NERSC Shifter Docker Image Will Not Build

[joeykleingers]

Hello,

I have been attempting to build the NERSC shifter docker image, but I am getting an error when it executes line 57 to install Jupyter lab extensions in the DockerFile. In order to look at the log files inside the DockerFile, I commented out the DockerFile from line 57 all the way to the bottom, built that Docker image, navigated into the running Docker container and launched a bash shell, and then began manually installing the lab extensions that are listed on line 57 in the DockerFile.

I ran this command: jupyter labextension install jupyter-matplotlib.

Here is the output from the log file:

Node v13.13.0

Yarn configuration loaded.
> /opt/conda/bin/npm pack jupyter-matplotlib
npm notice
npm notice 📦  [email protected]
npm notice === Tarball Contents ===
npm notice 169B   .prettierrc
npm notice 594B   src/mpl_widget.css
npm notice 336B   .eslintrc.js
npm notice 22.7kB dist/index.js
npm notice 184B   src/index.js
npm notice 437B   src/lab_extension.js
npm notice 21.8kB src/mpl_widget.js
npm notice 312B   src/nb_extension.js
npm notice 612B   src/nb_index.js
npm notice 5.5kB  src/toolbar_widget.js
npm notice 651B   src/utils.js
npm notice 2.7kB  webpack.config.js
npm notice 1.9kB  package.json
npm notice 76.6kB dist/index.js.map
npm notice 161B   README.md
npm notice === Tarball Details ===
npm notice name:          jupyter-matplotlib
npm notice version:       0.8.2
npm notice filename:      jupyter-matplotlib-0.8.2.tgz
npm notice package size:  36.8 kB
npm notice unpacked size: 134.7 kB
npm notice shasum:        97a357ecf9dec8eba9cda7d486a973c0bfe2b880
npm notice integrity:     sha512-2j81aEDe2Xsjp[...]LCe/dukMB5//A==
npm notice total files:   15
npm notice
jupyter-matplotlib-0.8.2.tgz

Node v13.13.0

Yarn configuration loaded.
Building jupyterlab assets (build:prod:minimize)
> node /opt/conda/lib/python3.8/site-packages/jupyterlab/staging/yarn.js install --non-interactive
yarn install v1.21.1
[1/5] Validating package.json...
[2/5] Resolving packages...
[3/5] Fetching packages...
info [email protected]: The platform "linux" is incompatible with this module.
info "[email protected]" is an optional dependency and failed compatibility check. Excluding it from installation.
info [email protected]: The platform "linux" is incompatible with this module.
info "[email protected]" is an optional dependency and failed compatibility check. Excluding it from installation.
[4/5] Linking dependencies...
warning " > @lumino/[email protected]" has unmet peer dependency "[email protected]".
[5/5] Building fresh packages...
error /opt/conda/share/jupyter/lab/staging/node_modules/jupyter-matplotlib: Command failed.
Exit code: 1
Command: npm run build
Arguments:
Directory: /opt/conda/share/jupyter/lab/staging/node_modules/jupyter-matplotlib
Output:
npm WARN lifecycle The node binary used for scripts is /tmp/yarn--1610735981021-0.8672339414699104/node but npm is using /opt/conda/bin/node itself. Use the `--scripts-prepend->

> [email protected] build /opt/conda/share/jupyter/lab/staging/node_modules/jupyter-matplotlib
> webpack && npm run build:labextension

Hash: 0659dc8e03cbf5eaeb49b80fac93cd37f5fed1ea32955f3439476b78d7da
Version: webpack 4.44.1
Child
    Hash: 0659dc8e03cbf5eaeb49
    Time: 523ms
    Built at: 01/15/2021 6:39:42 PM
           Asset     Size  Chunks             Chunk Names
    extension.js  1.1 KiB       0  [emitted]  main
    Entrypoint main = extension.js
    [0] ./src/nb_extension.js 312 bytes {0} [built]

