source: gs2-extensions/parallel-building/trunk/src/src/java/org/nzdl/gsdl/HadoopGreenstoneIngest.java@ 27571

Last change on this file since 27571 was 27571, checked in by jmt12, 11 years ago

increase timeout to 4 hours per map
File size: 14.2 KB
Line 
1/** jmt12 **/
2package org.nzdl.gsdl;
3
4import java.io.BufferedOutputStream;
5import java.io.BufferedReader;
6import java.io.File;
7import java.io.FileOutputStream;
8import java.io.FileWriter;
9import java.io.InputStream;
10import java.io.InputStreamReader;
11import java.io.IOException;
12import java.io.PrintWriter;
13import java.lang.ProcessBuilder;
14import java.lang.ProcessBuilder.*;
15import java.lang.Thread;
16import java.net.InetAddress;
17import java.util.Map;
18
19import org.apache.hadoop.fs.Path;
20import org.apache.hadoop.conf.*;
21import org.apache.hadoop.io.*;
22import org.apache.hadoop.mapreduce.*;
23import org.apache.hadoop.mapreduce.Mapper.Context;
24import org.apache.hadoop.mapreduce.lib.input.FileInputFormat;
25import org.apache.hadoop.mapreduce.lib.input.FileSplit;
26import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat;
27import org.apache.hadoop.mapreduce.lib.output.NullOutputFormat;
28import org.apache.hadoop.mapreduce.lib.output.TextOutputFormat;
29import org.apache.hadoop.util.*;
30
31/** @class WordCount
32 */
33public class HadoopGreenstoneIngest
34{
35
36 /** @class GSFileRecordReader
37 */
38 public static class GSFileRecordReader
39 extends RecordReader<Text, IntWritable>
40 {
41 /** Uncompressed file name */
42 private Text current_key;
43
44 private IntWritable current_value = new IntWritable(1);
45
46 /** Used to indicate progress */
47 private boolean is_finished = false;
48
49 /**
50 */
51 @Override
52 public void initialize( InputSplit inputSplit, TaskAttemptContext taskAttemptContext )
53 throws IOException, InterruptedException
54 {
55 FileSplit split = (FileSplit) inputSplit;
56 current_key = new Text(split.getPath().toString());
57 }
58 /** initialize() **/
59
60 /**
61 * We only ever have a single key/value
62 */
63 @Override
64 public boolean nextKeyValue()
65 throws IOException, InterruptedException
66 {
67 if (!is_finished)
68 {
69 is_finished = true;
70 return true;
71 }
72 return false;
73 }
74 /** nextKeyValue() **/
75
76 /** @function getProgress
77 * Rather than calculating progress, we just keep it simple
78 */
79 @Override
80 public float getProgress()
81 throws IOException, InterruptedException
82 {
83 return is_finished ? 1 : 0;
84 }
85 /** getProgress() **/
86
87 /**
88 * Returns the current key (name of the zipped file)
89 */
90 @Override
91 public Text getCurrentKey()
92 throws IOException, InterruptedException
93 {
94 return current_key;
95 }
96 /** getCurrentKey() **/
97
98 /**
99 * Returns the current value (contents of the zipped file)
100 */
101 @Override
102 public IntWritable getCurrentValue()
103 throws IOException, InterruptedException
104 {
105 return current_value;
106 }
107 /** getCurrentValue() **/
108
109 /**
110 * Close quietly, ignoring any exceptions
111 */
112 @Override
113 public void close()
114 throws IOException
115 {
116 // nothing to do
117 }
118 /** close() **/
119
120 }
121 /** GSFileRecordReader **/
122
123 /** @class GSFileInputFormat
124 */
125 public static class GSFileInputFormat
126 extends FileInputFormat<Text, IntWritable>
127 {
128 /**
129 * Don't split the files
130 */
131 @Override
132 protected boolean isSplitable(JobContext context, Path filename)
133 {
134 return false;
135 }
136 /** isSplitable() **/
137
138 /**
139 */
140 @Override
141 public RecordReader<Text, IntWritable> createRecordReader(InputSplit split, TaskAttemptContext content)
142 throws IOException, InterruptedException
143 {
144 return new GSFileRecordReader();
145 }
146 /** createRecordReader() **/
147
148 }
149 /** class GSFileInputFormat **/
150
151 /** @class GSMap
152 */
153 public static class GSMap
154 extends Mapper<Text, IntWritable, Text, IntWritable>
155 {
156 /** @function map
157 * The key is the full path (HDFS) of the file to be processed.
