My docker script is this:
docker run --interactive --tty --rm \
--volume=$HOME/neo4j/data:/data \
--volume=$HOME/neo4j/backups:/backups \
neo4j/neo4j-admin:4.4.9 \
neo4j-admin load --database=neo4j --from=/backups/neo4j.dump
When I run it, I'm getting:
docker: invalid reference format.
See 'docker run --help'.
zsh: no such file or directory: --volume=/Users/ironside/neo4j/backups:/backups
zsh: no such file or directory: neo4j/neo4j-admin:4.4.9
But if I do cd $HOME/neo4j/backups and pwd I get /Users/ironside/neo4j/backups. So it exists. Same with the .dump file. It's there.
The data part works, which is very confusing. I'm trying to follow this part from the docs:
https://neo4j.com/docs/operations-manual/current/docker/maintenance/#docker-neo4j-dump
docker run --interactive --tty --rm \
--volume=$HOME/neo4j/data:/data \
--volume=$HOME/neo4j/backups:/backups \
neo4j/neo4j-admin:4.4.9 \
neo4j-admin load --database=neo4j --from=/backups/<dump-name>.dump
What am I missing here?
I'm using a MAC (MacBook Pro (16-inch, 2021)) with Apple M1 Pro chip.
Related
Im currently struggling to run a container and execute a command within this container.I'm trying to use NanoSNP (https://github.com/huangnengCSU/NanoSNP), which is an image available from dockerhub. After fulling this docker, the following command would be sufficient to run the the container:
docker run \
-v "${INPUT_DIR}":"${INPUT_DIR}" \
-v "${OUTPUT_DIR}":"${OUTPUT_DIR}" \
--gpus all \
huangnengcsu/nanosnp:v2.1-gpu \
run_caller.sh \
-b "${INPUT_DIR}/input.bam" \
-f "${INPUT_DIR}/reference.fa" \
-t "${THREADS}" \
-c "${COVERAGE}" \
-o "${OUTPUT_DIR}"
When trying to run the code: I get the following error: Invalid reference format.
This didn't happen before. When inactivating the -v it doesn't give the error again. I'm working with WSL, in VCS with a python script, and running my docker command via subprocess.run, so the following code looks like this (I only included the -v because that's where the error occurred:
subprocess.run(["sudo", "docker", "run", \
"-v", "${INPUT_DIR}",":","${INPUT_DIR}", \
"-v", "${OUTPUT_DIR}",":","${OUTPUT_DIR}", \
If anyone knows or sees the problem, let me know.
With the following command, I tried to boot directly into an OS X shell with no display (Xvfb) [HEADLESS], using the sickcodes/docker-osx:naked docker image with a custom Mojave image.
# run your own image headless + SSH
docker run -it \
--device /dev/kvm \
-p 50922:10022 \
-v "${PWD}/mac_hdd_ng.img:/image" \
sickcodes/docker-osx:naked
However it ends up with the following error message:
nohup: appending output to 'nohup.out'
nohup: failed to run command 'Xvfb': No such file or directory
Details to reproduce:
The version of the sickcodes/docker-osx:naked docker image is: https://hub.docker.com/layers/docker-osx/sickcodes/docker-osx/naked/images/sha256-ffff65c24b7a1588dd665f07f52a48ef5efb9941c2e2fa07573e66524029ab08
The custom image - mac_hdd_ng.img is generated by running:
docker run -it \
--device /dev/kvm \
-p 50922:10022 \
-v /tmp/.X11-unix:/tmp/.X11-unix \
-e "DISPLAY=${DISPLAY:-:0.0}" \
sickcodes/docker-osx:mojave
sudo find /var/lib/docker -size +10G | grep mac_hdd_ng.img # https://github.com/sickcodes/Docker-OSX#container-creation-examples
This youtube video provides a detailed example of using sickcodes/docker-osx to run Mac OS X in Docker.
Building and using the Docker Image using https://github.com/sickcodes/Docker-OSX/blob/master/Dockerfile.naked with the following edits solved the issue.
Replace Line 63 in Dockerfile.naked
RUN pacman -Syu xorg-server-xvfb wget xterm xorg-xhost xorg-xrandr sshpass --noconfirm \
With
RUN pacman -Sy xorg-server-xvfb wget xterm xorg-xhost xorg-xrandr sshpass --noconfirm \
References:
https://github.com/sickcodes/Docker-OSX/issues/515
https://github.com/sickcodes/Docker-OSX/issues/498
envs:
host:centos
docker:ubuntu 16 nivida-docker
program:c++ websocket
desc:
when I use gdb in docker ,I can't use breakpoint ,it just says:warning: error disabling address space randomization: operation not permitted.I see alot of resolutions to this question,all of them tell me to add :--cap-add=SYS_PTRACE --security-opt seccomp=unconfinedto my docker file ,so I did it.here is my docker file:
!/bin/sh
SCRIPT_DIR=$(cd $(dirname "${BASH_SOURCE[0]}") && pwd)
PROJECT_ROOT="$( cd "${SCRIPT_DIR}/.." && pwd )"
echo "PROJECT_ROOT = ${PROJECT_ROOT}"
run_type=$1
docker_name=$2
sudo docker run \
--name=${docker_name} \
--privileged \
--network host \
-it --rm \
--cap-add=SYS_PTRACE --security-opt seccomp=unconfined \
-v ${PROJECT_ROOT}/..:/home \
-v /ssd3:/ssd3 \
xxxx/xx/xxxx:xxxx \
bash
but when restart the container and run gdb ,it always killed like below:
(gdb) r -c conf/a.json -p 8075
Starting program: /home/Service/bin/Service --args -c conf/a.json -p 8075
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
Killed
I don't known where is wrong ,anyone have any opinions?
