[REVIEW]: NiMARE: Neuroimaging Meta-Analysis Research Environment

[roboneuro]

Submitting author: @tsalo (Taylor Salo) Repository: https://github.com/NBCLab/nimare-paper Editor: @pbellec Reviewers: @agahkarakuzu Jupyter Book: http://neurolibre-data-prod.conp.cloud/book-artifacts/roboneurolibre/github.com/nimare-paper/0195c842c8b6f5d42150df814500a9aadb05cc75/_build/html/ Repository archive: 10.5281/zenodo.6624793 Data archive: 10.5281/zenodo.6624795 Book archive: 10.5281/zenodo.6624790 Docker archive: 10.5281/zenodo.6624797

Status

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Reviewer instructions & questions

@ltetrel, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @pbellec know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @ltetrel

Conflict of interest

• [ ] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• [ ] I confirm that I read and will adhere to the NeuroLibre code of conduct.

General checks

• [ ] Repository: Is the source code for this software available at the repository url?
• [ ] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [ ] Contribution and authorship: Has the submitting author (@tsalo) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [ ] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• [ ] Installation: Does installation proceed as outlined in the documentation?
• [ ] Functionality: Have the functional claims of the software been confirmed?
• [ ] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• [ ] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [ ] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [ ] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [ ] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [ ] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [ ] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• [ ] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [ ] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [ ] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [ ] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[roboneuro]

Hello human, I'm @roboneuro, a robot that can help you with some common editorial tasks. @ltetrel it looks like you're currently assigned to review this paper :tada:.

:star: Important :star:

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/neurolibre/neurolibre-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

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@roboneuro commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@roboneuro generate pdf

[roboneuro]

:point_right::page_facing_up: View built NeuroLibre Notebook :page_facing_up::point_left:

[roboneuro]

PDF failed to compile for issue #7 with the following error:

[WARNING] Could not convert image '/tmp/tex2pdf.-717850ee2d77f491/3bf6210ae27218adb13345ecb2c5cbeeb7270898.shtml': Cannot load file Jpeg Invalid marker used PNG Invalid PNG file, signature broken Bitmap Invalid Bitmap magic identifier GIF Invalid Gif signature :

HDR Invalid radiance file signature Tiff Invalid endian tag value TGA Invalid bit depth (104) Error producing PDF. ! LaTeX Error: Cannot determine size of graphic in /tmp/tex2pdf.-717850ee2d77f4 91/3bf6210ae27218adb13345ecb2c5cbeeb7270898.shtml (no BoundingBox).

See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ...

l.372 ...0ae27218adb13345ecb2c5cbeeb7270898.shtml}

[ltetrel]

@roboneuro commands

[roboneuro]

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[ltetrel]

@roboneuro generate nl-notebook

[roboneuro]

:seedling: We are currently building your NeuroLibre notebook! Good things take time :seedling:

[ltetrel]

@tsalo we will see at the end of the day.

🤞

[roboneuro]

:point_right::page_facing_up: View built NeuroLibre Notebook :page_facing_up::point_left:

[ltetrel]

@tsalo you forgot to remove the jupyter cache folder so it can re-execute on the cluster.

[tsalo]

Sorry about that. The build files should be gone now.

[ltetrel]

@roboneuro generate nl-notebook

[roboneuro]

:seedling: We are currently building your NeuroLibre notebook! Good things take time :seedling:

[roboneuro]

