configure-basic fails out-of-the-box
Closed this issue · 5 comments
dmd commented
[ddrucker@micpacs ~]$ git clone https://github.com/MonashBI/xnat-docker-compose.git
Cloning into 'xnat-docker-compose'...
remote: Enumerating objects: 25, done.
remote: Counting objects: 100% (25/25), done.
remote: Compressing objects: 100% (20/20), done.
remote: Total 615 (delta 11), reused 9 (delta 5), pack-reused 590
Receiving objects: 100% (615/615), 123.11 KiB | 0 bytes/s, done.
Resolving deltas: 100% (357/357), done.
[ddrucker@micpacs ~]$ cd xnat-docker-compose/
[ddrucker@micpacs xnat-docker-compose]$ ./configure-basic.sh
[... stuff happens ...]
Creating xnat-docker-compose_cadvisor_1 ...
Creating xnat-docker-compose_xnat-db_1 ... done
Creating xnat-docker-compose_xnat-backup_1 ... error
Creating xnat-docker-compose_cadvisor_1 ... done
ERROR: for xnat-docker-compose_xnat-backup_1 Cannot create container for service xnat-backup: create .: volume name is too sCreating xnat-docker-compose_xnat-web_1 ... done
Creating xnat-docker-compose_prometheus_1 ... done
Creating xnat-docker-compose_xnat-nginx_1 ... error
ERROR: for xnat-docker-compose_xnat-nginx_1 Cannot start service xnat-nginx: OCI runtime create failed: container_linux.go:346: starting container process caused "process_linux.go:449: container init caused \"rootfs_linux.go:58: mounting \\\"/home/ddrucker/xnat-docker-compose/nginx/nginx-ssl.conf\\\" to rootfs \\\"/var/lib/docker/overlay2/5afb159efc0a5c39f9d15e0006fc4089dfa910b1516bae16b1c9cb7001dc38d0/merged\\\" at \\\"/var/lib/docker/overlay2/5afb159efc0a5c39f9d15e0006fc4089dfa910b1516bae16b1c9cb7001dc38d0/merged/etc/nginx/nginx.conf\\\" caused \\\"not a directory\\\"\"": unknown: Are you trying to mount a directory onto a file (or vice-versa)? Check if the specified host path exists and is the expected type
ERROR: for xnat-backup Cannot create container for service xnat-backup: create .: volume name is too short, names should be at least two alphanumeric characters
ERROR: for xnat-nginx Cannot start service xnat-nginx: OCI runtime create failed: container_linux.go:346: starting container process caused "process_linux.go:449: container init caused \"rootfs_linux.go:58: mounting \\\"/home/ddrucker/xnat-docker-compose/nginx/nginx-ssl.conf\\\" to rootfs \\\"/var/lib/docker/overlay2/5afb159efc0a5c39f9d15e0006fc4089dfa910b1516bae16b1c9cb7001dc38d0/merged\\\" at \\\"/var/lib/docker/overlay2/5afb159efc0a5c39f9d15e0006fc4089dfa910b1516bae16b1c9cb7001dc38d0/merged/etc/nginx/nginx.conf\\\" caused \\\"not a directory\\\"\"": unknown: Are you trying to mount a directory onto a file (or vice-versa)? Check if the specified host path exists and is the expected type
ERROR: Encountered errors while bringing up the project.
Full log is attached.
tclose commented
Which version of docker / docker compose are you running?
Are you trying to run the “basic” demo config or the full config? Can you
paste the command you are using to bring up docker compose?
The second “nginx” error is likely caused by trying to start the “full
config” (I.e. without manually specifying the docker file) without having
run configure.sh. As it looks like the nginx.conf wasn’t created and Docker
automatically created it for you as a directory when it tried to mount it
into the container.
Try
$ docker-compose -f docker-compose.yml
Instead
On Fri, 21 Feb 2020 at 4:00 am, Daniel M. Drucker ***@***.***> wrote:
***@***.*** ~]$ git clone https://github.com/MonashBI/xnat-docker-compose.git
Cloning into 'xnat-docker-compose'...
remote: Enumerating objects: 25, done.
remote: Counting objects: 100% (25/25), done.
remote: Compressing objects: 100% (20/20), done.
remote: Total 615 (delta 11), reused 9 (delta 5), pack-reused 590
Receiving objects: 100% (615/615), 123.11 KiB | 0 bytes/s, done.