Try this
docker run --cap-add=SYS_PTRACE --security-opt seccomp=unconfined
Is there a way to run Podman inside Podman, similar to the way you can run Docker inside Docker?
Here is a snippet of my Dockerfile which is strongly based on another question:
FROM debian:10.6
RUN apt update && apt upgrade -qqy && \
apt install -qqy iptables bridge-utils \
qemu-kvm libvirt-daemon libvirt-clients virtinst libvirt-daemon-system \
cpu-checker kmod && \
apt -qqy install curl sudo gnupg2 && \
echo "deb https://download.opensuse.org/repositories/devel:/kubic:/libcontainers:/stable/Debian_10/ /" > /etc/apt/sources.list.d/devel:kubic:libcontainers:stable.list && \
curl -L https://download.opensuse.org/repositories/devel:/kubic:/libcontainers:/stable/Debian_10/Release.key | sudo apt-key add - && \
apt update && \
apt -qqy install podman
Now trying some tests:
$ podman run -it my/test bash -c "podman --storage-driver=vfs info"
... (long output; this works fine)
$ podman run -it my/test bash -c "podman --storage-driver=vfs images"
ERRO[0000] unable to write system event: "write unixgram #000ec->/run/systemd/journal/socket: sendmsg: no such file or directory"
REPOSITORY TAG IMAGE ID CREATED SIZE
$ podman run -it my/test bash -c "podman --storage-driver=vfs run docker.io/library/hello-world"
ERRO[0000] unable to write system event: "write unixgram #000ef->/run/systemd/journal/socket: sendmsg: no such file or directory"
Trying to pull docker.io/library/hello-world...
Getting image source signatures
Copying blob 0e03bdcc26d7 done
Copying config bf756fb1ae done
Writing manifest to image destination
Storing signatures
ERRO[0003] unable to write pod event: "write unixgram #000ef->/run/systemd/journal/socket: sendmsg: no such file or directory"
ERRO[0003] Error preparing container 66692b7ff496775499d405d538769a078f2794549955cf2409fcbcbf87f42e94: error creating network namespace for container 66692b7ff496775499d405d538769a078f2794549955cf2409fcbcbf87f42e94: mount --make-rshared /var/run/netns failed: "operation not permitted"
Error: failed to mount shm tmpfs "/var/lib/containers/storage/vfs-containers/66692b7ff496775499d405d538769a078f2794549955cf2409fcbcbf87f42e94/userdata/shm": operation not permitted
I've also tried a suggestion from the other question, passing --cgroup-manager=cgroupfs, but without success:
$ podman run -it my/test bash -c "podman --storage-driver=vfs --cgroup-manager=cgroupfs run docker.io/library/hello-world"
Trying to pull docker.io/library/hello-world...
Getting image source signatures
Copying blob 0e03bdcc26d7 done
Copying config bf756fb1ae done
Writing manifest to image destination
Storing signatures
ERRO[0003] unable to write pod event: "write unixgram #000f3->/run/systemd/journal/socket: sendmsg: no such file or directory"
ERRO[0003] Error preparing container c3fff4d8161903aaebd6f89f3b3c06b55038e11e07b6b561dc6576ca675747a3: error creating network namespace for container c3fff4d8161903aaebd6f89f3b3c06b55038e11e07b6b561dc6576ca675747a3: mount --make-rshared /var/run/netns failed: "operation not permitted"
Error: failed to mount shm tmpfs "/var/lib/containers/storage/vfs-containers/c3fff4d8161903aaebd6f89f3b3c06b55038e11e07b6b561dc6576ca675747a3/userdata/shm": operation not permitted
Seems like some network configuration is needed. I found the project below which suggests that some tweaking on network configurations might be necessary, but I don't know what would be the context of that and whether it would apply here or not.
https://github.com/joshkunz/qemu-docker
EDIT: I've just discovered /var/run/podman.sock, but also without success:
$ sudo podman run -it -v /run/podman/podman.sock:/run/podman/podman.sock my/test bash -c "podman --storage-driver=vfs --cgroup-manager=cgroupfs run docker.io/library/hello-world"
Trying to pull my/test...
denied: requested access to the resource is denied
Trying to pull my:test...
unauthorized: access to the requested resource is not authorized
Error: unable to pull my/text: 2 errors occurred:
* Error initializing source docker://my/test: Error reading manifest latest in docker.io/my/test: errors:
denied: requested access to the resource is denied
unauthorized: authentication required
* Error initializing source docker://quay.io/my/test:latest: Error reading manifest latest in quay.io/my/test: unauthorized: access to the requested resource is not authorized
Seems like root cannot see the images I've created under my user.
