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Megalinter v6 freezes in Gitlab CI
Megalinter v6 is freezing in Gitlab CI and I'm not sure how to debug. v5.17.0 works flawlessly.
Description
Running megalinter in Gitlab on a shared runner using your suggested template. I disabled parallel execution to debug.
lint-megalinter:
stage: lint
image: oxsecurity/megalinter:v6.5.0
rules:
- if: $CI_MERGE_REQUEST_ID
script: ["true"]
variables:
# All available variables are described in documentation
# https://megalinter.github.io/configuration/
DEFAULT_WORKSPACE: $CI_PROJECT_DIR
PARALLEL: "false"
artifacts:
when: always
paths:
- megalinter-reports
expire_in: 1 week
interruptible: true
It successfully pulls the image and runs until hadolint:
Running with gitlab-runner 15.3.0~beta.42.gdb7789ca (db7789ca)
on blue-4.shared.runners-manager.gitlab.com/default J2nyww-s
Preparing the "docker+machine" executor 03:46
Using Docker executor with image oxsecurity/megalinter:v6.5.0 ...
Pulling docker image oxsecurity/megalinter:v6.5.0 ...
Using docker image sha256:5edff1422a258f93f1ba19a9c48ef1328ef50cabd87054f69eaf9a1aa10970bd for oxsecurity/megalinter:v6.5.0 with digest oxsecurity/megalinter@sha256:586effe9bec89667601bd2168e5576970a648c79b8b5bd2bf19c4440edfb257d ...
Preparing environment 00:04
Running on runner-j2nyww-s-project-18942007-concurrent-0 via runner-j2nyww-s-shared-1660928858-82342b69...
Getting source from Git repository 00:03
$ eval "$CI_PRE_CLONE_SCRIPT"
Fetching changes with git depth set to 50...
Initialized empty Git repository in /builds/schorlton/test/.git/
Created fresh repository.
Checking out 2697be3c as refs/merge-requests/874/head...
Skipping Git submodules setup
Executing "step_script" stage of the job script
Using docker image sha256:5edff1422a258f93f1ba19a9c48ef1328ef50cabd87054f69eaf9a1aa10970bd for oxsecurity/megalinter:v6.5.0 with digest oxsecurity/megalinter@sha256:586effe9bec89667601bd2168e5576970a648c79b8b5bd2bf19c4440edfb257d ...
Setting git safe.directory default: /github/workspace ...
Setting git safe.directory to /tmp/lint ...
[MegaLinter init] ONE-SHOT RUN
[config] /builds/schorlton/test/.mega-linter.yml + Environment variables
----------------------------------------------------------------------------------------------------
------------------------------------ MegaLinter, by OX Security ------------------------------------
----------------------------------------------------------------------------------------------------
- Image Creation Date: 2022-08-15T19:43:12Z
- Image Revision: eca13fcbb
- Image Version: v6.5.0
----------------------------------------------------------------------------------------------------
The MegaLinter documentation can be found at:
- https://oxsecurity.github.io/megalinter/latest
----------------------------------------------------------------------------------------------------
MegaLinter initialization (expand for details)
[Activation] EDITORCONFIG_EDITORCONFIG_CHECKER has been set inactive, as none of these files has been found: ['.editorconfig']
[Activation] JAVASCRIPT_ES has been set inactive, as none of these files has been found: ['.eslintrc.json', '.eslintrc.yml', '.eslintrc.yaml', '.eslintrc.js', '.eslintrc.cjs', 'package.json:eslintConfig']
[Activation] JSX_ESLINT has been set inactive, as none of these files has been found: ['.eslintrc.json', '.eslintrc.yml', '.eslintrc.yaml', '.eslintrc.js', '.eslintrc.cjs', 'package.json:eslintConfig']
[Activation] REPOSITORY_GOODCHECK has been set inactive, as none of these files has been found: ['goodcheck.yml']
[Activation] SPELL_PROSELINT has been set inactive, as none of these files has been found: ['.proselintrc', 'proselint/config.json']
[Activation] SQL_SQLFLUFF has been set inactive, as none of these files has been found: ['.sqlfluff']
[Activation] SWIFT_SWIFTLINT has been set inactive, as none of these files has been found: ['.swiftlint.yml']
[Activation] TSX_ESLINT has been set inactive, as none of these files has been found: ['.eslintrc.json', '.eslintrc.yml', '.eslintrc.yaml', '.eslintrc.js', '.eslintrc.cjs', 'package.json:eslintConfig']
[Activation] TYPESCRIPT_ES has been set inactive, as none of these files has been found: ['.eslintrc.json', '.eslintrc.yml', '.eslintrc.yaml', '.eslintrc.js', '.eslintrc.cjs', 'package.json:eslintConfig']
MARKDOWN_REMARK_LINT has been temporary disabled in MegaLinter, please use a previous MegaLinter version or wait for the next one !
