Closed erikr closed 3 years ago
Hi @erikr thanks for the detailed report. It's definitely a good idea to add the channels at the top of the yml file, can you create a pull request? The required channels are added as one of the steps in the dockerfile, but they will be useful if people try to install it locally just as you did.
As for the crashes, it appears that the workers are killed for an unrelated reason. Could it be a memory issue?
Hi @prhoda, thanks for the input. Yes, will fork and open PR.
Previously I used a VM with 4 GB of RAM. Now I am using 32 GB RAM and cannot reproduce the error. It would be ideal to have a clearer understanding of minimum memory requirements, e.g., if the README
says "If running BioPhi
on a local machine or server, we recommend having at least x
GB of RAM".
(now that I can successfully run docker-build
, I now have a positive control to assess if my PR breaks setup)
I will close this issue now since the problem disappeared, but if there is interest to hunt down the root cause, this issue can always be re-opened.
@erikr FYI We set up the university server on Ubuntu without Docker. Feel free to use this repo as a guide: https://github.com/lich-uct/biophi.dichlab.org
I also added this link to the README.
Also FYI, I removed the mongodb
and beat
services from the docker-compose file because these are actually not needed anymore.
Error description
I freshly cloned this repo on a new Ubuntu 20.04 VM, installed
miniconda3
, and followed the instructions at Run BioPhi dev server through Docker Compose.Running
make docker-build
throws an error:So I ran
make env-create
:So I added the env name and channels to
environment.yml
:and re-ran
make env-create
, which now gives a new error:Expected behavior
make env-create
does not throw an error. Strangely this worked last night but the errors began around 10 pm EST.