1- # ' Creates a configuration file for the user's cluster setup.
1+ # ' Creates a credentials file for rAzureBatch package authentication
22# '
3- # ' @param fileName Cluster configuration's file name.
3+ # ' @param fileName Credentials file name
44# ' @param ... Further named parameters
55# ' \itemize{
66# ' \item{"batchAccount"}: {A list of files that the Batch service will download to the compute node before running the command line.}
1111# '}
1212# ' @return The request to the Batch service was successful.
1313# ' @examples {
14- # ' generateClusterConfig ("test_config.json")
15- # ' generateClusterConfig ("test_config.json", batchAccount = "testbatchaccount", batchKey = "test_batch_account_key", batchUrl = "http://testbatchaccount.azure.com", storageAccount = "teststorageaccount", storageKey = "test_storage_account_key")
14+ # ' generateCredentialsConfig ("test_config.json")
15+ # ' generateCredentialsConfig ("test_config.json", batchAccount = "testbatchaccount", batchKey = "test_batch_account_key", batchUrl = "http://testbatchaccount.azure.com", storageAccount = "teststorageaccount", storageKey = "test_storage_account_key")
1616# ' }
17- generateClusterConfig <- function (fileName , ... ){
17+ # ' @export
18+ generateCredentialsConfig <- function (fileName , ... ){
1819 args <- list (... )
1920
2021 batchAccount <- ifelse(is.null(args $ batchAccount ), " batch_account_name" args $ batchAccount )
@@ -31,35 +32,64 @@ generateClusterConfig <- function(fileName, ...){
3132 batchAccount = list (
3233 name = batchAccount ,
3334 key = batchKey ,
34- url = batchUrl ,
35- pool = list (
36- name = " myPoolName"
37- vmSize = " Standard_D2_v2"
38- maxTasksPerNode = 1 ,
39- poolSize = list (
40- minNodes = 3 ,
41- maxNodes = 10 ,
42- autoscaleFormula = " QUEUE"
43- )
44- ),
45- rPackages = list (
46- cran = vector(),
47- github = vector()
48- )
35+ url = batchUrl
4936 ),
5037 storageAccount = list (
5138 name = storageName ,
5239 key = storageKey
53- ),
54- settings = list (
55- verbose = FALSE
5640 )
5741 )
5842
5943 configJson <- jsonlite :: toJSON(config , auto_unbox = TRUE , pretty = TRUE )
6044 write(configJson , file = paste0(getwd(), " /" fileName ))
6145
6246 print(sprintf(" A config file has been generated %s. Please enter your Batch credentials." " /" fileName )))
47+ }
48+ }
49+
50+ # ' Creates a configuration file for the user's cluster setup.
51+ # '
52+ # ' @param fileName Cluster settings file name
53+ # ' @return The request to the Batch service was successful.
54+ # ' @examples {
55+ # ' generateClusterConfig("test_config.json")
56+ # ' generateClusterConfig("test_config.json")
57+ # ' }
58+ # '
59+ # ' @export
60+ generateClusterConfig <- function (fileName , ... ){
61+ args <- list (... )
62+
63+ packages <- ifelse(is.null(args $ packages ), list (), args $ packages )
64+
65+ if (! file.exists(fileName ) || ! file.exists(paste0(getwd(), " /" fileName ))){
66+ config <- list (
67+ pool = list (
68+ name = " myPoolName"
69+ vmSize = " Standard_D2_v2"
70+ maxTasksPerNode = 1 ,
71+ poolSize = list (
72+ dedicatedNodes = list (
73+ min = 3 ,
74+ max = 3
75+ ),
76+ lowPriorityNodes = list (
77+ min = 3 ,
78+ max = 3
79+ ),
80+ autoscaleFormula = " QUEUE"
81+ )
82+ ),
83+ rPackages = list (
84+ cran = vector(),
85+ github = vector()
86+ )
87+ )
88+
89+ configJson <- jsonlite :: toJSON(config , auto_unbox = TRUE , pretty = TRUE )
90+ write(configJson , file = paste0(getwd(), " /" fileName ))
91+
92+ print(sprintf(" A cluster settings has been generated %s. Please enter your cluster specification." " /" fileName )))
6393 print(" Note: To maximize all CPU cores, set the maxTasksPerNode property up to 4x the number of cores for the VM size."
6494 }
6595}
@@ -69,35 +99,48 @@ generateClusterConfig <- function(fileName, ...){
6999# ' @param fileName Cluster configuration's file name
70100# ' @param fullName A boolean flag for checking the file full name
71101# ' @param wait A boolean flag to wait for all nodes to boot up
102+ # ' @param resourceFiles A list of files that Batch will download to the compute node before running the command line
72103# '
73104# ' @return The request to the Batch service was successful.
