Develop Reference

MapReduce WordCount example issue

I was trying to run the basic WordCount example of Apache MapReduce 2.7 from here:
https://hadoop.apache.org/docs/r2.7.0/hadoop-mapreduce-client/hadoop-mapreduce-client-core/MapReduceTutorial.html#Example:_WordCount_v1.0
I put the input files at : /user/hadoopLearning/WordCount/input/
Output path : /user/hadoopLearning/WordCount/output/
then I ran the following command :
hadoop jar wc.jar WordCount /user/hadoopLearning/WordCount/input/file01 /user/hadoopLearning/WordCount/output
However on running I am getting the following error:
Exception in thread "main" org.apache.hadoop.mapred.FileAlreadyExistsException: **Output directory** hdfs://sandbox.hortonworks.com:8020/user/hadoopLearning/WordCount/**input**/file01 already exists
I haven't written a single piece of code and copied everything from above location from Apache's website.
I understand the error , but the if we closely look at the error it says the output directory already exists and in the stack trace it gives the path of input directory.
Please can anyone help me. I am a beginner in the field of hadoop. Thanks in advance.

You're trying to create a file which already exists.
HDFS doesn't allow that.
replace your output path ('/user/hadoopLearning/WordCount/output'), with something else.
try this command
hadoop jar wc.jar WordCount /user/hadoopLearning/WordCount/input/file01 /user/hadoopLearning/WordCount/new_output_path

Java error while running maxent in biomod2

I am running maxent from R, in the package biomod2 and the following error appeared. I do not come from a technical background and wasn't sure why is this error happening. Is it a memory problem or someone said the java path is not set. But I followed the instructions to set maxent to run in R and also downloaded Java Platform, Standard Edition Development Kit and set a path for it as explained in this pdf: http://modata.ceoe.udel.edu/dev/dhaulsee/class_rcode/r_pkgmanuals/MAXENT4R_directions.pdf
I would be really grateful if you could help me understand this problem and any solution to it.
Thanks a lot
Error in file(file, "rt") : cannot open the connection
In addition: Warning messages:
1: running command 'java' had status 1
2: running command 'java -mx512m -jar E:\bioclim_2.5min\model/maxent.jar environmentallayers
="rainfed/models/1432733200/m_47203134/Back_swd.csv"
samplesfile="rainfed/models/1432733200/m_47203134/Sp_swd.csv"
projectionlayers="rainfed/models/1432733200/m_47203134/Predictions/Pred_swd.csv"
outputdirectory="rainfed/models/1432733200/rainfed_PA1_Full_MAXENT_outputs"
outputformat=logistic redoifexists visible=FALSE linear=TRUE quadratic=TRUE
product=TRUE threshold=TRUE hinge=TRUE lq2lqptthreshold=80 l2lqthreshold=10
hingethreshold=15 beta_threshold=-1 beta_categorical=-1 beta_lqp=-1
beta_hinge=-1 defaultprevalence=0.5 autorun nowarnings notooltips
noaddsamplestobackground' had status 1
3: In file(file, "rt") :
cannot open file 'rainfed/models/1432733200/rainfed_PA1_Full_MAXENT_outputs/rainfed_PA1_
Full_Pred_swd.csv': No such file or directory

I've just manage to solve this problem - it is a problem with the file path specified. For me, I had a space in one of the folder names which was not accepted in the path to the maxent.jar file. From looking at your error, it looks like it might be the two backslashes.
E:\bioclim_2.5min\model/maxent.jar
should probably read
E:/bioclim_2.5min/model/maxent.jar

