I have a script which contains this line:
fgrep -m 1 'PostgreSQL init process complete' <( docker run --name test-postgres-migration \
-a STDOUT -p 5432:5432 postgres:9.4 )
However, even if I change it to:
fgrep -m 1 'PostgreSQL init process complete' <( docker run --name test-postgres-migration \
-a STDOUT -p 5432:5432 postgres:9.4 </dev/null )
or:
fgrep -m 1 'PostgreSQL init process complete' <( docker run --name test-postgres-migration \
-a STDOUT -p 5432:5432 postgres:9.4 </dev/null ) </dev/null
or even when I put the entire line in a separate shell script and wrap it in nohup:
nohup ./boot-container.sh
the docker container still dies if the script is killed (by emacs) when it is on a later line. This happens because the docker client command is still running, and even though it has PID 1 as its parent, for some mysterious reason (maybe due to a shared stdin file handle or tty) it gets killed too when the script gets killed, which in turn causes the docker container it has started to die. How can I prevent this?
In this situation, even nohup isn't sufficient - it's necessary to use setsid:
fgrep -m 1 'PostgreSQL init process complete' <( setsid docker run --name test-postgres-migration \
-a STDOUT -p 5432:5432 postgres:9.4 )
This solves my problem on Linux - I haven't verified whether the problem occurs on Mac or Unixes, or if this unofficial port of setsid to Mac and other Unixes fixes it.
Related
I am running the below script and getting error.
#!/bin/bash
webproxy=$(sudo docker ps -a --format "{{.Names}}"|grep webproxy)
webproxycheck="curl -k -s https://localhost:\${nginx_https_port}/HealthCheckService"
if [ -n "$webproxy" ] ; then
sudo docker exec $webproxy sh -c "$webproxycheck"
fi
Here is my docker ps -a output
$sudo docker ps -a --format "{{.Names}}"|grep webproxy
webproxy-dev-01
webproxy-dev2-01
when i run the command individually it works. For Example:
$sudo docker exec webproxy-dev-01 sh -c 'curl -k -s https://localhost:${nginx_https_port}/HealthCheckService'
HEALTHCHECK_OK
$sudo docker exec webproxy-dev2-01 sh -c 'curl -k -s https://localhost:${nginx_https_port}/HealthCheckService'
HEALTHCHECK_OK
Here is the error i get.
$ sh healthcheck.sh
OCI runtime exec failed: exec failed: container_linux.go:348: starting container process caused "exec: \"webproxy-dev-01\": executable file not found in $PATH": unknown
Could someone please help me with the error. Any help will be greatly appreciated.
Because the variable contains two tokens (on two separate lines) that's what the variable expands to. You are running
sudo docker exec webproxy-dev-01 webproxy-dev2-01 ...
which of course is an error.
It's not clear what you actually expect to happen, but if you want to loop over those values, that's
for host in $webproxy; do
sudo docker exec "$host" sh -c "$webproxycheck"
done
which will conveniently loop zero times if the variable is empty.
If you just want one value, maybe add head -n 1 to the pipe, or pass a more specific regular expression to grep so it only matches one container. (If you have control over these containers, probably run them with --name so you can unambiguously identify them.)
Based on your given script, you are trying to "exec" the following
sudo docker exec webproxy-dev2-01
webproxy-dev-01 sh -c "curl -k -s https://localhost:${nginx_https_port}/HealthCheckService"
As you see, here is your error.
sudo docker exec webproxy-dev2-01
webproxy-dev-01 [...]
The problem is this line:
webproxy=$(sudo docker ps -a --format "{{.Names}}"|grep webproxy)
which results in the following (you also posted this):
webproxy-dev2-01
webproxy-dev-01
Now, the issue is, that your docker exec command now takes both images names (coming from the variable assignment $webproxy), interpreting the second entry (which is webproxy-dev-01 and sepetrated by \n) as the exec command. This is now intperreted as the given command which is not valid and cannot been found: That's what the error tells you.
A workaround would be the following:
webproxy=$(sudo docker ps -a --format "{{.Names}}"| grep webproxy | head -n 1)
It only graps the first entry of your output. You can of course adapt this to do this in a loop.
A small snippet:
#!/bin/bash
webproxy=$(sudo docker ps -a --format "{{.Names}}"| grep webproxy )
echo ${webproxy}
webproxycheck="curl -k -s https://localhost:\${nginx_https_port}/HealthCheckService"
while IFS= read -r line; do
if [ -n "$line" ] ; then
echo "sudo docker exec ${line} sh -c \"${webproxycheck}\""
fi
done <<< "$webproxy"
I have a simple bash script 'test.sh' in the root of mounted folder :
#!/bin/bash
Rscript -e "source('/home/rstudio/mount-folder/src/controller.R')";
However, when i try to mount folder and start the container with docker run as follows:
docker run -d -p 8000:8787 -e ROOT=true -e DISABLE_AUTH=true --name container -v mount-folder/:/home/rstudio/ image_name /home/rstudio/test.sh
above run command starts the container but exits automatically.
I am looking for a docker run command that starts the container , mounts the folder and then executes the bash script which is in the mount-folder without exiting the container.
(** dont want to go with docker exec command as it is not suitable for my use case for other reasons)
Dockerfile:
FROM rocker/rstudio:4.0.2
//some RUN commands to install necessary r packages
EXPOSE 8787
CMD tail -f /dev/null
Other details :
Image that i am using is rstudio server from rocker and container runs on AWS ubuntu machine.
Edit :
have also tried adding CMD tail -f /dev/null at the end of dockerfile as suggested in http://bigdatums.net/2017/11/07/how-to-keep-docker-containers-running/ even then the container exits.
Docker containers shutdown automatically when run in detached mode. I think this article proposes a nice solution:
http://bigdatums.net/2017/11/07/how-to-keep-docker-containers-running/
You could add tail -f /dev/null as the last command in your bash script instead so that the script will never halt unless it is told to do so.
When you do docker run [options] image_name [cmd] the command you specify becomes the command for the container and replaces any the command specified in the dockerfile (that's why adding CMD tail -f /dev/null doesn't do anything). If you ran your container without the /home/rstudio/test.sh at the end, it should stay running.
The solution would be to update your script to add the tail command at the end.
#!/bin/bash
Rscript -e "source('/home/rstudio/mount-folder/src/controller.R')";
exec tail -f /dev/null
If you can't update that script, you could instead add it to the command being passed to the container, with something like:
docker run [options] image_name bash -c '/home/rstudio/test.sh && exec tail -f /dev/null'
I'm attempting to craft system admin bash tools for starting up a Docker image.
But such docker run keeps dying on me after its bash script exited.
The actual working bash script in question is:
#!/bin/sh
docker run \
--name publicnginx1 \
-v /var/www:/usr/share/nginx/html:ro \
-v /var/nginx/conf:/etc/nginx:ro \
--rm \
-p 80 \
-p 443 \
-d \
nginx
docker ps
Executing the simple script resulted in:
# ./docker-run-nginx.sh
743a6eaa33f435e3e0d211c4047bc9af4d4667dc31cd249e481850f40f848c83
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
743a6eaa33f4 nginx "nginx -g 'daemon of…" 1 second ago Up Less than a second 0.0.0.0:32778->80/tcp, 0.0.0.0:32777->443/tcp publicnginx1
And after that bash script gets completed, I executed 'docker ps'
# docker ps
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
There is no Docker running.
What did I do wrong?
Try to run it without --rm.
You can see all container (including the one that already died using this command):
> docker ps -a
CONTAINER ID IMAGE COMMAND CREATED STATUS
743a6eaa33f4 nginx "nginx -g 'daemon of…" 1 second ago Exited (??) ??
^^^^^
You should be able to look at what is the exit code of the container. Using the container id, you can also look into it's log to understand better what is going on:
docker logs 743a6eaa33f4
If you still can't figure it out, you can start the container with tty to run bash, and try to run the command inside it.
docker run -it -v /var/www:/usr/share/nginx/html:ro -v /var/nginx/conf:/etc/nginx:ro --rm -p 80 -p 443 nginx bash
I am trying with a bash script to run a docker container then print a message. However the finished message is executed whilst the container is still running - I can exec into it and see PID 1 and multiple other processes.
How can I force the docker run command to complete first?
docker run --name registr \
-v ~/v1:/v1 \
-v ~/logging.yaml:/root/logging.yaml \
-v ~/.aws:/root/.aws \
-v ~/luigi.cfg:/root/luigi.cfg \
-v ~/params:/root/params \
-p 8082:8082 \
simonm3/registr
echo "docker finished"
The docker image has CMD ["python", "/root/worker/start.py"]
I have a shell script which runs as follows :
image_id=$(docker ps -a | grep postgres | awk -F' ' '{print $1}')
full_id=$(docker ps -a --no-trunc -q | grep $image_id)
docker exec -i -t $full_id bash
When I run this from the base linux OS, I expect to actually enter the postgres container which is a running container. But the issue is that the shell script hangs on 3rd line during ' docker exec' step.
My end goal is using the bash script, enter a running postgres container and run another bash script inside that container.
However the same command when I run it from command line, it works fine and gets me into the postgres container.
Please help, I have spent hours and hours to solve this but no progress.
Thanks again
Your setup is a bit more complex than it needs to be.
Docker ps can filter containers directly with the --filter= option
docker ps --no-trunc --quiet --filter="ancestor=postgres"
You can also --name containers when you run them which will be less fraught with danger than the script you are attempting
docker run --detach --name postgres_whatever postgres
docker exec -ti postgres_whatever bash
I'm not sure that your script is hanging as opposed to sitting there waiting for input. Try running a command directly
Using naming
exec_test.sh
#!/usr/bin/env bash
docker exec postgres_whatever echo "I have run the test"
When run
$ ./exec_test.sh
I have run the test
Without naming
exec_filter_test.sh
#!/usr/bin/env bash
id=$(docker ps --no-trunc --quiet --filter="ancestor=postgres")
[ -z "$id" ] && echo "no id" && exit 1
docker exec "${id}" echo "I have run the test"
When run
$ ./exec_filter_test.sh
I have run the test