SNAKEMAKE_SNAKEFMT has been temporary disabled in MegaLinter, please use a previous MegaLinter version or wait for the next one !
Skipped linters: ACTION_ACTIONLINT, ANSIBLE_ANSIBLE_LINT, EDITORCONFIG_EDITORCONFIG_CHECKER, JAVASCRIPT_ES, JAVASCRIPT_PRETTIER, JSX_ESLINT, KUBERNETES_KUBECONFORM, KUBERNETES_KUBEVAL, MARKDOWN_REMARK_LINT, PYTHON_BANDIT, PYTHON_MYPY, REPOSITORY_CHECKOV, REPOSITORY_DEVSKIM, REPOSITORY_GOODCHECK, REPOSITORY_SECRETLINT, REPOSITORY_SEMGREP, REPOSITORY_TRIVY, SALESFORCE_SFDX_SCANNER_APEX, SALESFORCE_SFDX_SCANNER_AURA, SALESFORCE_SFDX_SCANNER_LWC, SNAKEMAKE_SNAKEFMT, SPELL_CSPELL, SPELL_PROSELINT, SQL_SQLFLUFF, SWIFT_SWIFTLINT, TERRAFORM_KICS, TERRAFORM_TERRASCAN, TSX_ESLINT, TYPESCRIPT_ES, TYPESCRIPT_PRETTIER
To receive reports as email, please set variable EMAIL_REPORTER_EMAIL
MegaLinter now collects the files to analyse (expand for details)
Listing all files in directory [/builds/schorlton/test], then filter with:
- File extensions: , .R, .RMD, .Rmd, .bash, .c, .c++, .cc, .cdxml, .clj, .cljc, .cljs, .coffee, .cpp, .cs, .css, .cu, .cuh, .cxx, .dart, .dash, .edn, .env, .feature, .go, .gradle, .graphql, .groovy, .gvy, .h, .h++, .hcl, .hh, .hpp, .htm, .html, .hxx, .java, .js, .json, .json5, .jsonc, .ksh, .kt, .kts, .lua, .md, .nf, .p6, .php, .pl, .pl6, .pm, .pm6, .pp, .proto, .ps1, .ps1xml, .psd1, .psm1, .psrc, .pssc, .py, .r, .raku, .rakumod, .rakutest, .rb, .rs, .rst, .saas, .scala, .scss, .sh, .smk, .sql, .t, .tex, .tf, .ts, .vb, .xml, .yaml, .yml
- File names (regex): Dockerfile, Jenkinsfile, Makefile, Snakefile
- Excluding regex: (redacted)
- Excluding .gitignored files [1]: /builds/schorlton/test/megalinter-reports/megalinter.log
Kept [297] files on [316] found files
+----MATCHING LINTERS-------------------+--------------------------------------+----------------+------------+
| Descriptor | Linter | Criteria | Matching files | Format/Fix |
+------------+--------------------------+--------------------------------------+----------------+------------+
| PYTHON | pylint | .py | 84 | no |
| PYTHON | black | .py | 84 | no |
| PYTHON | flake8 | .py | 84 | no |
| PYTHON | isort | .py | 84 | no |
| BASH | bash-exec | .sh|.bash|.dash|.ksh | 26 | no |
| BASH | shellcheck | .sh|.bash|.dash|.ksh | 26 | no |
| BASH | shfmt | .sh|.bash|.dash|.ksh | 26 | no |
| COPYPASTE | jscpd | | project | no |
| DOCKERFILE | hadolint | Dockerfile | 50 | no |
| GROOVY | npm-groovy-lint | .groovy|.gvy|.gradle|.nf|Jenkinsfile | 55 | no |
| JSON | jsonlint | .json | 7 | no |
| JSON | eslint-plugin-jsonc | .json|.json5|.jsonc | 7 | no |
| JSON | v8r | .json | 7 | no |
| JSON | prettier | .json | 7 | no |
| MARKDOWN | markdownlint | .md | 5 | no |
| MARKDOWN | markdown-link-check | .md | 5 | no |
| MARKDOWN | markdown-table-formatter | .md | 5 | no |
| PROTOBUF | protolint | .proto | 1 | no |
| REPOSITORY | dustilock | | project | no |
| REPOSITORY | git_diff | | project | no |
| REPOSITORY | gitleaks | | project | no |
| REPOSITORY | syft | | project | no |
| SPELL | misspell | | 297 | no |
| TERRAFORM | tflint | .tf | 6 | no |
| TERRAFORM | terragrunt | .hcl | 1 | no |
| TERRAFORM | terraform-fmt | .tf | 6 | no |