158 */
159 public void map(Text key, IntWritable value, Context context)
160 throws IOException, InterruptedException
161 {
162 String file_path = key.toString();
163 // - configuration for the task
164 Configuration conf = context.getConfiguration();
165 String gsdlhome = conf.get("gsdlhome");
166 String hdfs_prefix = conf.get("hdfsprefix");
167 String hadoop_prefix = conf.get("hadoopprefix");
168 String collection = conf.get("collection");
169 String task_id = conf.get("mapred.task.id");
170 task_id = task_id.substring(8); // remove "attempt_" prefix
171 // Programatically rewrite the protocol as appropriate for the given
172 // archives directory
173 file_path = file_path.replace("hdfs://", hdfs_prefix);
174 // - create a temporary directory
175 File greenstone_tmp_dir = new File("/tmp/greenstone");
176 if (!greenstone_tmp_dir.isDirectory())
177 {
178 greenstone_tmp_dir.mkdir();
179 }
180 // - open a unique log file
181 File import_process_log = new File("/tmp/greenstone/import-hadoop-" + task_id + ".log");
182 // - start the log by writing the time and the manifest line
183 FileWriter fw1 = new FileWriter(import_process_log, true);
184 long start_time = System.currentTimeMillis()/1000;
185 StringBuffer header_block = new StringBuffer("[Started:");
186 header_block.append(start_time);
187 header_block.append("]\n[Host:");
188 header_block.append(InetAddress.getLocalHost().getHostName());
189 header_block.append("]\n[CPU:");
190 String getcpu_executable_cmd = gsdlhome + "/ext/parallel-building/linux/bin/getcpu";
191 File getcpu_executable = new File(getcpu_executable_cmd);
192 if (getcpu_executable.exists())
193 {
194 header_block.append(runCommand(getcpu_executable_cmd));
195 }
196 else
197 {
198 header_block.append("0");
199 }
200 header_block.append("]\n[Task:");
201 header_block.append(task_id);
202 header_block.append("]\n[Map:");
203 header_block.append(file_path);
204 header_block.append("=>");
205 header_block.append(value);
206 header_block.append("]\n");
207 fw1.write(header_block.toString());
208 header_block = null;
209
210 // - create a temporary manifest file to process this file. Overwrite any
211 // existing file
212 File manifest_path = new File("/tmp/greenstone/manifest" + task_id + ".xml");
213 FileWriter manifest_writer = new FileWriter(manifest_path);
214 manifest_writer.write("<Manifest version=\"2.0\">\n");
215 manifest_writer.write("\t<Index>\n");
216 manifest_writer.write("\t\t<Filename>" + file_path + "</Filename>\n");
217 manifest_writer.write("\t</Index>\n");
218 manifest_writer.write("</Manifest>\n");
219 manifest_writer.close();
220
221 // - call Greenstone passing in the path to the manifest
222 ProcessBuilder import_process_builder
223 = new ProcessBuilder("time", "-p", "import.pl", "-manifest", manifest_path.toString(), "-keepold", "-verbosity", "42", "-archivedir", hdfs_prefix + "/user/jmt12/gsdl/collect/" + collection + "/archives", collection);
224 fw1.write("[Command:" + import_process_builder.command() + "]\n");
225 // - alter environment
226 Map<String, String> import_process_env = import_process_builder.environment();
227 // - path
228 String path = import_process_env.get("PATH");
229 path = gsdlhome + "/ext/parallel-building/bin/script:" + path;
230 path = gsdlhome + "/ext/parallel-building/linux/bin:" + path;
231 path = hadoop_prefix + "/bin:" + path;
232 path = gsdlhome + "/ext/tdb-edit/linux/bin:" + path;
233 path = gsdlhome + "/ext/tdb-edit/bin/script:" + path;
234 path = gsdlhome + "/ext/video-and-audio/linux/bin:" + path;
