public static boolean runJob(DMLConfig conf) throws Exception {
boolean ret = false;
try {
JobConf job;
job = new JobConf(CleanupMR.class);
job.setJobName("Cleanup-MR");
// set up SystemML local tmp dir
String dir = conf.getTextValue(DMLConfig.LOCAL_TMP_DIR);
MRJobConfiguration.setSystemMLLocalTmpDir(job, dir);
// set mappers, reducers
int numNodes = InfrastructureAnalyzer.getRemoteParallelNodes();
job.setMapperClass(CleanupMapper.class); // map-only
job.setNumMapTasks(numNodes); // numMappers
job.setNumReduceTasks(0);
// set input/output format, input path
String inFileName = conf.getTextValue(DMLConfig.SCRATCH_SPACE) + "/cleanup_tasks";
job.setInputFormat(NLineInputFormat.class);
job.setOutputFormat(NullOutputFormat.class);
Path path = new Path(inFileName);
FileInputFormat.setInputPaths(job, path);
writeCleanupTasksToFile(path, numNodes);
// disable automatic tasks timeouts and speculative task exec
job.setInt(MRConfigurationNames.MR_TASK_TIMEOUT, 0);
job.setMapSpeculativeExecution(false);
/////
// execute the MR job
RunningJob runjob = JobClient.runJob(job);
ret = runjob.isSuccessful();
} catch (Exception ex) {
// don't raise an exception, just gracefully an error message.
LOG.error("Failed to run cleanup MR job. ", ex);
}
return ret;
}
/**
* @param pfid
* @param program
* @param taskFile
* @param resultFile
* @param _enableCPCaching
* @param mode
* @param numMappers
* @param replication
* @return
* @throws DMLRuntimeException
*/
public static RemoteParForJobReturn runJob(
long pfid,
String program,
String taskFile,
String resultFile,
MatrixObject colocatedDPMatrixObj, // inputs
boolean enableCPCaching,
int numMappers,
int replication,
int max_retry,
long minMem,
boolean jvmReuse) // opt params
throws DMLRuntimeException {
RemoteParForJobReturn ret = null;
String jobname = "ParFor-EMR";
long t0 = DMLScript.STATISTICS ? System.nanoTime() : 0;
JobConf job;
job = new JobConf(RemoteParForMR.class);
job.setJobName(jobname + pfid);
// maintain dml script counters
Statistics.incrementNoOfCompiledMRJobs();
try {
/////
// configure the MR job
// set arbitrary CP program blocks that will perform in the mapper
MRJobConfiguration.setProgramBlocks(job, program);
// enable/disable caching
MRJobConfiguration.setParforCachingConfig(job, enableCPCaching);
// set mappers, reducers, combiners
job.setMapperClass(RemoteParWorkerMapper.class); // map-only
// set input format (one split per row, NLineInputFormat default N=1)
if (ParForProgramBlock.ALLOW_DATA_COLOCATION && colocatedDPMatrixObj != null) {
job.setInputFormat(RemoteParForColocatedNLineInputFormat.class);
MRJobConfiguration.setPartitioningFormat(job, colocatedDPMatrixObj.getPartitionFormat());
MatrixCharacteristics mc = colocatedDPMatrixObj.getMatrixCharacteristics();
MRJobConfiguration.setPartitioningBlockNumRows(job, mc.getRowsPerBlock());
MRJobConfiguration.setPartitioningBlockNumCols(job, mc.getColsPerBlock());
MRJobConfiguration.setPartitioningFilename(job, colocatedDPMatrixObj.getFileName());
} else // default case
{
job.setInputFormat(NLineInputFormat.class);
}
// set the input path and output path
FileInputFormat.setInputPaths(job, new Path(taskFile));
// set output format
job.setOutputFormat(SequenceFileOutputFormat.class);
// set output path
MapReduceTool.deleteFileIfExistOnHDFS(resultFile);
