Unfortunately I'm still getting stuck indexing.   It at least appears to me that I have such a large number of password protected docs and scanned PDFs without OCR enabled that the job is dying on me before it even finds all the "good" docs.    It will die with the error "Error: Repeated service interruptions - failure processing document Server at http://localhost:8983/solr returned non ok status:500, message:Server Error".   My job tells me there are 168,595 documents, with 73,238 currently active, and 106,291 processed.    At this point, if I keep restarting the job, it slowly adds a small number of new docs, but then dies again with the same error.    The thing is, it has not indexed a large number of documents that should be indexable.  
 
To help clarify, it may be helpful to note that I am indexing a folder that contains thousands of folders within that which are named after companies we have associated with, with several files and folders within each.   If I test searches in SOLR by reviewing a document and then performing a search based on that text, I get the expected search results consistently when I am searching files that are within folders with company names beginning with A, B, C, D, etc.   However, I do not get results if I search for files within folders with company names beginning with R,S,T,U,V, etc. 
 
We are looking into whether we should batch convert the scanned PDFs to support OCR and thereby cut down on the number of problem docs, but for now, I'd like to just get all of the indexable documents into SOLR. 
 
Going back to my original question, should I consider breaking this single job into multiple jobs based on the letter of the alphabet?   If so, I haven't been able to figure out a working regex to tell it to just pick up all files and folders within a folder which name begins with R-Z, for example.    And if not that workaround, where do you suggest I go to resolve this?    I'm not entirely sure what is causing all of the files and folders not to be traversed before my job dies (is this a ManifoldCF thing or a SOLR thing?)
 
Thanks again for your help.


>>> Ian Zapczynski 3/20/2015 2:25 PM >>>
Thanks for the help, Karl.    Yup, I was using the simple-to-set-up single process configuration, and silly me.... after I restarted from scratch at one point, I completely failed to update the combined-options-env.win config file that you referred to, so MCF was still set to use only 256 Mb despite my thinking otherwise.   I've bumped it up to 4 Gb, and the job recovered and is finally again moving along.  
-Ian

>>> Karl Wright <daddywri@gmail.com> 3/20/2015 10:55 AM >>>
Hi Ian,

HSQLDB is an interesting database in that it is *not* memory constrained. It attempts to keep everything in memory.

I'd strongly suggest either giving the MCF agents process a lot more memory, say 2G, if you want to keep using hsqldb. A better choice would be postgresql or mysql. There's a configuration file where you can put java switches for all of the processes; start by doing that.