    WARNING in configuration
    The 'mode' option has not been set, webpack will fallback to 'production' for this value. Set 'mode' option to 'development' or 'production' to enable defaults for each env>
    You can also set it to 'none' to disable any default behavior. Learn more: https://webpack.js.org/configuration/mode/
Child
    Hash: b80fac93cd37f5fed1ea
    Time: 1135ms
    Built at: 01/15/2021 6:39:43 PM
           Asset      Size  Chunks                   Chunk Names
        index.js  22.3 KiB       0  [emitted]        main
    index.js.map  66.6 KiB       0  [emitted] [dev]  main
    Entrypoint main = index.js index.js.map
    [0] ./package.json 1.85 KiB {0} [built]
    [1] external "@jupyter-widgets/base" 42 bytes {0} [built]
    [2] ./src/nb_index.js 612 bytes {0} [built]
    [3] ./src/utils.js 651 bytes {0} [built]
    [4] ./src/mpl_widget.css 446 bytes {0} [built]
    [5] ../css-loader/dist/cjs.js!./src/mpl_widget.css 759 bytes {0} [built]
    [6] ../css-loader/dist/runtime/api.js 2.61 KiB {0} [built]
    [7] ../style-loader/dist/runtime/injectStylesIntoStyleTag.js 6.75 KiB {0} [built]
    [8] ./src/index.js + 2 modules 26.9 KiB {0} [built]
        | ./src/index.js 184 bytes [built]
        | ./src/toolbar_widget.js 5.38 KiB [built]
        | ./src/mpl_widget.js 21.3 KiB [built]

    WARNING in configuration
    The 'mode' option has not been set, webpack will fallback to 'production' for this value. Set 'mode' option to 'development' or 'production' to enable defaults for each env>
    You can also set it to 'none' to disable any default behavior. Learn more: https://webpack.js.org/configuration/mode/
Child
    Hash: 32955f3439476b78d7da
    Time: 1055ms
    Built at: 01/15/2021 6:39:43 PM
           Asset      Size  Chunks                   Chunk Names
        index.js  22.2 KiB       0  [emitted]        main
    index.js.map    66 KiB       0  [emitted] [dev]  main
    Entrypoint main = index.js index.js.map
    [0] ./package.json 1.85 KiB {0} [built]
    [1] external "@jupyter-widgets/base" 42 bytes {0} [built]
    [2] ./src/utils.js 651 bytes {0} [built]
    [3] ./src/mpl_widget.css 446 bytes {0} [built]
    [4] ../css-loader/dist/cjs.js!./src/mpl_widget.css 759 bytes {0} [built]
    [5] ../css-loader/dist/runtime/api.js 2.61 KiB {0} [built]
    [6] ../style-loader/dist/runtime/injectStylesIntoStyleTag.js 6.75 KiB {0} [built]
    [7] ./src/index.js + 2 modules 26.9 KiB {0} [built]
        | ./src/index.js 184 bytes [built]
        | ./src/toolbar_widget.js 5.38 KiB [built]
        | ./src/mpl_widget.js 21.3 KiB [built]

    WARNING in configuration
    The 'mode' option has not been set, webpack will fallback to 'production' for this value. Set 'mode' option to 'development' or 'production' to enable defaults for each env>
    You can also set it to 'none' to disable any default behavior. Learn more: https://webpack.js.org/configuration/mode/
npm WARN lifecycle The node binary used for scripts is /tmp/yarn--1610735981021-0.8672339414699104/node but npm is using /opt/conda/bin/node itself. Use the `--scripts-prepend->

> [email protected] build:labextension /opt/conda/share/jupyter/lab/staging/node_modules/jupyter-matplotlib
> jupyter labextension build .

Please supply at least one subcommand: check, disable, enable, install, link, list, uninstall, unlink, update
npm ERR! code ELIFECYCLE
npm ERR! errno 1
npm ERR! [email protected] build:labextension: `jupyter labextension build .`
npm ERR! Exit status 1
npm ERR!
npm ERR! Failed at the [email protected] build:labextension script.
npm ERR! This is probably not a problem with npm. There is likely additional logging output above.

npm ERR! A complete log of this run can be found in:
npm ERR!     /home/jovyan/.npm/_logs/2021-01-15T18_39_44_306Z-debug.log
npm ERR! code ELIFECYCLE
npm ERR! errno 1
npm ERR! [email protected] build: `webpack && npm run build:labextension`
npm ERR! Exit status 1
npm ERR!
npm ERR! Failed at the [email protected] build script.
npm ERR! This is probably not a problem with npm. There is likely additional logging output above.

