shadanan / hadooplink Goto Github PK
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License: Other
Mathematica package for reading files off of HDFS
License: Other
Very strange error.
The whole package worked nicely before my cluster crashed one time. After reinstall the OS and everything, lots of errors emerge including this one.
2016-02-11 19:35:06,117 INFO org.apache.hadoop.metrics.jvm.JvmMetrics: Initializing JVM Metrics with processName=MAP, sessionId=
2016-02-11 19:35:06,184 INFO org.apache.hadoop.mapred.MapTask: io.sort.mb = 100
2016-02-11 19:35:06,208 INFO org.apache.hadoop.mapred.MapTask: data buffer = 79691776/99614720
2016-02-11 19:35:06,208 INFO org.apache.hadoop.mapred.MapTask: record buffer = 262144/327680
2016-02-11 19:35:06,231 INFO org.apache.hadoop.util.NativeCodeLoader: Loaded the native-hadoop library
2016-02-11 19:35:06,233 INFO org.apache.hadoop.io.compress.zlib.ZlibFactory: Successfully loaded & initialized native-zlib library
2016-02-11 19:35:06,233 INFO org.apache.hadoop.io.compress.CodecPool: Got brand-new decompressor
2016-02-11 19:35:06,726 WARN org.apache.hadoop.mapred.TaskTracker: Error running child
java.lang.StringIndexOutOfBoundsException: String index out of range: -6
at java.lang.String.substring(String.java:1967)
at com.wolfram.hadoop.mapreduce.MapReduceKernelLink.loadPackageFromJar(Unknown Source)
at com.wolfram.hadoop.mapreduce.MapReduceKernelLink.get(Unknown Source)
at com.wolfram.hadoop.mapreduce.MathematicaMapper.setup(Unknown Source)
at org.apache.hadoop.mapreduce.Mapper.run(Mapper.java:142)
at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:518)
at org.apache.hadoop.mapred.MapTask.run(MapTask.java:303)
at org.apache.hadoop.mapred.Child.main(Child.java:170)
2016-02-11 19:35:06,730 INFO org.apache.hadoop.mapred.TaskRunner: Runnning cleanup for the task
Located at:
String packagePath = packageURL.getPath();
int n = packagePath.lastIndexOf("!");
String jarPath = packagePath.substring(5, n);
Right now the input and output format for HadoopLink MapReduce jobs are hard-coded as SequenceFileInputFormat and SequenceFileOutputFormat respectively:
[paul-jean@paul-jeanmaclap: hadoop-link]$ grep "setInputFormatClass" src/java/com/wolfram/hadoop/mapreduce/MathematicaJob.java
job.setInputFormatClass(SequenceFileInputFormat.class);
[paul-jean@paul-jeanmaclap: hadoop-link]$ grep "setOutputFormatClass" src/java/com/wolfram/hadoop/mapreduce/MathematicaJob.java
job.setOutputFormatClass(SequenceFileOutputFormat.class);
I would be nice to be able to choose alternative input/output formats.
The cleanest way that comes to mind is to add options "InputFormat" and "OutputFormat" to the HadoopMapReduceJob function:
HadoopMapReduceJob[
$$link,
"blah blah",
inputfile,
outputdir,
Function[{k,v}, ...],
Function[{k,vs}, ...],
"InputFormat" -> "Text",
"OutputFormat" -> "SequenceFile" (* or Automatic *)
]
The reason I want this at the moment is so I can write a simple job that turns text files into Sequence files:
Clear[GenomeIndexMapper];
GenomeIndexMapper := Function[{k, v},
Yield[k, v]
]
Clear[GenomeIndexReducer];
GenomeIndexReducer := Function[{k, vs},
While[vs@hasNext[],
Yield[k, vs@next[]]
]
]
With[{
input =
DFSFileNames[$$link, "*.fa",
"/user/paul-jean/hadooplink/genomes/hs/"],
out = "/user/paul-jean/hadooplink/genomes/test"},
If[DFSFileExistsQ[$$link, out], DFSDeleteDirectory[$$link, out]];
HadoopMapReduceJob[
$$link,
"test identity mappers/reducers",
input,
out,
GenomeIndexMapper,
GenomeIndexReducer,
"InputFormat" -> "Text",
"OutputFormat" -> "SequenceFile"
]
]
When use DFSImport[h_HadoopLink, file_String, "SequenceFile"]
it reports :
cannot load java class: com.wolfram.hadoop.dfs.SequenceFileImportReader
link = OpenHadoopLink[
"fs.default.name" -> "hdfs://hadoopheadlx.wolfram.com:8020",
"mapred.job.tracker" -> "hadoopheadlx.wolfram.com:8021"];
DFSFileNames[link]
Java::excptn: A Java exception occurred: java.lang.ClassNotFoundException: org.apache.hadoop.fs.FileSystem
at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:249).
LoadJavaClass::fail: Java failed to load class org.apache.hadoop.fs.FileSystem. >>
Java::excptn: A Java exception occurred: java.lang.ClassNotFoundException: org.apache.hadoop.conf.Configuration
at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:249).
LoadJavaClass::fail: Java failed to load class org.apache.hadoop.conf.Configuration. >>
KeepJavaObject::obj: At least one argument to KeepJavaObject was not a valid Java object. >>
Java::excptn: A Java exception occurred: java.lang.ClassNotFoundException: org.apache.hadoop.fs.Path
at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:249).
General::stop: Further output of Java::excptn will be suppressed during this calculation. >>
LoadJavaClass::fail: Java failed to load class org.apache.hadoop.fs.Path. >>
General::stop: Further output of LoadJavaClass::fail will be suppressed during this calculation. >>
StringMatchQ::strse: String or list of strings expected at position 1 in StringMatchQ[OperatingSystem->Unix,*]. >>
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