Thanks,
Karl




On Fri, Mar 20, 2015 at 9:29 AM, Ian Zapczynski <Ian.Zapczynski@veritablelp.com> wrote:
Hi Karl,
I have SOLR and ManifoldCF running with Tomcat on a Windows 2012 R2 server. Linux would have been my preference, but various logistics prevented me from using that. I have set the maximum document length to be 3072000. I chose a larger size than what might be normal because when I first did a test, I could see that a lot of docs were getting rejected based on size, and it seems folks around here don't reduce/shrink the size of their PDFs.
The errors from the log are below. I was more busy paying attention to the errors spit out to the console, which didn't so obviously point to the backend database being the culprit. I'm guessing that I'm pushing the database too hard and should really be using PostgreSQL, right? I don't know why, but I didn't see or reference the deployment documentation that covered using various other databases until now. I was working off of the ManifoldCF End User Documentation as well as a (mostly) helpful blog post I found elsewhere.
Much thanks,
-Ian
WARN 2015-03-19 18:30:48,030 (Worker thread '34') - Solr exception during indexing file://///host.domain.com/FileShare1/Data/Manager%20Information/<foldername>/file1.pdf (500): Server at http://localhost:8983/solr returned non ok status:500, message:Server Error
org.apache.solr.common.SolrException: Server at http://localhost:8983/solr returned non ok status:500, message:Server Error
at org.apache.manifoldcf.agents.output.solr.ModifiedHttpSolrServer.request(ModifiedHttpSolrServer.java:303)
at org.apache.solr.client.solrj.impl.HttpSolrServer.request(HttpSolrServer.java:206)
at org.apache.solr.client.solrj.request.AbstractUpdateRequest.process(AbstractUpdateRequest.java:124)
at org.apache.manifoldcf.agents.output.solr.HttpPoster$IngestThread.run(HttpPoster.java:894)
WARN 2015-03-19 18:30:48,030 (Worker thread '34') - Service interruption reported for job 1426796577848 connection 'MACLSTR file server': Solr exception during indexing file://///host.domain.com/FileShare1/Data/Manager%20Information/<foldername>/file3.pdf (500): Server at http://localhost:8983/solr returned non ok status:500, message:Server Error
ERROR 2015-03-19 18:31:45,730 (Job delete thread) - Job delete thread aborting and restarting due to database connection reset: Database exception: SQLException doing query (S1000): java.lang.OutOfMemoryError: GC overhead limit exceeded
ERROR 2015-03-19 18:31:45,309 (Finisher thread) - Finisher thread aborting and restarting due to database connection reset: Database exception: SQLException doing query (S1000): java.lang.OutOfMemoryError: GC overhead limit exceeded
ERROR 2015-03-19 18:31:43,043 (Set priority thread) - Set priority thread aborting and restarting due to database connection reset: Database exception: SQLException doing query (S1000): java.lang.OutOfMemoryError: GC overhead limit exceeded
ERROR 2015-03-19 18:32:02,292 (Job notification thread) - Job notification thread aborting and restarting due to database connection reset: Database exception: SQLException doing query (S1000): java.lang.OutOfMemoryError: GC overhead limit exceeded
FATAL 2015-03-19 18:32:05,870 (Thread-3838608) - C:\apache-manifoldcf-2.0.1\example\.\./dbname.data getFromFile out of mem 531146
WARN 2015-03-19 18:32:09,167 (Assessment thread) - Found a long-running query (64919 ms): [SELECT id,status,connectionname FROM jobs WHERE assessmentstate=? FOR UPDATE]
WARN 2015-03-19 18:32:09,167 (Assessment thread) - Parameter 0: 'N'
ERROR 2015-03-19 18:32:09,167 (Job reset thread) - Job reset thread aborting and restarting due to database connection reset: Database exception: SQLException doing query (S1000): java.lang.RuntimeException: Logging failed when attempting to log: C:\apache-manifoldcf-2.0.1\example\.\./dbname.data getFromFile out of mem 531146 java.lang.RuntimeException: Logging failed when attempting to log: C:\apache-manifoldcf-2.0.1\example\.\./dbname.data getFromFile out of mem 531146
org.apache.manifoldcf.core.interfaces.ManifoldCFException: Database exception: SQLException doing query (S1000): java.lang.RuntimeException: Logging failed when attempting to log: C:\apache-manifoldcf-2.0.1\example\.\./dbname.data getFromFile out of mem 531146 java.lang.RuntimeException: Logging failed when attempting to log: C:\apache-manifoldcf-2.0.1\example\.\./dbname.data getFromFile out of mem 531146
at org.apache.manifoldcf.core.database.Database$ExecuteQueryThread.finishUp(Database.java:702)
at org.apache.manifoldcf.core.database.Database.executeViaThread(Database.java:728)
at org.apache.manifoldcf.core.database.Database.executeUncachedQuery(Database.java:771)
at org.apache.manifoldcf.core.database.Database$QueryCacheExecutor.create(Database.java:1444)
at org.apache.manifoldcf.core.cachemanager.CacheManager.findObjectsAndExecute(CacheManager.java:146)
at org.apache.manifoldcf.core.database.Database.executeQuery(Database.java:191)
at org.apache.manifoldcf.core.database.DBInterfaceHSQLDB.performModification(DBInterfaceHSQLDB.java:750)
at org.apache.manifoldcf.core.database.DBInterfaceHSQLDB.performUpdate(DBInterfaceHSQLDB.java:296)
at org.apache.manifoldcf.core.database.BaseTable.performUpdate(BaseTable.java:80)
at org.apache.manifoldcf.crawler.jobs.JobQueue.noDocPriorities(JobQueue.java:967)
at org.apache.manifoldcf.crawler.jobs.JobManager.noDocPriorities(JobManager.java:8148)