| TERRAFORM | checkov | .tf | 6 | no |
| YAML | prettier | .yml|.yaml | 8 | no |
| YAML | yamllint | .yml|.yaml | 8 | no |
| YAML | v8r | .yml|.yaml | 8 | no |
+------------+--------------------------+--------------------------------------+----------------+------------+
✅ Linted [PYTHON] files with [pylint] successfully - (14.14s) (expand for details)
- Using [pylint v2.14.5] https://oxsecurity.github.io/megalinter/latest/v6.5.0/descriptors/python_pylint
- MegaLinter key: [PYTHON_PYLINT]
- Rules config: [.pylintrc]
- Number of files analyzed: [84]
✅ Linted [PYTHON] files with [black] successfully - (3.62s) (expand for details)
- Using [black v22.6.0] https://oxsecurity.github.io/megalinter/latest/v6.5.0/descriptors/python_black
- MegaLinter key: [PYTHON_BLACK]
- Rules config: [pyproject.toml]
- Number of files analyzed: [84]
✅ Linted [PYTHON] files with [flake8] successfully - (2.62s) (expand for details)
- Using [flake8 v5.0.4] https://oxsecurity.github.io/megalinter/latest/v6.5.0/descriptors/python_flake8
- MegaLinter key: [PYTHON_FLAKE8]
- Rules config: [/builds/schorlton/test/.flake8]
- Number of files analyzed: [84]
✅ Linted [PYTHON] files with [isort] successfully - (0.3s) (expand for details)
- Using [isort v5.10.1] https://oxsecurity.github.io/megalinter/latest/v6.5.0/descriptors/python_isort
- MegaLinter key: [PYTHON_ISORT]
- Rules config: [/builds/schorlton/test/.isort.cfg]
- Number of files analyzed: [84]
✅ Linted [BASH] files with [bash-exec] successfully - (0.11s) (expand for details)
- Using [bash-exec v5.1.16] https://oxsecurity.github.io/megalinter/latest/v6.5.0/descriptors/bash_bash_exec
- MegaLinter key: [BASH_EXEC]
- Rules config: identified by [bash-exec]
- Number of files analyzed: [26]
✅ Linted [BASH] files with [shellcheck] successfully - (0.57s) (expand for details)
- Using [shellcheck v0.8.0] https://oxsecurity.github.io/megalinter/latest/v6.5.0/descriptors/bash_shellcheck
- MegaLinter key: [BASH_SHELLCHECK]
- Rules config: identified by [shellcheck]
- Number of files analyzed: [26]
✅ Linted [BASH] files with [shfmt] successfully - (0.11s) (expand for details)
- Using [shfmt v3.6.0] https://oxsecurity.github.io/megalinter/latest/v6.5.0/descriptors/bash_shfmt
- MegaLinter key: [BASH_SHFMT]
- Rules config: identified by [shfmt]
- Number of files analyzed: [26]
✅ Linted [COPYPASTE] files with [jscpd] successfully - (4.07s) (expand for details)
- Using [jscpd v3.3.26] https://oxsecurity.github.io/megalinter/latest/v6.5.0/descriptors/copypaste_jscpd
- MegaLinter key: [COPYPASTE_JSCPD]
- Rules config: [.jscpd.json]
✅ Linted [DOCKERFILE] files with [hadolint] successfully - (3.33s) (expand for details)
- Using [hadolint v2.10.0] https://oxsecurity.github.io/megalinter/latest/v6.5.0/descriptors/dockerfile_hadolint
- MegaLinter key: [DOCKERFILE_HADOLINT]
- Rules config: [/builds/schorlton/test/.hadolint.yaml]
- Number of files analyzed: [50]
At this point, it times out after an hour. The linting works flawlessly in v6 locally and is quick. When I follow along locally, it seems that npm-groovy-lint runs after hadolint, so I wonder if this is what is freezing?