Resolving deltas: 100% (357/357), done.
***@***.*** ~]$ cd xnat-docker-compose/
***@***.*** xnat-docker-compose]$ ./configure-basic.sh
[... stuff happens ...]
Creating xnat-docker-compose_cadvisor_1 ...
Creating xnat-docker-compose_xnat-db_1 ... done
Creating xnat-docker-compose_xnat-backup_1 ... error
Creating xnat-docker-compose_cadvisor_1 ... done
ERROR: for xnat-docker-compose_xnat-backup_1 Cannot create container for service xnat-backup: create .: volume name is too sCreating xnat-docker-compose_xnat-web_1 ... done
Creating xnat-docker-compose_prometheus_1 ... done
Creating xnat-docker-compose_xnat-nginx_1 ... error
ERROR: for xnat-docker-compose_xnat-nginx_1 Cannot start service xnat-nginx: OCI runtime create failed: container_linux.go:346: starting container process caused "process_linux.go:449: container init caused \"rootfs_linux.go:58: mounting \\\"/home/ddrucker/xnat-docker-compose/nginx/nginx-ssl.conf\\\" to rootfs \\\"/var/lib/docker/overlay2/5afb159efc0a5c39f9d15e0006fc4089dfa910b1516bae16b1c9cb7001dc38d0/merged\\\" at \\\"/var/lib/docker/overlay2/5afb159efc0a5c39f9d15e0006fc4089dfa910b1516bae16b1c9cb7001dc38d0/merged/etc/nginx/nginx.conf\\\" caused \\\"not a directory\\\"\"": unknown: Are you trying to mount a directory onto a file (or vice-versa)? Check if the specified host path exists and is the expected type
ERROR: for xnat-backup Cannot create container for service xnat-backup: create .: volume name is too short, names should be at least two alphanumeric characters
ERROR: for xnat-nginx Cannot start service xnat-nginx: OCI runtime create failed: container_linux.go:346: starting container process caused "process_linux.go:449: container init caused \"rootfs_linux.go:58: mounting \\\"/home/ddrucker/xnat-docker-compose/nginx/nginx-ssl.conf\\\" to rootfs \\\"/var/lib/docker/overlay2/5afb159efc0a5c39f9d15e0006fc4089dfa910b1516bae16b1c9cb7001dc38d0/merged\\\" at \\\"/var/lib/docker/overlay2/5afb159efc0a5c39f9d15e0006fc4089dfa910b1516bae16b1c9cb7001dc38d0/merged/etc/nginx/nginx.conf\\\" caused \\\"not a directory\\\"\"": unknown: Are you trying to mount a directory onto a file (or vice-versa)? Check if the specified host path exists and is the expected type
ERROR: Encountered errors while bringing up the project.
Full log is attached.
log.txt
<https://github.com/MonashBI/xnat-docker-compose/files/4231992/log.txt>
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Imaging Informatics Officer
*Monash Biomedical Imaging*
Monash University
Room 139, 770 Blackburn Rd
Clayton Campus, Clayton VIC 3800
Australia
T: +61 3 9902 9804
M: +61 491 141 390
E: tom.close@monash.edu
mbi.monash.edu.au
tclose commented
You should also delete the nginx.conf directory that was created too
On Fri, 21 Feb 2020 at 6:30 am, Thomas Close ***@***.***> wrote:
Which version of docker / docker compose are you running?
Are you trying to run the “basic” demo config or the full config? Can you
paste the command you are using to bring up docker compose?
The second “nginx” error is likely caused by trying to start the “full
config” (I.e. without manually specifying the docker file) without having
run configure.sh. As it looks like the nginx.conf wasn’t created and Docker
automatically created it for you as a directory when it tried to mount it
into the container.
Try
$ docker-compose -f docker-compose.yml
Instead
On Fri, 21 Feb 2020 at 4:00 am, Daniel M. Drucker <
***@***.***> wrote:
> ***@***.*** ~]$ git clone https://github.com/MonashBI/xnat-docker-compose.git
> Cloning into 'xnat-docker-compose'...
> remote: Enumerating objects: 25, done.
> remote: Counting objects: 100% (25/25), done.
> remote: Compressing objects: 100% (20/20), done.