We ran into a problem building your book. :(

Click here to see build log

      ["Cloning into '/tmp/repo2dockermet4gz9z'...\\n", "HEAD is now at 099fa11 Remove build files so it will execute on NeuroLibre.\\n", "Using PythonBuildPack builder\\n", "Step 1/51 : FROM buildpack-deps:bionic", "\\n", " ---> cb3fc72df6ea\\n", "Step 2/51 : ENV DEBIAN_FRONTEND=noninteractive", "\\n", " ---> Using cache\\n", " ---> 72acdf6eec08\\n", "Step 3/51 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends locales > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*", "\\n", " ---> Using cache\\n", " ---> f214f4f3bf44\\n", "Step 4/51 : RUN echo \\\"en_US.UTF-8 UTF-8\\\" > /etc/locale.gen &&     locale-gen", "\\n", " ---> Using cache\\n", " ---> 272e81f97e82\\n", "Step 5/51 : ENV LC_ALL en_US.UTF-8", "\\n", " ---> Using cache\\n", " ---> 1d018c152688\\n", "Step 6/51 : ENV LANG en_US.UTF-8", "\\n", " ---> Using cache\\n", " ---> 6db3fe2db2c9\\n", "Step 7/51 : ENV LANGUAGE en_US.UTF-8", "\\n", " ---> Using cache\\n", " ---> a8006ae656a8\\n", "Step 8/51 : ENV SHELL /bin/bash", "\\n", " ---> Using cache\\n", " ---> c9c153c437dd\\n", "Step 9/51 : ARG NB_USER", "\\n", " ---> Using cache\\n", " ---> 5b3a4e779e3b\\n", "Step 10/51 : ARG NB_UID", "\\n", " ---> Using cache\\n", " ---> 3ac38dfe60a4\\n", "Step 11/51 : ENV USER ${NB_USER}", "\\n", " ---> Using cache\\n", " ---> ecb84a25dfb6\\n", "Step 12/51 : ENV HOME /home/${NB_USER}", "\\n", " ---> Using cache\\n", " ---> 646007b142dd\\n", "Step 13/51 : RUN groupadd         --gid ${NB_UID}         ${NB_USER} &&     useradd         --comment \\\"Default user\\\"         --create-home         --gid ${NB_UID}         --no-log-init         --shell /bin/bash         --uid ${NB_UID}         ${NB_USER}", "\\n", " ---> Using cache\\n", " ---> 1a6b5dec6d96\\n", "Step 14/51 : RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key |  apt-key add - &&     DISTRO=\\\"bionic\\\" &&     echo \\\"deb https://deb.nodesource.com/node_14.x $DISTRO main\\\" >> /etc/apt/sources.list.d/nodesource.list &&     echo \\\"deb-src https://deb.nodesource.com/node_14.x $DISTRO main\\\" >> /etc/apt/sources.list.d/nodesource.list", "\\n", " ---> Using cache\\n", " ---> 32b750d70868\\n", "Step 15/51 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends        less        nodejs        unzip        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*", "\\n", " ---> Using cache\\n", " ---> 0ef56e9173a5\\n", "Step 16/51 : EXPOSE 8888", "\\n", " ---> Using cache\\n", " ---> 40dfbe8cd55f\\n", "Step 17/51 : ENV APP_BASE /srv", "\\n", " ---> Using cache\\n", " ---> 6098a639283d\\n", "Step 18/51 : ENV NPM_DIR ${APP_BASE}/npm", "\\n", " ---> Using cache\\n", " ---> 01b8f22c7c90\\n", "Step 19/51 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc", "\\n", " ---> Using cache\\n", " ---> 345e5c4b8ca1\\n", "Step 20/51 : ENV CONDA_DIR ${APP_BASE}/conda", "\\n", " ---> Using cache\\n", " ---> 5eba253d8b0a\\n", "Step 21/51 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook", "\\n", " ---> Using cache\\n", " ---> a468da77aa68\\n", "Step 22/51 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock", "\\n", " ---> Using cache\\n", " ---> e00d76c2d1e8\\n", "Step 23/51 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}", "\\n", " ---> Using cache\\n", " ---> 2e3bf763600b\\n", "Step 24/51 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}", "\\n", " ---> Using cache\\n", " ---> 0916f8beeff0\\n", "Step 25/51 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2factivate-2dconda-2esh-391af5 /etc/profile.d/activate-conda.sh", "\\n", " ---> Using cache\\n", " ---> 9ca86ff64b56\\n", "Step 26/51 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2epy-2d3-2e7-2elock-4f1154 /tmp/env/environment.lock", "\\n", " ---> Using cache\\n", " ---> 35e64af9a217\\n", "Step 27/51 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2finstall-2dminiforge-2ebash-514214 /tmp/install-miniforge.bash", "\\n", " ---> Using cache\\n", " ---> 5967f5817f5f\\n", "Step 28/51 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}", "\\n", " ---> Using cache\\n", " ---> a98db9c66e77\\n", "Step 29/51 : USER ${NB_USER}", "\\n", " ---> Using cache\\n", " ---> d91473d71da3\\n", "Step 30/51 : RUN npm config --global set prefix ${NPM_DIR}", "\\n", " ---> Using cache\\n", " ---> 13947f195972\\n", "Step 31/51 : USER root", "\\n", " ---> Using cache\\n", " ---> 3c0507fc7bee\\n", "Step 32/51 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm -rf /tmp/install-miniforge.bash /tmp/env", "\\n", " ---> Using cache\\n", " ---> a5bef3504f13\\n", "Step 33/51 : ARG REPO_DIR=${HOME}", "\\n", " ---> Using cache\\n", " ---> 917d5ab6ceaa\\n", "Step 34/51 : ENV REPO_DIR ${REPO_DIR}", "\\n", " ---> Using cache\\n", " ---> 3bc3a53544d4\\n", "Step 35/51 : WORKDIR ${REPO_DIR}", "\\n", " ---> Using cache\\n", " ---> d9143e5fd05a\\n", "Step 36/51 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}", "\\n", " ---> Using cache\\n", " ---> ad54a4a5a927\\n", "Step 37/51 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}", "\\n", " ---> Using cache\\n", " ---> 6ec422525566\\n", "Step 38/51 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}", "\\n", " ---> Using cache\\n", " ---> 24f0c971901e\\n", "Step 39/51 : COPY --chown=1000:1000 src/binder/requirements.txt ${REPO_DIR}/binder/requirements.txt", "\\n", " ---> Using cache\\n", " ---> 5a2e900153dd\\n", "Step 40/51 : USER ${NB_USER}", "\\n", " ---> Using cache\\n", " ---> ba2b26fcdf25\\n", "Step 41/51 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r \\\"binder/requirements.txt\\\"", "\\n", " ---> Using cache\\n", " ---> 4d5da7870846\\n", "Step 42/51 : COPY --chown=1000:1000 src/ ${REPO_DIR}", "\\n", " ---> 8a11f869fb88\\n", "Step 43/51 : LABEL repo2docker.ref=\\\"099fa11dd7678afec6915e381a8fe3fe473f7d20\\\"", "\\n", " ---> Running in f92084a107ea\\n", "Removing intermediate container f92084a107ea\\n", " ---> ac09eef02760\\n", "Step 44/51 : LABEL repo2docker.repo=\\\"https://github.com/NBCLab/nimare-paper\\\"", "\\n", " ---> Running in 6b59a9253003\\n", "Removing intermediate container 6b59a9253003\\n", " ---> e5632be7e4f9\\n", "Step 45/51 : LABEL repo2docker.version=\\\"2021.08.0\\\"", "\\n", " ---> Running in c03e5d5a3d4b\\n", "Removing intermediate container c03e5d5a3d4b\\n", " ---> f7e6fdf3ba84\\n", "Step 46/51 : USER ${NB_USER}", "\\n", " ---> Running in dba2a31cad5c\\n", "Removing intermediate container dba2a31cad5c\\n", " ---> 1b20f002a5a3\\n", "Step 47/51 : ENV PYTHONUNBUFFERED=1", "\\n", " ---> Running in aa46e0ddf245\\n", "Removing intermediate container aa46e0ddf245\\n", " ---> b4034bb12187\\n", "Step 48/51 : COPY /python3-login /usr/local/bin/python3-login", "\\n", " ---> e9687e163938\\n", "Step 49/51 : COPY /repo2docker-entrypoint /usr/local/bin/repo2docker-entrypoint", "\\n", " ---> 6fc1055b7022\\n", "Step 50/51 : ENTRYPOINT [\\\"/usr/local/bin/repo2docker-entrypoint\\\"]", "\\n", " ---> Running in 2e8780c4b441\\n", "Removing intermediate container 2e8780c4b441\\n", " ---> 03a7620869e8\\n", "Step 51/51 : CMD [\\\"jupyter\\\", \\\"notebook\\\", \\\"--ip\\\", \\\"0.0.0.0\\\"]", "\\n", " ---> Running in 6f9bf86f0803\\n", "Removing intermediate container 6f9bf86f0803\\n", " ---> 50e71f5825ee\\n", "{\\\"aux\\\": {\\\"ID\\\": \\\"sha256:50e71f5825ee2ff9624d2ca559c88e1ae7ea9d77f1ae1ed1bc42b640505bf2d2\\\"}}", "Successfully built 50e71f5825ee\\n", "Successfully tagged binder-registry.conp.cloud/binder-registry.conp.cloud/binder-nbclab-2dnimare-2dpaper-3e379f:099fa11dd7678afec6915e381a8fe3fe473f7d20\\n", "Pushing image\\n\", \"progress\": {\"b9380779ad7f\": 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\"dfafca59dbc4\": \"Layer already exists\", \"a389027da55b\": \"Layer already exists\", \"2a5c062238ae\": \"Layer already exists\", \"47fce20e9787\": \"Layer already exists\", \"862636b3aca5\": \"Layer already exists\", \"2a06b1849fd3\": \"Layer already exists\", \"0f8c4e4b509c\": \"Layer already exists\", \"285aab7aae38\": \"Layer already exists\", \"0c2c837b295e\": \"Layer already exists\", \"2e6bfb4089f3\": \"Layer already exists\", \"b0eb2032f1da\": \"Layer already exists\", \"1ab6ee41ee9a\": \"Layer already exists\", \"824821e7a1be\": \"Layer already exists\", \"824bf068fd3d\": \"Layer already exists\"}, \"layers\": {\"b9380779ad7f\": {\"status\": \"Pushed\", \"progressDetail\": {}, \"id\": \"b9380779ad7f\"}, \"b324385f0c96\": {\"status\": \"Pushed\", \"progressDetail\": {}, \"id\": \"b324385f0c96\"}, \"633f008b83bf\": {\"status\": \"Pushed\", \"progressDetail\": {}, \"id\": \"633f008b83bf\"}, \"b64f374f2875\": {\"status\": \"Layer already exists\", \"progressDetail\": {}, \"id\": 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\"2a06b1849fd3\": {\"status\": \"Layer already exists\", \"progressDetail\": {}, \"id\": \"2a06b1849fd3\"}, \"0f8c4e4b509c\": {\"status\": \"Layer already exists\", \"progressDetail\": {}, \"id\": \"0f8c4e4b509c\"}, \"285aab7aae38\": {\"status\": \"Layer already exists\", \"progressDetail\": {}, \"id\": \"285aab7aae38\"}, \"0c2c837b295e\": {\"status\": \"Layer already exists\", \"progressDetail\": {}, \"id\": \"0c2c837b295e\"}, \"2e6bfb4089f3\": {\"status\": \"Layer already exists\", \"progressDetail\": {}, \"id\": \"2e6bfb4089f3\"}, \"b0eb2032f1da\": {\"status\": \"Layer already exists\", \"progressDetail\": {}, \"id\": \"b0eb2032f1da\"}, \"1ab6ee41ee9a\": {\"status\": \"Layer already exists\", \"progressDetail\": {}, \"id\": \"1ab6ee41ee9a\"}, \"824821e7a1be\": {\"status\": \"Layer already exists\", \"progressDetail\": {}, \"id\": \"824821e7a1be\"}, \"824bf068fd3d\": {\"status\": \"Layer already exists\", \"progressDetail\": {}, \"id\": \"824bf068fd3d\"}", "Successfully pushed binder-registry.conp.cloud/binder-registry.conp.cloud/binder-nbclab-2dnimare-2dpaper-3e379f:099fa11dd7678afec6915e381a8fe3fe473f7d20", "Built image, launching...\\n", "server running at https://binder.conp.cloud/jupyter/user/nbclab-nimare-paper-54fetsl0/\\n\", \"image\": \"binder-registry.conp.cloud/binder-registry.conp.cloud/binder-nbclab-2dnimare-2dpaper-3e379f:099fa11dd7678afec6915e381a8fe3fe473f7d20\", \"repo_url\": \"https://github.com/NBCLab/nimare-paper\", \"token\": \"pHjXcrPZRc-P0gYlrErbUQ\", \"binder_ref_url\": \"https://github.com/NBCLab/nimare-paper/tree/099fa11dd7678afec6915e381a8fe3fe473f7d20\", \"binder_launch_host\": \"https://binder.conp.cloud/\", \"binder_request\": \"v2/gh/NBCLab/nimare-paper.git/099fa11dd7678afec6915e381a8fe3fe473f7d20\", \"binder_persistent_request\": \"v2/gh/NBCLab/nimare-paper/099fa11dd7678afec6915e381a8fe3fe473f7d20"]
      

[ltetrel]

Just added a check to create the (empty) jupyter cache directory if does not exist, so jupyter-book build does not fail.

[ltetrel]

@roboneuro generate nl-notebook

[roboneuro]

:seedling: We are currently building your NeuroLibre notebook! Good things take time :seedling:

[ltetrel]

@tsalo the book execution is at this stage after 3 hours, does that makes sense for you?

Running Jupyter-Book v0.11.3
Source Folder: /home/jovyan/content
Config Path: /home/jovyan/content/_config.yml
Output Path: /mnt/books/NBCLab/github.com/nimare-paper/099fa11dd7678afec6915e381a8fe3fe473f7d20/_build/html
Running Sphinx v3.5.4
Adding copy buttons to code blocks...
Adding copy buttons to code blocks...
[etoc] Changing master_doc to 'abstract'
checking for /home/jovyan/paper.bib in bibtex cache... not found
parsing bibtex file /home/jovyan/paper.bib... parsed 97 entries
myst v0.13.7: MdParserConfig(renderer='sphinx', commonmark_only=False, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, update_mathjax=True, enable_extensions=['colon_fence', 'dollarmath', 'linkify', 'substitution'], disable_syntax=[], url_schemes=['mailto', 'http', 'https'], heading_anchors=None, html_meta=[], footnote_transition=True, substitutions=[], sub_delimiters=['{', '}'])
MyST-NB: Excluded Paths: set()
loading intersphinx inventory from _static/nimare_v0_0_10_objects.inv...
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 18 source files that are out of date
updating environment: MyST-NB: Potential docnames to execute: ['acknowledgements', 'ibma', 'abstract', 'bibliography', 'decoding', 'future_directions', 'introduction', 'summary', 'about_derivative_analyses', 'macm', 'cbma', 'appendices/brainmap_decoding', 'resources', 'overview', 'annotation', 'subtraction', 'correction', 'appendices/neurosynth_decoding']
executing outdated notebooks... Executing: /home/jovyan/content/ibma.md
Execution Succeeded: /home/jovyan/content/ibma.md
Executing: /home/jovyan/content/decoding.md
Executing: /home/jovyan/content/macm.md
Executing: /home/jovyan/content/cbma.md
Executing: /home/jovyan/content/resources.md
Executing: /home/jovyan/content/annotation.md
Executing: /home/jovyan/content/subtraction.md
Executing: /home/jovyan/content/correction.md

[tsalo]

I think that makes sense. When I ran it on my university's HPC, the correction step was the last slow one and it took ~1 hour.

[ltetrel]

ok good, it is the first time that we test the caching mechanism with retries, so I wanted to make sure that it works well :)

[ltetrel]

Hmm I think there was an issue with the caching, just pushed a fix and re-trying

[ltetrel]

@roboneuro generate nl-notebook

[roboneuro]

:seedling: We are currently building your NeuroLibre notebook! Good things take time :seedling:

[ltetrel]

@tsalo it will help me if you are able to give some minimalistic benchmarks for your notebooks, i.e. time execution for each. I am trying to understand how the jupyter-book caching works, and how it can be used with our limitations.

[tsalo]

I've added a couple of lines to print out the duration of each notebook. Should I build it on the FIU HPC and paste the durations here after it finishes, or would the log from the NeuroLibre build work?

[ltetrel]

Because we never succeded to build it once from zero, I think we have no choice to have from your HPC yes :'(

[ltetrel]

The issue might be because jupyter cache save its state notebook-wise and not cell-wise. So if one notebook takes more than 1h to run (hitting our 1h limit for one pass), it will in-definitively try to re-execute without cache re-use (cache not saved since whole notebook did not complete). Still investigating anyway :)

[tsalo]

Here are the durations from the FIU HPC:

• resources: 0:22:56.817754
• cbma: 0:21:25.588111
• ibma: 0:01:04.950397
• correction: 1:07:13.050189
• subtraction: 0:45:12.813117
• macm: 0:11:49.228726
• annotation: 0:02:17.743660
• decoding: 0:42:19.029345

I ended up pushing the HTML files so I could check the results easily, but I can remove them so that the book will build from scratch if you ask roboneuro to generate it again. Should I remove those files?

[ltetrel]

alright thanks @tsalo. Because the build does not use this folder anymore, it will not change the build status. You pushed all the build content or just some files ?

[tsalo]

It should be all of the build content. I'm glad it won't cause any problems.

[ltetrel]

Ok, I am still investigating if the issue is on jupyter caching. Comparing an old cache vs the most recent one.

[ltetrel]

Alright, @tsalo I think this is definitively due to the fact that correction.md takes more than one hour. Looking at the jupyter-book cache, it is indeed notebook-wise and not cell-wise as I thought (not sure why they did that, the ipynb checkpoints are cell-wise....). For example, this is your cache:

get_cache("nimare_cache_ref").list_cache_records()[0].to_dict()
{'hashkey': '341799c0d9acea3225b6bd2fe301fb31', 'description': '', 'created': datetime.datetime(2021, 10, 17, 13, 16, 51, 452338), 'pk': 1, 'uri': '/home/data/nbc/misc-projects/Salo_NiMARE/nimare-paper/content/cbma.md', 'data': {'execution_seconds': 404.3186927679926}, 'accessed': datetime.datetime(2021, 10, 19, 2, 13, 15, 502273)}

Just to make sure I am doing a final test today (because I updated some cluster config) and if it fails, then I will need you to break your notebooks so all of them execute in less than an hour (correction.md). Will let you know,

[tsalo]

I can cut down the number of permutations in the multiple comparisons correction step, which should reduce its duration. If that's the only problematic notebook, then that one change should be enough, right?

