITY: enabled
    • "overlay":
      • CONFIG_OVERLAY_FS: enabled


Reply to this email directly or view it on GitHub
docker#10180.

Contributor

jessfraz commented Jan 19, 2015

I was under the impression coreos used btrfs as the backing filesystem.

On Mon, Jan 19, 2015 at 3:16 AM, Tatsuya Kawano notifications@github.com
wrote:

I started to use "overlay" driver today and seeing odd behaviors in my
containers (CentOS 6).

  1. yum install in Dockerfile always fails, but running it again in the
    same container always succeeds.
  2. tail -f doesn't show appended contents

For 1, this simple Dockerfile always fails at second yum install (for
perl)

FROM centos:centos6

RUN yum install -y sudo
RUN yum install -y perl

with this error:

Step 2 : RUN yum install -y perl
---> Running in 21669e152088
...
Rpmdb checksum is invalid: dCDPT(pkg checksums): perl-version.x86_64 3:0.77-136.el6_6.1 - u

INFO[0018] The command [/bin/sh -c yum install -y perl] returned a non-zero code: 1

However, running the same command twice in the same container always
succeeds.

FROM centos:centos6

RUN yum install -y sudo
RUN (yum install -y perl || yum install -y perl)

Step 2 : RUN (yum install -y perl || yum install -y perl)
---> Running in 5bf1177b4437
...

Rpmdb checksum is invalid: dCDPT(pkg checksums): perl-version.x86_64 3:0.77-136.el6_6.1 - u
Installing : 4:perl-5.10.1-136.el6_6.1.x86_64 6/6
Loaded plugins: fastestmirror
Setting up Install Process
Loading mirror speeds from cached hostfile

  • base: mirror.vastspace.net
  • extras: mirror.vastspace.net
  • updates: mirror.vastspace.net
    Package 4:perl-5.10.1-136.el6_6.1.x86_64 already installed and latest version
    Nothing to do
    ---> 2671034175e9
    Removing intermediate container 5bf1177b4437
    Successfully built 2671034175e9

Even though I change perl to something else, I get the same behavior.

For 2, I noticed that doing tail -f <application.log> first shows last 10
lines of the log file, then it doesn't show any appended contents. If I
press Ctrl+C and redo, it will show the most recent contents.

I have only tried the official centos:centos6 image so far, and the above
behavior is 100% reproducible. I didn't try other images.

Docker Host:

CoreOS latest alpha with ext4 root file system and "overlay" driver. I'm
running it on EC2, and recreated it once but the problem persists.

core@core-01 ~ $ cat /etc/os-release
NAME=CoreOS
ID=coreos
VERSION=561.0.0
VERSION_ID=561.0.0
BUILD_ID=
PRETTY_NAME="CoreOS 561.0.0"
ANSI_COLOR="1;32"
HOME_URL="https://coreos.com/"
BUG_REPORT_URL="https://github.com/coreos/bugs/issues"

Docker Version and Info:

core@core-01 ~ $ docker --version
Docker version 1.4.1, build 5bc2ff8-dirty

core@core-01 ~ $ docker info
Containers: 1
Images: 4
Storage Driver: overlay
Execution Driver: native-0.2
Kernel Version: 3.18.2
Operating System: CoreOS 561.0.0
CPUs: 1
Total Memory: 3.68 GiB
Name: core-01
ID: TM2L:NIZI:CUGT:EUKX:ACP3:EOFX:YQVR:CTL7:R7L2:ILQF:6E3H:HAHQ

Kernel Config:

core@core-01 ~ $ wget https://raw.githubusercontent.com/docker/docker/master/contrib/check-config.sh
...
2015-01-19 11:09:00 (133 MB/s) - 'check-config.sh' saved [4476/4476]

core@core-01 ~ $ chmod a+x check-config.sh
core@core-01 ~ $ ./check-config.sh
info: reading kernel config from /proc/config.gz ...

Generally Necessary:

  • cgroup hierarchy: properly mounted [/sys/fs/cgroup]
  • CONFIG_NAMESPACES: enabled
  • CONFIG_NET_NS: enabled
  • CONFIG_PID_NS: enabled
  • CONFIG_IPC_NS: enabled
  • CONFIG_UTS_NS: enabled
  • CONFIG_DEVPTS_MULTIPLE_INSTANCES: enabled
  • CONFIG_CGROUPS: enabled
  • CONFIG_CGROUP_CPUACCT: enabled
  • CONFIG_CGROUP_DEVICE: enabled
  • CONFIG_CGROUP_FREEZER: enabled
  • CONFIG_CGROUP_SCHED: enabled
  • CONFIG_MACVLAN: enabled
  • CONFIG_VETH: enabled
  • CONFIG_BRIDGE: enabled
  • CONFIG_NF_NAT_IPV4: enabled
  • CONFIG_IP_NF_FILTER: enabled
  • CONFIG_IP_NF_TARGET_MASQUERADE: enabled
  • CONFIG_NETFILTER_XT_MATCH_ADDRTYPE: enabled
  • CONFIG_NETFILTER_XT_MATCH_CONNTRACK: enabled
  • CONFIG_NF_NAT: enabled
  • CONFIG_NF_NAT_NEEDED: enabled
  • CONFIG_POSIX_MQUEUE: enabled

Optional Features:

  • CONFIG_MEMCG_SWAP: enabled
  • CONFIG_RESOURCE_COUNTERS: enabled
  • CONFIG_CGROUP_PERF: enabled
  • Storage Drivers:
    • "aufs":
      • CONFIG_AUFS_FS: missing
      • CONFIG_EXT4_FS_POSIX_ACL: enabled
      • CONFIG_EXT4_FS_SECURITY: enabled
    • "btrfs":
      • CONFIG_BTRFS_FS: enabled
    • "devicemapper":
      • CONFIG_BLK_DEV_DM: enabled
      • CONFIG_DM_THIN_PROVISIONING: enabled
      • CONFIG_EXT4_FS: enabled
      • CONFIG_EXT4_FS_POSIX_ACL: enabled
      • CONFIG_EXT4_FS_SECURITY: enabled
    • "overlay":
      • CONFIG_OVERLAY_FS: enabled


Reply to this email directly or view it on GitHub
docker#10180.

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unclejack Jan 19, 2015

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Overlay is currently experimental and not officially supported.

CentOS 6.x has user space tooling and configuration that's only supported with the provided kernel, 2.6.32. We can't provide support for custom kernels on this distribution - nor on RHEL or any other RHEL/CentOS derived distribution.

Please take a look at these comments for more information:
comment from me on the matter: docker#9696 (comment)
official comment from jperrin who works on CentOS: docker#9696 (comment)

Overlay has some known problems and I wouldn't be surprised to track down these problems to the following overlay related problems:
docker#9572
docker#9874
docker#10169

I'm going to close this issue now because 1) we're tracking overlay issues in multiple other issues already 2) this overlay problem is reported on an unsupported setup - CentOS 6 with custom kernel

Debian jessie with kernel 3.18.x, Ubuntu 14.04/14.10 with kernel 3.18.x and Fedora with kernel 3.18.x would be better setups for testing overlay.

Contributor

unclejack commented Jan 19, 2015

Overlay is currently experimental and not officially supported.

CentOS 6.x has user space tooling and configuration that's only supported with the provided kernel, 2.6.32. We can't provide support for custom kernels on this distribution - nor on RHEL or any other RHEL/CentOS derived distribution.

Please take a look at these comments for more information:
comment from me on the matter: docker#9696 (comment)
official comment from jperrin who works on CentOS: docker#9696 (comment)

Overlay has some known problems and I wouldn't be surprised to track down these problems to the following overlay related problems:
docker#9572
docker#9874
docker#10169

I'm going to close this issue now because 1) we're tracking overlay issues in multiple other issues already 2) this overlay problem is reported on an unsupported setup - CentOS 6 with custom kernel

Debian jessie with kernel 3.18.x, Ubuntu 14.04/14.10 with kernel 3.18.x and Fedora with kernel 3.18.x would be better setups for testing overlay.

@unclejack unclejack closed this Jan 19, 2015

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tatsuya6502 Jan 19, 2015

I was under the impression coreos used btrfs as the backing filesystem.

Here is the release notes of the CoreOS release I'm using.

Release notes: https://coreos.com/releases/#561.0.0

  • Linux 3.18.2
  • Switch to ext4 as the default root filesystem. Existing systems using btrfs are unaffected.

More info will be found here.

CoreOS looks to move from Btrfs to overlayfs

I was under the impression coreos used btrfs as the backing filesystem.

Here is the release notes of the CoreOS release I'm using.

Release notes: https://coreos.com/releases/#561.0.0

  • Linux 3.18.2
  • Switch to ext4 as the default root filesystem. Existing systems using btrfs are unaffected.

More info will be found here.

CoreOS looks to move from Btrfs to overlayfs

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unclejack Jan 19, 2015

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@tatsuya6502 I apologize, I was under the impression you're on CentOS.

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unclejack commented Jan 19, 2015

@tatsuya6502 I apologize, I was under the impression you're on CentOS.

