Error when mounting volume

[ehsueh]

Hi again,

I'm experiencing an error when I try to mount a volume for the postgres db by changing the "volumes" section of docker-compose.yml for db to:

`volumes:

• /absolute/path/to/data/on/host:/var/lib/postgresql/data/:rw `

When I try to run docker-compose up db I get:

db_1 | chmod: changing permissions of ‘/var/lib/postgresql/data/’: Operation not permitted

At first I thought maybe it's due to permission or configuration issues on my host machine, so I tried looking into selinux but with no success. When I created a simplified container building from erasche/chado:1.31-jenkins97-pg9.5, I was able to mount a host data directory on /foo and read and write smoothly through /foo to the directory on host. However, if I mount the same host data directory to the same container but on /var/lib/postgresql/data (instead of /foo), the build crashes. :confounded:

Do you know what might be the problem? What could I try to trace the problem further?

Thank you for your time. :smile:

[hexylena]

That's quite interesting. Just checking, your docker-compose.yml looks the same as in this repo, except

diff --git a/docker-compose.yml b/docker-compose.yml
index bbe50fd..4057d48 100644
--- a/docker-compose.yml
+++ b/docker-compose.yml
@@ -30,7 +30,8 @@ services:
         - INSTALL_YEAST_DATA=0
         - PGDATA=/var/lib/postgresql/data/
       volumes:
-        - /var/lib/postgresql/data/
+        - /home/hxr/work/docker-chado/test:/var/lib/postgresql/data/:rw
+        #- /var/lib/postgresql/data/

     elasticsearch:
       image: elasticsearch

Or no? With that change even, I can bring up the container without issue.

For a simpler test, this works as well for me.

$ docker run -itP -v /home/hxr/work/docker-chado/test:/var/lib/postgresql/data/:rw erasche/chado:1.31-jenkins97-pg9.5

The chown that's happening is probably https://github.com/docker-library/postgres/blob/master/9.5/docker-entrypoint.sh#L33, are you starting it with --user or anything? Sorry I'm not more help / this is so many bugs.

[ehsueh]

Thanks for getting back to me so quickly. Yes, my docker-compose.yml looks the same the current one in this repo except for that line. And no, running that simple test (exact command but with different host dir path) gave me the same chmod error :cry: I'm not specifying --user or anything so the user at that point should be root with no permission problem on executing chmod for that dir, right?

[hexylena]

so the user at that point should be root with no permission problem on executing chmod for that dir, right?

yes! exactly.

If the simple version fails.. gosh. Maybe the image got updated? docker pull erasche/chado:1.31-jenkins97-pg9.5 if you haven't already tried that?

docker pull erasche/chado:1.31-jenkins97-pg9.5
1.31-jenkins97-pg9.5: Pulling from erasche/chado
Digest: sha256:24b13869f0ac639aefccffd9c49415e76e4e2d03ac8c34ef61c50e38a4dff389

sha256 in case you need to confirm.

Hmm. I'm guessing you found the selinux stuff from here or so https://github.com/docker-library/postgres/issues/116. Does the :z instead of :rw help? (never heard of that one before, no idea how it behaves. Edit: https://docs.docker.com/engine/reference/commandline/run/#/mount-volumes-from-container---volumes-from)

Maybe the other selinux chcon stuff? Or try wiping out the directory and re-running the container? Sorry I'm not able to be more helpful

[ehsueh]

Thanks, Eric.

The image is up to date with sha256.

1.31-jenkins97-pg9.5: Pulling from erasche/chado
Digest: sha256:24b13869f0ac639aefccffd9c49415e76e4e2d03ac8c34ef61c50e38a4dff389
Status: Image is up to date for erasche/chado:1.31-jenkins97-pg9.5

Yes I've tried suggestions from those links. I tried the :z fix again just now. Same error. All the selinux chcon suggestions I found don't seem to solve my error either. I've tried set up a new directory and re-run the whole thing but I still have the same error.

However, I was able to bring up a working instance (with mounted volume) on another box where my user (call it "myhostuser") is a sudo-er. I notice that the data directory on my host changed ownership from "myhostuser.myhostuser" to "guest-c1aswz.myhostuser" with subdirectories written by Postgres with ownership "guest-c1aswz.docker". From my host machine, I needed to use sudo to access, read and write to the modified data directory. (Is this normal?)

I'm still not sure why it doesn't work on that other machine. I'll update you if I find a solution to it. :smile:

Thanks again!

[hexylena]

Thanks for the update @ehsueh! Interesting, very interesting that you have to be a sudoer. I wonder why that is.

Yes, normal to have to sudo to access the pgdata directory that's volume mounted, the chown inside the container startup usually changes permissions away from the current user (unless remapped with --user).

Please do update if you find out! :)