I had successfully configure MongoDB(5.3.1) and Nutch(2.3), when I run the command "./bin/nutch index -all" some errors printed after inject/generate/fetch/parse/updatedb commands work,the error details like:
SolrIndexerJob: java.lang.RuntimeException: job failed: name=apache-nutch-2.3.1.jar, jobid=job_local140530148_0001
at org.apache.nutch.util.NutchJob.waitForCompletion(NutchJob.java:120)
at org.apache.nutch.indexer.IndexingJob.run(IndexingJob.java:154)
at org.apache.nutch.indexer.IndexingJob.index(IndexingJob.java:176)
at org.apache.nutch.indexer.IndexingJob.run(IndexingJob.java:202)
at org.apache.hadoop.util.ToolRunner.run(ToolRunner.java:70)
at org.apache.nutch.indexer.IndexingJob.main(IndexingJob.java:211)
I had configure the file in $NUTCH_HOME/runtime/local/conf/nutch-site.xml
details:
If all the others steps was running, it would be not a problem with mongodb but with solr (your nutch-site.xml suggests that you wanted index your data in solr). As far that i remember, when i used solr, i precised the core name, it would be something like that :
http://localhost:8983/solr/mycore/
Related
I am running a streaming beam job on a flink cluster where I am getting the following exception.
Caused by: org.apache.beam.sdk.util.UserCodeException: org.apache.flink.streaming.runtime.tasks.ExceptionInChainedOperatorException: Could not forward element to next operator
at org.apache.beam.sdk.util.UserCodeException.wrap(UserCodeException.java:34)
at org.apache.beam.sdk.transforms.MapElements$1$DoFnInvoker.invokeProcessElement(Unknown Source)
at org.apache.beam.runners.core.SimpleDoFnRunner.invokeProcessElement(SimpleDoFnRunner.java:218)
at org.apache.beam.runners.core.SimpleDoFnRunner.processElement(SimpleDoFnRunner.java:183)
at org.apache.beam.runners.flink.metrics.DoFnRunnerWithMetricsUpdate.processElement(DoFnRunnerWithMetricsUpdate.java:62)
at org.apache.beam.runners.flink.translation.wrappers.streaming.DoFnOperator.processElement(DoFnOperator.java:544)
at org.apache.flink.streaming.runtime.io.StreamInputProcessor.processInput(StreamInputProcessor.java:202)
at org.apache.flink.streaming.runtime.tasks.OneInputStreamTask.run(OneInputStreamTask.java:105)
at org.apache.flink.streaming.runtime.tasks.StreamTask.invoke(StreamTask.java:302)
at org.apache.flink.runtime.taskmanager.Task.run(Task.java:711)
at java.lang.Thread.run(Thread.java:748)
Caused by: org.apache.flink.streaming.runtime.tasks.ExceptionInChainedOperatorException: Could not forward element to next operator
at org.apache.flink.streaming.runtime.tasks.OperatorChain$CopyingChainingOutput.pushToOperator(OperatorChain.java:596)
at org.apache.flink.streaming.runtime.tasks.OperatorChain$CopyingChainingOutput.collect(OperatorChain.java:554)
at org.apache.flink.streaming.runtime.tasks.OperatorChain$CopyingChainingOutput.collect(OperatorChain.java:534)
at org.apache.flink.streaming.api.operators.AbstractStreamOperator$CountingOutput.collect(AbstractStreamOperator.java:718)
at org.apache.flink.streaming.api.operators.AbstractStreamOperator$CountingOutput.collect(AbstractStreamOperator.java:696)
at org.apache.beam.runners.flink.translation.wrappers.streaming.DoFnOperator$BufferedOutputManager.emit(DoFnOperator.java:941)
at org.apache.beam.runners.flink.translation.wrappers.streaming.DoFnOperator$BufferedOutputManager.output(DoFnOperator.java:895)
at org.apache.beam.runners.core.SimpleDoFnRunner.outputWindowedValue(SimpleDoFnRunner.java:252)
at org.apache.beam.runners.core.SimpleDoFnRunner.access$700(SimpleDoFnRunner.java:74)
at org.apache.beam.runners.core.SimpleDoFnRunner$DoFnProcessContext.output(SimpleDoFnRunner.java:576)
at org.apache.beam.sdk.transforms.DoFnOutputReceivers$WindowedContextOutputReceiver.output(DoFnOutputReceivers.java:71)
at org.apache.beam.sdk.transforms.MapElements$1.processElement(MapElements.java:139)
Caused by: org.apache.beam.sdk.util.UserCodeException: java.lang.IllegalArgumentException: Expect srcResourceIds and destResourceIds have the same scheme, but received alluxio, file.
