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Binder Environment using SageMath is not loading

asked 2021-09-29 16:49:41 +0100

cwarnock gravatar image

updated 2021-10-05 16:53:29 +0100

FrédéricC gravatar image

We have been using a Binder environment linked to Github to run SageMath files for our calculus labs for our university (University of South Carolina). Starting last Tuesday or Wednesday, the Binder server stopped loading the environment and stays on the command "Launching Server..." I have tested other Binder environments on the web which run SageMath and none of them seem to be working anymore. Nothing has changed in my Dockerfile, so I think that the issue is with SageMath. My Github repository is github.com/calculuslab/Calculus_Lab. Does anyone know how to get SageMath to work in Binder again? Is there a different way to load it in the Dockerfile which will work?

Thank you,

-Cuyler

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same goes for me at https://github.com/mmosmond/eeb430. I've asked about this in two places as well: https://github.com/sagemath/sage-binder-env/issues/9 (https://github.com/sagemath/sage-bind...), https://github.com/jupyterhub/binderhub/issues/1409 (https://github.com/jupyterhub/binderh...) -Matt

mmosmond gravatar imagemmosmond ( 2021-10-06 22:47:35 +0100 )edit

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answered 2021-10-09 11:31:41 +0100

enriqueartal gravatar image

updated 2021-10-10 13:01:55 +0100

slelievre gravatar image

I had the same issue. I put the logs of two different notebooks if this may help (thee is a "spawn failed" in one of them):

a

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Waiting for build to start...
Built image, launching...
Launching server...
Server requested
2021-10-09T09:06:12.557710Z [Normal] Successfully assigned turing/jupyter-enriqueartal-2dqu-2dformsingularity-2dhak2yp3i to aks-user-14930255-vmss00000j
2021-10-09T09:06:13Z [Normal] Container image "jupyterhub/mybinder.org-tc-init:2020.12.4-n655.hfe65496" already present on machine
2021-10-09T09:06:13Z [Normal] Created container tc-init
2021-10-09T09:06:13Z [Normal] Started container tc-init
2021-10-09T09:06:14Z [Normal] Pulling image "turingmybinder/binder-prod-r2d-g5b5b759-enriqueartal-2dquadraticformsingularity-5b0133:3af764e78f2ec3a2bd5b10e5713be2222f9c2202"
2021-10-09T09:07:04Z [Normal] Successfully pulled image "turingmybinder/binder-prod-r2d-g5b5b759-enriqueartal-2dquadraticformsingularity-5b0133:3af764e78f2ec3a2bd5b10e5713be2222f9c2202"
2021-10-09T09:07:10Z [Normal] Created container notebook
2021-10-09T09:07:10Z [Normal] Started container notebook
Spawn failed: Timeout
Launch attempt 1 failed, retrying...
Server requested
2021-10-09T09:11:16.991402Z [Normal] Successfully assigned turing/jupyter-enriqueartal-2dqu-2dformsingularity-2d86zjjq1g to aks-user-14930255-vmss00000j
2021-10-09T09:11:17Z [Normal] Container image "jupyterhub/mybinder.org-tc-init:2020.12.4-n655.hfe65496" already present on machine
2021-10-09T09:11:18Z [Normal] Created container tc-init
2021-10-09T09:11:18Z [Normal] Started container tc-init
2021-10-09T09:11:18Z [Normal] Container image "turingmybinder/binder-prod-r2d-g5b5b759-enriqueartal-2dquadraticformsingularity-5b0133:3af764e78f2ec3a2bd5b10e5713be2222f9c2202" already present on machine
2021-10-09T09:11:18Z [Normal] Created container notebook
2021-10-09T09:11:19Z [Normal] Started container notebook
Spawn failed: Timeout
Launch attempt 2 failed, retrying...
Server requested
2021-10-09T09:16:27.056172Z [Normal] Successfully assigned turing/jupyter-enriqueartal-2dqu-2dformsingularity-2d719v46if to aks-user-14930255-vmss00000j
2021-10-09T09:16:27Z [Normal] Container image "jupyterhub/mybinder.org-tc-init:2020.12.4-n655.hfe65496" already present on machine
2021-10-09T09:16:28Z [Normal] Created container tc-init
2021-10-09T09:16:28Z [Normal] Started container tc-init
2021-10-09T09:16:28Z [Normal] Container image "turingmybinder/binder-prod-r2d-g5b5b759-enriqueartal-2dquadraticformsingularity-5b0133:3af764e78f2ec3a2bd5b10e5713be2222f9c2202" already present on machine
2021-10-09T09:16:28Z [Normal] Created container notebook
2021-10-09T09:16:28Z [Normal] Started container notebook
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