[ltetrel]

I can cut down the number of permutations in the multiple comparisons correction step, which should reduce its duration. If that's the only problematic notebook, then that one change should be enough, right?

Yes! Ideally if you make it run in ~50min (to take into account potential additionnal usage on our side) that would be great.

[tsalo]

I cut the number of iterations from 10000 to 5000 just now, so that should substantially reduce the build time for that notebook.

[ltetrel]

@roboneuro generate nl-notebook

[roboneuro]

:seedling: We are currently building your NeuroLibre notebook! Good things take time :seedling:

[roboneuro]

We ran into a problem building your book. :(

Click here to see build log

      ["Cloning into '/tmp/repo2dockermt3g8uxo'...\\n", "HEAD is now at eaf0b42 Cut Monte Carlo iterations to 5000.\\n", "Using PythonBuildPack builder\\n", "Step 1/51 : FROM buildpack-deps:bionic", "\\n", " ---> cb3fc72df6ea\\n", "Step 2/51 : ENV DEBIAN_FRONTEND=noninteractive", "\\n", " ---> Using cache\\n", " ---> 02b5fe258a88\\n", "Step 3/51 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends locales > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*", "\\n", " ---> Using cache\\n", " ---> 7723e2ab2b36\\n", "Step 4/51 : RUN echo \\\"en_US.UTF-8 UTF-8\\\" > /etc/locale.gen &&     locale-gen", "\\n", " ---> Using cache\\n", " ---> f359f24d94b5\\n", "Step 5/51 : ENV LC_ALL en_US.UTF-8", "\\n", " ---> Using cache\\n", " ---> 6276e131c31e\\n", "Step 6/51 : ENV LANG en_US.UTF-8", "\\n", " ---> Using cache\\n", " ---> f938f4c705c2\\n", "Step 7/51 : ENV LANGUAGE en_US.UTF-8", "\\n", " ---> Using cache\\n", " ---> 315ab9f77383\\n", "Step 8/51 : ENV SHELL /bin/bash", "\\n", " ---> Using cache\\n", " ---> 9085d274d9a3\\n", "Step 9/51 : ARG NB_USER", "\\n", " ---> Using cache\\n", " ---> b0d7321ef3bb\\n", "Step 10/51 : ARG NB_UID", "\\n", " ---> Using cache\\n", " ---> a7c1356f3093\\n", "Step 11/51 : ENV USER ${NB_USER}", "\\n", " ---> Using cache\\n", " ---> 2aa184680286\\n", "Step 12/51 : ENV HOME /home/${NB_USER}", "\\n", " ---> Using cache\\n", " ---> 1ddd30194e07\\n", "Step 13/51 : RUN groupadd         --gid ${NB_UID}         ${NB_USER} &&     useradd         --comment \\\"Default user\\\"         --create-home         --gid ${NB_UID}         --no-log-init         --shell /bin/bash         --uid ${NB_UID}         ${NB_USER}", "\\n", " ---> Using cache\\n", " ---> b4f39039ff5c\\n", "Step 14/51 : RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key |  apt-key add - &&     DISTRO=\\\"bionic\\\" &&     echo \\\"deb https://deb.nodesource.com/node_14.x $DISTRO main\\\" >> /etc/apt/sources.list.d/nodesource.list &&     echo \\\"deb-src https://deb.nodesource.com/node_14.x $DISTRO main\\\" >> /etc/apt/sources.list.d/nodesource.list", "\\n", " ---> Using cache\\n", " ---> 63401797a001\\n", "Step 15/51 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends        less        nodejs        unzip        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*", "\\n", " ---> Using cache\\n", " ---> 3de70ee474b7\\n", "Step 16/51 : EXPOSE 8888", "\\n", " ---> Using cache\\n", " ---> 767a3594a01b\\n", "Step 17/51 : ENV APP_BASE /srv", "\\n", " ---> Using cache\\n", " ---> 2927326a645b\\n", "Step 18/51 : ENV NPM_DIR ${APP_BASE}/npm", "\\n", " ---> Using cache\\n", " ---> c73216c94c36\\n", "Step 19/51 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc", "\\n", " ---> Using cache\\n", " ---> fce96bf8747f\\n", "Step 20/51 : ENV CONDA_DIR ${APP_BASE}/conda", "\\n", " ---> Using cache\\n", " ---> 1df834c2d52e\\n", "Step 21/51 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook", "\\n", " ---> Using cache\\n", " ---> b1b0f8b85487\\n", "Step 22/51 : ENV NB_ENVIRONMENT_FILE /tmp/env/environment.lock", "\\n", " ---> Using cache\\n", " ---> 11c076718dec\\n", "Step 23/51 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}", "\\n", " ---> Using cache\\n", " ---> ba856f66cd22\\n", "Step 24/51 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}", "\\n", " ---> Using cache\\n", " ---> c1d9814cc1b9\\n", "Step 25/51 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2factivate-2dconda-2esh-391af5 /etc/profile.d/activate-conda.sh", "\\n", " ---> Using cache\\n", " ---> 847820fe0b21\\n", "Step 26/51 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2epy-2d3-2e7-2elock-4f1154 /tmp/env/environment.lock", "\\n", " ---> Using cache\\n", " ---> 1823a219cfa4\\n", "Step 27/51 : COPY --chown=1000:1000 build_script_files/-2fusr-2flib-2fpython3-2e8-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2finstall-2dminiforge-2ebash-514214 /tmp/install-miniforge.bash", "\\n", " ---> Using cache\\n", " ---> a219e5b3836a\\n", "Step 28/51 