Thanks for any tips!
I would try running with LOG_LEVEL: DEBUG and DISABLE_LINTERS: GROOVY. If you can prove that a particular linter is hanging, then I would try running it directly to assess whether the issue is related to MegaLinter.
@schorlton I recently released a new npm-groovy-lint version that can accept a list of files Please could you disable groovy like suggested by @Kurt-von-Laven , so we can know if npm-groovy-lint is responsible for the timeout ?
Or any chance we could have access to the gitlab repo ?
(if npm-groovy-lint is guilty, you may also use GROOVY_NPM_GROOVY_LINT_CLI_LINT_MODE: file, it will be slower but may work before a fix is published )
Thank you both for your feedback. I'm confirming it's npm-groovy-lint, and changing GROOVY_NPM_GROOVY_LINT_CLI_LINT_MODE did not help. The linting works locally which makes me think maybe it's a resource limitation of the GitLab CI environment? It's weird that it broke going from v5 to v6. I unfortunately cannot provide access to our repo, but please let me know if there's any other debugging I can help with. You may be able to reproduce this issue by simply running a big (several hundred line) file through npm-groovy-lint on GitLab CI - in file mode, it looks like it was frozen on the first file.
Please can you try defining the following in your MegaLinter config file ?
GROOVY_NPM_GROOVY_LINT_ARGUMENTS: --noserver
Please can you try defining the following in your MegaLinter config file ? GROOVY_NPM_GROOVY_LINT_ARGUMENTS: --noserver
Should I also keep GROOVY_NPM_GROOVY_LINT_CLI_LINT_MODE: file or remove that before running?
you can try first to remove GROOVY_NPM_GROOVY_LINT_CLI_LINT_MODE: file and see what happens with only GROOVY_NPM_GROOVY_LINT_ARGUMENTS: --noserver :)
you can try first to remove
GROOVY_NPM_GROOVY_LINT_CLI_LINT_MODE: fileand see what happens with onlyGROOVY_NPM_GROOVY_LINT_ARGUMENTS: --noserver:)
That fixed it!! :smile:
Addendum: premature excitement. It got further but freezes on:
npm-groovy-lint results in 128 linted files:
┌─────────┬───────────┬─────────────┐
│ (index) │ Severity │ Total found │
├─────────┼───────────┼─────────────┤
│ 0 │ 'Error' │ 0 │
│ 1 │ 'Warning' │ 7 │
│ 2 │ 'Info' │ 129 │
└─────────┴───────────┴─────────────┘
Failure: 0 error(s) have been found
7 warning(s) have been found
129 info(s) have been found
Linter version command: ['/node-deps/node_modules/.bin/npm-groovy-lint', '--version']
You may want to try running npm-groovy-lint directly in GitLab CI (without MegaLinter). If you can reproduce the hang that way, this probably belongs in npm-groovy-lint's issue tracker. Maybe they need to expose a config option that limits resource consumption in some way?
@schorlton Oh, so the --version is boring :o Do you have some public repo where I could see the problem ?
@Kurt-von-Laven "they" is kind of .... me 🤣 I'm the creator/maintainer of npm-groovy-lint... and only maintainer 😭
@Kurt-von-Laven - yes I'm sorry for polluting megalinter repo with likely external issue. Thanks for understanding. @nvuillam - big thanks for your help on debugging. Unfortunately, this is a private repo and I can't share as it's protected IP. My best suggestion is to try running in gitlab CI on ~128 nextflow files with ~129 infos and ~7 warnings...perhaps running on one of the nf-core repos may reproduce?
That may indeed be caused by the big amount of nextflow files.... I'll test with npm-groovy-lint and try to pimp it :)
@nvuillam, wondering if you've been able to reproduce? Would be really nice to switch to Megalinter v6 with all of its improvements, but this is precluding the switch. Thanks!
@schorlton I'm finalizing a pull request on codenarc to arrange that, then it will arrive in npm-groovy-lint, then megalinter :) Slow but progressing :)
Amazing. If I understand, it was a performance issue? Was too many files crashing it on Gitlab due to resource constraints?
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@schorlton I have to wait for CodeNarc new release... they are not frequent as MegaLinter... ^^
https://github.com/CodeNarc/CodeNarc