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From Ian Boston <...@tfd.co.uk>
Subject Re: Intermittent Slow Down
Date Mon, 17 Dec 2012 23:34:07 GMT
On 18 December 2012 09:57, Morrell Jacobs <mjacobs@maned.com> wrote:
> Thanks Ian, will try.
>
> I added the -server flag earlier today so I'll see if it helps.  I've used the JMX tools
(VisualVM) and running GC manually seems to drop back down to a base level (or close).
>
> When tomcat / web app is idle, the heap usage seems to be a saw tooth pattern, which
isn't a surprise.  The test takes a while to run so have to wait and see if -server helps.
>
> I'm using JVM 6.

I think -server will switch to the ParallelGC. If you still have
problems read the section on  Ergonomics [1], and if the adjustments
there make no difference think about switching to the Concurrent GC,
however if you have no free cores for long periods the Concurrent GC
may not get enough time to free tenured space which will lead to a JVM
pause.  [2]

VisualVM should show you which pool is being exhausted and give you a
clue to the root cause of a GC related pause to the application
threads.

(if you wanted to get forensic you could turn on GC logging leave it
for 24h and then graph the output in a spreadsheet.).

HTH
Ian


1 http://www.oracle.com/technetwork/java/javase/gc-tuning-6-140523.html#par_gc.ergonomics

2 http://www.oracle.com/technetwork/java/javase/gc-tuning-6-140523.html#cms.concurrent_mode_failure