at org.apache.manifoldcf.crawler.jobs.JobManager.finishJobStops(JobManager.java:8123)
at org.apache.manifoldcf.crawler.system.JobResetThread.run(JobResetThread.java:69)
Caused by: java.sql.SQLException: java.lang.RuntimeException: Logging failed when attempting to log: C:\apache-manifoldcf-2.0.1\example\.\./dbname.data getFromFile out of mem 531146 java.lang.RuntimeException: Logging failed when attempting to log: C:\apache-manifoldcf-2.0.1\example\.\./dbname.data getFromFile out of mem 531146
at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source)
at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source)
at org.hsqldb.jdbc.JDBCPreparedStatement.fetchResult(Unknown Source)
at org.hsqldb.jdbc.JDBCPreparedStatement.executeUpdate(Unknown Source)
at org.apache.manifoldcf.core.database.Database.execute(Database.java:903)
at org.apache.manifoldcf.core.database.Database$ExecuteQueryThread.run(Database.java:683)
Caused by: org.hsqldb.HsqlException: java.lang.RuntimeException: Logging failed when attempting to log: C:\apache-manifoldcf-2.0.1\example\.\./dbname.data getFromFile out of mem 531146
at org.hsqldb.error.Error.error(Unknown Source)
at org.hsqldb.result.Result.newErrorResult(Unknown Source)
at org.hsqldb.StatementDMQL.execute(Unknown Source)
at org.hsqldb.Session.executeCompiledStatement(Unknown Source)
at org.hsqldb.Session.execute(Unknown Source)
... 4 more
Caused by: java.lang.RuntimeException: Logging failed when attempting to log: C:\apache-manifoldcf-2.0.1\example\.\./dbname.data getFromFile out of mem 531146
at org.hsqldb.lib.FrameworkLogger.privlog(Unknown Source)
at org.hsqldb.lib.FrameworkLogger.severe(Unknown Source)
at org.hsqldb.persist.Logger.logSevereEvent(Unknown Source)
at org.hsqldb.persist.DataFileCache.logSevereEvent(Unknown Source)
at org.hsqldb.persist.DataFileCache.getFromFile(Unknown Source)
at org.hsqldb.persist.DataFileCache.get(Unknown Source)
at org.hsqldb.persist.RowStoreAVLDisk.get(Unknown Source)
at org.hsqldb.index.NodeAVLDisk.findNode(Unknown Source)
at org.hsqldb.index.NodeAVLDisk.getRight(Unknown Source)
at org.hsqldb.index.IndexAVL.next(Unknown Source)
at org.hsqldb.index.IndexAVL.next(Unknown Source)
at org.hsqldb.index.IndexAVL$IndexRowIterator.getNextRow(Unknown Source)
at org.hsqldb.RangeVariable$RangeIteratorMain.findNext(Unknown Source)
at org.hsqldb.RangeVariable$RangeIteratorMain.next(Unknown Source)
at org.hsqldb.StatementDML.executeUpdateStatement(Unknown Source)
at org.hsqldb.StatementDML.getResult(Unknown Source)
... 7 more
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:483)
... 23 more
Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded
WARN 2015-03-19 18:32:09,167 (Assessment thread) - Plan: isDistinctSelect=[false]
WARN 2015-03-19 18:32:09,182 (Assessment thread) - Plan: isGrouped=[false]
WARN 2015-03-19 18:32:09,182 (Assessment thread) - Plan: isAggregated=[false]
WARN 2015-03-19 18:32:09,182 (Assessment thread) - Plan: columns=[ COLUMN: PUBLIC.JOBS.ID not nullable
WARN 2015-03-19 18:32:09,182 (Assessment thread) - Plan: COLUMN: PUBLIC.JOBS.STATUS not nullable
WARN 2015-03-19 18:32:09,182 (Assessment thread) - Plan: COLUMN: PUBLIC.JOBS.CONNECTIONNAME not nullable
WARN 2015-03-19 18:32:09,182 (Assessment thread) - Plan:
WARN 2015-03-19 18:32:09,182 (Assessment thread) - Plan: ]
WARN 2015-03-19 18:32:09,182 (Assessment thread) - Plan: [range variable 1
WARN 2015-03-19 18:32:09,182 (Assessment thread) - Plan: join type=INNER
WARN 2015-03-19 18:32:09,182 (Assessment thread) - Plan: table=JOBS
WARN 2015-03-19 18:32:09,182 (Assessment thread) - Plan: cardinality=5
WARN 2015-03-19 18:32:09,182 (Assessment thread) - Plan: access=FULL SCAN
WARN 2015-03-19 18:32:09,182 (Assessment thread) - Plan: join condition = [index=SYS_IDX_SYS_PK_10234_10237
WARN 2015-03-19 18:32:09,182 (Assessment thread) - Plan: other condition=[
WARN 2015-03-19 18:32:09,182 (Assessment thread) - Plan: EQUAL arg_left=[ COLUMN: PUBLIC.JOBS.ASSESSMENTSTATE
WARN 2015-03-19 18:32:09,182 (Assessment thread) - Plan: ] arg_right=[ DYNAMIC PARAM: , TYPE = CHARACTER
WARN 2015-03-19 18:32:09,182 (Assessment thread) - Plan: ]]
WARN 2015-03-19 18:32:09,182 (Assessment thread) - Plan: ]
WARN 2015-03-19 18:32:09,182 (Assessment thread) - Plan: ]]
WARN 2015-03-19 18:32:09,182 (Assessment thread) - Plan: PARAMETERS=[
WARN 2015-03-19 18:32:09,182 (Assessment thread) - Plan: @0[DYNAMIC PARAM: , TYPE = CHARACTER
WARN 2015-03-19 18:32:09,182 (Assessment thread) - Plan: ]]
WARN 2015-03-19 18:32:09,182 (Assessment thread) - Plan: SUBQUERIES[]
WARN 2015-03-19 18:32:09,182 (Assessment thread) -
FATAL 2015-03-19 18:32:09,198 (Job notification thread) - JobNotificationThread initialization error tossed: GC overhead limit exceeded
java.lang.OutOfMemoryError: GC overhead limit exceeded
FATAL 2015-03-19 18:32:09,198 (Set priority thread) - SetPriorityThread initialization error tossed: GC overhead limit exceeded
java.lang.OutOfMemoryError: GC overhead limit exceeded
FATAL 2015-03-19 18:32:09,198 (Finisher thread) - FinisherThread initialization error tossed: GC overhead limit exceeded
java.lang.OutOfMemoryError: GC overhead limit exceeded
FATAL 2015-03-19 18:32:09,198 (Job delete thread) - JobDeleteThread initialization error tossed: GC overhead limit exceeded
java.lang.OutOfMemoryError: GC overhead limit exceeded
FATAL 2015-03-19 18:32:09,198 (Seeding thread) - SeedingThread initialization error tossed: GC overhead limit exceeded
java.lang.OutOfMemoryError: GC overhead limit exceeded