DBPedia extraction framework failure during extraction of DBPedia Dump

While working on DBpedia extraction framework, I am facing issues with the csv files from the Core Dataset.
I'm interested in extracting data (in my case, abstract of all company's wikipedia page) from dbpedia dumps (RDF format). I'm following the instructions from DBpedia Abstract Extractioin Step-by-step Guide
Commands used:
$ git clone git://github.com/dbpedia/extraction-framework.git
$ cd extraction-framework
$ mvn clean install
$ cd dump
$ ../run download config=download.minimal.properties
$ ../run extraction extraction.default.properties
I get the below error when executing the last command "./run extraction extraction.properties.file". Can anyone point out wh at mistake am I making. Is there any specific csv file i need to process or some configur ation issue. I have the full "mediawiki-1.24.1".
Also please note th at pages-articles.xml.bz2, I download it partially upto 256MB only. Please help
parsing /opt/extraction-framework-master/DumpsD ata/wikid atawiki/20150113/wikipedias.csv
java.lang.reflect.Invoc ationTargetException
at sun.reflect.N ativeMethodAccessorImpl.invoke0(N ative Method)
at sun.reflect.N ativeMethodAccessorImpl.invoke(N ativeMethodAccessorImpl.java:62)
at sun.reflect.Deleg atingMethodAccessorImpl.invoke(Deleg atingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:483)
at scala_maven_executions.MainHelper.runMain(MainHelper.java:164)
at scala_maven_executions.MainWithArgsInFile.main(MainWithArgsInFile.java:26)
Caused by: java.lang.Exception: expected [15] fields, found [1] in line [%21%21%21 http://www.w3.org/2000/01/rdf-schema#label !!! l]
at org.dbpedia.extraction.util.WikiInfo$.fromLine(WikiInfo.scala:60)
at org.dbpedia.extraction.util.WikiInfo$$anonfun$fromLines$1.apply(WikiInfo.scala:49)
at org.dbpedia.extraction.util.WikiInfo$$anonfun$fromLines$1.apply(WikiInfo.scala:49)
at scala.collection.Iter ator$class.foreach(Iter ator.scala:743)
at scala.collection.AbstractIter ator.foreach(Iter ator.scala:1195)
at org.dbpedia.extraction.util.WikiInfo$.fromLines(WikiInfo.scala:49)
at org.dbpedia.extraction.util.WikiInfo$.fromSource(WikiInfo.scala:36)
at org.dbpedia.extraction.util.WikiInfo$.fromFile(WikiInfo.scala:27)
at org.dbpedia.extraction.util.ConfigUtils$.parseLanguages(ConfigUtils.scala:83)
at org.dbpedia.extraction.dump.sql.Import$.main(Import.scala:29)
at org.dbpedia.extraction.dump.sql.Import.main(Import.scala)

i was facing above issue because of incomplete download of enwiki-20150205-pages-articles.xml.bz2 file using
$ ../run download config=download.minimal.properties
but yet failing to resolve abstract extraction issue as i am expecting long abstract from bdpedia dump.
$ ../run extraction extraction extraction.abstracts.properties
it builds completely and perform extraction over 1 cr+ pages but not reflecting any data in long_abstracts_en.nt
i followed instruction to put mediawiki php and mysql etc.

Gpj installation error in Linux

i am new to java card development. i want to write java applet and create .cap file to the smart card.so i read https://www.opensc-project.org/opensc/wiki/JavaCard this article and i in download the gpj-20120310.zip and try to install that one in the Linux flat form.when i try to install using read readMe file when i entered java -jar gpj.jar command it gives java.security.NoSuchAlgorithmException: Error constructing implementation (algorithm: PC/SC, provider: SunPCSC, class: sun.security.smartcardio.SunPCSC$Factory Error.Can anyone tell me what is the wrong..
Thanks
SSV

tdbloader on Cygwin: Gettging FileNotFoundException: d:\cygdrive\d\....\node2id.idn