at org.apache.beam.sdk.util.UserCodeException.wrap(UserCodeException.java:34)
at org.apache.beam.sdk.io.WriteFiles$FinalizeTempFileBundles$FinalizeFn$DoFnInvoker.invokeProcessElement(Unknown Source)
at org.apache.beam.runners.core.SimpleDoFnRunner.invokeProcessElement(SimpleDoFnRunner.java:218)
at org.apache.beam.runners.core.SimpleDoFnRunner.processElement(SimpleDoFnRunner.java:183)
at org.apache.beam.runners.flink.metrics.DoFnRunnerWithMetricsUpdate.processElement(DoFnRunnerWithMetricsUpdate.java:62)
at org.apache.beam.runners.flink.translation.wrappers.streaming.DoFnOperator.processElement(DoFnOperator.java:544)
at org.apache.flink.streaming.runtime.tasks.OperatorChain$CopyingChainingOutput.pushToOperator(OperatorChain.java:579)
at org.apache.flink.streaming.runtime.tasks.OperatorChain$CopyingChainingOutput.collect(OperatorChain.java:554)
at org.apache.flink.streaming.runtime.tasks.OperatorChain$CopyingChainingOutput.collect(OperatorChain.java:534)
at org.apache.flink.streaming.api.operators.AbstractStreamOperator$CountingOutput.collect(AbstractStreamOperator.java:718)
at org.apache.flink.streaming.api.operators.AbstractStreamOperator$CountingOutput.collect(AbstractStreamOperator.java:696)
at org.apache.beam.runners.flink.translation.wrappers.streaming.DoFnOperator$BufferedOutputManager.emit(DoFnOperator.java:941)
at org.apache.beam.runners.flink.translation.wrappers.streaming.DoFnOperator$BufferedOutputManager.output(DoFnOperator.java:895)
at org.apache.beam.runners.core.SimpleDoFnRunner.outputWindowedValue(SimpleDoFnRunner.java:252)
at org.apache.beam.runners.core.SimpleDoFnRunner.access$700(SimpleDoFnRunner.java:74)
at org.apache.beam.runners.core.SimpleDoFnRunner$DoFnProcessContext.output(SimpleDoFnRunner.java:576)
at org.apache.beam.sdk.transforms.DoFnOutputReceivers$WindowedContextOutputReceiver.output(DoFnOutputReceivers.java:71)
at org.apache.beam.sdk.transforms.MapElements$1.processElement(MapElements.java:139)
at org.apache.beam.sdk.transforms.MapElements$1$DoFnInvoker.invokeProcessElement(Unknown Source)
at org.apache.beam.runners.core.SimpleDoFnRunner.invokeProcessElement(SimpleDoFnRunner.java:218)
at org.apache.beam.runners.core.SimpleDoFnRunner.processElement(SimpleDoFnRunner.java:183)
at org.apache.beam.runners.flink.metrics.DoFnRunnerWithMetricsUpdate.processElement(DoFnRunnerWithMetricsUpdate.java:62)
at org.apache.beam.runners.flink.translation.wrappers.streaming.DoFnOperator.processElement(DoFnOperator.java:544)
at org.apache.flink.streaming.runtime.io.StreamInputProcessor.processInput(StreamInputProcessor.java:202)
at org.apache.flink.streaming.runtime.tasks.OneInputStreamTask.run(OneInputStreamTask.java:105)
at org.apache.flink.streaming.runtime.tasks.StreamTask.invoke(StreamTask.java:302)
at org.apache.flink.runtime.taskmanager.Task.run(Task.java:711)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.IllegalArgumentException: Expect srcResourceIds and destResourceIds have the same scheme, but received alluxio, file.
at org.apache.beam.vendor.guava.v26_0_jre.com.google.common.base.Preconditions.checkArgument(Preconditions.java:141)
at org.apache.beam.sdk.io.FileSystems.validateSrcDestLists(FileSystems.java:428)
at org.apache.beam.sdk.io.FileSystems.rename(FileSystems.java:308)
at org.apache.beam.sdk.io.FileBasedSink$WriteOperation.moveToOutputFiles(FileBasedSink.java:755)
at org.apache.beam.sdk.io.WriteFiles$FinalizeTempFileBundles$FinalizeFn.process(WriteFiles.java:850)
The streaming job is getting data from the apache pulsar source and writing output data onto an Alluxio data lake in parquet file format. I am using Spotify's scio for writing this job in Scala. A little code chunk to emphasize what I am trying to achieve:
pulsarSource
.open(sc)
.withFixedWindows(Duration.standardSeconds(windowDuration))
.toSinkTap(sink)
From the exception, I can see that source and output paths should have the same URI scheme but I don't know how it is happening because I am using an alluxio path as an output directory. There are some temp directories that are being created on alluxio output directory but after the WindowDuration, when the output file is being created, this exception happens.