@unclejack unclejack reopened this Jan 19, 2015

@jessfraz jessfraz changed the title from CentOS 6 on docker + overlayfs fails to run yum install with a strange file checksum error to docker + overlayfs fails to run container with a strange file checksum error Jan 19, 2015

@jessfraz jessfraz changed the title from docker + overlayfs fails to run container with a strange file checksum error to overlayfs fails to run container with a strange file checksum error Jan 19, 2015

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tatsuya6502 Jan 19, 2015

@unclejack That's ok. I think the issue title I put was confusing.

@unclejack That's ok. I think the issue title I put was confusing.

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jessfraz Jan 19, 2015

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So overlay is currently an experimental graphdriver, there are some known issues with tests failing we are working on see #9874.
I wonder if this has anything to do with those.

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jessfraz commented Jan 19, 2015

So overlay is currently an experimental graphdriver, there are some known issues with tests failing we are working on see #9874.
I wonder if this has anything to do with those.

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tatsuya6502 Jan 19, 2015

@unclejack btw, thanks for the pointers for these issues. I'll take a look.

@unclejack btw, thanks for the pointers for these issues. I'll take a look.

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tatsuya6502 Jan 19, 2015

@jfrazelle Thanks for the info. I think this issue may be related to the following test case as my problem only happens after switching containers. (Run a container, modify the image, stop the container, run a new container with the image, try to modify the image -> error)

#9874

--- FAIL: TestSaveAndLoadRepoFlags (0.47s)
    docker_cli_save_load_test.go:266: inspect is not the same after a save / load

@jfrazelle Thanks for the info. I think this issue may be related to the following test case as my problem only happens after switching containers. (Run a container, modify the image, stop the container, run a new container with the image, try to modify the image -> error)

#9874

--- FAIL: TestSaveAndLoadRepoFlags (0.47s)
    docker_cli_save_load_test.go:266: inspect is not the same after a save / load
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porjo Feb 27, 2015

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I use CoreOS and have just switched from Btrfs to Ext4 and I having the same issue. I was also seeing errors like this:

error: rpmdb: BDB0689 Packages page 122 is on free list with type 7
error: rpmdb: BDB0061 PANIC: Invalid argument
error: db5 error(-30973) from dbcursor->c_put: BDB0087 DB_RUNRECOVERY: Fatal error, run database recovery
error: error(-30973) adding header #163 record
error: rpmdb: BDB0060 PANIC: fatal region error detected; run recovery
error: db5 error(-30973) from dbcursor->c_close: BDB0087 DB_RUNRECOVERY: Fatal error, run database recovery
error: rpmdb: BDB0060 PANIC: fatal region error detected; run recovery
error: db5 error(-30973) from db->sync: BDB0087 DB_RUNRECOVERY: Fatal error, run database recovery

I found that inserting RUN rpm --rebuilddb prior to yum install -y <pkg> resolved both errors, however that should not be necessary.

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porjo commented Feb 27, 2015

I use CoreOS and have just switched from Btrfs to Ext4 and I having the same issue. I was also seeing errors like this:

error: rpmdb: BDB0689 Packages page 122 is on free list with type 7
error: rpmdb: BDB0061 PANIC: Invalid argument
error: db5 error(-30973) from dbcursor->c_put: BDB0087 DB_RUNRECOVERY: Fatal error, run database recovery
error: error(-30973) adding header #163 record
error: rpmdb: BDB0060 PANIC: fatal region error detected; run recovery
error: db5 error(-30973) from dbcursor->c_close: BDB0087 DB_RUNRECOVERY: Fatal error, run database recovery
error: rpmdb: BDB0060 PANIC: fatal region error detected; run recovery
error: db5 error(-30973) from db->sync: BDB0087 DB_RUNRECOVERY: Fatal error, run database recovery

I found that inserting RUN rpm --rebuilddb prior to yum install -y <pkg> resolved both errors, however that should not be necessary.

@porjo porjo referenced this issue in coreos/bugs Feb 27, 2015

Open

Docker w/overlayfs and hard links #285

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marineam Feb 27, 2015

iirc Linux 3.19 or 4.0 adds support for multiple read-only layers in overlayfs which could allow using overlayfs to handle stacking layers instead of re-copying the whole filesystem tree in every layer.

iirc Linux 3.19 or 4.0 adds support for multiple read-only layers in overlayfs which could allow using overlayfs to handle stacking layers instead of re-copying the whole filesystem tree in every layer.

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oszi Mar 1, 2015

I also have this issue with CoreOS 598 and Fedora Rawhide containers.

oszi commented Mar 1, 2015

I also have this issue with CoreOS 598 and Fedora Rawhide containers.