FileOutputFormat.setOutputPath(job, new Path(resultFile));
// set the output key, value schema
job.setMapOutputKeyClass(LongWritable.class);
job.setMapOutputValueClass(Text.class);
job.setOutputKeyClass(LongWritable.class);
job.setOutputValueClass(Text.class);
//////
// set optimization parameters
// set the number of mappers and reducers
job.setNumMapTasks(numMappers); // numMappers
job.setNumReduceTasks(0);
// job.setInt("mapred.map.tasks.maximum", 1); //system property
// job.setInt("mapred.tasktracker.tasks.maximum",1); //system property
// job.setInt("mapred.jobtracker.maxtasks.per.job",1); //system property
// use FLEX scheduler configuration properties
if (ParForProgramBlock.USE_FLEX_SCHEDULER_CONF) {
job.setInt("flex.priority", 0); // highest
job.setInt("flex.map.min", 0);
job.setInt("flex.map.max", numMappers);
job.setInt("flex.reduce.min", 0);
job.setInt("flex.reduce.max", numMappers);
}
// set jvm memory size (if require)
String memKey = "mapred.child.java.opts";
if (minMem > 0 && minMem > InfrastructureAnalyzer.extractMaxMemoryOpt(job.get(memKey))) {
InfrastructureAnalyzer.setMaxMemoryOpt(job, memKey, minMem);
LOG.warn("Forcing '" + memKey + "' to -Xmx" + minMem / (1024 * 1024) + "M.");
}
// disable automatic tasks timeouts and speculative task exec
job.setInt("mapred.task.timeout", 0);
job.setMapSpeculativeExecution(false);
// set up map/reduce memory configurations (if in AM context)
DMLConfig config = ConfigurationManager.getConfig();
DMLAppMasterUtils.setupMRJobRemoteMaxMemory(job, config);
// enables the reuse of JVMs (multiple tasks per MR task)
if (jvmReuse) job.setNumTasksToExecutePerJvm(-1); // unlimited
// set sort io buffer (reduce unnecessary large io buffer, guaranteed memory consumption)
job.setInt(MRConfigurationNames.MR_TASK_IO_SORT_MB, 8); // 8MB
// set the replication factor for the results
job.setInt("dfs.replication", replication);
// set the max number of retries per map task
// disabled job-level configuration to respect cluster configuration
// note: this refers to hadoop2, hence it never had effect on mr1
// job.setInt("mapreduce.map.maxattempts", max_retry);
// set unique working dir
MRJobConfiguration.setUniqueWorkingDir(job);
/////
// execute the MR job
RunningJob runjob = JobClient.runJob(job);
// Process different counters
Statistics.incrementNoOfExecutedMRJobs();
Group pgroup = runjob.getCounters().getGroup(ParForProgramBlock.PARFOR_COUNTER_GROUP_NAME);
int numTasks = (int) pgroup.getCounter(Stat.PARFOR_NUMTASKS.toString());
int numIters = (int) pgroup.getCounter(Stat.PARFOR_NUMITERS.toString());
if (DMLScript.STATISTICS && !InfrastructureAnalyzer.isLocalMode()) {
Statistics.incrementJITCompileTime(pgroup.getCounter(Stat.PARFOR_JITCOMPILE.toString()));
Statistics.incrementJVMgcCount(pgroup.getCounter(Stat.PARFOR_JVMGC_COUNT.toString()));
Statistics.incrementJVMgcTime(pgroup.getCounter(Stat.PARFOR_JVMGC_TIME.toString()));
Group cgroup =
runjob.getCounters().getGroup(CacheableData.CACHING_COUNTER_GROUP_NAME.toString());
CacheStatistics.incrementMemHits(
(int) cgroup.getCounter(CacheStatistics.Stat.CACHE_HITS_MEM.toString()));
CacheStatistics.incrementFSBuffHits(
(int) cgroup.getCounter(CacheStatistics.Stat.CACHE_HITS_FSBUFF.toString()));
CacheStatistics.incrementFSHits(