235 path = gsdlhome + "/bin/script:" + path;
236 path = gsdlhome + "/bin/linux:" + path;
237 import_process_env.put("PATH", path);
238 fw1.write("[PATH: " + path + "]\n");
239 // - ld_library_path
240 import_process_env.put("LD_LIBRARY_PATH", gsdlhome + "/ext/parallel-building/linux/lib:" + gsdlhome + "/ext/hadoop/linux/lib:" + gsdlhome + "/ext/video-and-audio/linux/lib:" + gsdlhome + "/ext/tdb-edit/linux/lib");
241 // - dyld_library_path
242 import_process_env.put("DYLD_LIBRARY_PATH", gsdlhome + "/ext/video-and-audio/linux/lib");
243 // - misc
244 import_process_env.put("GSDLHOME", gsdlhome);
245 import_process_env.put("GSDLOS", "linux");
246 import_process_env.put("GSDLEXTS", "parallel-building:tdb-edit:video-and-audio");
247 // - installed extension paths
248 import_process_env.put("GEXTPARALLELBUILDING", gsdlhome + "/ext/parallel-building");
249 import_process_env.put("GEXTPARALLELBUILDING_INSTALLED", gsdlhome + "/ext/parallel-building/linux");
250 import_process_env.put("GEXTTDBEDIT_INSTALLED", gsdlhome + "/ext/tdb-edit/linux");
251 import_process_env.put("GEXTVIDEO_INSTALLED", gsdlhome + "/ext/video-and-audio/linux");
252 // - Hadoop specific
253 import_process_env.put("HADOOP_PREFIX", hadoop_prefix);
254 fw1.write("[HADOOP_PREFIX: " + hadoop_prefix + "]\n");
255
256 // - change working directory
257 import_process_builder.directory(new File(gsdlhome));
258 // - close our output to the log before opening in the process
259 fw1.close();
260
261 // - write output to log
262 import_process_builder.redirectErrorStream(true);
263 import_process_builder.redirectOutput(Redirect.appendTo(import_process_log));
264
265 // - create progress reporter (so Hadoop doesn't time us out)
266 Thread reporter = new HadoopProgressReporter(context, import_process_log);
267 reporter.start();
268
269 // - run process
270 Process import_process = import_process_builder.start();
271 try
272 {
273 int import_status = import_process.waitFor();
274 if (import_status != 0)
275 {
276 throw new Exception("exit status: " + import_status);
277 }
278 }
279 catch (Exception e)
280 {
281 System.err.println("Error! Import command failed (" + e.toString() + ")");
282 }
283
284 // - stop the progress reporter as, one way or another, there will be no
285 // more progress
286 reporter.interrupt();
287 reporter = null; // force gc
288
289 // - write end time to log
290 FileWriter fw2 = new FileWriter(import_process_log, true);
291 long end_time = System.currentTimeMillis()/1000;
292 fw2.write("[Completed:" + end_time + "]\n");
293 fw2.close();
294
295 // - for now return a dummy output. In the future I may want to parse the
296 // output from Greenstone as output and allow reducing to make me a
297 // pretty timebased log
298 context.write(key, value);
299 }
300 /** map(LongWritable,Text,Context) **/
301
302 }
303 /** class GSMap **/
304
305 /** @function main
306 */
307 public static void main(String[] args)
308 throws Exception
309 {
310 if (args.length < 6)
311 {
312 System.out.println("Usage: bin/hadoop jar hadoop-greenstone.jar org.nzdl.gsdl.HadoopGreenstoneIngest <gsdlhome> <hdfsprefix> <hadoop prefix> <collection> <hdfsin> <hdfsout>\n");
313 System.exit(0);
314 }
315
316 Configuration conf = new Configuration();
317 conf.set("gsdlhome", args[0]);
318 conf.set("hdfsprefix", args[1]); // HDThriftFS or HDFSShell
319 conf.set("hadoopprefix", args[2]);
320 conf.set("collection", args[3]);
321 // Set the number of retries to 1 - hopefully one of the following will work
322 conf.setInt("mapred.map.max.attempts", 1); // Old Hadoop
323 conf.setInt("mapreduce.map.maxattempts", 1); // Hadoop 2.0.3-alpha
324 conf.setInt("mapreduce.map.max.attempts", 1); // Solution on Web
325 // prevent timeouts
326 long milli_seconds = 4*60*60*1000; // 4 hour
327 conf.setLong("mapred.task.timeout", milli_seconds);
328 Job job = new Job(conf, "hadoopgreenstoneingest");
329 job.setJarByClass(HadoopGreenstoneIngest.class);
330
331 job.setOutputKeyClass(Text.class);
332 job.setOutputValueClass(IntWritable.class);
333
334 // Register the map, combiner, and reducer classes
335 job.setMapperClass(GSMap.class);
336 // - in theory, uses the IdentityReducer by default, which simply returns
337 // the input as the output (so no processing)
338 job.setNumReduceTasks(0);
339
340 // Sets the input and output handlers - may need to adjust input to provide me
341 // a series of filenames (TextInputFormat will instead read in a text file and
342 // return each line...)
343 job.setInputFormatClass(GSFileInputFormat.class);
344 job.setOutputFormatClass(NullOutputFormat.class);
345 //job.setOutputFormatClass(TextOutputFormat.class);
346
347 // Register the input and output paths
348 // - this input path should be to a file (in HDFS) that lists the paths to
349 // the manifest files
350 FileInputFormat.setInputPaths(job, new Path(args[4]));
351 // - for now the output isn't that important, but in the future I may use
352 // this mechanism to produce a time based log.
353 FileOutputFormat.setOutputPath(job, new Path(args[5]));
354
355 // Recommended notation despite my hatiness of ?: syntax
356 System.exit(job.waitForCompletion(true)?0:1);
357 }
358 /** main(String[]) **/
359
360 /** @function runCommand()
361 *
362 * A convenience method that calls an external command and returns its
363 * standard out as a string. Warning! Not safe if the command could return a
364 * large amount of text in the STDERR stream - may infinitely block.
365 *
366 */
367 public static String runCommand(String command)
368 {
369 StringBuffer result = new StringBuffer();
370 try
371 {
372 Runtime run = Runtime.getRuntime() ;
373 Process pr = run.exec(command) ;
374 pr.waitFor() ;
375 BufferedReader buf = new BufferedReader( new InputStreamReader( pr.getInputStream() ) ) ;
376 String line;
377 while ( ( line = buf.readLine() ) != null )
378 {
379 result.append(line);
380 }
381 }
382 catch (Exception ex)
383 {
384 System.err.println("Error! " + ex.getMessage());
385 }
386 return result.toString();
387 }
388 /** runCommand() **/
389}
390
391class HadoopProgressReporter
392extends Thread
393{
394
395 private Context hadoop_process;
396
397 private File log_file;
398
399 HadoopProgressReporter(Context hadoop_process, File log_file)
400 {
401 this.hadoop_process = hadoop_process;
402 //this.log_file = log_file;
403 this.log_file = new File("/tmp/hadoop_progress_reporter.log");
404 }
405
406 public void run()
407 {
408 try
409 {
410 while (!this.isInterrupted())
411 {
412 sleep(60000); // Wait a minute
413 //FileWriter fw1 = new FileWriter(this.log_file, true);
414 //long time = System.currentTimeMillis()/1000;
415 //fw1.write("[" + time + "] HadoopProgressReporter.progress()\n");
416 //fw1.close();
417 this.hadoop_process.progress(); // Inform Hadoop we are still processing
418 }
419 }
420 catch (InterruptedException iex)
421 {
422 // We've been interrupted: no more progress
423 }
424 catch (Exception ex)
425 {
426 ex.printStackTrace();
427 }
428 }
429}
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