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}", "\\n", " ---> Using cache\\n", " ---> 4cdc2be62996\\n", "Step 29/51 : USER ${NB_USER}", "\\n", " ---> Using cache\\n", " ---> e68790eb2eb7\\n", "Step 30/51 : RUN npm config --global set prefix ${NPM_DIR}", "\\n", " ---> Using cache\\n", " ---> 167cf6a99158\\n", "Step 31/51 : USER root", "\\n", " ---> Using cache\\n", " ---> c569a97625e5\\n", "Step 32/51 : RUN TIMEFORMAT='time: %3R' bash -c 'time /tmp/install-miniforge.bash' && rm -rf /tmp/install-miniforge.bash /tmp/env", "\\n", " ---> Using cache\\n", " ---> c2985f604c42\\n", "Step 33/51 : ARG REPO_DIR=${HOME}", "\\n", " ---> Using cache\\n", " ---> 7f3d1f5072d2\\n", "Step 34/51 : ENV REPO_DIR ${REPO_DIR}", "\\n", " ---> Using cache\\n", " ---> 515ed35d6be5\\n", "Step 35/51 : WORKDIR ${REPO_DIR}", "\\n", " ---> Using cache\\n", " ---> 4ab86ee14a53\\n", "Step 36/51 : RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR}", "\\n", " ---> Using cache\\n", " ---> 9112082605e9\\n", "Step 37/51 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}", "\\n", " ---> Using cache\\n", " ---> 618fab06d00a\\n", "Step 38/51 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}", "\\n", " ---> Using cache\\n", " ---> 6720236bb76e\\n", "Step 39/51 : COPY --chown=1000:1000 src/binder/requirements.txt ${REPO_DIR}/binder/requirements.txt", "\\n", " ---> Using cache\\n", " ---> 13be4d14872f\\n", "Step 40/51 : USER ${NB_USER}", "\\n", " ---> Using cache\\n", " ---> ee1ee6c04e43\\n", "Step 41/51 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r \\\"binder/requirements.txt\\\"", "\\n", " ---> Using cache\\n", " ---> a41fcf850dff\\n", "Step 42/51 : COPY --chown=1000:1000 src/ ${REPO_DIR}", "\\n", " ---> 9b49d3238042\\n", "Step 43/51 : LABEL repo2docker.ref=\\\"eaf0b42c8794f59b511d4aec9d26d1da672cd907\\\"", "\\n", " ---> Running in 10307e1293a8\\n", "Removing intermediate container 10307e1293a8\\n", " ---> 3721cb95f04e\\n", "Step 44/51 : LABEL repo2docker.repo=\\\"https://github.com/NBCLab/nimare-paper\\\"", "\\n", " ---> Running in 850c78deee83\\n", "Removing intermediate container 850c78deee83\\n", " ---> 26ccdfd3aeba\\n", "Step 45/51 : LABEL repo2docker.version=\\\"2021.08.0\\\"", "\\n", " ---> Running in 35385392fe17\\n", "Removing intermediate container 35385392fe17\\n", " ---> a9725b16196e\\n", "Step 46/51 : USER ${NB_USER}", "\\n", " ---> Running in 1e7434b12dae\\n", "Removing intermediate container 1e7434b12dae\\n", " ---> 253c6cebadaf\\n", "Step 47/51 : ENV PYTHONUNBUFFERED=1", "\\n", " ---> Running in ac92220114f7\\n", "Removing intermediate container ac92220114f7\\n", " ---> a4fc31bb527a\\n", "Step 48/51 : COPY /python3-login /usr/local/bin/python3-login", "\\n", " ---> d099333a4eaf\\n", "Step 49/51 : COPY /repo2docker-entrypoint /usr/local/bin/repo2docker-entrypoint", "\\n", " ---> c759129f19bd\\n", "Step 50/51 : ENTRYPOINT [\\\"/usr/local/bin/repo2docker-entrypoint\\\"]", "\\n", " ---> Running in 36bd860ff1f7\\n", "Removing intermediate container 36bd860ff1f7\\n", " ---> 506b21f3ff24\\n", "Step 51/51 : CMD [\\\"jupyter\\\", \\\"notebook\\\", \\\"--ip\\\", \\\"0.0.0.0\\\"]", "\\n", " ---> Running in e1f2f9b2e692\\n", "Removing intermediate container e1f2f9b2e692\\n", " ---> 69036594fbe4\\n", "{\\\"aux\\\": {\\\"ID\\\": \\\"sha256:69036594fbe459a0d02759e983b6db34b82ee301ba820e26aa95b3b9abc00df4\\\"}}", "Successfully built 69036594fbe4\\n", "Successfully tagged binder-registry.conp.cloud/binder-registry.conp.cloud/binder-nbclab-2dnimare-2dpaper-3e379f:eaf0b42c8794f59b511d4aec9d26d1da672cd907\\n", "Pushing image\\n\", \"progress\": {\"f534f4e5d85b\": \"Pushed\", \"aca1e90d4add\": \"Pushed\", 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\"progressDetail\": {}, \"id\": \"824821e7a1be\"}, \"824bf068fd3d\": {\"status\": \"Layer already exists\", \"progressDetail\": {}, \"id\": \"824bf068fd3d\"}", "Successfully pushed binder-registry.conp.cloud/binder-registry.conp.cloud/binder-nbclab-2dnimare-2dpaper-3e379f:eaf0b42c8794f59b511d4aec9d26d1da672cd907", "Built image, launching...\\n", "server running at https://binder.conp.cloud/jupyter/user/nbclab-nimare-paper-lh8iz0jr/\\n\", \"image\": \"binder-registry.conp.cloud/binder-registry.conp.cloud/binder-nbclab-2dnimare-2dpaper-3e379f:eaf0b42c8794f59b511d4aec9d26d1da672cd907\", \"repo_url\": \"https://github.com/NBCLab/nimare-paper\", \"token\": \"wfZKrUufR8CwcvS9Vgi7vQ\", \"binder_ref_url\": \"https://github.com/NBCLab/nimare-paper/tree/eaf0b42c8794f59b511d4aec9d26d1da672cd907\", \"binder_launch_host\": \"https://binder.conp.cloud/\", \"binder_request\": \"v2/gh/NBCLab/nimare-paper.git/eaf0b42c8794f59b511d4aec9d26d1da672cd907\", \"binder_persistent_request\": \"v2/gh/NBCLab/nimare-paper/eaf0b42c8794f59b511d4aec9d26d1da672cd907"]
      