74105# ' @examples
75106# ' cluster <- makeCluster("cluster_config.json", fullName = TRUE, wait = TRUE)
76- makeCluster <- function (fileName = " az_config.json" fullName = FALSE , wait = TRUE , resourceFiles = list ()){
77- setPoolOption(fileName , fullName )
107+ # ' @export
108+ makeCluster <- function (clusterSetting = " cluster_settings.json" fullName = FALSE , wait = TRUE , resourceFiles = list ()){
109+ if (fullName ){
110+ pool <- rjson :: fromJSON(file = paste0(clusterSetting ))
111+ }
112+ else {
113+ pool <- rjson :: fromJSON(file = paste0(getwd(), " /" clusterSetting ))
114+ }
115+
78116 config <- getOption(" az_config"
79- pool <- config $ batchAccount $ pool
117+ if (is.null(config )){
118+ stop(" Credentials were not set."
119+ }
120+
121+ config $ poolId = pool $ pool $ name
122+ options(" az_config" = config )
80123
81124 packages <- NULL
82- if (! is.null(config $ batchAccount $ rPackages ) && ! is.null(config $ batchAccount $ rPackages $ cran ) && length(config $ batchAccount $ rPackages $ cran ) > 0 ){
83- packages <- getInstallationCommand(config $ batchAccount $ rPackages $ cran )
125+ if (! is.null(pool $ rPackages ) && ! is.null(pool $ rPackages $ cran ) && length(pool $ rPackages $ cran ) > 0 ){
126+ packages <- getInstallationCommand(pool $ rPackages $ cran )
84127 }
85128
86- if (! is.null(config $ batchAccount $ rPackages ) && ! is.null(config $ batchAccount $ rPackages $ github ) && length(config $ batchAccount $ rPackages $ github ) > 0 ){
129+ if (! is.null(pool $ rPackages ) && ! is.null(pool $ rPackages $ github ) && length(pool $ rPackages $ github ) > 0 ){
87130 if (is.null(packages )){
88- packages <- getGithubInstallationCommand(config $ batchAccount $ rPackages $ github )
131+ packages <- getGithubInstallationCommand(pool $ rPackages $ github )
89132 }
90133 else {
91- packages <- paste0(packages , " ;" config $ batchAccount $ rPackages $ github ))
134+ packages <- paste0(packages , " ;" pool $ rPackages $ github ))
92135 }
93136 }
94137
95138 response <- .addPool(
96- pool = pool ,
139+ pool = pool $ pool ,
97140 packages = packages ,
98141 resourceFiles = resourceFiles )
99142
100- pool <- getPool(pool $ name )
143+ pool <- getPool(pool $ pool $ name )
101144
102145 if (grepl(" AuthenticationFailed" response )){
103146 stop(" Check your credentials and try again."
@@ -108,36 +151,49 @@ makeCluster <- function(fileName = "az_config.json", fullName = FALSE, wait = TR
108151 }
109152 else {
110153 if (wait ){
111- waitForNodesToComplete(pool $ id , 60000 , targetDedicated = pool $ targetDedicated )
154+ waitForNodesToComplete(pool $ id , 60000 )
112155 }
113156 }
114157
115158 print(" Your pool has been registered."
116- print(sprintf(" Node Count: %i" pool $ targetDedicated ))
159+ print(sprintf(" Dedicated Node Count: %i" pool $ targetDedicatedNodes ))
160+ print(sprintf(" Low Priority Node Count: %i" pool $ targetLowPriorityNodes ))
117161 return (getOption(" az_config"
118162}
119163
120164# ' Deletes the cluster from your Azure account.
121165# '
122166# ' @param cluster The cluster configuration that was created in \code{makeCluster}
123167# '
124- # ' @return The request to the Batch service was successful.
125168# ' @examples
126- # ' clusterConfiguration <- makeCluster("pool_configuration .json")
169+ # ' clusterConfiguration <- makeCluster("cluster_settings .json")
127170# ' stopCluster(clusterConfiguration)
171+ # ' @export
128172stopCluster <- function (cluster ){
129- deletePool(pool $ batchAccount $ pool $ name )
173+ deletePool(cluster $ poolId )
174+
175+ print(sprintf(" Your %s cluster has been destroyed." cluster $ poolId ))
130176}
131177
132- setPoolOption <- function (fileName = " az_config.json" fullName = FALSE ){
133- if (fullName ){
178+ # ' Deletes the cluster from your Azure account.
179+ # '
180+ # ' @param fileName The cluster configuration that was created in \code{makeCluster}
181+ # '
182+ # ' @return The request to the Batch service was successful.
183+ # ' @examples
184+ # ' clusterConfiguration <- makeCluster("cluster_settings.json")
185+ # ' stopCluster(clusterConfiguration)
186+ # ' @export
187+ setCredentials <- function (fileName = " az_config.json"
188+ if (file.exists(fileName )){
134189 config <- rjson :: fromJSON(file = paste0(fileName ))
135190 }
136191 else {
137192 config <- rjson :: fromJSON(file = paste0(getwd(), " /" fileName ))
138193 }
139194
140195 options(" az_config" = config )
196+ print(" Your azure credentials have been set."
141197}
142198
143199getPoolWorkers <- function (poolId , ... ){
0 commit comments