This repository has been archived by the owner on Oct 12, 2023. It is now read-only.
-
Notifications
You must be signed in to change notification settings - Fork 49
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Moved all rAzureBatch logic to doAzureParallel
- Loading branch information
Showing
4 changed files
with
194 additions
and
13 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,177 @@ | ||
| .addTask <- function(jobId, taskId, ...){ | ||
| storageCredentials <- getStorageCredentials() | ||
|
|
||
| args <- list(...) | ||
| .doAzureBatchGlobals <- args$envir | ||
| argsList <- args$args | ||
| packages <- args$packages | ||
| dependsOn <- args$dependsOn | ||
|
|
||
| if(!is.null(argsList)){ | ||
| assign('argsList', argsList, .doAzureBatchGlobals) | ||
| } | ||
|
|
||
| envFile <- paste0(taskId, ".rds") | ||
| saveRDS(.doAzureBatchGlobals, file = envFile) | ||
| uploadBlob(jobId, paste0(getwd(), "/", envFile)) | ||
| file.remove(envFile) | ||
|
|
||
| sasToken <- constructSas("r", "c", jobId, storageCredentials$key) | ||
|
|
||
| taskPrep <- getInstallationCommand(packages) | ||
| rCommand <- sprintf("Rscript --vanilla --verbose $AZ_BATCH_JOB_PREP_WORKING_DIR/%s %s %s > %s.txt", "worker.R", "$AZ_BATCH_TASK_WORKING_DIR", envFile, taskId) | ||
|
|
||
| resultFile <- paste0(taskId, "-result", ".rds") | ||
| logsCommand <- sprintf("env PATH=$PATH blobxfer %s %s %s --upload --saskey $BLOBXFER_SASKEY --remoteresource logs/%s", storageCredentials$name, jobId, paste0(taskId, ".txt"), paste0(taskId, ".txt")) | ||
| autoUploadCommand <- sprintf("env PATH=$PATH blobxfer %s %s %s --upload --saskey $BLOBXFER_SASKEY --remoteresource result/%s", storageCredentials$name, jobId, resultFile, resultFile) | ||
| downloadCommand <- sprintf("env PATH=$PATH blobxfer %s %s %s --download --saskey $BLOBXFER_SASKEY --remoteresource . --include result/*.rds", storageCredentials$name, jobId, "$AZ_BATCH_TASK_WORKING_DIR") | ||
| logsCommand <- sprintf("env PATH=$PATH blobxfer %s %s %s --upload --saskey $BLOBXFER_SASKEY --remoteresource logs/%s", storageCredentials$name, jobId, paste0(taskId, ".txt"), paste0(taskId, ".txt")) | ||
|
|
||
| commands <- c("export PATH=/anaconda/envs/py35/bin:$PATH", downloadCommand, rCommand, logsCommand, autoUploadCommand) | ||
| if(taskPrep != ""){ | ||
| commands <- c(taskPrep, commands) | ||
| } | ||
|
|
||
| sasToken <- constructSas("rwcl", "c", jobId, storageCredentials$key) | ||
| sasQuery <- generateSasUrl(sasToken) | ||
|
|
||
| setting = list(name = "BLOBXFER_SASKEY", | ||
| value = sasQuery) | ||
|
|
||
| resourceFiles <- list(generateResourceFile(storageCredentials$name, jobId, envFile, sasToken)) | ||
|
|
||
| addTask(jobId, | ||
| taskId, | ||
| environmentSettings = list(setting), | ||
| resourceFiles = resourceFiles, | ||
| commandLine = linuxWrapCommands(commands)) | ||
| } | ||
|
|
||
| .addTaskMerge <- function(jobId, taskId, ...){ | ||
| storageCredentials <- getStorageCredentials() | ||
|
|
||
| args <- list(...) | ||
| .doAzureBatchGlobals <- args$envir | ||
| argsList <- args$args | ||
| packages <- args$packages | ||
| numOfTasks <- args$numOfTasks | ||
| dependsOn <- args$dependsOn | ||
|
|
||
| if(!is.null(argsList)){ | ||
| assign('argsList', argsList, .doAzureBatchGlobals) | ||
| } | ||
|
|
||
| envFile <- paste0(taskId, ".rds") | ||
| saveRDS(.doAzureBatchGlobals, file = envFile) | ||
| uploadBlob(jobId, paste0(getwd(), "/", envFile)) | ||
| file.remove(envFile) | ||
|
|
||
| sasToken <- constructSas("r", "c", jobId, storageCredentials$key) | ||
|
|
||
| taskPrep <- getInstallationCommand(packages) | ||
| rCommand <- sprintf("Rscript --vanilla --verbose $AZ_BATCH_JOB_PREP_WORKING_DIR/%s %s %s %s %s %s > %s.txt", "merger.R", "$AZ_BATCH_TASK_WORKING_DIR", envFile, length(dependsOn), jobId, numOfTasks, taskId) | ||
|
|
||
| resultFile <- paste0(taskId, "-result", ".rds") | ||