(int) cgroup.getCounter(CacheStatistics.Stat.CACHE_HITS_FS.toString()));
CacheStatistics.incrementHDFSHits(
(int) cgroup.getCounter(CacheStatistics.Stat.CACHE_HITS_HDFS.toString()));
CacheStatistics.incrementFSBuffWrites(
(int) cgroup.getCounter(CacheStatistics.Stat.CACHE_WRITES_FSBUFF.toString()));
CacheStatistics.incrementFSWrites(
(int) cgroup.getCounter(CacheStatistics.Stat.CACHE_WRITES_FS.toString()));
CacheStatistics.incrementHDFSWrites(
(int) cgroup.getCounter(CacheStatistics.Stat.CACHE_WRITES_HDFS.toString()));
CacheStatistics.incrementAcquireRTime(
cgroup.getCounter(CacheStatistics.Stat.CACHE_TIME_ACQR.toString()));
CacheStatistics.incrementAcquireMTime(
cgroup.getCounter(CacheStatistics.Stat.CACHE_TIME_ACQM.toString()));
CacheStatistics.incrementReleaseTime(
cgroup.getCounter(CacheStatistics.Stat.CACHE_TIME_RLS.toString()));
CacheStatistics.incrementExportTime(
cgroup.getCounter(CacheStatistics.Stat.CACHE_TIME_EXP.toString()));
}
// read all files of result variables and prepare for return
LocalVariableMap[] results = readResultFile(job, resultFile);
ret = new RemoteParForJobReturn(runjob.isSuccessful(), numTasks, numIters, results);
} catch (Exception ex) {
throw new DMLRuntimeException(ex);
} finally {
// remove created files
try {
MapReduceTool.deleteFileIfExistOnHDFS(new Path(taskFile), job);
MapReduceTool.deleteFileIfExistOnHDFS(new Path(resultFile), job);
} catch (IOException ex) {
throw new DMLRuntimeException(ex);
}
}
if (DMLScript.STATISTICS) {
long t1 = System.nanoTime();
Statistics.maintainCPHeavyHitters("MR-Job_" + jobname, t1 - t0);
}
return ret;
}
/**
* Starts a Rand MapReduce job which will produce one or more random objects.
*
* @param numRows number of rows for each random object
* @param numCols number of columns for each random object
* @param blockRowSize number of rows in a block for each random object
* @param blockColSize number of columns in a block for each random object
* @param minValue minimum of the random values for each random object
* @param maxValue maximum of the random values for each random object
* @param sparsity sparsity for each random object
* @param pdf probability density function for each random object
* @param replication file replication
* @param inputs input file for each random object
* @param outputs output file for each random object
* @param outputInfos output information for each random object
* @param instructionsInMapper instruction for each random object
* @param resultIndexes result indexes for each random object
* @return matrix characteristics for each random object
* @throws Exception if an error occurred in the MapReduce phase
*/
public static JobReturn runJob(
MRJobInstruction inst,
String[] dataGenInstructions,
String instructionsInMapper,
String aggInstructionsInReducer,
String otherInstructionsInReducer,
int numReducers,
int replication,
byte[] resultIndexes,
String dimsUnknownFilePrefix,
String[] outputs,
OutputInfo[] outputInfos)
throws Exception {
JobConf job = new JobConf(DataGenMR.class);
job.setJobName("DataGen-MR");
// whether use block representation or cell representation
MRJobConfiguration.setMatrixValueClass(job, true);
byte[] realIndexes = new byte[dataGenInstructions.length];
for (byte b = 0; b < realIndexes.length; b++) realIndexes[b] = b;
String[] inputs = new String[dataGenInstructions.length];
