167 lines
10 KiB
YAML
167 lines
10 KiB
YAML
when:
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event: [manual]
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skip_clone: true
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depends_on:
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- warm_up_build
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matrix:
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include:
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# - PLATFORM: redhat-9
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# BLOCK: 4810:length(pkgs)
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# ARCH: arm64
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# NCPUS: 2
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# MEMORY: 29Gi
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# STRATEGY: future.callr::callr
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# - PLATFORM: redhat-8
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# BLOCK: 4503:length(pkgs)
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# ARCH: arm64
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# NCPUS: 2
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# MEMORY: 29Gi
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# STRATEGY: future.callr::callr
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# - PLATFORM: ubuntu-2404
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# BLOCK: 5301:length(pkgs)
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# ARCH: arm64
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# NCPUS: 2
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# MEMORY: 29Gi
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# STRATEGY: future.callr::callr
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# - PLATFORM: ubuntu-2204
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# BLOCK: 5849:length(pkgs)
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# ARCH: arm64
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# NCPUS: 2
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# MEMORY: 29Gi
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# STRATEGY: future.callr::callr
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- PLATFORM: alpine-320
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BLOCK: 4602:length(pkgs)
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ARCH: arm64
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NCPUS: 2
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MEMORY: 29Gi
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STRATEGY: multisession
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# ### AMD
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# - PLATFORM: redhat-9
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# BLOCK: 4573:length(pkgs)
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# ARCH: amd64
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# NCPUS: 2
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# MEMORY: 29Gi
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# STRATEGY: future.callr::callr
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# - PLATFORM: redhat-8
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# BLOCK: 3908:length(pkgs)
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# ARCH: amd64
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# NCPUS: 2
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# MEMORY: 29Gi
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# STRATEGY: future.callr::callr
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# - PLATFORM: ubuntu-2404
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# BLOCK: 6256:length(pkgs)
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# ARCH: amd64
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# NCPUS: 2
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# MEMORY: 29Gi
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# STRATEGY: future.callr::callr
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# - PLATFORM: ubuntu-2204
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# BLOCK: 7293:length(pkgs)
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# ARCH: amd64
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# NCPUS: 2
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# MEMORY: 29Gi
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# STRATEGY: future.callr::callr
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- PLATFORM: alpine-320
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BLOCK: 4487:length(pkgs)
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ARCH: amd64
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NCPUS: 2
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MEMORY: 29Gi
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STRATEGY: multisession
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steps:
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- name: 'Build binaries (${PLATFORM}: ${BLOCK})'
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secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token, GITHUB_PAT]
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image: docker.io/devxygmbh/${ARCH}-binaries-r-${PLATFORM}
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pull: true
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# to ensure the PACKAGES upload step is being executed
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failure: ignore
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environment:
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GIT_USER: pat-s
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# set the location of the 'pkgcache' cache dir which persists the R package dependencies needed to install the packages themselves
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R_PKG_CACHE_DIR: /mnt/cache/pkgcache
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R_LIBS_USER: /mnt/cache/R-pkgs
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CCACHE_DIR: /mnt/cache/ccache
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volumes:
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- ${ARCH}-binaries-r-dep-cache-${PLATFORM}:/mnt/cache
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commands:
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# download latest package version (avoid having to rebuild image every time)
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# rscript_startup arg: required to pass down global option to future workers https://github.com/HenrikBengtsson/future/issues/134#issuecomment-2245666169
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- git clone https://pat-s:$$git_ro_token@git.devxy.io/devxy/r-pkg-binaries.git .
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- rm -rf /mnt/cache/R-pkgs/00LOCK-r-pkg-binaries /mnt/cache/R-pkgs/00LOCK-bincraftR
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# for some reason paks pkgcache is often corrupt
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- rm -rf /mnt/cache/R-pkgs/pkgcache/ /mnt/cache/pkgcache/ /root/.cache/R/
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- R -q -e 'pak::meta_update()'
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- R CMD INSTALL .
