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 == "ubuntu-2204-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-ubuntu-2204
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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: ubuntu-2204
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BLOCK: 20653: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-ubuntu-2204:/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 /mnt/cache/R-pkgs/gert
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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 -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/jammy/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 == 'ubuntu-2204', arch == 'arm64') |> distinct(name) |> pull(name); pkgs <- dput(cran_pkgs[cran_pkgs %nin% foo][0:300]); options(progressr.enable = TRUE); pkgs = c('aIc', 'asremlPlus', 'assignR', 'BiplotGUI', 'blatr', 'BNSP', 'BRugs', 'clrng', 'deeptrafo', 'doconv', 'excel.link', 'fBasics', 'filters', 'gpuR', 'imbalanceDatRel', 'IMIFA', 'KeyboardSimulator', 'KSgeneral', 'lgpr', 'MDSGUI', 'MediaNews', 'minired', 'R2PPT', 'R2wd', 'Racmacs', 'ravetools', 'Rblpapi', 'Rcplex', 'RcppCWB', 'redatamx', 'rFUSION', 'Rmpi', 'RWinEdt', 'simplexreg', 'simplextree', 'simPop', 'simputation', 'SimReg', 'simRestore', 'SiMRiv', 'simStateSpace', 'simstudy', 'SimSurvNMarker', 'simts', 'singR', 'SiPhyNetwork', 'SIRmcmc', 'sirt', 'sirus', 'sisireg', 'SIT', 'SITH', 'sitmo', 'sits', 'SK4FGA', 'SKAT', 'sketching', 'SKFCPD', 'sklarsomega', 'skm', 'skpr', 'slasso', 'slcm', 'sld', 'sleev', 'slfm', 'SLHD', 'SLOPE', 'slp', 'smaa', 'smam', 'smartsnp', 'smcryptoR', 'smfishHmrf', 'smfsb', 'smile', 'SMITIDvisu', 'SMMA', 'SMME', 'smmR', 'smoof', 'smooth', 'SmoothHazard', 'smoothSurv', 'smurf', 'SMUT', 'sna', 'SnowballC', 'SNPknock', 'snplist', 'snpsettest', 'SNSeg', 'SobolSequence', 'socceR', 'social', 'sodium', 'SoftBart', 'softImpute', 'som', 'sorcering', 'SoundexBR', 'sourcetools', 'sox', 'sp', 'spAbundance', 'spacefillr', 'SpaceTimeBSS', 'SpaCOAP', 'SpaDES.tools', 'spam', 'spam64', 'spaMM', 'sparcl', 'SparseChol', 'sparseDFM', 'sparsegl', 'sparseHessianFD', 'sparseinv', 'SparseLPM', 'sparseLTSEigen', 'SparseM', 'SPARSEMODr', 'sparsereg', 'sparsesvd', 'sparseSVM', 'SparseTSCGM', 'sparsevb', 'sparsevctrs', 'sparsio', 'sparta', 'sparvaride', 'spass', 'spate', 'spatgraphs', 'spaths', 'spatial', 'SpatialBSS', 'SpatialEpi', 'SpatialExtremes', 'SpatialGEV', 'spatialising', 'SpatialKDE', 'SpatialKWD', 'SpatialPack', 'spatialreg', 'spatialrisk', 'SpatialTools', 'spatialwarnings', 'spatialwidget', 'SpatMCA', 'SpaTopic', 'SpatPCA', 'spatstat.Knet', 'spatstat.linnet', 'spatstat.model', 'spatstat.random', 'spatstat.sparse', 'spbal', 'spBayes', 'spBayesSurv', 'spBFA', 'Spbsampling', 'spc', 'spCP', 'spcr', 'spdep', 'spduration', 'speakeasyR', 'SPECIES', 'specklestar', 'specs', 'SpecsVerification', 'spectralGraphTopology', 'Spectran', 'spectre', 'spectrino', 'sped', 'speedytax', 'spfa', 'spFW', 'spGARCH', 'spgs', 'spgwr', 'sphunif', 'spiderbar', 'spikeslab', 'spinBayes', 'splancs', 'SPlit', 'SplitGLM', 'SplitReg', 'splmm', 'splusTimeDate', 'splusTimeSeries', 'spMC', 'spNNGP', 'spOccupancy', 'sport', 'spray', 'spreadr', 'springer', 'sprintr', 'SPSP', 'spsurv', 'spTDyn', 'SpTe2M', 'spTimer', 'squat', 'srm', 'ssh', 'Sshaped', 'SSLR', 'ssMousetrack', 'SSN2', 'SSOSVM', 'sspse', 'sstvars', 'stable', 'staggered', 'stan4bart', 'StanMoMo', 'STAREG', 'starma', 'starsExtra', 'STARTdesign', 'starvz', 'statcomp', 'statgenIBD', 'statgenQTLxT', 'statip', 'STB', 'stcos', 'stcpR6', 'stdvectors', 'steepness', 'stelfi', 'stepPlr', 'steps', 'StepSignalMargiLike', 'stepSplitReg', 'StepwiseTest', 'stfit', 'stima', 'stlplus', 'StochBlock', 'stochQN', 'stockR', 'stocks', 'stosim', 'stpm', 'stpp', 'stpphawkes', 'strat', 'stratEst', 'StrathE2E2', 'stratification', 'strawr', 'stream', 'streambugs', 'strex', 'strider', 'string2path', 'stringdist', 'stringfish', 'stringi', 'stringmagic', 'striprtf', 'strucchangeRcpp', 'StuteTest', 'subplex', 'subrank', 'SubTite', 'SubTS', 'sumFREGAT', 'SummaryLasso', 'sumR', 'sumSome', 'supclust', 'supercells', 'SuperExactTest', 'SuperGauss', 'SuperpixelImageSegmentation', 'SuperRanker', 'SuppDists', 'surbayes', 'sureLDA', 'SurrogateBMA', 'SurrogateRegression', 'surtvep', 'survAUC', 'survC1', 'surveil', 'SurvEval', 'surveybootstrap', 'surveygraph', 'surveysd', 'surveyvoi', 'survIDINRI', 'survidm', 'survival'); 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 = 'ubuntu-2204'))"
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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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