InputInfo[] inputInfos = new InputInfo[dataGenInstructions.length];
long[] rlens = new long[dataGenInstructions.length];
long[] clens = new long[dataGenInstructions.length];
int[] brlens = new int[dataGenInstructions.length];
int[] bclens = new int[dataGenInstructions.length];
FileSystem fs = FileSystem.get(job);
String dataGenInsStr = "";
int numblocks = 0;
int maxbrlen = -1, maxbclen = -1;
double maxsparsity = -1;
for (int i = 0; i < dataGenInstructions.length; i++) {
dataGenInsStr = dataGenInsStr + Lop.INSTRUCTION_DELIMITOR + dataGenInstructions[i];
MRInstruction mrins = MRInstructionParser.parseSingleInstruction(dataGenInstructions[i]);
MRINSTRUCTION_TYPE mrtype = mrins.getMRInstructionType();
DataGenMRInstruction genInst = (DataGenMRInstruction) mrins;
rlens[i] = genInst.getRows();
clens[i] = genInst.getCols();
brlens[i] = genInst.getRowsInBlock();
bclens[i] = genInst.getColsInBlock();
maxbrlen = Math.max(maxbrlen, brlens[i]);
maxbclen = Math.max(maxbclen, bclens[i]);
if (mrtype == MRINSTRUCTION_TYPE.Rand) {
RandInstruction randInst = (RandInstruction) mrins;
inputs[i] = LibMatrixDatagen.generateUniqueSeedPath(genInst.getBaseDir());
maxsparsity = Math.max(maxsparsity, randInst.getSparsity());
FSDataOutputStream fsOut = fs.create(new Path(inputs[i]));
PrintWriter pw = new PrintWriter(fsOut);
// for obj reuse and preventing repeated buffer re-allocations
StringBuilder sb = new StringBuilder();
// seed generation
Well1024a bigrand = LibMatrixDatagen.setupSeedsForRand(randInst.getSeed());
long[] nnz =
LibMatrixDatagen.computeNNZperBlock(
rlens[i], clens[i], brlens[i], bclens[i], randInst.getSparsity());
int nnzIx = 0;
for (long r = 0; r < rlens[i]; r += brlens[i]) {
long curBlockRowSize = Math.min(brlens[i], (rlens[i] - r));
for (long c = 0; c < clens[i]; c += bclens[i]) {
long curBlockColSize = Math.min(bclens[i], (clens[i] - c));
sb.append((r / brlens[i]) + 1);
sb.append(',');
sb.append((c / bclens[i]) + 1);
sb.append(',');
sb.append(curBlockRowSize);
sb.append(',');
sb.append(curBlockColSize);
sb.append(',');
sb.append(nnz[nnzIx++]);
sb.append(',');
sb.append(bigrand.nextLong());
pw.println(sb.toString());
sb.setLength(0);
numblocks++;
}
}
pw.close();
fsOut.close();
inputInfos[i] = InputInfo.TextCellInputInfo;
} else if (mrtype == MRINSTRUCTION_TYPE.Seq) {
SeqInstruction seqInst = (SeqInstruction) mrins;
inputs[i] = genInst.getBaseDir() + System.currentTimeMillis() + ".seqinput";
maxsparsity = 1.0; // always dense
double from = seqInst.fromValue;
double to = seqInst.toValue;
double incr = seqInst.incrValue;
// handle default 1 to -1 for special case of from>to
incr = LibMatrixDatagen.updateSeqIncr(from, to, incr);
// Correctness checks on (from, to, incr)
boolean neg = (from > to);
if (incr == 0) throw new DMLRuntimeException("Invalid value for \"increment\" in seq().");
if (neg != (incr < 0))
throw new DMLRuntimeException("Wrong sign for the increment in a call to seq()");
// Compute the number of rows in the sequence
long numrows = 1 + (long) Math.floor((to - from) / incr);
if (rlens[i] > 0) {
if (numrows != rlens[i])
throw new DMLRuntimeException(
"Unexpected error while processing sequence instruction. Expected number of rows does not match given number: "
+ rlens[i]
+ " != "
+ numrows);
} else {
rlens[i] = numrows;