| logsCommand <- sprintf("env PATH=$PATH blobxfer %s %s %s --upload --saskey $BLOBXFER_SASKEY --remoteresource logs/%s", storageCredentials$name, jobId, paste0(taskId, ".txt"), paste0(taskId, ".txt")) | ||
| autoUploadCommand <- sprintf("env PATH=$PATH blobxfer %s %s %s --upload --saskey $BLOBXFER_SASKEY --remoteresource result/%s", storageCredentials$name, jobId, resultFile, resultFile) | ||
| downloadCommand <- sprintf("env PATH=$PATH blobxfer %s %s %s --download --saskey $BLOBXFER_SASKEY --remoteresource . --include result/*.rds", storageCredentials$name, jobId, "$AZ_BATCH_TASK_WORKING_DIR") | ||
| logsCommand <- sprintf("env PATH=$PATH blobxfer %s %s %s --upload --saskey $BLOBXFER_SASKEY --remoteresource logs/%s", storageCredentials$name, jobId, paste0(taskId, ".txt"), paste0(taskId, ".txt")) | ||
|
|
||
| commands <- c("export PATH=/anaconda/envs/py35/bin:$PATH", downloadCommand, rCommand, logsCommand, autoUploadCommand) | ||
| if(taskPrep != ""){ | ||
| commands <- c(taskPrep, commands) | ||
| } | ||
|
|
||
| sasToken <- constructSas("rwcl", "c", jobId, storageCredentials$key) | ||
| sasQuery <- generateSasUrl(sasToken) | ||
|
|
||
| setting = list(name = "BLOBXFER_SASKEY", | ||
| value = sasQuery) | ||
|
|
||
| resourceFiles <- list(generateResourceFile(storageCredentials$name, jobId, envFile, sasToken)) | ||
|
|
||
| addTask(jobId, | ||
| taskId, | ||
| environmentSettings = list(setting), | ||
| resourceFiles = resourceFiles, | ||
| commandLine = linuxWrapCommands(commands), | ||
| dependsOn = list(taskIds = dependsOn)) | ||
| } | ||
|
|
||
| .addJob <- function(jobId, | ||
| poolId, | ||
| resourceFiles, | ||
| ...){ | ||
| args <- list(...) | ||
| packages <- args$packages | ||
|
|
||
| poolInfo <- list("poolId" = poolId) | ||
|
|
||
| commands <- linuxWrapCommands(c("ls")) | ||
| if(!is.null(packages)){ | ||
| commands <- paste0(commands, ";", getInstallationCommand(packages)) | ||
| } | ||
|
|
||
| jobPreparationTask <- list( | ||
| commandLine = commands, | ||
| userIdentity = list( | ||
| autoUser = list( | ||
| scope = "task", | ||
| elevationLevel = "admin" | ||
| ) | ||
| ), | ||
| waitForSuccess = TRUE, | ||
| resourceFiles = resourceFiles, | ||
| constraints = list( | ||
| maxTaskRetryCount = 2 | ||
| ) | ||
| ) | ||
|
|
||
| usesTaskDependencies <- TRUE | ||
|
|
||
| response <- addJob(jobId, | ||
| poolInfo = poolInfo, | ||
| jobPreparationTask = jobPreparationTask, | ||
| usesTaskDependencies = usesTaskDependencies, | ||
| raw = TRUE) | ||
|
|
||
| return(response) | ||
| } | ||
|
|
||
| .addPool <- function(pool, packages){ | ||
| commands <- c("sed -i -e 's/Defaults requiretty.*/ #Defaults requiretty/g' /etc/sudoers", | ||
| "export PATH=/anaconda/envs/py35/bin:$PATH", | ||
| "sudo env PATH=$PATH pip install --no-dependencies blobxfer") | ||
|
|
||
| commands <- paste0(linuxWrapCommands(commands), ";", packages) | ||
|
|
||
| startTask <- list( | ||
| commandLine = commands, | ||
| userIdentity = list( | ||
| autoUser = list( | ||
| scope = "task", | ||
| elevationLevel = "admin" | ||
| ) | ||
| ), | ||
| waitForSuccess = TRUE | ||
| ) | ||
|
|
||
| virtualMachineConfiguration <- list( | ||
| imageReference = list(publisher = "microsoft-ads", | ||
| offer = "linux-data-science-vm", | ||
| sku = "linuxdsvm", | ||
| version = "latest"), | ||
| nodeAgentSKUId ="batch.node.centos 7") | ||
|
|
||
| response <- addPool(pool$name, | ||
| pool$vmSize, | ||
| startTask = startTask, | ||
| virtualMachineConfiguration = virtualMachineConfiguration, | ||
| enableAutoScale = TRUE, | ||
| autoscaleFormula = getAutoscaleFormula(pool$poolSize$autoscaleFormula, pool$poolSize$minNodes, pool$poolSize$maxNodes), | ||
| autoScaleEvaluationInterval = "PT5M", | ||
| maxTasksPerNode = pool$maxTasksPerNode, | ||
| raw = TRUE) | ||
|
|
||
| return(response) | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters