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mindboggle docker installation problem #168

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SHJDwu opened this issue Mar 14, 2019 · 8 comments

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@SHJDwu
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commented Mar 14, 2019

Hi mindboggle experts,
I'm attempting a docker install of Mindboggle on Ubuntu 14. I’ve followed the recommendations here (https://mindboggle.readthedocs.io/en/latest/). Firstly, I installed docker following this web page(https://docs.docker.com/install/linux/docker-ce/ubuntu/). After docker installation, I used the following commandline

docker pull nipy/mindboggle

then, the status showed "Download newer image for nipy/mindboggle: latest". Since mindboggle was downloaded, how can I finish its installation for the next step?

In the installation section of "https://mindboggle.readthedocs.io/en/latest/", what does the follow two commandlines mean? I did not understand what their setting path was used for.

HOST=/Users/binarybottle
DOCK=/home/jovyan/work
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@binarybottle

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commented Mar 14, 2019

I don't know if there's a problem here. The next steps in the online documentation suggest setting environment variables so that you can access files from within the docker container, and then the command(s) for running mindlogger within the container.

@NPann

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commented Apr 19, 2019

This 2 environment variables are used to map the docker volume between your host machine and the docker container. HOST pointing to a folder on your host machine, DOCK pointing to a folder in the docker container so that when your run
docker run --rm -ti -v $HOST:/home/jovyan/work -p 8888:8888 nipy/mindboggle
you can access what is in the folder defined HOST from the docker container at the DOCK location.

Saying that, setting DOCK=/home/jovyan/work will not work because it seems that /home/jovyan/work has not been created in the container (Dockerfile). The doc seems is a bit outdated.

Also the jupyter notebook /opt/mindboggle/docs/mindboggle_tutorial.ipynb suggested in the the Getting help section returns: OSError: [Errno 99] Cannot assign requested address. I was able to launch the notebook with the following command:
jupyter notebook /opt/mindboggle/docs/mindboggle_tutorial.ipynb --ip=0.0.0.0 --allow-root if that's helpful

binarybottle added a commit that referenced this issue Jun 8, 2019

@PeerHerholz

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commented Jun 8, 2019

Hi @binarybottle & @NPann, maybe including
--run 'mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > ~/.jupyter/jupyter_notebook_config.py' \
in the neurodocker.sh file might help and will allow the classic call without the need to specify the IP/allowing root!? At least it did for some of the docker images I set up.

@binarybottle

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commented Jun 8, 2019

Thank you, @PeerHerholz !
I have added the line to neurodocker.sh and pushed to the repo.

@PeerHerholz and @NPann -- Before I update the docker container on dockerhub, could you please help me update the documentation as per "The doc seems is a bit outdated." comment above?

binarybottle pushed a commit that referenced this issue Jun 8, 2019

Arno Klein
Fix part of issue #168
Add --run 'mkdir -p ~/.jupyter && echo c.NotebookApp.ip = "0.0.0.0" > ~/.jupyter/jupyter_notebook_config.py' to neurodocker.sh
according to advice from @PeerHerholz
@PeerHerholz

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commented Jun 9, 2019

Sure thing! Did you have anything particular in mind? I'll build the image locally and test a bit around.

@binarybottle

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commented Jun 9, 2019

I'm just pushing a new version (1.3.1) to docker hub. I'll give each command a try and give you feedback in a bit...

@binarybottle

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commented Jun 9, 2019

Hi @binarybottle & @NPann, maybe including
--run 'mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > ~/.jupyter/jupyter_notebook_config.py' \
in the neurodocker.sh file might help and will allow the classic call without the need to specify the IP/allowing root!? At least it did for some of the docker images I set up.

I tried adding the following line to neurodocker.sh:

--run 'mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > ~/.jupyter/jupyter_notebook_config.py' \

but for the current docker image, I still needed "--ip=0.0.0.0 --allow-root" to open up a jupyter notebook.

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commented Jun 20, 2019

I am going to close this issue now that we have an updated docker container, updated instructions, and a working command to launch the jupyter notebook (from above):

jupyter notebook /opt/mindboggle/docs/mindboggle_tutorial.ipynb --ip=0.0.0.0 --allow-root

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