}
if (clens[i] > 0 && clens[i] != 1)
throw new DMLRuntimeException(
"Unexpected error while processing sequence instruction. Number of columns ("
+ clens[i]
+ ") must be equal to 1.");
else clens[i] = 1;
FSDataOutputStream fsOut = fs.create(new Path(inputs[i]));
PrintWriter pw = new PrintWriter(fsOut);
StringBuilder sb = new StringBuilder();
double temp = from;
double block_from, block_to;
for (long r = 0; r < rlens[i]; r += brlens[i]) {
long curBlockRowSize = Math.min(brlens[i], (rlens[i] - r));
// block (bid_i,bid_j) generates a sequence from the interval [block_from, block_to]
// (inclusive of both end points of the interval)
long bid_i = ((r / brlens[i]) + 1);
long bid_j = 1;
block_from = temp;
block_to = temp + (curBlockRowSize - 1) * incr;
temp = block_to + incr; // next block starts from here
sb.append(bid_i);
sb.append(',');
sb.append(bid_j);
sb.append(',');
/*
// Need not include block size while generating seq()
sb.append(curBlockRowSize);
sb.append(',');
sb.append(1);
sb.append(',');*/
sb.append(block_from);
sb.append(',');
sb.append(block_to);
sb.append(',');
sb.append(incr);
pw.println(sb.toString());
// System.out.println("MapTask " + r + ": " + sb.toString());
sb.setLength(0);
numblocks++;
}
pw.close();
fsOut.close();
inputInfos[i] = InputInfo.TextCellInputInfo;
} else {
throw new DMLRuntimeException("Unexpected Data Generation Instruction Type: " + mrtype);
}
}
dataGenInsStr = dataGenInsStr.substring(1); // remove the first ","
RunningJob runjob;
MatrixCharacteristics[] stats;
try {
// set up the block size
MRJobConfiguration.setBlocksSizes(job, realIndexes, brlens, bclens);
// set up the input files and their format information
MRJobConfiguration.setUpMultipleInputs(
job, realIndexes, inputs, inputInfos, brlens, bclens, false, ConvertTarget.BLOCK);
// set up the dimensions of input matrices
MRJobConfiguration.setMatricesDimensions(job, realIndexes, rlens, clens);
MRJobConfiguration.setDimsUnknownFilePrefix(job, dimsUnknownFilePrefix);
// set up the block size
MRJobConfiguration.setBlocksSizes(job, realIndexes, brlens, bclens);
// set up the rand Instructions
MRJobConfiguration.setRandInstructions(job, dataGenInsStr);
// set up unary instructions that will perform in the mapper
MRJobConfiguration.setInstructionsInMapper(job, instructionsInMapper);
// set up the aggregate instructions that will happen in the combiner and reducer
MRJobConfiguration.setAggregateInstructions(job, aggInstructionsInReducer);
// set up the instructions that will happen in the reducer, after the aggregation instrucions
MRJobConfiguration.setInstructionsInReducer(job, otherInstructionsInReducer);
// set up the replication factor for the results
job.setInt(MRConfigurationNames.DFS_REPLICATION, replication);
// set up map/reduce memory configurations (if in AM context)
DMLConfig config = ConfigurationManager.getDMLConfig();
DMLAppMasterUtils.setupMRJobRemoteMaxMemory(job, config);
// set up custom map/reduce configurations
MRJobConfiguration.setupCustomMRConfigurations(job, config);
// determine degree of parallelism (nmappers: 1<=n<=capacity)
// TODO use maxsparsity whenever we have a way of generating sparse rand data
int capacity = InfrastructureAnalyzer.getRemoteParallelMapTasks();
long dfsblocksize = InfrastructureAnalyzer.getHDFSBlockSize();