>
> Thanks!
>
>
> On Dec 17, 2012, at 5:16 PM, Ian Boston wrote:
>
>> Hi Morrell,
>> Sounds suspiciously like garbage collection activity. Rather than
>> attaching a profiler which may impact heap usage, try attaching a JMX
>> console which should be less impact (eg JConsole) and looking at the
>> graph of Garbage Collection activity during the slow down.
>>
>> If you see it taking up a significant amount of time and CPU, try
>> changing the type of garbage collector[1]. IIRC the default without
>> the -server flag is a serial GC. Increasing heap will lengthen the
>> time between these slowdowns but won't eliminate them.
>>
>> Also, you may be able to recreate the slowdown by forcing a full GC
>> operation from JConsole. Obviously if a full GC operation doesn't
>> leave the JVM with significantly more free heap, then you need to up
>> the limit to prevent the JVM spending all its time trying to free
>> more.
>>
>> You didn't say which JVM you are using, the link below is for 6.
>> Adjust appropriately.
>>
>> HTH
>> Ian
>>
>>
>> 1 http://www.oracle.com/technetwork/java/javase/gc-tuning-6-140523.html#available_collectors
>>
>> On 18 December 2012 05:14, Morrell Jacobs <mjacobs@maned.com> wrote:
>>> We're running MySQL 5.5.19 for Linux
>>>
>>> We had the blobs in the database because of clustering.  Since we've moved to
single stack, I suppose we could pull them out - not a long term solution, but we could try
and see if it helps.
>>>
>>> I'll have our MySQL experts review the settings, the restructuring may be accounting
for some of the slow down.  If we were seeing delays from MySQL, I wouldn't expect Tomcat's
CPU usage to be pegged though - I would think all the threads would be idle, waiting for a
response.  Does that sound right to you?
>>>
>>> Thanks
>>> Morrell
>>>
>>>
>>> On Dec 17, 2012, at 12:48 PM, Ron Wheeler wrote:
>>>
>>>> I would play with the JVM memory configuration.
>>>> It still looks very small.
>>>> Try doubling it and see if it changes anything.
>>>> If not, you can look elsewhere and if it does, try making it larger until
it stops improving things.
>>>>
>>>> What version of MySQL are you running?
>>>> Have you tuned your MySQL?
>>>> You might want to look at how MySQL is going to treat these objects and what
configuration parameters are recommended when you have large blobs.
>>>> Have you thought about getting your binary content out of the database. Databases
are not very good at 100Mb blobs.
>>>> Links to 100Mb blobs/files work much better.
>>>>
>>>> Is there a compelling reason to put the binary data inside a database?
>>>> Anytime MySQL has to restructure its indexes or physical storage, you are
going to see a pause in the action.
>>>>
>>>> Ron
>>>>
>>>> On 17/12/2012 12:04 PM, Morrell Jacobs wrote:
>>>>> Hello all,
>>>>>
>>>>> We're currently experience a problem where JackRabbit function will occasionally
slow down; according to our QA, the slow down comes in waves: good performance for a while
(hours) then bad for a while (minutes / hours).  The slow down is on the order of minutes
to perform create or modify an object (creation involves creating a 2-3 levels of nodes, and
setting properties).  Normally these operations take 100 - 300 ms, but during the slow down
they can take as much 5 minutes.
>>>>>
>>>>> The slow down does not seem to be connected to the load on the server:
we've seen it perform well, when many people are connecting, then slow down with only one
user.  I suspect the slow down is related to indexing, but that's just a guess on my part
- I'm looking for something that would happen at some interval.
>>>>>
>>>>>
>>>>> Environment:
>>>>> * JackRabbit is built into war running in Tomcat (was 7.0.25, recently
upgraded to 7.0.34)
>>>>> * Tomcat was running with default configs but recently up'd memory -
-Xms128M -Xmx512M -XX:MaxPermSize=256M
>>>>> * Repository XML is at end of email
>>>>> * JackRabbit was originally configured to be clustered, but is now running
as just a single instance.
>>>>>
>>>>>
>>>>> Data:
>>>>> * Our data is structured similar to a file system, except any object
can be both a file and contain other objects (files); each object has various metadata (some
in properties, some in child nodes), a file and child objects
>>>>> * We don't use full text searching and don't want file (binary) contents
indexed; the only way I was able to prevent the search index from examining the files (some
are large 100+ M) was to create my own node types for files.  My node types are identical
nt:file and nt:content, except that they are named prd:file and prd:content; the unrecognized
name seems to prevent indexing from touch them.
>>>>>
>>>>>
>>>>> When I've attempted to use profiling tools, it appears that during the
slow down the CPU is pegged; memory usage is also at or close to the limit.  In depth profiling
tools (NetBeans) get overwhelmed during the slow down.
>>>>>
>>>>> We're going thru a variety of tests, but any advice the community can
provide will be greatly appreciated.
>>>>>
>>>>> Here's the repository.xml:
>>>>> <Repository>
>>>>>    <FileSystem class="org.apache.jackrabbit.core.fs.db.DbFileSystem">
>>>>>        <param name="driver" value="com.mysql.jdbc.Driver"/>
>>>>>        <param name="url" value="jdbc:mysql://${pm.database.url}:${pm.database.port}/${pm.database.prefix}global_repository?autoReconnect=true&amp;createDatabaseIfNotExist=true"/>
>>>>>        <param name="schema" value="mysql"/>
>>>>>        <param name="schemaObjectPrefix" value="rep_"/>
>>>>>        <param name="user" value="${pm.database.user}"/>
>>>>>        <param name="password" value="${pm.database.pwd}"/>
>>>>>    </FileSystem>
>>>>>
>>>>>    <!--
>>>>>        security configuration
>>>>>    -->
>>>>>    <Security appName="Jackrabbit">
>>>>>        <!--
>>>>>            security manager:
>>>>>            class: FQN of class implementing the JackrabbitSecurityManager
interface
>>>>>        -->
>>>>>        <SecurityManager class="org.apache.jackrabbit.core.DefaultSecurityManager"
workspaceName="default">
>>>>>            <!--
>>>>>                workspace access:
>>>>>                class: FQN of class implementing the WorkspaceAccessManager
interface
>>>>>            -->
>>>>>            <!-- <WorkspaceAccessManager class="..."/> -->
>>>>>            <!-- <param name="config" value="${rep.home}/security.xml"/>
-->
>>>>>        </SecurityManager>
>>>>>        <!--
>>>>>            access manager:
>>>>>            class: FQN of class implementing the AccessManager interface
>>>>>        -->
