Clinical-Genomics-Lund / bonsai

Visualize and analyze resistance and outbreak of bacterial pathogen
https://bonsai-wgs.readthedocs.io/en/latest/
GNU General Public License v3.0
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Support request: error configuring network namespace [...] CNI network "bonsai_bonsai-net" not found #132

Closed samuell closed 10 months ago

samuell commented 10 months ago

I just thought to ask if you have any tips to share when getting the following errors, trying to do docker-compose up -d (after fixing an initial permissions issue with sudo chown -R root:docker /run/podman/ and sudo chmod g+rx /run/podman/):

Running:

docker-compose up -d |& tee out.log

... I get:

Starting mongodb ... 
Starting bonsai_redis_1 ... 
Starting bonsai_redis_1 ... error

ERROR: for bonsai_redis_1  Cannot start service redis: error configuring network namespace for container 82379018a770d08c713825dca5cafecaf963451b5d0377c4ddad9c91ceebc2be: CNI network "bonsai_bonsai-net" not found
Starting mongodb        ... error

ERROR: for mongodb  Cannot start service mongodb: error configuring network namespace for container 1fc3741d41ae6296688ad8694c42a6d68de1fe63ef3e5c469bdcb213fe108cce: CNI network "bonsai_bonsai-net" not found

ERROR: for redis  Cannot start service redis: error configuring network namespace for container 82379018a770d08c713825dca5cafecaf963451b5d0377c4ddad9c91ceebc2be: CNI network "bonsai_bonsai-net" not found

ERROR: for mongodb  Cannot start service mongodb: error configuring network namespace for container 1fc3741d41ae6296688ad8694c42a6d68de1fe63ef3e5c469bdcb213fe108cce: CNI network "bonsai_bonsai-net" not found
Encountered errors while bringing up the project.
mhkc commented 10 months ago

Can you post your docker-compose file?

samuell commented 10 months ago

Got this running with the help of @mhkc now!

Turned out I had accidentally installed podman, which "hijacked" the docker command with an alias pointing to podman, and it turns out they are not 100% compatible. E.g. there were complaints that the CNI version used is not supported.

After installing the docker.io package (in Linux Mint 21.1), things worked much better. Also I did upgrade to 0.2.0 instead of 0.1.0 of Bonsai.