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wuxxin Mar 8, 2015

same issue with: bare metal ubuntu trusty with:
kernel 3.18.8 and 3.19.1 both with overlay fs and ext4
docker 1.5 and 1.5.0-dev, build a78ce5c
container is fedora 21

wuxxin commented Mar 8, 2015

same issue with: bare metal ubuntu trusty with:
kernel 3.18.8 and 3.19.1 both with overlay fs and ext4
docker 1.5 and 1.5.0-dev, build a78ce5c
container is fedora 21

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Same issue here as well on CoreOS with 3.18.4 kernel.

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vaijab commented Mar 10, 2015

Same issue here as well on CoreOS with 3.18.4 kernel.

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t0mk Mar 12, 2015

same issue, coreos 607, kernel 3.18.6, docker 1.5.0, trying to build image from centos:6

Rpmdb checksum is invalid: dCDPT(pkg checksums): php-pdo.x86_64 0:5.3.3-40.el6_6 - u

Reverting to btrfs CoreOS used to help. "Used to" because I noticed that the 607 is stable now, so no non-overlay CoreOS in the offical channels. I guess that means I can't build the centos:6 image on CoreOS now.

t0mk commented Mar 12, 2015

same issue, coreos 607, kernel 3.18.6, docker 1.5.0, trying to build image from centos:6

Rpmdb checksum is invalid: dCDPT(pkg checksums): php-pdo.x86_64 0:5.3.3-40.el6_6 - u

Reverting to btrfs CoreOS used to help. "Used to" because I noticed that the 607 is stable now, so no non-overlay CoreOS in the offical channels. I guess that means I can't build the centos:6 image on CoreOS now.

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Same issue too. Coreos 607. Trying to build a CentOS container.

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cdrage commented Mar 22, 2015

Same issue too. Coreos 607. Trying to build a CentOS container.

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lypanov Mar 24, 2015

Same issue using out of box Google Compute Engine CoreOS stable images.... :( Wasted all morning on this. Never could have guessed it would be CoreOS itself.

(seen while trying to build a Fedora 21 image)

lypanov commented Mar 24, 2015

Same issue using out of box Google Compute Engine CoreOS stable images.... :( Wasted all morning on this. Never could have guessed it would be CoreOS itself.

(seen while trying to build a Fedora 21 image)

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t0mk Mar 24, 2015

Actually, at least in my case, the yum command quite succeeds, just the rpmdb checksum is invalid... A consequent yum install pkg tells me that pkg is already installed. I then suppress the error with " || true" after each in the RUN in Dockerfile. That way I can build the CentOS on CoreOS 607+.

t0mk commented Mar 24, 2015

Actually, at least in my case, the yum command quite succeeds, just the rpmdb checksum is invalid... A consequent yum install pkg tells me that pkg is already installed. I then suppress the error with " || true" after each in the RUN in Dockerfile. That way I can build the CentOS on CoreOS 607+.

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hany Mar 30, 2015

Experiencing the same issue with CoreOS 607.0.0 and CentOS 7 image:

Rpmdb checksum is invalid: dCDPT(pkg checksums): perl-HTTP-Tiny.noarch 0:0.033-3.el7 - u

I'm having the same issue with tailing the log as originally described. File system is ext4.

hany commented Mar 30, 2015

Experiencing the same issue with CoreOS 607.0.0 and CentOS 7 image:

Rpmdb checksum is invalid: dCDPT(pkg checksums): perl-HTTP-Tiny.noarch 0:0.033-3.el7 - u

I'm having the same issue with tailing the log as originally described. File system is ext4.

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Looks like Linux kernel 4.0 is shipping with multi read-only layers support in overlayfs.

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vaijab commented Mar 30, 2015

Looks like Linux kernel 4.0 is shipping with multi read-only layers support in overlayfs.

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Does anyone know that kernel patch that fixes this?

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crosbymichael commented Mar 30, 2015

Does anyone know that kernel patch that fixes this?