npm ERR! A complete log of this run can be found in:
npm ERR!     /home/jovyan/.npm/_logs/2021-01-15T18_39_44_318Z-debug.log
info Visit https://yarnpkg.com/en/docs/cli/install for documentation about this command.

npm dependencies failed to install
Traceback (most recent call last):

  File "/opt/conda/lib/python3.8/site-packages/jupyterlab/debuglog.py", line 47, in debug_logging
    yield

  File "/opt/conda/lib/python3.8/site-packages/jupyterlab/labextensions.py", line 104, in start
    build(clean_staging=self.should_clean,

  File "/opt/conda/lib/python3.8/site-packages/jupyterlab/commands.py", line 459, in build
    return handler.build(name=name, version=version, static_url=static_url,

  File "/opt/conda/lib/python3.8/site-packages/jupyterlab/commands.py", line 652, in build
    raise RuntimeError(msg)

RuntimeError: npm dependencies failed to install

Exiting application: jupyter

Here's the output from the complete run log file:

  GNU nano 4.8                                               /home/jovyan/.npm/_logs/2021-01-15T18_39_44_306Z-debug.log                                                          
0 info it worked if it ends with ok
1 verbose cli [
1 verbose cli   '/opt/conda/bin/node',
1 verbose cli   '/opt/conda/bin/npm',
1 verbose cli   'run',
1 verbose cli   'build:labextension'
1 verbose cli ]
2 info using [email protected]
3 info using [email protected]
4 verbose run-script [
4 verbose run-script   'prebuild:labextension',
4 verbose run-script   'build:labextension',
4 verbose run-script   'postbuild:labextension'
4 verbose run-script ]
5 info lifecycle [email protected]~prebuild:labextension: [email protected]
6 info lifecycle [email protected]~build:labextension: [email protected]
7 warn lifecycle The node binary used for scripts is /tmp/yarn--1610735981021-0.8672339414699104/node but npm is using /opt/conda/bin/node itself. Use the `--scripts-prepend-no>
8 verbose lifecycle [email protected]~build:labextension: unsafe-perm in lifecycle true
9 verbose lifecycle [email protected]~build:labextension: PATH: /opt/conda/lib/node_modules/npm/node_modules/npm-lifecycle/node-gyp-bin:/opt/conda/share/jupyter/lab/stag>
10 verbose lifecycle [email protected]~build:labextension: CWD: /opt/conda/share/jupyter/lab/staging/node_modules/jupyter-matplotlib
11 silly lifecycle [email protected]~build:labextension: Args: [ '-c', 'jupyter labextension build .' ]
12 silly lifecycle [email protected]~build:labextension: Returned: code: 1  signal: null
13 info lifecycle [email protected]~build:labextension: Failed to exec build:labextension script
14 verbose stack Error: [email protected] build:labextension: `jupyter labextension build .`
14 verbose stack Exit status 1
14 verbose stack     at EventEmitter.<anonymous> (/opt/conda/lib/node_modules/npm/node_modules/npm-lifecycle/index.js:332:16)
14 verbose stack     at EventEmitter.emit (events.js:315:20)
14 verbose stack     at ChildProcess.<anonymous> (/opt/conda/lib/node_modules/npm/node_modules/npm-lifecycle/lib/spawn.js:55:14)
14 verbose stack     at ChildProcess.emit (events.js:315:20)
14 verbose stack     at maybeClose (internal/child_process.js:1026:16)
14 verbose stack     at Process.ChildProcess._handle.onexit (internal/child_process.js:286:5)
15 verbose pkgid [email protected]
16 verbose cwd /opt/conda/share/jupyter/lab/staging/node_modules/jupyter-matplotlib
17 verbose Linux 4.19.121-linuxkit
18 verbose argv "/opt/conda/bin/node" "/opt/conda/bin/npm" "run" "build:labextension"
19 verbose node v13.13.0
20 verbose npm  v6.14.4
21 error code ELIFECYCLE
22 error errno 1
23 error [email protected] build:labextension: `jupyter labextension build .`
23 error Exit status 1
24 error Failed at the [email protected] build:labextension script.
24 error This is probably not a problem with npm. There is likely additional logging output above.
25 verbose exit [ 1, true ]

Can anyone tell me what's wrong with this and how to fix it?