I am trying to run a Docker container to analyze data in a Google Cloud Bucket.
I have been able to successfully mount the Bucket using
gcsfuse, and I tested that I could do thinks like create and delete files within the Bucket.
In order to be able to install other programs (and mount the bucket), I installed Docker (and didn’t use the Docker-optimized instance option). If I run Docker in interactive mode (without mounting a drive), it looks like it is working OK.
However, if I try to run Docker in interactive mode with the mounted drive (which is the gcsfuse-mounted Bucket), I get an error message:
[email protected]:~/bucket-name/subfolder$ docker run -it -v /home/user/bucket-name:/mnt/bucket-name gcr.io/deepvariant-docker/deepvariant docker: Error response from daemon: error while creating mount source path '/home/user/bucket-name': mkdir /home/user/bucket-name: file exists.
I hope that I am close to having this working: does anybody have any ideas about a relatively simple fix for this error message?
BTW, I realize that there are other ways to run DeepVariant on Google Cloud, but I am trying to makes things as similar as possible to what I am doing on AWS (plus, I may need to do some extra troubleshooting for analysis of one of my files).
Thank you very much for your help!
FYI, this is how I mounted the Bucket:
#mount directory: https://github.com/GoogleCloudPlatform/gcsfuse/blob/master/docs/installing.md export GCSFUSE_REPO=gcsfuse-`lsb_release -c -s` echo "deb http://packages.cloud.google.com/apt $GCSFUSE_REPO main" | sudo tee /etc/apt/sources.list.d/gcsfuse.list curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | sudo apt-key add - sudo apt-get update sudo apt-get -y install gcsfuse #restart and mount directory: https://cloud.google.com/storage/docs/gcs-fuse mkdir [bucket-name] gcsfuse [bucket-name] ./[bucket-name]
and this is how I installed Docker:
#install Docker for Debian: https://docs.docker.com/install/linux/docker-ce/debian/ sudo apt-get update sudo apt-get -y install apt-transport-https ca-certificates curl gnupg2 software-properties-common curl -fsSL https://download.docker.com/linux/debian/gpg | sudo apt-key add - sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/debian $(lsb_release -cs) stable" sudo apt-get update sudo apt-get -y install docker-ce docker-ce-cli containerd.io #fix Docker sock issue: https://stackoverflow.com/questions/47854463/got-permission-denied-while-trying-to-connect-to-the-docker-daemon-socket-at-uni sudo usermod -a -G docker [user] #have to restart after this