// correction max number of mappers on yarn clusters
if (InfrastructureAnalyzer.isYarnEnabled())
capacity = (int) Math.max(capacity, YarnClusterAnalyzer.getNumCores());
int nmapers =
Math.max(
Math.min((int) (8 * maxbrlen * maxbclen * (long) numblocks / dfsblocksize), capacity),
1);
job.setNumMapTasks(nmapers);
// set up what matrices are needed to pass from the mapper to reducer
HashSet<Byte> mapoutputIndexes =
MRJobConfiguration.setUpOutputIndexesForMapper(
job,
realIndexes,
dataGenInsStr,
instructionsInMapper,
null,
aggInstructionsInReducer,
otherInstructionsInReducer,
resultIndexes);
MatrixChar_N_ReducerGroups ret =
MRJobConfiguration.computeMatrixCharacteristics(
job,
realIndexes,
dataGenInsStr,
instructionsInMapper,
null,
aggInstructionsInReducer,
null,
otherInstructionsInReducer,
resultIndexes,
mapoutputIndexes,
false);
stats = ret.stats;
// set up the number of reducers
MRJobConfiguration.setNumReducers(job, ret.numReducerGroups, numReducers);
// print the complete MRJob instruction
if (LOG.isTraceEnabled()) inst.printCompleteMRJobInstruction(stats);
// Update resultDimsUnknown based on computed "stats"
byte[] resultDimsUnknown = new byte[resultIndexes.length];
for (int i = 0; i < resultIndexes.length; i++) {
if (stats[i].getRows() == -1 || stats[i].getCols() == -1) {
resultDimsUnknown[i] = (byte) 1;
} else {
resultDimsUnknown[i] = (byte) 0;
}
}
boolean mayContainCtable =
instructionsInMapper.contains("ctabletransform")
|| instructionsInMapper.contains("groupedagg");
// set up the multiple output files, and their format information
MRJobConfiguration.setUpMultipleOutputs(
job, resultIndexes, resultDimsUnknown, outputs, outputInfos, true, mayContainCtable);
// configure mapper and the mapper output key value pairs
job.setMapperClass(DataGenMapper.class);
if (numReducers == 0) {
job.setMapOutputKeyClass(Writable.class);
job.setMapOutputValueClass(Writable.class);
} else {
job.setMapOutputKeyClass(MatrixIndexes.class);
job.setMapOutputValueClass(TaggedMatrixBlock.class);
}
// set up combiner
if (numReducers != 0
&& aggInstructionsInReducer != null
&& !aggInstructionsInReducer.isEmpty()) job.setCombinerClass(GMRCombiner.class);
// configure reducer
job.setReducerClass(GMRReducer.class);
// job.setReducerClass(PassThroughReducer.class);
// By default, the job executes in "cluster" mode.
// Determine if we can optimize and run it in "local" mode.
MatrixCharacteristics[] inputStats = new MatrixCharacteristics[inputs.length];
for (int i = 0; i < inputs.length; i++) {
inputStats[i] = new MatrixCharacteristics(rlens[i], clens[i], brlens[i], bclens[i]);
}
// set unique working dir
MRJobConfiguration.setUniqueWorkingDir(job);
runjob = JobClient.runJob(job);
/* Process different counters */
Group group = runjob.getCounters().getGroup(MRJobConfiguration.NUM_NONZERO_CELLS);
for (int i = 0; i < resultIndexes.length; i++) {
// number of non-zeros
stats[i].setNonZeros(group.getCounter(Integer.toString(i)));
}
String dir = dimsUnknownFilePrefix + "/" + runjob.getID().toString() + "_dimsFile";
stats = MapReduceTool.processDimsFiles(dir, stats);
MapReduceTool.deleteFileIfExistOnHDFS(dir);
} finally {
for (String input : inputs) MapReduceTool.deleteFileIfExistOnHDFS(new Path(input), job);
}
return new JobReturn(stats, outputInfos, runjob.isSuccessful());
}