>>> Karl Wright <daddywri@gmail.com> 3/19/2015 3:34 PM >>>
Hi Ian,

ManifoldCF operates under what is known as a "bounded" memory model. That means that you should always be able to find a memory size that works (that isn't huge).

The only exception to this is for Solr indexing that does *not* go via the extracting update handler. The standard update handler unfortunately *requires* that the entire document fit in memory. If this is what you are doing, you must take steps to limit the maximum document size to prevent OOM's.

160,000 documents is quite small by MCF standards (we do 10 million to 50 million on some setups). So let's diagnose your problem before taking any bizarre actions. Can you provide an out-of-memory dump from the log, for instance? Can you let us know what deployment model you are using (e.g. single-process, etc.)?

Thanks,
Karl


On Thu, Mar 19, 2015 at 3:07 PM, Ian Zapczynski <Ian.Zapczynski@veritablelp.com> wrote:
Hello all. I am using ManifoldCF to index a Windows share containing well over 160,000 files (.xls, .pdf, .doc). I keep getting memory errors when I try to index the whole folder at once and have not been able to resolve this by throwing memory and CPU at Tomcat and the VM, so I thought I'd try this a different way.
What I'd like to do now is break what was a single job up into multiple jobs. Each job should index all indexable files under a parent folder, with one job indexing folders whose names begin with the letters A-G as well as all subfolders and files within, another job for H-M also with all subfolders/files, and so on. My problem is, somehow I can't manage to figure out what expression to use to get it to index what I want.
In the Job settings under Paths, I have specified the parent folder, and within there I've tried:
1. Include file(s) or directory(s) matching * (this works, but indexes every file in every folder within the parent, eventually causing me unresolvable GC memory overhead errors)
2. Include file(s) or directory(s) matching ^(?i)[A-G]* (this does not work; it supposedly indexes one file and then quits)
3. Include file(s) or directory(s) matching A* (this does not work; it supposedly indexes one file and then quits, and there are many folders directly under the parent that begin with 'A')
Can anyone help confirm what type of expression I should use in the paths to accomplish what I want?
Or alternately if you think I should be able to index 160,000+ files in one job without getting GC memory overhead errors, I'm open to hear your suggestions on resolving those. All I know to do is increase the maximum memory in Tomcat as well as on the OS, and that didn't help at all.
Thanks much!
-Ian