Repository: spark Updated Branches: refs/heads/master d7d9fa0b8 -> 835a79d78
[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....@intel.com> Closes #9390 from sun-rui/SPARK-10500. Project: http://git-wip-us.apache.org/repos/asf/spark/repo Commit: http://git-wip-us.apache.org/repos/asf/spark/commit/835a79d7 Tree: http://git-wip-us.apache.org/repos/asf/spark/tree/835a79d7 Diff: http://git-wip-us.apache.org/repos/asf/spark/diff/835a79d7 Branch: refs/heads/master Commit: 835a79d78ee879a3c36dde85e5b3591243bf3957 Parents: d7d9fa0 Author: Sun Rui <rui....@intel.com> Authored: Sun Nov 15 19:29:09 2015 -0800 Committer: Shivaram Venkataraman <shiva...@cs.berkeley.edu> Committed: Sun Nov 15 19:29:09 2015 -0800 ---------------------------------------------------------------------- R/install-dev.bat | 6 +++ R/install-dev.sh | 4 ++ R/pkg/R/sparkR.R | 14 ++++++- R/pkg/inst/profile/general.R | 3 +- R/pkg/inst/worker/daemon.R | 5 ++- R/pkg/inst/worker/worker.R | 3 +- .../scala/org/apache/spark/api/r/RBackend.scala | 1 + .../scala/org/apache/spark/api/r/RRDD.scala | 4 +- .../scala/org/apache/spark/api/r/RUtils.scala | 37 +++++++++++++---- .../org/apache/spark/deploy/RPackageUtils.scala | 26 ++++++++---- .../scala/org/apache/spark/deploy/RRunner.scala | 5 ++- .../org/apache/spark/deploy/SparkSubmit.scala | 43 ++++++++++++++++---- .../apache/spark/deploy/SparkSubmitSuite.scala | 5 +-- make-distribution.sh | 1 + 14 files changed, 121 insertions(+), 36 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/spark/blob/835a79d7/R/install-dev.bat ---------------------------------------------------------------------- diff --git a/R/install-dev.bat b/R/install-dev.bat index 008a5c6..ed1c91a 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 + http://git-wip-us.apache.org/repos/asf/spark/blob/835a79d7/R/install-dev.sh ---------------------------------------------------------------------- diff --git a/R/install-dev.sh b/R/install-dev.sh index 59d98c9..4972bb9 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 http://git-wip-us.apache.org/repos/asf/spark/blob/835a79d7/R/pkg/R/sparkR.R ---------------------------------------------------------------------- diff --git a/R/pkg/R/sparkR.R b/R/pkg/R/sparkR.R index ebe2b2b..7ff3fa6 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 http://git-wip-us.apache.org/repos/asf/spark/blob/835a79d7/R/pkg/inst/profile/general.R ---------------------------------------------------------------------- diff --git a/R/pkg/inst/profile/general.R b/R/pkg/inst/profile/general.R index 2a8a821..c55fe9b 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) } http://git-wip-us.apache.org/repos/asf/spark/blob/835a79d7/R/pkg/inst/worker/daemon.R ---------------------------------------------------------------------- diff --git a/R/pkg/inst/worker/daemon.R b/R/pkg/inst/worker/daemon.R index 3584b41..f55beac 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")) http://git-wip-us.apache.org/repos/asf/spark/blob/835a79d7/R/pkg/inst/worker/worker.R ---------------------------------------------------------------------- diff --git a/R/pkg/inst/worker/worker.R b/R/pkg/inst/worker/worker.R index 0c3b0d1..3ae072b 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")) http://git-wip-us.apache.org/repos/asf/spark/blob/835a79d7/core/src/main/scala/org/apache/spark/api/r/RBackend.scala ---------------------------------------------------------------------- diff --git a/core/src/main/scala/org/apache/spark/api/r/RBackend.scala b/core/src/main/scala/org/apache/spark/api/r/RBackend.scala index b7e72d4..8b3be0d 100644 --- a/core/src/main/scala/org/apache/spark/api/r/RBackend.scala +++ b/core/src/main/scala/org/apache/spark/api/r/RBackend.scala @@ -113,6 +113,7 @@ private[spark] object RBackend extends Logging { val dos = new DataOutputStream(new FileOutputStream(f)) dos.writeInt(boundPort) dos.writeInt(listenPort) + SerDe.writeString(dos, RUtils.rPackages.getOrElse("")) dos.close() f.renameTo(new File(path)) http://git-wip-us.apache.org/repos/asf/spark/blob/835a79d7/core/src/main/scala/org/apache/spark/api/r/RRDD.scala ---------------------------------------------------------------------- diff --git a/core/src/main/scala/org/apache/spark/api/r/RRDD.scala b/core/src/main/scala/org/apache/spark/api/r/RRDD.scala index 6b418e9..7509b3d 100644 --- a/core/src/main/scala/org/apache/spark/api/r/RRDD.scala +++ b/core/src/main/scala/org/apache/spark/api/r/RRDD.scala @@ -400,14 +400,14 @@ private[r] object RRDD { val rOptions = "--vanilla" val rLibDir = RUtils.sparkRPackagePath(isDriver = false) - val rExecScript = rLibDir + "/SparkR/worker/" + script + val rExecScript = rLibDir(0) + "/SparkR/worker/" + script val pb = new ProcessBuilder(Arrays.asList(rCommand, rOptions, rExecScript)) // Unset the R_TESTS environment variable for workers. // This is set by R CMD check as startup.Rs // (http://svn.r-project.org/R/trunk/src/library/tools/R/testing.R) // and confuses worker script which tries to load a non-existent file pb.environment().put("R_TESTS", "") - pb.environment().put("SPARKR_RLIBDIR", rLibDir) + pb.environment().put("SPARKR_RLIBDIR", rLibDir.mkString(",")) pb.environment().put("SPARKR_WORKER_PORT", port.toString) pb.redirectErrorStream(true) // redirect stderr into stdout val proc = pb.start() http://git-wip-us.apache.org/repos/asf/spark/blob/835a79d7/core/src/main/scala/org/apache/spark/api/r/RUtils.scala ---------------------------------------------------------------------- diff --git a/core/src/main/scala/org/apache/spark/api/r/RUtils.scala b/core/src/main/scala/org/apache/spark/api/r/RUtils.scala index fd5646b..1615741 100644 --- a/core/src/main/scala/org/apache/spark/api/r/RUtils.scala +++ b/core/src/main/scala/org/apache/spark/api/r/RUtils.scala @@ -23,6 +23,10 @@ import java.util.Arrays import org.apache.spark.{SparkEnv, SparkException} private[spark] object RUtils { + // Local path where R binary packages built from R source code contained in the spark + // packages specified with "--packages" or "--jars" command line option reside. + var rPackages: Option[String] = None + /** * Get the SparkR package path in the local spark distribution. */ @@ -34,11 +38,15 @@ private[spark] object RUtils { } /** - * Get the SparkR package path in various deployment modes. + * Get the list of paths for R packages in various deployment modes, of which the first + * path is for the SparkR package itself. The second path is for R packages built as + * part of Spark Packages, if any exist. Spark Packages can be provided through the + * "--packages" or "--jars" command line options. + * * This assumes that Spark properties `spark.master` and `spark.submit.deployMode` * and environment variable `SPARK_HOME` are set. */ - def sparkRPackagePath(isDriver: Boolean): String = { + def sparkRPackagePath(isDriver: Boolean): Seq[String] = { val (master, deployMode) = if (isDriver) { (sys.props("spark.master"), sys.props("spark.submit.deployMode")) @@ -51,15 +59,30 @@ private[spark] object RUtils { val isYarnClient = master != null && master.contains("yarn") && deployMode == "client" // In YARN mode, the SparkR package is distributed as an archive symbolically - // linked to the "sparkr" file in the current directory. Note