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# more complicated system dependencies which pak cannot resolve
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- mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages
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# set additional repos: important as otherwise some packages cannot be resolved (e.g. INLA). Also: setting our own binary repos so we can make use of them for dep installation at some point
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### Check
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# - Rsymphony/ROI.plugin.symphony/adea/PortfolioAnalytics -> can't install/link external SYMPHONY lib (only on RHEL, as for others syslib exists)
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# - Rglpk
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# biplotbootGUI: somehow ubuntu still hangs even when using xvfb-run
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- xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = ${NCPUS}, future.globals.onReference = NULL); pkgs = tools::CRAN_package_db()[[1]]; pkgs = setdiff(pkgs, c("biplotbootGUI", "Rsymphony", "PortfolioAnalytics", "ROI.plugin.symphony", "adea", "RInno", "skedastic", "RPushbullet", "SimNPH", "SimDesign","simCAT", "SIAmodules", "shinytest2", "shinyIRT", "ShinyItemAnalysis", "shiny.benchmark", "scDIFtest", "RSP", "ROracle", "ROI.plugin.qpoases", "ROI.plugin.cplex", "RmecabKo", "rmarchingcubes", "RcppMeCab", "Rcplex", "ravetools", "Rbeast", "Rblpapi", "RcppEnsmallen", "qtkit", "priorCON", "prior3D", "PerFit", "outlierensembles", "nomnoml", "mxfda", "MultBiplotR", "mstDIF", "mdsr", "makepipe", "lordif", "KSgeneral", "kequate", "jstager", "jrt", "irtreliability", "irtQ", "irtpwr", "irtawsi", "GRShiny", "gpuR", "googletraffic", "giacR", "gamstransfer", "aflps", "flow", "filters", "faoutlier", "equateIRT", "EnrichIntersect", "EFA.dimensions", "DFIT", "D3mirt", "ctgdist", "CoTiMA", "ConvertPar", "clrng", "bscui", "BifactorIndicesCalculator", "autoFC", "airt")); library(bincraftR); future::plan("${STRATEGY}", workers = ${NCPUS}, rscript_startup = quote(options(crayon.enabled = TRUE))); options(progressr.enable = TRUE); progressr::handlers("cli"); progressr::handlers(global = TRUE); foo = lapply(pkgs[${BLOCK}], function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = "${PLATFORM}"))'
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### Manual pkg builds
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# webshot2, tabledown, TestAnaAPP, trekcolors, Spectran, SimNPH, RPushbullet, SimDesign, simCAT, SIAmodules, shinytest2, ShinyItemAnalysis, shinyIRT, shiny.benchmark, scDIFtest, RSP, qtkit, PROsetta, prettifyAddins, PerFit, outlierensembles, nomnoml, mxfda, MultBiplotR, mstDIF, mdsr, makepipe, lordif, kequate, jstager, jrt, irtreliability, irtQ, irtpwr, irtGUI, irtawsi, GRShiny, GPCMlasso, googletraffic, giacR, flps, flow, faoutlier, equateIRT, EnrichIntersect, EFA.dimensions, DFIT, D3mirt, ctgdist, CoTiMA, ConvertPar, bscui, BifactorIndicesCalculator, autoFC, airt: wait for https://github.com/rstudio/r-system-requirements/pull/178
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# RInno: Windows-only
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# skedastic: waiting for ROI.plugin.qpoases (https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1)
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# rswipl: ccache issues: https://github.com/mgondan/rswipl/issues/3 -> solved
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# Rpoppler: https://github.com/rstudio/r-system-requirements/pull/179/
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# ROracle: sysdep missing -> create rule
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# ROI.plugin.qpoases: https://gitlab.com/roigrp/solver/ROI.plugin.qpoases/-/issues/1
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# ROI.plugin.cplex: checking for cplex... no -> requires propriatary software IBM Cplex
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# RmecabKo: fatal error: mecab.h: No such file or directory
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# rmarchingcubes: error: narrowing conversion of '-1' from 'int' to 'char' [-Wnarrowing] -> https://github.com/shwilks/rmarchingcubes/issues/3
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# RcppMeCab: /bin/bash: line 2: mecab-config: command not found -> https://github.com/rstudio/r-system-requirements/pull/180
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# Rcplex: checking for cplex... no -> requires propriatary software IBM Cplex
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# Rblpapi: Unknown architecture: aarch64. Exiting. -> https://github.com/Rblp/Rblpapi/issues/399
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# Rbeast: aarch64 issue -> https://github.com/zhaokg/Rbeast/issues/29
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# ravetools: checking for FFTW... configure: error: Package requirements (fftw3) were not met: -> fftw3 rule needed
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# Racmacs -> rmarchingcubes
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# minic: /usr/include/c++/13/bits/stl_algo.h:5805:5: note: template argument deduction/substitution failed:
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# KSgeneral -> aligned_mem.h:6:10: fatal error: mm_malloc.h: No such file or directory -> https://github.com/d-dimitrova/KSgeneral/issues/1
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# gpuR -> /usr/bin/ld: cannot find -lOpenCL: No such file or directory -> no GPU avail
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# clrng -> gpuR
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# BRugs: configure: error: OpenBUGS 3.2.2 or later not found. as it is only one package, not doing anything
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# gamstransfer -> gdx/src/gdlib/gmsstrm.cpp:85:70: error: narrowing conversion of '-1' from 'std::char_traits<char>::int_type' {aka 'int'} to 'char' [-Wnarrowing] -> https://github.com/GAMS-dev/transfer-r/issues/2
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# filters: <simpleError: `target` must be a character vector containing no `NA` values.> -> email sent
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# magickGUI, biplotbootGUI
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# ymd (alpine, voi)
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# tfrmtbuilder -> V8 (alpine)
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# Rcmdr (alpine)
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# readstata13 (alpine)
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# - xvfb-run R -q -e 'options(crayon.enabled = TRUE, Ncpus = ${NCPUS}, future.globals.onReference = NULL); pkgs = c( "RcmdrPlugin.orloca", "RcmdrPlugin.PcaRobust", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.ROC", "RcmdrPlugin.sos" , "RcmdrPlugin.survival", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.TeachStat", "RcmdrPlugin.temis", "RcmdrPlugin.UCA", "RcmdrPlugin.WorldFlora", "streamDAG", "stan4bart", "snplinkage", "saeHB.panel.beta", "rTwig", "rswipl", "RPointCloud", "rPDBapi", "rolog", "rmcfs", "rjags", "ResultModelManager", "RcppCWB", "RcmdrPlugin.WorldFlora", "RcmdrPlugin.UCA", "RcmdrPlugin.temis", "RcmdrPlugin.TeachStat", "RcmdrPlugin.TeachingDemos", "RcmdrPlugin.survival", "RcmdrPlugin.sos", "RcmdrPlugin.ROC", "RcmdrPlugin.RMTCJags", "RcmdrPlugin.RiskDemo", "RcmdrPlugin.PcaRobust", "RclusTool", "Rbeast", "rayrender", "quanteda.textmodels", "polmineR", "plotBart", "NlinTS", "ndtv", "overtureR", "mathml", "magickGUI", "lgpr", "KappaGUI", "historicalborrow", "GSODR", "GRIDCOPULA", "googleAnalyticsR", "fluidsynth", "EventDetectGUI", "evalITR", "EBcoBART", "deeptrafo", "dbarts", "CRE", "countSTAR", "bartMan", "bartCause", "altmeta", "EthSEQ", "dartR.spatial", "dartR.sim", "gwid", "Mega2R", "priorCON", "prior3D", "MCARtest", "designmatch", "highs", "ROI.plugin.highs", "GPCMlasso"); library(bincraftR); options(progressr.enable = TRUE); foo = lapply(pkgs, function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = "${PLATFORM}"))'
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backend_options:
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kubernetes:
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### PROD-parallel
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resources:
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requests:
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memory: ${MEMORY}
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cpu: 12000m
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limits:
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memory: ${MEMORY}
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cpu: 16000m
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### PROD-sequential
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# resources:
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# requests:
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# memory: ${MEMORY}
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# cpu: 2000m
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# limits:
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# memory: 29Gi
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# cpu: 4000m
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# DEBUG
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# resources:
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# requests:
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# memory: 4Gi
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# cpu: 2000m
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# limits:
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# memory: 4Gi
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# cpu: 2000m
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nodeSelector:
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kubernetes.io/arch: '${ARCH}'
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tolerations:
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- key: 'CI'
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operator: 'Equal'
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value: 'true'
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effect: 'NoSchedule'
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