[ltetrel]

@roboneuro generate nl-notebook

[roboneuro]

:seedling: We are currently building your NeuroLibre notebook! Good things take time :seedling:

[roboneuro]

:point_right::page_facing_up: View built NeuroLibre Notebook :page_facing_up::point_left:

[pbellec]

so the figures seem to be missing from the built notebook, and I also tried to re-run decoding.md on the server and it crashed :/

[ltetrel]

Re-tried another build under the hood, but it failed also (even though jupyter book build succeeded this time): http://neurolibre-data.conp.cloud/book-artifacts/NBCLab/github.com/nimare-paper/eaf0b42c8794f59b511d4aec9d26d1da672cd907/book-build.log

And no, jupyter-book does not give the option to fail a build if the underlying notebook execution failed, so basically the cluster thinks it succeded. I will have no choice to hack my way to scan the book log file and detect if execution failed or not...

[ltetrel]

so the figures seem to be missing from the built notebook, and I also tried to re-run decoding.md on the server and it crashed :/

Did not try yet to execute directly on the server, what was the output ?

[pbellec]

no output, kernel dies. It does not seem to run out of memory though (it caps at 1.2GB/2 GB, although it may simply not have time to update before dying).

[ltetrel]

Alright, I think I will need to upgarde the RAM to 4G on test anyway because it needs to be the same as prod.

[ltetrel]

@tsalo do you know the (peak) RAM consumption for your submission ? Just tried and it crashes also on mybinder.org

[ltetrel]

@roboneuro generate nl-notebook

[roboneuro]

:point_right::page_facing_up: View built NeuroLibre Notebook :page_facing_up::point_left:

[ltetrel]

ups, deleting old artifacts now...