I am completely new to Jena/TDB. All I want to do is to load data from some sample rdf, N3 etc file using tdb scripts or through java api.
I am tried to use tbdloader on Cygwin to load data (tdb-0.9.0, on Windows XP with IBM Java 1.6). Following are the command that I ran:
$ export TDBROOT=/cygdrive/d/Project/Store_DB/jena-tdb-0.9.0-incubating
$ export PATH=$TDBROOT/bin:$PATH
I also changed classpath for java in the tdbloader script as mentioned at tdbloader on Cygwin: java.lang.NoClassDefFoundError :
exec java $JVM_ARGS $SOCKS -cp "PATH_OF_JAR_FILES" "tdb.$TDB_CMD" $TDB_SPEC "$#"
So when I run $ tdbloader --help it shows the help correctly.
But when I run
$ tdbloader --loc /cygdrive/d/Project/Store_DB/data1
OR
$ tdbloader --loc /cygdrive/d/Project/Store_DB/data1 test.rdf
I am getting following exception:
com.hp.hpl.jena.tdb.base.file.FileException: Failed to open: d:\cygdrive\d\Project\Store_DB\data1\node2id.idn (mode=rw)
at com.hp.hpl.jena.tdb.base.file.ChannelManager.open$(ChannelManager.java:83)
at com.hp.hpl.jena.tdb.base.file.ChannelManager.openref$(ChannelManager.java:58)
at com.hp.hpl.jena.tdb.base.file.ChannelManager.acquire(ChannelManager.java:47)
at com.hp.hpl.jena.tdb.base.file.FileBase.<init>(FileBase.java:57)
at com.hp.hpl.jena.tdb.base.file.FileBase.<init>(FileBase.java:46)
at com.hp.hpl.jena.tdb.base.file.FileBase.create(FileBase.java:41)
at com.hp.hpl.jena.tdb.base.file.BlockAccessBase.<init>(BlockAccessBase.java:46)
at com.hp.hpl.jena.tdb.base.block.BlockMgrFactory.createStdFile(BlockMgrFactory.java:98)
at com.hp.hpl.jena.tdb.base.block.BlockMgrFactory.createFile(BlockMgrFactory.java:82)
at com.hp.hpl.jena.tdb.base.block.BlockMgrFactory.create(BlockMgrFactory.java:58)
at com.hp.hpl.jena.tdb.setup.Builder$BlockMgrBuilderStd.buildBlockMgr(Builder.java:196)
at com.hp.hpl.jena.tdb.setup.Builder$RangeIndexBuilderStd.createBPTree(Builder.java:165)
at com.hp.hpl.jena.tdb.setup.Builder$RangeIndexBuilderStd.buildRangeIndex(Builder.java:134)
at com.hp.hpl.jena.tdb.setup.Builder$IndexBuilderStd.buildIndex(Builder.java:112)
at com.hp.hpl.jena.tdb.setup.Builder$NodeTableBuilderStd.buildNodeTable(Builder.java:85)
at com.hp.hpl.jena.tdb.setup.DatasetBuilderStd$NodeTableBuilderRecorder.buildNodeTable(DatasetBuilderStd.java:389)
at com.hp.hpl.jena.tdb.setup.DatasetBuilderStd.makeNodeTable(DatasetBuilderStd.java:300)
at com.hp.hpl.jena.tdb.setup.DatasetBuilderStd._build(DatasetBuilderStd.java:167)
at com.hp.hpl.jena.tdb.setup.DatasetBuilderStd.build(DatasetBuilderStd.java:157)
at com.hp.hpl.jena.tdb.setup.DatasetBuilderStd.build(DatasetBuilderStd.java:70)
at com.hp.hpl.jena.tdb.StoreConnection.make(StoreConnection.java:132)
at com.hp.hpl.jena.tdb.transaction.DatasetGraphTransaction.<init>(DatasetGraphTransaction.java:46)
at com.hp.hpl.jena.tdb.sys.TDBMakerTxn._create(TDBMakerTxn.java:50)
at com.hp.hpl.jena.tdb.sys.TDBMakerTxn.createDatasetGraph(TDBMakerTxn.java:38)
at com.hp.hpl.jena.tdb.TDBFactory._createDatasetGraph(TDBFactory.java:166)
at com.hp.hpl.jena.tdb.TDBFactory.createDatasetGraph(TDBFactory.java:74)
at com.hp.hpl.jena.tdb.TDBFactory.createDataset(TDBFactory.java:53)
at tdb.cmdline.ModTDBDataset.createDataset(ModTDBDataset.java:95)
at arq.cmdline.ModDataset.getDataset(ModDataset.java:34)
at tdb.cmdline.CmdTDB.getDataset(CmdTDB.java:137)
at tdb.cmdline.CmdTDB.getDatasetGraph(CmdTDB.java:126)
at tdb.cmdline.CmdTDB.getDatasetGraphTDB(CmdTDB.java:131)
at tdb.tdbloader.loadQuads(tdbloader.java:163)
at tdb.tdbloader.exec(tdbloader.java:122)
at arq.cmdline.CmdMain.mainMethod(CmdMain.java:97)
at arq.cmdline.CmdMain.mainRun(CmdMain.java:59)
at arq.cmdline.CmdMain.mainRun(CmdMain.java:46)
at tdb.tdbloader.main(tdbloader.java:53)
Caused by: java.io.FileNotFoundException: d:\cygdrive\d\Project\Store_DB\data1\node2id.idn (The system cannot find the path specified.)
at java.io.RandomAccessFile.open(Native Method)
at java.io.RandomAccessFile.<init>(RandomAccessFile.java:222)
at java.io.RandomAccessFile.<init>(RandomAccessFile.java:107)
at com.hp.hpl.jena.tdb.base.file.ChannelManager.open$(ChannelManager.java:80)
... 37 more
I am not sure what node2id.idn file is and why is it expecting it?

The file node2id.idn is one of TDB's internal index files. It's not something that you have to create or manage for yourself. I've just tried tdbloader on cygwin myself, it it worked OK for me. I can think of two basic possibilities:
your disk is full
the TDB index is corrupted
If this is the first file you are loading into an otherwise emtpy TDB, the second possibility is unlikely. If you are loading into a non-empty TDB, try deleting the TDB image and starting again. Note that TDB by itself does not manage concurrent writes: if you have more than one process writing to a single TDB image, you must handle locking at the application level, or use TDB's transactions.
The final possibility, of course, is that your disk is flaky. You might want to try your code on another machine.
If none of these suggestions help, please send a complete minimal test case to the Jena users list.