I had a doubt that temp location might be configured by default to the local filesystem, so I did set that to output directory path (alluxio dir path) but it didn't change anything.
sc.options.setTempLocation(outputDir)
I want to do remote debugging in order to figure out the issue. I have tried this document to do remote debugging on the task executor node, but once my IntelliJ IDE connects with the node, I don't get hit on my breakpoint.
Can someone suggest, how can I debug or get more information about this issue.
Thanks
Remote debugging might be quite hard, but let's try this first: Make sure you connect to the task manager and not job manager (easy to verify with thread names). Then make sure to have a high number of retries, such that you don't miss the task execution, as attaching the debugging might take a while.
It's also helpful to double check that line numbers of the stack trace match your code version in the IDE. If Flink/Beam is preinstalled, they might run a slightly different version and your break point is void. Just paste the stack trace in your IDE and check if each line matches the expectation. Finally, add a few more breakpoint at central places like org.apache.flink.streaming.runtime.io.StreamInputProcessor.processInput(StreamInputProcessor.java:202) to make sure if the setup is working at all.
However, remote debugging is usually not the recommended option for big data systems. You'd first ensure locally that most of the things work on their own with some IT tests and local runners. Then, you might want to add e2e tests with docker containers and a local mini cluster. Additionally, you'd add a ton of logging statements, which you can turn on and off with your logging configuration. Similarly, if you set logging level to debug, the existing log statements of the frameworks might already be enough to gain some insights. One important thing that you should always look at is the generated topology that you can see in Web UI. Maybe it already tells you the paths in question.
One question as just starting to use karate-gatling: is it possible to aggregate the reports generated? So after multiple runs to get one single report? It would be nice to be able to compare somehow the performance - to get automatically the information if there is a performance degradation or not. What I did try but did not work, was to copy the simulation logs and afterwards only generate the reports ("gatling.bat -ro simulations") but this did not work. The error that I got was:
gatling.bat -ro simulations/catskaratesimulation-1544015145031
GATLING_HOME is set to "D:\AutomationTeam\gatling-charts-highcharts-bundle-3.0.1.1"
JAVA = ""C:\Program Files\Java\jdk1.8.0_131\bin\java.exe""
Parsing log file(s)...
Exception in thread "main" java.lang.NumberFormatException: For input string: "catskaratesimulation"
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Long.parseLong(Long.java:589)
at java.lang.Long.parseLong(Long.java:631)
at scala.collection.immutable.StringLike.toLong(StringLike.scala:305)
at scala.collection.immutable.StringLike.toLong$(StringLike.scala:305)
at scala.collection.immutable.StringOps.toLong(StringOps.scala:29)
at io.gatling.charts.stats.LogFileReader.$anonfun$firstPass$1(LogFileReader.scala:102)
at scala.collection.Iterator.foreach(Iterator.scala:937)
at scala.collection.Iterator.foreach$(Iterator.scala:937)
at scala.collection.AbstractIterator.foreach(Iterator.scala:1425)
at io.gatling.charts.stats.LogFileReader.firstPass(LogFileReader.scala:86)
at io.gatling.charts.stats.LogFileReader.$anonfun$x$4$1(LogFileReader.scala:125)
at io.gatling.charts.stats.LogFileReader.parseInputFiles(LogFileReader.scala:63)
at io.gatling.charts.stats.LogFileReader.(LogFileReader.scala:125)
at io.gatling.app.RunResultProcessor.initLogFileReader(RunResultProcessor.scala:67)
at io.gatling.app.RunResultProcessor.processRunResult(RunResultProcessor.scala:49)
at io.gatling.app.Gatling$.start(Gatling.scala:81)
at io.gatling.app.Gatling$.fromArgs(Gatling.scala:46)
at io.gatling.app.Gatling$.main(Gatling.scala:38)
at io.gatling.app.Gatling.main(Gatling.scala)
Is there another way to do it? Should I somehow reconfigure gatling? Thanks!