that this does not apply - // to the driver in client mode because it is run outside of the cluster. + // linked to the "sparkr" file in the current directory and additional R packages + // are distributed as an archive symbolically linked to the "rpkg" file in the + // current directory. + // + // Note that this does not apply to the driver in client mode because it is run + // outside of the cluster. if (isYarnCluster || (isYarnClient && !isDriver)) { - new File("sparkr").getAbsolutePath + val sparkRPkgPath = new File("sparkr").getAbsolutePath + val rPkgPath = new File("rpkg") + if (rPkgPath.exists()) { + Seq(sparkRPkgPath, rPkgPath.getAbsolutePath) + } else { + Seq(sparkRPkgPath) + } } else { // Otherwise, assume the package is local // TODO: support this for Mesos - localSparkRPackagePath.getOrElse { - throw new SparkException("SPARK_HOME not set. Can't locate SparkR package.") + val sparkRPkgPath = localSparkRPackagePath.getOrElse { + throw new SparkException("SPARK_HOME not set. Can't locate SparkR package.") + } + if (!rPackages.isEmpty) { + Seq(sparkRPkgPath, rPackages.get) + } else { + Seq(sparkRPkgPath) } } } http://git-wip-us.apache.org/repos/asf/spark/blob/835a79d7/core/src/main/scala/org/apache/spark/deploy/RPackageUtils.scala ---------------------------------------------------------------------- diff --git a/core/src/main/scala/org/apache/spark/deploy/RPackageUtils.scala b/core/src/main/scala/org/apache/spark/deploy/RPackageUtils.scala index 7d160b6..d46dc87 100644 --- a/core/src/main/scala/org/apache/spark/deploy/RPackageUtils.scala +++ b/core/src/main/scala/org/apache/spark/deploy/RPackageUtils.scala @@ -100,20 +100,29 @@ private[deploy] object RPackageUtils extends Logging { * Runs the standard R package installation code to build the R package from source. * Multiple runs don't cause problems. */ - private def rPackageBuilder(dir: File, printStream: PrintStream, verbose: Boolean): Boolean = { + private def rPackageBuilder( + dir: File, + printStream: PrintStream, + verbose: Boolean, + libDir: String): Boolean = { // this code should be always running on the driver. - val pathToSparkR = RUtils.localSparkRPackagePath.getOrElse( - throw new SparkException("SPARK_HOME not set. Can't locate SparkR package.")) val pathToPkg = Seq(dir, "R", "pkg").mkString(File.separator) - val installCmd = baseInstallCmd ++ Seq(pathToSparkR, pathToPkg) + val installCmd = baseInstallCmd ++ Seq(libDir, pathToPkg) if (verbose) { print(s"Building R package with the command: $installCmd", printStream) } try { val builder = new ProcessBuilder(installCmd.asJava) builder.redirectErrorStream(true) + + // Put the SparkR package directory into R library search paths in case this R package + // may depend on SparkR. val env = builder.environment() - env.clear() + val rPackageDir = RUtils.sparkRPackagePath(isDriver = true) + env.put("SPARKR_PACKAGE_DIR", rPackageDir.mkString(",")) + env.put("R_PROFILE_USER", + Seq(rPackageDir(0), "SparkR", "profile", "general.R").mkString(File.separator)) + val process = builder.start() new RedirectThread(process.getInputStream, printStream, "redirect R packaging").start() process.waitFor() == 0 @@ -170,8 +179,11 @@ private[deploy] object RPackageUtils extends Logging { if (checkManifestForR(jar)) { print(s"$file contains R source code. Now installing package.", printStream, Level.INFO) val rSource = extractRFolder(jar, printStream, verbose) + if (RUtils.rPackages.isEmpty) { + RUtils.rPackages = Some(Utils.createTempDir().getAbsolutePath) + } try { - if (!rPackageBuilder(rSource, printStream, verbose)) { + if (!rPackageBuilder(rSource, printStream, verbose, RUtils.rPackages.get)) { print(s"ERROR: Failed to build R package in $file.", printStream) print(RJarDoc, printStream) } @@ -208,7 +220,7 @@ private[deploy] object RPackageUtils extends Logging { } } - /** Zips all the libraries found with SparkR in the R/lib directory for distribution with Yarn. */ + /** Zips all the R libraries built for distribution to the cluster. */ private[deploy] def zipRLibraries(dir: File, name: String): File = { val filesToBundle = listFilesRecursively(dir, Seq(".zip")) // create a zip file from scratch, do not append to existing file. http://git-wip-us.apache.org/repos/asf/spark/blob/835a79d7/core/src/main/scala/org/apache/spark/deploy/RRunner.scala ---------------------------------------------------------------------- diff --git a/core/src/main/scala/org/apache/spark/deploy/RRunner.scala b/core/src/main/scala/org/apache/spark/deploy/RRunner.scala index ed183cf..661f731 100644 --- a/core/src/main/scala/org/apache/spark/deploy/RRunner.scala +++ b/core/src/main/scala/org/apache/spark/deploy/RRunner.scala @@ -82,9 +82,10 @@ object RRunner { val env = builder.environment() env.put("EXISTING_SPARKR_BACKEND_PORT", sparkRBackendPort.toString) val rPackageDir = RUtils.sparkRPackagePath(isDriver = true) - env.put("SPARKR_PACKAGE_DIR", rPackageDir) + // Put the R package directories into an env variable of comma-separated paths + env.put("SPARKR_PACKAGE_DIR", rPackageDir.mkString(",")) env.put("R_PROFILE_USER", - Seq(rPackageDir, "SparkR", "profile", "general.R").mkString(File.separator)) + Seq(rPackageDir(0), "SparkR", "profile", "general.R").mkString(File.separator)) builder.redirectErrorStream(true) // Ugly but needed for stdout and stderr to synchronize val process = builder.start() http://git-wip-us.apache.org/repos/asf/spark/blob/835a79d7/core/src/main/scala/org/apache/spark/deploy/SparkSubmit.scala ---------------------------------------------------------------------- diff --git a/core/src/main/scala/org/apache/spark/deploy/SparkSubmit.scala b/core/src/main/scala/org/apache/spark/deploy/SparkSubmit.scala index 09d2ec9..2e912b5 100644 --- a/core/src/main/scala/org/apache/spark/deploy/SparkSubmit.scala +++ b/core/src/main/scala/org/apache/spark/deploy/SparkSubmit.scala @@ -83,6 +83,7 @@ object SparkSubmit { private val PYSPARK_SHELL = "pyspark-shell" private val SPARKR_SHELL = "sparkr-shell" private val SPARKR_PACKAGE_ARCHIVE = "sparkr.zip" + private val R_PACKAGE_ARCHIVE = "rpkg.zip" private val CLASS_NOT_FOUND_EXIT_STATUS = 101 @@ -362,22 +363,46 @@ object SparkSubmit { } } - // In YARN mode for an R app, add the SparkR package archive to archives - // that can be distributed with the job + // In YARN mode for an R app, add the SparkR package archive and the R package + // archive containing all of the built R libraries to archives so that they can + // be distributed with the job if (args.isR && clusterManager == YARN) { - val rPackagePath = RUtils.localSparkRPackagePath - if (rPackagePath.isEmpty) { + val sparkRPackagePath = RUtils.localSparkRPackagePath + if (sparkRPackagePath.isEmpty) { printErrorAndExit("SPARK_HOME does not exist for R application in YARN mode.") } - val rPackageFile = - RPackageUtils.zipRLibraries(new File(rPackagePath.get), SPARKR_PACKAGE_ARCHIVE) - if (!rPackageFile.exists()) { + val sparkRPackageFile = new File(sparkRPackagePath.get, SPARKR_PACKAGE_ARCHIVE) + if (!sparkRPackageFile.exists()) { printErrorAndExit(s"$SPARKR_PACKAGE_ARCHIVE does not exist for R application in YARN mode.") } - val localURI = Utils.resolveURI(rPackageFile.getAbsolutePath) + val sparkRPackageURI = Utils.resolveURI(sparkRPackageFile.getAbsolutePath).toString + // Distribute the SparkR package. // Assigns a symbol link name "sparkr" to the shipped package. - args.archives = mergeFileLists(args.archives, localURI.toString + "#sparkr") + args.archives = mergeFileLists(args.archives, sparkRPackageURI + "#sparkr") + + // Distribute the R package archive containing all the built R packages. + if (!RUtils.rPackages.isEmpty) { + val rPackageFile = + RPackageUtils.zipRLibraries(new File(RUtils.rPackages.get), R_PACKAGE_ARCHIVE) + if (!rPackageFile.exists()) { + printErrorAndExit("Failed to zip all the built R packages.") + } + + val rPackageURI = Utils.resolveURI(rPackageFile.getAbsolutePath).toString + // Assigns a symbol link name "rpkg" to the shipped package. + args.archives = mergeFileLists(args.archives, rPackageURI + "#rpkg") + } + } + + // TODO: Support distributing R packages with standalone cluster + if (args.isR && clusterManager == STANDALONE && !RUtils.rPackages.isEmpty) { + printErrorAndExit("Distributing R packages with standalone cluster is not supported.") + } + + // TODO: Support SparkR with mesos cluster + if (args.isR && clusterManager == MESOS) { + printErrorAndExit("SparkR is not supported for Mesos cluster.") } // If we're running a R app, set the main class to our specific R runner http://git-wip-us.apache.org/repos/asf/spark/blob/835a79d7/core/src/test/scala/org/apache/spark/deploy/SparkSubmitSuite.scala ---------------------------------------------------------------------- diff --git a/core/src/test/scala/org/apache/spark/deploy/SparkSubmitSuite.scala b/core/src/test/scala/org/apache/spark/deploy/SparkSubmitSuite.scala index 66a5051..42e748e 100644 --- a/core/src/test/scala/org/apache/spark/deploy/SparkSubmitSuite.scala +++ b/core/src/test/scala/org/apache/spark/deploy/SparkSubmitSuite.scala @@ -28,6 +28,7 @@ import org.scalatest.concurrent.Timeouts import org.scalatest.time.SpanSugar._ import org.apache.spark._ +import org.apache.spark.api.r.RUtils import org.apache.spark.deploy.SparkSubmit._ import org.apache.spark.deploy.SparkSubmitUtils.MavenCoordinate import org.apache.spark.util.{ResetSystemProperties, Utils} @@ -369,9 +370,6 @@ class SparkSubmitSuite } test("correctly builds R packages included in a jar with --packages") { - // TODO(SPARK-9603): Building a package to $SPARK_HOME/R/lib is unavailable on Jenkins. - // It's hard to write the test in SparkR (because we can't create the repository dynamically) - /* assume(RUtils.isRInstalled, "R isn't installed on this machine.") val main = MavenCoordinate("my.great.lib", "mylib", "0.1") val sparkHome = sys.props.getOrElse("spark.test.home", fail("spark.test.home is not set!")) @@ -389,7 +387,6 @@ class SparkSubmitSuite rScriptDir) runSparkSubmit(args) } - */ } test("resolves command line argument paths correctly") { http://git-wip-us.apache.org/repos/asf/spark/blob/835a79d7/make-distribution.sh ---------------------------------------------------------------------- diff --git a/make-distribution.sh b/make-distribution.sh index e1c2afd..d7d27e2 100755 --- a/make-distribution.sh +++ b/make-distribution.sh @@ -220,6 +220,7 @@ cp -r "$SPARK_HOME/ec2" "$DISTDIR" if [ -d "$SPARK_HOME"/R/lib/SparkR ]; then mkdir -p "$DISTDIR"/R/lib cp -r "$SPARK_HOME/R/lib/SparkR" "$DISTDIR"/R/lib + cp "$SPARK_HOME/R/lib/sparkr.zip" "$DISTDIR"/R/lib fi # Download and copy in tachyon, if requested --------------------------------------------------------------------- To unsubscribe, e-mail: commits-unsubscr...@spark.apache.org For additional commands, e-mail: commits-h...@spark.apache.org
