I’m brand new to docker, and not sure i’m getting the concepts and terminology 100% correct, so please forgive me and interpret with that in mind.
I have installed a docker container containing a package called tailseeker onto a Centos 7 server, following instructions on https://github.com/hyeshik/tailseeker#running-with-docker
Before I run tailseeker proper, i have to “extend the Docker image to supplement a genome reference database” which involves “building the Docker image from an empty directory” so i type:
docker build -t tailseeker:GRCm38–build-arg genome=GRCm38 .
This returns a very lengthy message, ending in:
OSError: [Errno 28] No space left on device
I know there are several other posts about this error, but none have given me what i need. I’m not running out of space on the server (nor the partition). I have replaced /var/lib/docker with a link to /home/docker, to avoid problems that it was causing there. I’m using docker version 1.13.0. Lots of the solutions I find online seem to be specific to older versions. I have tried various commands to clean out old docker images and files. They run successfully, but they don’t solve the problem.
I have only a beginners understanding of docker’s storage, but have tried a few ways to modify things to increase it: I was previously getting an error about the size of my “thin pool”, I found and ran a solution to that, by asking for 250GB rather than the default 100GB:
sudo dd if=/dev/zero of=/home/docker/devicemapper/devicemapper/data bs=1G count=0 seek=250
….which solved that problem, but now I get the “No space left on device” error instead. Further increasing the thin pool size (up to 2000GB) makes no further difference.
I have also tried the following command, and several variations on it:
sudo dockerd --storage-opt dm.basesize=20G
….which returns the following, and then hangs for (at least) several hours:
INFO[0000] libcontainerd: new containerd process, pid: 115819
WARN[0000] containerd: low RLIMIT_NOFILE changing to max current=1024 max=4096
WARN[0001] devmapper: Can’t shrink loopback file /home/docker/devicemapper/devicemapper/data
WARN[0001] devmapper: Usage of loopback devices is strongly discouraged for production use. Please use --storage-opt dm.thinpooldev or use man docker to refer to dm.thinpooldev section.
WARN[0001] devmapper: Base device already exists and has filesystem xfs on it. User specified filesystem will be ignored.
INFO[0001] [graphdriver] using prior storage driver: devicemapper
INFO[0001] Graph migration to content-addressability took 0.00 seconds
WARN[0001] mountpoint for pids not found
INFO[0001] Loading containers: start.
INFO[0001] Firewalld running: true
INFO[0001] Default bridge (docker0) is assigned with an IP address 172.17.0.0/16. Daemon option --bip can be used to set a preferred IP address
INFO[0002] Loading containers: done.
INFO[0002] Daemon has completed initialization
INFO[0002] Docker daemon commit=49bf474 graphdriver=devicemapper version=1.13.0
INFO[0002] API listen on /var/run/docker.sock
Googling these warnings doesn’t give me much that I can make use of.
Any explanation or advice would be greatly appreciated.
Thanks!