[SPARK-10500][SPARKR] sparkr.zip cannot be created if /R/lib is unwritable

The basic idea is that:
The archive of the SparkR package itself, that is sparkr.zip, is created during build process and is contained in the Spark binary distribution. No change to it after the distribution is installed as the directory it resides ($SPARK_HOME/R/lib) may not be writable.

When there is R source code contained in jars or Spark packages specified with "--jars" or "--packages" command line option, a temporary directory is created by calling Utils.createTempDir() where the R packages built from the R source code will be installed. The temporary directory is writable, and won't interfere with each other when there are multiple SparkR sessions, and will be deleted when this SparkR session ends. The R binary packages installed in the temporary directory then are packed into an archive named rpkg.zip.

sparkr.zip and rpkg.zip are distributed to the cluster in YARN modes.

The distribution of rpkg.zip in Standalone modes is not supported in this PR, and will be address in another PR.

Various R files are updated to accept multiple lib paths (one is for SparkR package, the other is for other R packages)  so that these package can be accessed in R.

Author: Sun Rui <rui.sun@intel.com>

Closes #9390 from sun-rui/SPARK-10500.

6 files changed, 30 insertions, 5 deletions

diff --git a/R/install-dev.bat b/R/install-dev.bat
index 008a5c668b..ed1c91ae3a 100644
--- a/R/install-dev.bat
+++ b/R/install-dev.bat
@@ -25,3 +25,9 @@ set SPARK_HOME=%~dp0..
 MKDIR %SPARK_HOME%\R\lib
 
 R.exe CMD INSTALL --library="%SPARK_HOME%\R\lib"  %SPARK_HOME%\R\pkg\
+
+rem Zip the SparkR package so that it can be distributed to worker nodes on YARN
+pushd %SPARK_HOME%\R\lib
+%JAVA_HOME%\bin\jar.exe cfM "%SPARK_HOME%\R\lib\sparkr.zip" SparkR
+popd
+
diff --git a/R/install-dev.sh b/R/install-dev.sh
index 59d98c9c7a..4972bb9217 100755
--- a/R/install-dev.sh
+++ b/R/install-dev.sh
@@ -42,4 +42,8 @@ Rscript -e ' if("devtools" %in% rownames(installed.packages())) { library(devtoo
 # Install SparkR to $LIB_DIR
 R CMD INSTALL --library=$LIB_DIR $FWDIR/pkg/
 
+# Zip the SparkR package so that it can be distributed to worker nodes on YARN
+cd $LIB_DIR
+jar cfM "$LIB_DIR/sparkr.zip" SparkR
+
 popd > /dev/null
diff --git a/R/pkg/R/sparkR.R b/R/pkg/R/sparkR.R
index ebe2b2b8dc..7ff3fa628b 100644
--- a/R/pkg/R/sparkR.R
+++ b/R/pkg/R/sparkR.R
@@ -48,6 +48,12 @@ sparkR.stop <- function() {
       }
     }
 
+    # Remove the R package lib path from .libPaths()
+    if (exists(".libPath", envir = env)) {
+      libPath <- get(".libPath", envir = env)
+      .libPaths(.libPaths()[.libPaths() != libPath])
+    }
+
     if (exists(".backendLaunched", envir = env)) {
       callJStatic("SparkRHandler", "stopBackend")
     }
@@ -155,14 +161,20 @@ sparkR.init <- function(
     f <- file(path, open="rb")
     backendPort <- readInt(f)
     monitorPort <- readInt(f)
+    rLibPath <- readString(f)
     close(f)
     file.remove(path)
     if (length(backendPort) == 0 || backendPort == 0 ||
-        length(monitorPort) == 0 || monitorPort == 0) {
+        length(monitorPort) == 0 || monitorPort == 0 ||
+        length(rLibPath) != 1) {
       stop("JVM failed to launch")
     }
     assign(".monitorConn", socketConnection(port = monitorPort), envir = .sparkREnv)
     assign(".backendLaunched", 1, envir = .sparkREnv)
+    if (rLibPath != "") {
+      assign(".libPath", rLibPath, envir = .sparkREnv)
+      .libPaths(c(rLibPath, .libPaths()))
+    }
   }
 
   .sparkREnv$backendPort <- backendPort
diff --git a/R/pkg/inst/profile/general.R b/R/pkg/inst/profile/general.R
index 2a8a8213d0..c55fe9ba7a 100644
--- a/R/pkg/inst/profile/general.R
+++ b/R/pkg/inst/profile/general.R
@@ -17,6 +17,7 @@
 
 .First <- function() {
   packageDir <- Sys.getenv("SPARKR_PACKAGE_DIR")
-  .libPaths(c(packageDir, .libPaths()))
+  dirs <- strsplit(packageDir, ",")[[1]]
+  .libPaths(c(dirs, .libPaths()))
   Sys.setenv(NOAWT=1)
 }
diff --git a/R/pkg/inst/worker/daemon.R b/R/pkg/inst/worker/daemon.R
index 3584b418a7..f55beac6c8 100644
--- a/R/pkg/inst/worker/daemon.R
+++ b/R/pkg/inst/worker/daemon.R
@@ -18,10 +18,11 @@
 # Worker daemon
 
 rLibDir <- Sys.getenv("SPARKR_RLIBDIR")
-script <- paste(rLibDir, "SparkR/worker/worker.R", sep = "/")
+dirs <- strsplit(rLibDir, ",")[[1]]
+script <- file.path(dirs[[1]], "SparkR", "worker", "worker.R")
 
 # preload SparkR package, speedup worker
-.libPaths(c(rLibDir, .libPaths()))
+.libPaths(c(dirs, .libPaths()))
 suppressPackageStartupMessages(library(SparkR))
 
 port <- as.integer(Sys.getenv("SPARKR_WORKER_PORT"))
diff --git a/R/pkg/inst/worker/worker.R b/R/pkg/inst/worker/worker.R
index 0c3b0d1f4b..3ae072beca 100644
--- a/R/pkg/inst/worker/worker.R
+++ b/R/pkg/inst/worker/worker.R
@@ -35,10 +35,11 @@ bootTime <- currentTimeSecs()
 bootElap <- elapsedSecs()
 
 rLibDir <- Sys.getenv("SPARKR_RLIBDIR")
+dirs <- strsplit(rLibDir, ",")[[1]]
 # Set libPaths to include SparkR package as loadNamespace needs this
 # TODO: Figure out if we can avoid this by not loading any objects that require
 # SparkR namespace
-.libPaths(c(rLibDir, .libPaths()))
+.libPaths(c(dirs, .libPaths()))
 suppressPackageStartupMessages(library(SparkR))
 
 port <- as.integer(Sys.getenv("SPARKR_WORKER_PORT"))