138 lines
12 KiB
YAML
138 lines
12 KiB
YAML
when:
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- event: manual
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evaluate: 'build == "all"'
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- event: manual
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evaluate: 'build == "redhat-8-arm64"'
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- event: manual
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evaluate: 'build == "all-arm64"'
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skip_clone: true
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steps:
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- name: 'Warming up'
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image: busybox:latest
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failure: ignore
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commands:
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- sleep 300
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- echo "Warmed Up"
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backend_options:
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kubernetes:
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resources:
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requests:
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memory: 14Gi
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cpu: 3000m
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limits:
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memory: 14Gi
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cpu: 3000m
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nodeSelector:
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kubernetes.io/arch: arm64
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node.kubernetes.io/instance-type: cax31
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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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- name: 'Build binaries'
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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/arm64-binaries-r-redhat-8
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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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PLATFORM: redhat-8
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BLOCK: 20500:length(pkgs)
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ARCH: arm64
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NCPUS: 2
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MEMORY: 14Gi
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INSTANCE_TYPE: cax31
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STRATEGY: multisession
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volumes:
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- arm64-binaries-r-dep-cache-redhat-8:/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::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git")'
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- R -q -e 'packageVersion("bincraftR")'
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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, repos = structure(c(devxy = 'https://cran.devxy.io/arm64/rhel8/latest', CRAN = 'https://cloud.r-project.org'))); library(dplyr); library(bincraftR); cran_pkgs = tools::CRAN_package_db()[['Package']]; '%nin%' <- Negate('%in%'); foo = query_metadata_table() |> filter(platform == 'redhat-8', arch == 'arm64') |> distinct(name) |> pull(name); pkgs <- dput(cran_pkgs[cran_pkgs %nin% foo][0:300]); options(progressr.enable = TRUE); pkgs = c('excel.link', 'facmodTS', 'fastFMM', 'FIESTA', 'FIESTAutils', 'filters', 'finch', 'fitbitViz', 'fitlandr', 'forestdata', 'FORTLS', 'FPCdpca', 'frscore', 'fsbrain', 'fsn', 'FTSgof', 'FuzzyImputationTest', 'geoidep', 'geojson', 'geojsonio', 'geppe', 'gerbil', 'ggfacto', 'ggpicrust2', 'glmtoolbox', 'googletraffic', 'gp', 'gpg', 'gpuR', 'handwriterApp', 'handwriterRF', 'HDiR', 'highd2means', 'hillshader', 'HLAtools', 'hypergeo2', 'imbalanceDatRel', 'IMIFA', 'InteRD', 'interpolation', 'irtQ', 'jack', 'kDGLM', 'KeyboardSimulator', 'KMD', 'KPC', 'KSgeneral', 'lgpr', 'LipidomicsR', 'LorMe', 'mapping', 'mathml', 'matRiks', 'mbr', 'mcradds', 'MDSGUI', 'MediaNews', 'mergedblocks', 'metaGE', 'metajam', 'meteo', 'MetSizeR', 'mfpp', 'micd', 'miceRanger', 'minired', 'mixgb', 'mixpoissonreg', 'MLE', 'mlmts', 'MMOC', 'MN', 'moc.gapbk', 'modgo', 'ModTools', 'MonoPhy', 'morphomap', 'mregions2', 'multibiplotGUI', 'mvcauchy', 'mvcor', 'mvhtests', 'naive', 'nebula', 'negligible', 'neo4jshell', 'nesRdata', 'nestedcv', 'NetFACS', 'NetSci', 'nflverse', 'NGBVS', 'NGCHM', 'nlgm', 'nlmixr2', 'nlmixr2plot', 'nmrrr', 'npcurePK', 'obfuscatoR', 'OpenCL', 'parTimeROC', 'Patterns', 'pbANOVA', 'pcaL1', 'pcds.ugraph', 'pchc', 'PCRA', 'pgKDEsphere', 'phylotypr', 'phylter', 'plumberDeploy', 'PNAR', 'polyhedralCubature', 'popstudy', 'PoweREST', 'PPbigdata', 'ppsbm', 'praatpicture', 'practicalSigni', 'PRTree', 'qspray', 'qsub', 'QUALYPSO', 'R2PPT', 'R2wd', 'Racmacs', 'RandomWalker', 'RankAggSIgFUR', 'RAppArmor', 'RationalMatrix', 'ratioOfQsprays', 'ravetools', 'raymolecule', 'Rblpapi', 'Rcatch22', 'rcccd', 'rcompanion', 'rcontroll', 'Rcplex', 'RcppCWB', 'RcppMagicEnum', 'rdflib', 'Rdimtools', 'RDM', 'redland', 'regda', 'resultant', 'Rfast2', 'rFUSION', 'Riemann', 'RInno', 'rmapzen', 'rmarchingcubes', 'RmecabKo', 'Rmpi', 'robin', 'RobRegression', 'robustarima', 'ROI.plugin.cplex', 'ROI.plugin.qpoases', 'ROI.plugin.symphony', 'ROracle', 'RPatternJoin', 'RQuantLib', 'RSP', 'RSquaredMI', 'rStrava', 'Rsymphony', 'rties', 'Rtropical', 'rvMF', 'RWinEdt', 'satdad', 'scDIFtest', 'scMappR', 'segen', 'SEIRfansy', 'SelectBoost', 'SEMdeep', 'sendigR', 'seq2R', 'sevenbridges2', 'SherlockHolmes', 'shiny.benchmark', 'shinyExprPortal', 'shinyIRT', 'shinylive', 'shinyMixR', 'shinyQueryBuilder', 'shinytest2', 'shrinkTVPVAR', 'SIAmodules', 'simCAT', 'simDAG', 'SimNPH', 'smartsnp', 'smcryptoR', 'smvgraph', 'SOMMD', 'SpaCCI', 'spaceNet', 'sparseCov', 'spaths', 'spectralR', 'Spectran', 'spectrino', 'Spectrum', 'splusTimeSeries', 'spStack', 'ssh', 'SSHAARP', 'stppSim', 'surveyvoi', 'symbolicQspray', 'T4cluster', 'tabxplor', 'tame', 'taskscheduleR', 'TDAkit', 'theft', 'theftdlc', 'tidyclust', 'tiledb', 'TML', 'Toothnroll', 'TreeDimensionTest', 'triptych', 'trtswitch', 'truh', 'TSCI', 'tsmarch', 'tspredit', 'twl', 'UBayFS', 'valhallr', 'voiceR', 'vvdoctor', 'WaverideR', 'WCluster', 'webglobe', 'WRI'); pkgs = setdiff(pkgs, c('RInno', 'MediaNews')); progressr::handlers('cli'); progressr::handlers(global = TRUE); foo = lapply(pkgs, function(x) bincraftR::build_binary_package(x, debug = FALSE, force = TRUE, platform = 'redhat-8'))"
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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, debug = FALSE, force = TRUE, platform = "arm64"))'
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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: 14Gi
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cpu: 3000m
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limits:
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memory: 14Gi
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cpu: 3000m
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### PROD-sequential
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# resources:
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# requests:
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# memory: 14Gi
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# cpu: 2000m
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# limits:
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# memory: 14Gi
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# cpu: 3000m
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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: arm64
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node.kubernetes.io/instance-type: cax31
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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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