b

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Waiting for build to start...
Picked Git content provider.
Cloning into '/tmp/repo2docker3adasz6z'...
HEAD is now at 6d2ef09 Update sage version in Dockerfile
Using DockerBuildPack builder
Step 1/2 : FROM sagemath/sagemath:9.1
Fetching base image...
Fetching base image...
Fetching base image...
Fetching base image...
Fetching base image...
...
Fetching base image...
Fetching base image...
Fetching base image...
Fetching base image...
Fetching base image...
 ---> b08484514181
Step 2/2 : COPY --chown=sage:sage . ${HOME}
 ---> 95b2f00651b9
{"aux": {"ID": "sha256:95b2f00651b985556e71eb056703d9f0935118282270e1ff0a81debfe743b8d8"}}[Warning] One or more build-args [NB_USER NB_UID] were not consumed
Successfully built 95b2f00651b9
Successfully tagged gcr.io/binderhub-288415/r2d-staging-g5b5b759-enriqueartal-2dartinkernels-fe5d7b:6d2ef09f87fa3d5a3f5eae885172d009525ea064
Successfully pushed gcr.io/binderhub-288415/r2d-staging-g5b5b759-enriqueartal-2dartinkernels-fe5d7b:6d2ef09f87fa3d5a3f5eae885172d009525ea064Built image, launching...
Launching server...
Server requested
2021-10-09T09:16:08.033842Z [Normal] Successfully assigned prod/jupyter-enriqueartal-2dartinkernels-2dpe4fkdvd to gke-prod-user-202009-b9c03ca0-hc1p
2021-10-09T09:16:09Z [Normal] Container image "jupyterhub/mybinder.org-tc-init:2020.12.4-n655.hfe65496" already present on machine
2021-10-09T09:16:09Z [Normal] Created container tc-init
2021-10-09T09:16:09Z [Normal] Started container tc-init
2021-10-09T09:16:10Z [Normal] Pulling image "gcr.io/binderhub-288415/r2d-staging-g5b5b759-enriqueartal-2dartinkernels-fe5d7b:6d2ef09f87fa3d5a3f5eae885172d009525ea064"
2021-10-09T09:16:10Z [Normal] Successfully pulled image "gcr.io/binderhub-288415/r2d-staging-g5b5b759-enriqueartal-2dartinkernels-fe5d7b:6d2ef09f87fa3d5a3f5eae885172d009525ea064" in 385.01784ms
2021-10-09T09:16:10Z [Normal] Created container notebook
2021-10-09T09:16:10Z [Normal] Started container notebook
Spawn failed: pod prod/jupyter-enriqueartal-2dartinkernels-2dpe4fkdvd did not start in 300 seconds!
Launch attempt 1 failed, retrying...
Server requested
2021-10-09T09:20:48.053642Z [Normal] Successfully assigned prod/jupyter-enriqueartal-2dartinkernels-2d8rz7i76o to gke-prod-user-202009-b9c03ca0-dw4f
2021-10-09T09:20:49Z [Normal] Container image "jupyterhub/mybinder.org-tc-init:2020.12.4-n655.hfe65496" already present on machine
2021-10-09T09:20:49Z [Normal] Created container tc-init
2021-10-09T09:20:49Z [Normal] Started container tc-init
2021-10-09T09:20:50Z [Normal] Pulling image "gcr.io/binderhub-288415/r2d-staging-g5b5b759-enriqueartal-2dartinkernels-fe5d7b:6d2ef09f87fa3d5a3f5eae885172d009525ea064"
2021-10-09T09:20:50Z [Normal] Successfully pulled image "gcr.io/binderhub-288415/r2d-staging-g5b5b759-enriqueartal-2dartinkernels-fe5d7b:6d2ef09f87fa3d5a3f5eae885172d009525ea064" in 365.923976ms
2021-10-09T09:20:51Z [Normal] Created container notebook
2021-10-09T09:20:51Z [Normal] Started container notebook
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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Comments

1

It works with the following dockerfile:

FROM sagemathinc/cocalc:latest

COPY --chown=sage:sage ./* /home/sage/

enriqueartal gravatar imageenriqueartal ( 2021-10-11 12:16:51 +0100 )edit

thanks for the tip but this doesnt work for me (https://github.com/mmosmond/eeb430, https://mybinder.org/v2/gh/mmosmond/eeb430/HEAD)

can you point me to a repo that successfully uses this so i can see what i'm missing?

mmosmond gravatar imagemmosmond ( 2021-10-12 18:02:49 +0100 )edit

This dockerfile worked for me and opened the right folder in this repo https://github.com/enriqueartal/QuadraticFormSingularity

FROM sagemathinc/cocalc:latest

COPY --chown=sage:sage ./*.ipynb /home/sage/

WORKDIR "/home/sage/"

enriqueartal gravatar imageenriqueartal ( 2021-10-20 00:50:34 +0100 )edit
1

answered 2021-09-30 11:01:00 +0100

eric_g gravatar image

I confirm the issue: the notebooks posted at https://sagemanifolds.obspm.fr/exampl... are no longer working in Binder, while they used to work some time ago. I've reported the issue on Sage Devel forum.

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Asked: 2021-09-29 16:49:41 +0100

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Last updated: Oct 10