It worked when using the same version (2.2.4) via gatling.bat -ro folder_with_simulations.
I am using Hadoop on Windows Server 2008 - Hortonworks distribution
We are using PIG and trying to write the data into MongoDB; I am not able to read or write to the MongoDB; not sure what the issue we get an error 2116 which states that the mongodb schema is empty
Command to read -
register 'D:\hdp\pig-0.12.1.2.1.1.0-1621\lib\mongo-hadoop-core-1.2.0.jar'
register 'D:\mongo-hadoop-2.2-1.2.0\mongo-hadoop-2.2-1.2.0\mongo-hadoop-1.2.0.jar'
register 'D:\mongo-hadoop-2.2-1.2.0\mongo-hadoop-2.2-1.2.0\mongo-hadoop-pig-1.2.0.jar'
register 'D:\hdp\hadoop-2.4.0.2.1.1.0-1621\lib\mongo-2.6.1.jar'
set mapred.map.tasks.speculative.execution false;
set mapred.reduce.tasks.speculative.execution false;
SET mapreduce.fileoutputcommitter.marksuccessfuljobs false;
SalesLoading = load 'mongodb://localhost/benvenuedb.SalesData' using com.mongodb.hadoop.pig.MongoLoader();
store SalesLoading into 'mongodb://localhost:27017/benvenuedb.SalesData1' using com.mongodb.hadoop.pig.MongoStorage();
Error Messages
Pig Stack Trace
---------------
ERROR 2116:
<line 5, column 0> Output Location Validation Failed for: 'mongodb://127.0.0.1:27017/benvenuedb.SalesData More info to follow:
The value of property mongo.pig.output.schema must not be null
org.apache.pig.impl.logicalLayer.FrontendException: ERROR 1002: Unable to store alias salesLoading
at org.apache.pig.PigServer$Graph.registerQuery(PigServer.java:1637)
at org.apache.pig.PigServer.registerQuery(PigServer.java:577)
at org.apache.pig.tools.grunt.GruntParser.processPig(GruntParser.java:1093)
at org.apache.pig.tools.pigscript.parser.PigScriptParser.parse(PigScriptParser.java:501)
at org.apache.pig.tools.grunt.GruntParser.parseStopOnError(GruntParser.java:198)
at org.apache.pig.tools.grunt.GruntParser.parseStopOnError(GruntParser.java:173)
at org.apache.pig.tools.grunt.Grunt.run(Grunt.java:69)
at org.apache.pig.Main.run(Main.java:541)
at org.apache.pig.Main.main(Main.java:156)
Caused by: org.apache.pig.impl.plan.VisitorException: ERROR 2116:
<line 5, column 0> Output Location Validation Failed for: 'mongodb://127.0.0.1:27017/benvenuedb.SalesData More info to follow:
The value of property mongo.pig.output.schema must not be null
at org.apache.pig.newplan.logical.rules.InputOutputFileValidator$InputOutputFileVisitor.visit(InputOutputFileValidator.java:75)
at org.apache.pig.newplan.logical.relational.LOStore.accept(LOStore.java:66)
at org.apache.pig.newplan.DepthFirstWalker.depthFirst(DepthFirstWalker.java:64)
at org.apache.pig.newplan.DepthFirstWalker.depthFirst(DepthFirstWalker.java:66)
at org.apache.pig.newplan.DepthFirstWalker.walk(DepthFirstWalker.java:53)
at org.apache.pig.newplan.PlanVisitor.visit(PlanVisitor.java:52)
at org.apache.pig.newplan.logical.rules.InputOutputFileValidator.validate(InputOutputFileValidator.java:45)
at org.apache.pig.backend.hadoop.executionengine.HExecutionEngine.compile(HExecutionEngine.java:303)
at org.apache.pig.PigServer.compilePp(PigServer.java:1382)
at org.apache.pig.PigServer.executeCompiledLogicalPlan(PigServer.java:1307)
at org.apache.pig.PigServer.execute(PigServer.java:1299)
at org.apache.pig.PigServer.access$400(PigServer.java:124)
at org.apache.pig.PigServer$Graph.registerQuery(PigServer.java:1632)
... 8 more
Caused by: java.lang.IllegalArgumentException: The value of property mongo.pig.output.schema must not be null
at com.google.common.base.Preconditions.checkArgument(Preconditions.java:88)
at org.apache.hadoop.conf.Configuration.set(Configuration.java:971)
at org.apache.hadoop.conf.Configuration.set(Configuration.java:953)
at com.mongodb.hadoop.pig.MongoStorage.setStoreLocation(MongoStorage.java:249)
at org.apache.pig.newplan.logical.rules.InputOutputFileValidator$InputOutputFileVisitor.visit(InputOutputFileValidator.java:68)
... 20 more
I have issued netstat -an to see the open ports
The local address is 10.69.148.89; I do not see the port 27017 open in this IP; however 127.0.0.1 has 27017 open. There is something simple we are overlooking.
Need some help; we have spent over 2 days with no resolution
Have you tried setting the property it says is missing?
The value of property mongo.pig.output.schema must not be null
There are some issues in writing to MongoDB from PIG especially when you use Hortonworks windows distribution. I have broken this into Three steps;
Write to HDFS filesystem as a json file using JSONStorage( );
Move the HDFS file to windows filesystem
Load the json file into MongoDB
I am open if anyone has attempted this in a different way
On starting jboss I am getting the following error :
--- MBEANS THAT ARE THE ROOT CAUSE OF THE PROBLEM ---
ObjectName: jboss.jca:service=DataSourceBinding,name=DefaultDS
State: NOTYETINSTALLED
Depends On Me:
jboss.ejb:service=EJBTimerService,persistencePolicy=database
jboss:service=KeyGeneratorFactory,type=HiLo
jboss.mq:service=StateManager
jboss.mq:service=PersistenceManager
And for all database connections in the servlet I get the following exception :
org.postgresql.util.PSQLException: FATAL: password a
uthentication failed for user "poll"
It was working fine and all of a sudden I started getting these errors. My password is correct. I even tried changing the password and then tried again it showed the same exception. What is happening here?
The DefaultDS data source is what the name suggests; the default datasource. It ships with JBoss and is configured to use the Hypersonic (ie in-memory) database. JBoss uses the DefaultDS datasource to read/write internal queues, timed events, etc
Check the file ../conf/standardjbosscmp-jdbc.xml to see what you've got configured for the DefaultDS datasource. It sounds like you've edited that file unintentionally. Unless you need to persist internal queues etc across boots, just leave it as shipped using Hypersonic.
See the JBoss doc for more.
Sorry for the big wall of text, but its mostly logs
Thx for any help in any of my problems
I've been trying to get help from Seam forums, but in vain.
I'm trying this Setup mentioned in the title, but unsuccessfully.
I have it all installed correctly and the problems start with the seam-gen.
This is my build.properties
#Generated by seam setup
#Sat Aug 29 19:12:18 BRT 2009
hibernate.connection.password=abc123
workspace.home=/home/rgoytacaz/workspace
hibernate.connection.dataSource_class=org.postgresql.ds.PGConnectionPoolDataSource
model.package=com.atom.Commerce.model
hibernate.default_catalog=PostgreSQL
driver.jar=/home/rgoytacaz/postgresql-8.4-701.jdbc4.jar
action.package=com.atom.Commerce.action
test.package=com.atom.Commerce.test
database.type=postgres
richfaces.skin=glassX
glassfish.domain=domain1
hibernate.default_schema=Core
database.drop=n
project.name=Commerce
hibernate.connection.username=postgres
glassfish.home=C\:/Program Files/glassfish-v2.1
hibernate.connection.driver_class=org.postgresql.Driver
hibernate.cache.provider_class=org.hibernate.cache.HashtableCacheProvider
jboss.domain=default
project.type=ear
icefaces.home=
database.exists=y
jboss.home=/srv/jboss-5.1.0.GA
driver.license.jar=
hibernate.dialect=org.hibernate.dialect.PostgreSQLDialect
hibernate.connection.url=jdbc\:postgresql\:Atom
icefaces=n
./seam create-project works okay, but when I try generate-entities, I get the following...
generate-model:
[echo] Reverse engineering database using JDBC driver /home/rgoytacaz/postgresql-8.4-701.jdbc4.jar
[echo] project=/home/rgoytacaz/workspace/Commerce
[echo] model=com.atom.Commerce.model
[hibernate] Executing Hibernate Tool with a JDBC Configuration (for reverse engineering)
[hibernate] 1. task: hbm2java (Generates a set of .java files)
[hibernate] log4j:WARN No appenders could be found for logger (org.hibernate.cfg.Environment).
[hibernate] log4j:WARN Please initialize the log4j system properly.