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wuxxin Mar 31, 2015

tested with kernel 4.0-rc5 , docker-1.5-dev build f0ddbba (downloaded an hour ago), overlay fs, ext4 backend: still same problem.

if you follow the commits of the overlay graphdriver, beside 35a22c9
nothing serious has changed in the overlay graphdriver since
the source drop of the overlayfs graphdriver which happened on 19. August 2014

UPDATE: after branching current docker and patching it using a7d1ca3 and 18e37f1
i can include kernel 3.16 (ubuntu utopic kernel on trusty lts) to the not working list i tried so far:

all configurations fail with "Rpmdb checksum is invalid: dCDPT(pkg checksums)":
overlay/overlayfs, dist: ubuntu: kernel: 3.16, 3.18, 3.19, 4.0-rc5, docker 1.4.1, docker 1.5, docker 1.5-dev (up to current), with ext4, container: centos 6, fedora:21

side note: the old overlayfs is behaving with current docker the same way as the new overlay fs.

the possibilities i found:

  • maybe there is a bug/semantics issue in the overlay kernel module since before it was included in the kernel at 3.18, including 4.0rc5.
  • maybe docker is using the semantics of the old overlayfs module so there was no bug in docker until usage of the new overlay fs, with the same code written for the old overlayfs (see update)
  • It didn't work in the first place: the old overlayfs module and the first docker overlayfs implementation also did not work for redhat container.

wuxxin commented Mar 31, 2015

tested with kernel 4.0-rc5 , docker-1.5-dev build f0ddbba (downloaded an hour ago), overlay fs, ext4 backend: still same problem.

if you follow the commits of the overlay graphdriver, beside 35a22c9
nothing serious has changed in the overlay graphdriver since
the source drop of the overlayfs graphdriver which happened on 19. August 2014

UPDATE: after branching current docker and patching it using a7d1ca3 and 18e37f1
i can include kernel 3.16 (ubuntu utopic kernel on trusty lts) to the not working list i tried so far:

all configurations fail with "Rpmdb checksum is invalid: dCDPT(pkg checksums)":
overlay/overlayfs, dist: ubuntu: kernel: 3.16, 3.18, 3.19, 4.0-rc5, docker 1.4.1, docker 1.5, docker 1.5-dev (up to current), with ext4, container: centos 6, fedora:21

side note: the old overlayfs is behaving with current docker the same way as the new overlay fs.

the possibilities i found:

  • maybe there is a bug/semantics issue in the overlay kernel module since before it was included in the kernel at 3.18, including 4.0rc5.
  • maybe docker is using the semantics of the old overlayfs module so there was no bug in docker until usage of the new overlay fs, with the same code written for the old overlayfs (see update)
  • It didn't work in the first place: the old overlayfs module and the first docker overlayfs implementation also did not work for redhat container.

wuxxin added a commit to wuxxin/docker that referenced this issue Apr 1, 2015

wuxxin added a commit to wuxxin/docker that referenced this issue Apr 1, 2015

@cloudnautique cloudnautique referenced this issue in rancher/os Apr 1, 2015

Closed

Vagrant Host Permission #120

@stefancocora stefancocora referenced this issue in UKHomeOffice/application-container-platform Aug 17, 2016

Closed

fix the RPM db corruption issue #307

thaJeztah added a commit to thaJeztah/docker that referenced this issue Aug 17, 2016

Add a note about the open(2) and rename(2) on AUFS and OverlayFS
Close #25409
Update #10180

Signed-off-by: Akihiro Suda <suda.akihiro@lab.ntt.co.jp>
(cherry picked from commit aab101a)
Signed-off-by: Sebastiaan van Stijn <github@gone.nl>

AkihiroSuda added a commit to AkihiroSuda/issues-docker that referenced this issue Aug 18, 2016

dekkagaijin added a commit to dekkagaijin/docker that referenced this issue Aug 18, 2016

Add a note about the open(2) and rename(2) on AUFS and OverlayFS
Close #25409
Update #10180

Signed-off-by: Akihiro Suda <suda.akihiro@lab.ntt.co.jp>
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xavierbaude Oct 10, 2016

There is a yum patch, simply add this in your Dockerfile :

RUN yum install -y yum-plugin-ovl

Tested in Centos 7/6 + RHEL 7/6

http://man7.org/linux/man-pages/man1/yum-ovl.1.html

Enjoy Docker/overlay :)

There is a yum patch, simply add this in your Dockerfile :

RUN yum install -y yum-plugin-ovl

Tested in Centos 7/6 + RHEL 7/6

http://man7.org/linux/man-pages/man1/yum-ovl.1.html

Enjoy Docker/overlay :)

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popomore Nov 25, 2016

@xavierbaude I also get the checksum error when install yum-plugin-ovl 😢

@xavierbaude I also get the checksum error when install yum-plugin-ovl 😢

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Stelminator Nov 25, 2016

@popomore you'll probably have to build that layer on something else before moving it to overlayfs. If it works after that, I'd build it into a base image.

@popomore you'll probably have to build that layer on something else before moving it to overlayfs. If it works after that, I'd build it into a base image.

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@popomore the CentOS 6 base containers have had yum-plugin-ovl in them for several months now. perhaps you need to update, or are you using something other than centos?

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jperrin commented Nov 25, 2016

@popomore the CentOS 6 base containers have had yum-plugin-ovl in them for several months now. perhaps you need to update, or are you using something other than centos?

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popomore Nov 25, 2016

I have try the way in docker#10180 (comment) , it works for me, but I don't know why.

I have try the way in docker#10180 (comment) , it works for me, but I don't know why.

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alanfranz Dec 2, 2016

I'm experiencing the issue with the very latest centos 7 image.

https://hub.docker.com/r/alanfranz/drb-epel-7-x86-64/builds/byquwcmv6kmzxt2wwdvkswb/

I have just forced the sha256 for what is currently (December 2nd) tagged with centos:7, I have forced the install of yum-plugin-ovl (by the way it's already installed) but I still get the error.

I'm experiencing the issue with the very latest centos 7 image.

https://hub.docker.com/r/alanfranz/drb-epel-7-x86-64/builds/byquwcmv6kmzxt2wwdvkswb/

I have just forced the sha256 for what is currently (December 2nd) tagged with centos:7, I have forced the install of yum-plugin-ovl (by the way it's already installed) but I still get the error.

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@dmcgowan any ideas? ^^

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thaJeztah commented Dec 2, 2016

@dmcgowan any ideas? ^^

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@alanfranz ensure plugins=1 is set in your /etc/yum.conf file. The base image has this set and the ovl plugin installed.

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dmcgowan commented Dec 5, 2016

@alanfranz ensure plugins=1 is set in your /etc/yum.conf file. The base image has this set and the ovl plugin installed.

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alanfranz Dec 6, 2016

I confirm everything is working properly for both centos 6 and 7 if plugins=1 is enabled in yum.conf.

I confirm everything is working properly for both centos 6 and 7 if plugins=1 is enabled in yum.conf.

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xiaoshengaimm Dec 10, 2016

i got this issue too. however plugins=1 in /etc/yum.conf and RUN yum install -y yum-plugin-ovl both not work for me.

my host system is 7.2.1511 with 4.4.9-1.el7.elrepo.x86_64

docker version 1.11.1 with overlayfs

build image from centos 6.6.....

i got this issue too. however plugins=1 in /etc/yum.conf and RUN yum install -y yum-plugin-ovl both not work for me.

my host system is 7.2.1511 with 4.4.9-1.el7.elrepo.x86_64

docker version 1.11.1 with overlayfs

build image from centos 6.6.....

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alanfranz Dec 10, 2016

@xiaoshengaimm post your Dockerfile. Also, please be advised that plugins=1 and yum-plugin-ovl must be employed together, not alternatively. The first command enables plugins, the second installs the plugin to support overlay.

centos 6.6 is an old centos release (two years old, I think?) and most probably the fix is not baked in that image. Use the latest centos:6 release and most probably you won't experience any issue out of the box, as long as plugins=1 is in yum.conf.

alanfranz commented Dec 10, 2016

@xiaoshengaimm post your Dockerfile. Also, please be advised that plugins=1 and yum-plugin-ovl must be employed together, not alternatively. The first command enables plugins, the second installs the plugin to support overlay.

centos 6.6 is an old centos release (two years old, I think?) and most probably the fix is not baked in that image. Use the latest centos:6 release and most probably you won't experience any issue out of the box, as long as plugins=1 is in yum.conf.

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@jperrin did something change recently with the centos builds? I swear the "yum" checksum problem with overlay2 was fixed before I made a recent docker pull of centos.

Maybe yum-utils used to include yum-plugin-ovl but it no longer does?

This is necessary for overlayfs to work, please add yum-plugin-ovl back in. I guess I should file another bug please let me know what project.

# docker info
Containers: 48
 Running: 38
 Paused: 0
 Stopped: 10
Images: 81
Server Version: 1.12.4
Storage Driver: overlay2
 Backing Filesystem: extfs
Logging Driver: json-file
Cgroup Driver: cgroupfs
Plugins:
 Volume: local
 Network: bridge null host overlay
Swarm: inactive
Runtimes: runc
Default Runtime: runc
Security Options: apparmor seccomp
Kernel Version: 4.4.0-53-generic
Operating System: Ubuntu 16.04.1 LTS
OSType: linux
Architecture: x86_64
CPUs: 4
Total Memory: 31.31 GiB
Name: 63
ID: AUQE:OS5D:5RNW:SBMA:ZMSP:M5PG:7URM:5XTE:CSN2:4JVM:5C6E:JPYG
Docker Root Dir: /var/lib/docker
Debug Mode (client): false
Debug Mode (server): false
Registry: https://index.docker.io/v1/
WARNING: No swap limit support
Labels:
 provider=generic
Insecure Registries:
 127.0.0.0/8
# cat | docker build -
FROM centos:7.2.1511
RUN yum update -y && yum install -y curl which initscripts net-tools bind-utils
RUN yum install -y openssh-server

Sending build context to Docker daemon 2.048 kB
Step 1 : FROM centos:7.2.1511
7.2.1511: Pulling from library/centos
a2392627bec4: Pull complete 
Digest: sha256:2632572665fc957592ae2332662c11a380fdb869eec172eaa0fa25d673a82ac6
Status: Downloaded newer image for centos:7.2.1511
 ---> feac5e0dfdb2
Step 2 : RUN yum update -y && yum install -y curl which initscripts net-tools bind-utils
...
Step 3 : RUN yum install -y openssh-server
Running transaction
  Installing : fipscheck-lib-1.4.1-5.el7.x86_64                             1/5 
  Installing : fipscheck-1.4.1-5.el7.x86_64                                 2/5 
  Installing : openssh-6.6.1p1-31.el7.x86_64                                3/5 
  Installing : tcp_wrappers-libs-7.6-77.el7.x86_64                          4/5 
  Installing : openssh-server-6.6.1p1-31.el7.x86_64                         5/5

Rpmdb checksum is invalid: dCDPT(pkg checksums): openssh.x86_64 0:6.6.1p1-31.el7 - u
 
The command '/bin/sh -c yum install -y openssh-server' returned a non-zero code: 1
Contributor

jamshid commented Dec 23, 2016

@jperrin did something change recently with the centos builds? I swear the "yum" checksum problem with overlay2 was fixed before I made a recent docker pull of centos.

Maybe yum-utils used to include yum-plugin-ovl but it no longer does?

This is necessary for overlayfs to work, please add yum-plugin-ovl back in. I guess I should file another bug please let me know what project.

# docker info
Containers: 48
 Running: 38
 Paused: 0
 Stopped: 10
Images: 81
Server Version: 1.12.4
Storage Driver: overlay2
 Backing Filesystem: extfs
Logging Driver: json-file
Cgroup Driver: cgroupfs
Plugins:
 Volume: local
 Network: bridge null host overlay
Swarm: inactive
Runtimes: runc
Default Runtime: runc
Security Options: apparmor seccomp
Kernel Version: 4.4.0-53-generic
Operating System: Ubuntu 16.04.1 LTS
OSType: linux
Architecture: x86_64
CPUs: 4
Total Memory: 31.31 GiB
Name: 63
ID: AUQE:OS5D:5RNW:SBMA:ZMSP:M5PG:7URM:5XTE:CSN2:4JVM:5C6E:JPYG
Docker Root Dir: /var/lib/docker
Debug Mode (client): false
Debug Mode (server): false
Registry: https://index.docker.io/v1/
WARNING: No swap limit support
Labels:
 provider=generic
Insecure Registries:
 127.0.0.0/8
# cat | docker build -
FROM centos:7.2.1511
RUN yum update -y && yum install -y curl which initscripts net-tools bind-utils
RUN yum install -y openssh-server

Sending build context to Docker daemon 2.048 kB
Step 1 : FROM centos:7.2.1511
7.2.1511: Pulling from library/centos
a2392627bec4: Pull complete 
Digest: sha256:2632572665fc957592ae2332662c11a380fdb869eec172eaa0fa25d673a82ac6
Status: Downloaded newer image for centos:7.2.1511
 ---> feac5e0dfdb2
Step 2 : RUN yum update -y && yum install -y curl which initscripts net-tools bind-utils
...
Step 3 : RUN yum install -y openssh-server
Running transaction
  Installing : fipscheck-lib-1.4.1-5.el7.x86_64                             1/5 
  Installing : fipscheck-1.4.1-5.el7.x86_64                                 2/5 
  Installing : openssh-6.6.1p1-31.el7.x86_64                                3/5 
  Installing : tcp_wrappers-libs-7.6-77.el7.x86_64                          4/5 
  Installing : openssh-server-6.6.1p1-31.el7.x86_64                         5/5

Rpmdb checksum is invalid: dCDPT(pkg checksums): openssh.x86_64 0:6.6.1p1-31.el7 - u
 
The command '/bin/sh -c yum install -y openssh-server' returned a non-zero code: 1

@jamshid jamshid referenced this issue in CentOS/sig-cloud-instance-images Dec 23, 2016