>>>>>        <AccessManager class="org.apache.jackrabbit.core.security.DefaultAccessManager">
>>>>>            <!-- <param name="config" value="${rep.home}/access.xml"/>
-->
>>>>>        </AccessManager>
>>>>>                 <LoginModule class="org.apache.jackrabbit.core.security.authentication.DefaultLoginModule">
>>>>>            <!--
>>>>>                anonymous user name ('anonymous' is the default value)
>>>>>            -->
>>>>>            <param name="anonymousId" value="anonymous"/>
>>>>>            <!--
>>>>>                administrator user id (default value if param is missing
is 'admin')
>>>>>            -->
>>>>>            <param name="adminId" value="admin"/>
>>>>>        </LoginModule>
>>>>>    </Security>
>>>>>         <!--
>>>>>        location of workspaces root directory and name of default workspace
>>>>>    -->
>>>>>    <Workspaces rootPath="${rep.home}/workspaces" defaultWorkspace="default"/>
>>>>>         <!--
>>>>>        workspace configuration template:
>>>>>        used to create the initial workspace if there's no workspace yet
>>>>>    -->
>>>>> <!--    <Workspace name="default">-->
>>>>>    <Workspace name="default">
>>>>>        <!--
>>>>>            virtual file system of the workspace:
>>>>>            class: FQN of class implementing the FileSystem interface
>>>>>        -->
>>>>>        <FileSystem class="org.apache.jackrabbit.core.fs.local.LocalFileSystem">
>>>>>            <param name="path" value="${wsp.home}"/>
>>>>>        </FileSystem>
>>>>>        <!--
>>>>>            persistence manager of the workspace:
>>>>>            class: FQN of class implementing the PersistenceManager interface
>>>>>        -->
>>>>>        <PersistenceManager class="org.apache.jackrabbit.core.persistence.pool.MySqlPersistenceManager">
>>>>>            <param name="driver" value="com.mysql.jdbc.Driver"/>
>>>>>            <param name="url" value="jdbc:mysql://${pm.database.url}:${pm.database.port}/${pm.database.prefix}product?createDatabaseIfNotExist=true"/>
>>>>>            <param name="user" value="${pm.database.user}"/>
>>>>>            <param name="password" value="${pm.database.pwd}"/>
>>>>>            <param name="schemaObjectPrefix" value="Product_"/>
>>>>>            <param name="schema" value="mysql"/>
>>>>>        </PersistenceManager>
>>>>>        <!--
>>>>>            Search index and the file system it uses.
>>>>>            class: FQN of class implementing the QueryHandler interface
>>>>>        -->
>>>>>        <SearchIndex class="org.apache.jackrabbit.core.query.lucene.SearchIndex">
>>>>>            <param name="path" value="${wsp.home}/index"/>
>>>>>            <!--<param name="textFilterClasses"
>>>>>                value="org.apache.jackrabbit.extractor.PlainTextExtractor,org.apache.jackrabbit.extractor.MsWordTextExtractor,org.apache.jackrabbit.extractor.MsExcelTextExtractor,org.apache.jackrabbit.extractor.MsPowerPointTextExtractor,org.apache.jackrabbit.extractor.PdfTextExtractor,org.apache.jackrabbit.extractor.OpenOfficeTextExtractor,org.apache.jackrabbit.extractor.RTFTextExtractor,org.apache.jackrabbit.extractor.HTMLTextExtractor,org.apache.jackrabbit.extractor.XMLTextExtractor"/>
>>>>>            <param name="extractorPoolSize" value="2"/>
>>>>>            <param name="supportHighlighting" value="true"/> -->
>>>>>        </SearchIndex>
>>>>>    </Workspace>
>>>>>         <!--
>>>>>        Configures the versioning
>>>>>    -->
>>>>>    <Versioning rootPath="${rep.home}/version">
>>>>>        <!--
>>>>>            Configures the filesystem to use for versioning for the respective
>>>>>            persistence manager
>>>>>        -->
>>>>>        <FileSystem class="org.apache.jackrabbit.core.fs.local.LocalFileSystem">
>>>>>            <param name="path" value="${rep.home}/version"/>
>>>>>        </FileSystem>
>>>>>        <!--
>>>>>            Configures the persistence manager to be used for persisting
version state.
>>>>>            Please note that the current versioning implementation is
based on
>>>>>            a 'normal' persistence manager, but this could change in future
>>>>>            implementations.
>>>>>        -->
>>>>>        <PersistenceManager class="org.apache.jackrabbit.core.persistence.pool.MySqlPersistenceManager">
>>>>>            <param name="driver" value="com.mysql.jdbc.Driver"/>
>>>>>            <param name="url" value="jdbc:mysql://${pm.database.url}:${pm.database.port}/${pm.database.prefix}truedit_versions?createDatabaseIfNotExist=true"/>
>>>>>            <param name="user" value="${pm.database.user}"/>
>>>>>            <param name="password" value="${pm.database.pwd}"/>
>>>>>            <param name="schemaObjectPrefix" value="version_"/>
>>>>>            <param name="schema" value="mysql"/>
>>>>>        </PersistenceManager>
>>>>>    </Versioning>
>>>>>         <!--
>>>>>        Configures the Data Store for large binary objects.
>>>>>    -->
>>>>>    <DataStore class="org.apache.jackrabbit.core.data.FileDataStore">
>>>>>        <param name="path" value="${datastore.location.path}"/>
>>>>>        <param name="minRecordLength" value="100"/>
>>>>>    </DataStore>
>>>>>    <!--
>>>>>    <Cluster id="${cluster.id}" syncDelay="2000">
>>>>>        <Journal class="org.apache.jackrabbit.core.journal.DatabaseJournal">
>>>>>            <param name="driver" value="com.mysql.jdbc.Driver" />
>>>>>            <param name="url" value="jdbc:mysql://${pm.database.url}:${pm.database.port}/${pm.database.prefix}journal?autoReconnect=true&amp;createDatabaseIfNotExist=true"/>
>>>>>            <param name="schemaObjectPrefix" value="journal_"/>
>>>>>            <param name="databaseType" value="mysql"/>
>>>>>            <param name="user" value="${pm.database.user}"/>
>>>>>            <param name="password" value="${pm.database.pwd}"/>
>>>>>        </Journal>
>>>>>    </Cluster>
>>>>>    -->
>>>>>
>>>>> </Repository>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Morrell Jacobs
>>>>> Chief Software Architect
>>>>> MEI
>>>>> 610 Old York Road, Suite 250
>>>>> Jenkintown, PA 19046
>>>>> Phone: 215-886-5662, ext. 252
>>>>> Fax: 215-886-5681
>>>>> http://www.maned.com
>>>>> E-mail: mjacobs@maned.com
>>>>> AOL IM: MorrellMEI
>>>>>
>>>>> Have you seen Nervous Pixel, MEI's creative services division?
>>>>> www.nervouspixel.com
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Ron Wheeler
>>>> President
>>>> Artifact Software Inc
>>>> email: rwheeler@artifact-software.com
>>>> skype: ronaldmwheeler
>>>> phone: 866-970-2435, ext 102
>>>>
>>>
>

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