[javaformatter] Java formatting of 4 files completed. Skipped 0 file(s).
this is problem no.1. How do I fix this? What is this? I had to do this in eclipse. It worked.
Then I import the seam-gen created project into eclipse, and deploy to JBoss 5.1. While my servers start I've noticed the following..
03:18:56,405 ERROR [SchemaUpdate] Unsuccessful: alter table PostgreSQL.atom.productsculturedetail add constraint FKBD5D849BC0A26E19 foreign key (culture_Id) references PostgreSQL.atom.cultures
03:18:56,406 ERROR [SchemaUpdate] ERROR: cross-database references are not implemented: "postgresql.atom.productsculturedetail"
03:18:56,407 ERROR [SchemaUpdate] Unsuccessful: alter table PostgreSQL.atom.productsculturedetail add constraint FKBD5D849BFFFC9417 foreign key (product_Id) references PostgreSQL.atom.products
03:18:56,408 ERROR [SchemaUpdate] ERROR: cross-database references are not implemented: "postgresql.atom.productsculturedetail"*
03:18:56,408 INFO [SchemaUpdate] schema update complete
Problem no.2. What is this cross-database references?
What about this..
03:18:55,089 INFO [SettingsFactory] JDBC driver: PostgreSQL Native Driver, version: PostgreSQL 8.4 JDBC3 (build 701)
Problem no.3 I've said in the build.properties to use JDBC4 driver, I don't know why seam insists to use JDBC3 driver. Where do I change this?
When I go into http://localhost:5443/Commerce and try to browse the auto-generated CRUD UI.
I get this error.. Error reading 'resultList' on type com.atom.Commerce.action.ProductsList_$$_javassist_seam_2
And this is what is showing in my server logs...
03:34:00,828 INFO [STDOUT] Hibernate:
select
products0_.product_Id as product1_0_,
products0_.active as active0_
from
PostgreSQL.atom.products products0_ limit ?
03:34:00,848 WARN [JDBCExceptionReporter] SQL Error: 0, SQLState: 0A000
03:34:00,849 ERROR [JDBCExceptionReporter] ERROR: cross-database references are not implemented: "postgresql.atom.products"
Position: 81
03:34:00,871 SEVERE [viewhandler] Error Rendering View[/ProductsList.xhtml]
javax.el.ELException: /ProductsList.xhtml: Error reading 'resultList' on type com.atom.Commerce.action.ProductsList_$$_javassist_seam_2
Caused by: javax.persistence.PersistenceException: org.hibernate.exception.GenericJDBCException: could not execute query
Problem no.4 What is going on here? Cross-database references?
Thx for any help in any of my problems.
You did receive a few answers on the Seam forums (here and here), but you didn't follow up. Anyway, all these are actually caused by one problem:
As Stuart Douglas told you, you shouldn't use a catalog when connecting to PostgreSQL. To fix this, replace the property "hibernate.default_catalog=PostgreSQL" in your properties file by the property: "hibernate.default_catalog.null=", so that your file looks like this:
...
model.package=com.atom.Commerce.model
hibernate.default_catalog.null= # <-- This is the replaced property
driver.jar=/home/rgoytacaz/postgresql-8.4-701.jdbc4.jar
...
You should be able to use seam generate-entities fine afterwards (assuming the rest of your configuration is correct). I'd recommend doing the generation into a clean folder.
Cross-database references is when a query tries to access two or more different databases. PostgreSQL does not support this, and thus complains when there is more than 1 period in the table name, so in PostgreSQL.atom.productsculturedetail, the bold part should be removed. Hibernate adds this prefix when you tell it to use a default catalog, which we already fixed in step 1 above (by telling it not to use a catalog), so this problem should be fixed after you regenerate your entities.
(Note that this is effectively the same as what Stuart Douglas told you, that you should remove the catalog="PostgreSQL" attribute in the annotations on your entity classes.)
When you specified the postgresql-8.4-701.jdbc4.jar file in the properties file, this didn't mean that the driver supports JDBC4. Although the name of the file would suggest so, the driver's website clearly states that "The driver provides a reasonably complete implementation of the JDBC 3 specification". This shouldn't be a problem for you, as you're not using the driver directly (or at least you're not supposed to). The driver is sufficient for Hibernate to fulfill its requirements and provide the required functionality.
This issue is caused by the same problem above. Hibernate is unable to read data from the database because of the incorrect query. Fixing the catalog problem should fix this issue.