Any ideas? Thanks.
Assume we would like to run ls / in a docker.io/library/alpine container.
Standard Podman
podman run --rm docker.io/library/alpine ls /
Podman in Podman
Let's run ls / in a docker.io/library/alpine container, but this time we run podman in a quay.io/podman/stable container.
Update June 2021
A GitHub issue comment shows an example of how to run Podman in Podman as a non-root user both on the host and in the outer container. Slightly modified it would look like this:
podman \
run \
--rm \
--security-opt label=disable \
--user podman \
quay.io/podman/stable \
podman \
run \
--rm \
docker.io/library/alpine \
ls /
Here is a full example:
$ podman --version
podman version 3.2.1
$ cat /etc/fedora-release
Fedora release 34 (Thirty Four)
$ uname -r
5.12.11-300.fc34.x86_64
$ podman \
run \
--rm \
--security-opt label=disable \
--user podman \
quay.io/podman/stable \
podman \
run \
--rm \
docker.io/library/alpine \
ls /
Trying to pull docker.io/library/alpine:latest...
Getting image source signatures
Copying blob sha256:5843afab387455b37944e709ee8c78d7520df80f8d01cf7f861aae63beeddb6b
Copying config sha256:d4ff818577bc193b309b355b02ebc9220427090057b54a59e73b79bdfe139b83
Writing manifest to image destination
Storing signatures
bin
dev
etc
home
lib
media
mnt
opt
proc
root
run
sbin
srv
sys
tmp
usr
var
$
To avoid repeatedly downloading the inner container image,
create a volume
podman volume create mystorage
and add the command-line option
-v mystorage:/home/podman/.local/share/containers:rw
to the outer Podman command. In other words
podman \
run \
-v mystorage:/home/podman/.local/share/containers:rw \
--rm \
--security-opt label=disable \
--user podman \
quay.io/podman/stable \
podman \
run \
--rm \
docker.io/library/alpine \
ls /
Podman in Podman (outdated answer)
(The old outdated answer from Dec 2020. I'll probably remove this when it's clear that the method described here is outdated)
Let's run ls / in a docker.io/library/alpine container, but this time we run podman in a quay.io/podman/stable container.
The command will look like this:
podman \
run \
--privileged \
--rm \
--ulimit host \
-v /dev/fuse:/dev/fuse:rw \
-v ./mycontainers:/var/lib/containers:rw \
quay.io/podman/stable \
podman \
run \
--rm \
--user 0 \
docker.io/library/alpine ls
(The directory ./mycontainers is here used for container storage)
Here is a full example
$ podman --version
podman version 2.1.1
$ mkdir mycontainers
$ podman run --privileged --rm --ulimit host -v /dev/fuse:/dev/fuse:rw -v ./mycontainers:/var/lib/containers:rw quay.io/podman/stable podman run --rm --user 0 docker.io/library/alpine ls | head -5
Trying to pull docker.io/library/alpine...
Getting image source signatures
Copying blob sha256:188c0c94c7c576fff0792aca7ec73d67a2f7f4cb3a6e53a84559337260b36964
Copying config sha256:d6e46aa2470df1d32034c6707c8041158b652f38d2a9ae3d7ad7e7532d22ebe0
Writing manifest to image destination
Storing signatures
bin
dev
etc
home
lib
$ podman run --privileged --rm --ulimit host -v /dev/fuse:/dev/fuse:rw -v ./mycontainers:/var/lib/containers:rw quay.io/podman/stable podman images
REPOSITORY TAG IMAGE ID CREATED SIZE
docker.io/library/alpine latest d6e46aa2470d 4 days ago 5.85 MB
If you would leave out -v ./mycontainers:/var/lib/containers:rw you might see the slightly confusing error message
Error: executable file `ls` not found in $PATH: No such file or directory: OCI runtime command not found error
References:
How to use Podman inside of a container Red Hat blog post from July 2021.
discussion.fedoraproject.org (discussion about not found in $PATH)
github comment (that gives advice about the correct way to run Podman in Podman)
I want to install the vendor folder of a project on docker, and I try to use this command:
winpty docker run --rm --interactive --tty \ --volume $(pwd):/app \ composer install
but after running it, I get the error message
C:/Program Files/Docker/Docker/Resources/bin/docker.exe: invalid
reference format.
is there any solution to fix it?
In powershell you should use ${pwd} instead of $(pwd)