122 lines
12 KiB
YAML
122 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-9-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-9
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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-9
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BLOCK: 20615: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-9:/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/rhel9/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-9', arch == 'arm64') |> distinct(name) |> pull(name); pkgs <- dput(cran_pkgs[cran_pkgs %nin% foo][0:300]); options(progressr.enable = TRUE); pkgs = c('adamethods', 'adaptIVPT', 'AFM', 'aIc', 'alphashape3d', 'Anthropometry', 'Apollonius', 'archeoViz', 'Arothron', 'atom4R', 'bigGP', 'bio.infer', 'BiplotGUI', 'blatr', 'BNSP', 'bpca', 'brainKCCA', 'brainR', 'BRugs', 'candisc', 'ChaosGame', 'choosepc', 'circularEV', 'ClaimsProblems', 'clintrialx', 'clrng', 'ClusROC', 'cncaGUI', 'concom', 'ConfidenceEllipse', 'ConsRank', 'ConsRankClass', 'controlfunctionIV', 'cops', 'CovTools', 'crumble', 'cubing', 'curvHDR', 'dataone', 'datapack', 'dbcsp', 'dcortools', 'dcorVS', 'deductive', 'deepgp', 'deform', 'deformula', 'degreenet', 'Delaporte', 'deldir', 'demu', 'DendSer', 'denim', 'densEstBayes', 'depcache', 'depcoeff', 'DepthProc', 'descr', 'deseats', 'desla', 'deSolve', 'detectRUNS', 'DetMCD', 'DetR', 'detrendr', 'devEMF', 'devoid', 'dexter', 'dexterMST', 'dfcomb', 'dfms', 'dfmta', 'dfphase1', 'dfsaneacc', 'dggridR', 'dglars', 'DGM', 'dgof', 'DGP4LCF', 'dgumbel', 'diagis', 'DiceDesign', 'DiceKriging', 'diceR', 'didimputation', 'DIDmultiplegtDYN', 'diffIRT', 'diffmatchpatch', 'diffobj', 'diffudist', 'DIFM', 'digest', 'DIME', 'dina', 'dipm', 'dipsaus', 'diptest', 'Dire', 'DIRECT', 'DirichletReg', 'DirStats', 'disaggregation', 'disbayes', 'disclapmix2', 'DiSCos', 'DiscreteDists', 'discretefit', 'disk.frame', 'dismo', 'dispeRse', 'distances', 'distcomp', 'distops', 'distory', 'divDyn', 'diveR', 'diversitree', 'diversityForest', 'divest', 'divo', 'dixon', 'dixonTest', 'do3PCA', 'doMPI', 'doolkit', 'dti', 'dymo', 'eDITH', 'eegkit', 'espadon', 'ETRep', 'Evomorph', 'excel.link', 'export', 'fabisearch', 'facmodTS', 'fdaPDE', 'filters', 'fingerPro', 'fitbitViz', 'fmdu', 'FPCdpca', 'fsbrain', 'gellipsoid', 'gensphere', 'geoelectrics', 'GoodFibes', 'GPGame', 'GPoM', 'gpuR', 'Greymodels', 'gyro', 'HDiR', 'hillshader', 'HUM', 'HybridMicrobiomes', 'hyper.fit', 'icosa', 'ICSClust', 'IOLS', 'ivdoctr', 'JFM', 'JSDNE', 'kernhaz', 'KernSmoothIRT', 'KeyboardSimulator', 'kml3d', 'kpcaIG', 'KSgeneral', 'lgpr', 'LSAfun', 'Maeswrap', 'maotai', 'mcauchyd', 'MDSGUI', 'MDSMap', 'MediaNews', 'metadynminer3d', 'metajam', 'mggd', 'minired', 'MLE', 'moc.gapbk', 'molaR', 'morph', 'Morpho', 'morphomap', 'MorphoTools2', 'mregions2', 'mstudentd', 'mully', 'multibiplotGUI', 'MultiscaleDTM', 'MultivariateAnalysis', 'mvhist', 'mvinfluence', 'mvmesh', 'nat', 'nat.nblast', 'nat.templatebrains', 'nesRdata', 'NGCHM', 'nltm', 'Nmix', 'nmixgof', 'nmslibR', 'nnet', 'nnlib2Rcpp', 'nnls', 'nodeSub', 'noisysbmGGM', 'noncompliance', 'nonlinearTseries', 'nonmem2rx', 'nonneg.cg', 'nonprobsvy', 'nopaco', 'norm', 'NormPsy', 'nortestARMA', 'not', 'np', 'NPBayesImputeCat', 'npcp', 'npcure', 'NPflow', 'npregfast', 'nprobust', 'npROCRegression', 'npsf', 'npsp', 'NScluster', 'nse', 'numbat', 'numberofalleles', 'Numero', 'numOSL', 'NUSS', 'nvmix', 'o2geosocial', 'o2plsda', 'obliqueRSF', 'OBsMD', 'oc', 'oce', 'OceanView', 'ocf', 'OCNet', 'odbc', 'odeGUTS', 'ODRF', 'oeli', 'oem', 'offlineChange', 'ohenery', 'ohoegdm', 'olctools', 'OncoBayes2', 'oncomsm', 'ondisc', 'oneclust', 'onehot', 'onemap', 'onion', 'onlineCOV', 'onlineforecast', 'onlinePCA', 'ontologySimilarity', 'opa', 'OpenCL', 'openCR', 'opencv', 'OpenImageR', 'OpenMx', 'openssl', 'openxlsx', 'oppr', 'Opt5PL', 'OptCirClust', 'OptGS', 'OptHedging', 'optimization', 'optiSel', 'optmatch', 'optpart', 'opusminer', 'orca', 'Orcs', 'ordinalgmifs', 'ore', 'orf', 'ORION', 'orsk', 'orthoDr', 'osc', 'oscar', 'OSFD', 'oskeyring', 'osmdata', 'osqp'); 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-9'))"
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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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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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