> remote: Total 615 (delta 11), reused 9 (delta 5), pack-reused 590
> Receiving objects: 100% (615/615), 123.11 KiB | 0 bytes/s, done.
> Resolving deltas: 100% (357/357), done.
> ***@***.*** ~]$ cd xnat-docker-compose/
> ***@***.*** xnat-docker-compose]$ ./configure-basic.sh
>
> [... stuff happens ...]
>
> Creating xnat-docker-compose_cadvisor_1 ...
> Creating xnat-docker-compose_xnat-db_1 ... done
> Creating xnat-docker-compose_xnat-backup_1 ... error
> Creating xnat-docker-compose_cadvisor_1 ... done
>
> ERROR: for xnat-docker-compose_xnat-backup_1 Cannot create container for service xnat-backup: create .: volume name is too sCreating xnat-docker-compose_xnat-web_1 ... done
> Creating xnat-docker-compose_prometheus_1 ... done
> Creating xnat-docker-compose_xnat-nginx_1 ... error
>
> ERROR: for xnat-docker-compose_xnat-nginx_1 Cannot start service xnat-nginx: OCI runtime create failed: container_linux.go:346: starting container process caused "process_linux.go:449: container init caused \"rootfs_linux.go:58: mounting \\\"/home/ddrucker/xnat-docker-compose/nginx/nginx-ssl.conf\\\" to rootfs \\\"/var/lib/docker/overlay2/5afb159efc0a5c39f9d15e0006fc4089dfa910b1516bae16b1c9cb7001dc38d0/merged\\\" at \\\"/var/lib/docker/overlay2/5afb159efc0a5c39f9d15e0006fc4089dfa910b1516bae16b1c9cb7001dc38d0/merged/etc/nginx/nginx.conf\\\" caused \\\"not a directory\\\"\"": unknown: Are you trying to mount a directory onto a file (or vice-versa)? Check if the specified host path exists and is the expected type
>
> ERROR: for xnat-backup Cannot create container for service xnat-backup: create .: volume name is too short, names should be at least two alphanumeric characters
>
> ERROR: for xnat-nginx Cannot start service xnat-nginx: OCI runtime create failed: container_linux.go:346: starting container process caused "process_linux.go:449: container init caused \"rootfs_linux.go:58: mounting \\\"/home/ddrucker/xnat-docker-compose/nginx/nginx-ssl.conf\\\" to rootfs \\\"/var/lib/docker/overlay2/5afb159efc0a5c39f9d15e0006fc4089dfa910b1516bae16b1c9cb7001dc38d0/merged\\\" at \\\"/var/lib/docker/overlay2/5afb159efc0a5c39f9d15e0006fc4089dfa910b1516bae16b1c9cb7001dc38d0/merged/etc/nginx/nginx.conf\\\" caused \\\"not a directory\\\"\"": unknown: Are you trying to mount a directory onto a file (or vice-versa)? Check if the specified host path exists and is the expected type
> ERROR: Encountered errors while bringing up the project.
>
> Full log is attached.
>
> log.txt
> <https://github.com/MonashBI/xnat-docker-compose/files/4231992/log.txt>
>
> —
> You are receiving this because you are subscribed to this thread.
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--
*THOMAS G. CLOSE, PHD*
Imaging Informatics Officer
*Monash Biomedical Imaging*
Monash University
Room 139, 770 Blackburn Rd
Clayton Campus, Clayton VIC 3800
Australia
T: +61 3 9902 9804
M: +61 491 141 390
E: ***@***.***
mbi.monash.edu.au
--
*THOMAS G. CLOSE, PHD*
Imaging Informatics Officer
*Monash Biomedical Imaging*
Monash University
Room 139, 770 Blackburn Rd
Clayton Campus, Clayton VIC 3800
Australia
T: +61 3 9902 9804
M: +61 491 141 390
E: tom.close@monash.edu
mbi.monash.edu.au
dmd commented
Ooops! Yes, this was a missing -f docker-compose.yml ... I had assumed that because that is the default filename, it wasn't necessary to pass that option! (Why is it!?)
dmd commented
Aha - there's a docker-compose.override.yml file, which automatically gets read if -f docker-compose.yml is not explicitly stated. Ok.
dmd commented
[Closed with OOPS I DO NOT FOLLOW DIRECTIONS]