Open

The return of yum failure "Rpmdb checksum is invalid" #74

heikoengel pushed a commit to heikoengel/docker-ci-containers that referenced this issue Feb 9, 2017

rodrigo-tsuru added a commit to rodrigo-tsuru/wsrr-docker that referenced this issue Feb 21, 2017

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MattGat Apr 25, 2017

I have the same issue with Docker version 17.03.1-ce, build c6d412e and CENTOS 7

RUN rpm --rebuilddb && yum install -y XXX => This solution has resolved this issue

MattGat commented Apr 25, 2017

I have the same issue with Docker version 17.03.1-ce, build c6d412e and CENTOS 7

RUN rpm --rebuilddb && yum install -y XXX => This solution has resolved this issue

@AkihiroSuda AkihiroSuda referenced this issue in containerd/containerd May 10, 2017

Closed

linux: build-in naive snapshotter #830

lukaszx0 added a commit to lukaszx0/protobuf that referenced this issue May 11, 2017

Workaround the docker bug when compiling artifacts
This is a workaround (moby/moby#10180 (comment)) the docker issue (moby/moby#10180) which breaks protoc-artifacts build process with following error

```Rpmdb checksum is invalid: dCDPT(pkg checksums): devtoolset-1.1-elfutils.x86_64 0:0.154-6.el6 - u

The command '/bin/sh -c yum clean all && yum install -y devtoolset-1.1                    devtoolset-1.1-libstdc++-devel                    devtoolset-1.1-libstdc++-devel.i686' returned a non-zero code: 1```

moby/moby#10180 (comment)

@mhart mhart referenced this issue in lambci/docker-lambda Jun 16, 2017

Closed

yum install issues in the build version #38

@vrothberg vrothberg referenced this issue in openSUSE/docker-containers Jun 20, 2017

Closed

Tumbleweed repo actions broken after few days in docker #57

mkosieradzki added a commit to mkosieradzki/protobuf that referenced this issue Jul 4, 2017

Workaround the docker bug when compiling artifacts
This is a workaround (moby/moby#10180 (comment)) the docker issue (moby/moby#10180) which breaks protoc-artifacts build process with following error

```Rpmdb checksum is invalid: dCDPT(pkg checksums): devtoolset-1.1-elfutils.x86_64 0:0.154-6.el6 - u

The command '/bin/sh -c yum clean all && yum install -y devtoolset-1.1                    devtoolset-1.1-libstdc++-devel                    devtoolset-1.1-libstdc++-devel.i686' returned a non-zero code: 1```

moby/moby#10180 (comment)

mkosieradzki added a commit to mkosieradzki/protobuf that referenced this issue Jul 4, 2017

Workaround the docker bug when compiling artifacts
This is a workaround (moby/moby#10180 (comment)) the docker issue (moby/moby#10180) which breaks protoc-artifacts build process with following error

```Rpmdb checksum is invalid: dCDPT(pkg checksums): devtoolset-1.1-elfutils.x86_64 0:0.154-6.el6 - u

The command '/bin/sh -c yum clean all && yum install -y devtoolset-1.1                    devtoolset-1.1-libstdc++-devel                    devtoolset-1.1-libstdc++-devel.i686' returned a non-zero code: 1```

moby/moby#10180 (comment)

@cmarcelo cmarcelo referenced this issue in clearlinux/bundle-chroot-builder Aug 3, 2017

Closed

Don't use os-core chroot as base for other bundles #7

dklawren added a commit to mozilla-conduit/docker-bmo that referenced this issue Aug 24, 2017

nehaljwani added a commit to conda/conda-docker that referenced this issue Aug 24, 2017

@mhart mhart referenced this issue in lambci/docker-lambda Dec 11, 2017

Closed

Trying to install postgresql fails #60

kinogmt added a commit to kinogmt/centos-ssh that referenced this issue Feb 14, 2018

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orodbhen Apr 2, 2018

If you're unable to install the yum plugin because of dependency conflicts (e.g. an older base image), You can work around this with touch /var/lib/rpm/*. See the bug report for details.

orodbhen commented Apr 2, 2018

If you're unable to install the yum plugin because of dependency conflicts (e.g. an older base image), You can work around this with touch /var/lib/rpm/*. See the bug report for details.

lae added a commit to lae/ansible-role-travis-lxc that referenced this issue May 1, 2018

Install yum-plugin-ovl in RHEL-based containers to fix rpmdb errors o…
…n OverlayFS

Yum reports rpmdb checksum failures on OverlayFS. This plugin fixes that.
See moby/moby#10180 for more information.
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