[GeoNetwork-users] help. geonetwork - McKoy

Ivan_Marchesini3 · April 18, 2010, 4:19pm

Dear Geonetwork users,
I have this problem:

I'm running geonetwork on a JVM version is 1.5.0_06-b05

since this night Geonetwork and Geoserver stopped to run..

I did a lot of things:
stopping catalina
killing java processes
removing tomcat lock files
looking if some other process was running on the same port

but nothing!!!

I have noted that, looking at "top" results, the cpu usage was really
hight
It seems there are some processes that use a lot of cpu

PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+
COMMAND
4600 root 20 0 2488m 143m 39m R 109 0.8 480:35.39 java

In the list of Geoerver Italian Users, someone suggest me to try to
execute some java diagnostic tools.
In particular, looking at the output of jstack:
________________________________________________--

Thread 4600: (state = IN_NATIVE)
- java.io.RandomAccessFile.readBytes(byte, int, int) @bci=0

(Compiled

frame; information may be imprecise)
- java.io.RandomAccessFile.read(byte, int, int) @bci=4, line=315
(Compiled frame)
- com.mckoi.store.JournalledSystem$Resource.read(long, byte, int)
@bci=341, line=1546 (Compiled frame)
- com.mckoi.store.LoggingBufferManager$BMPage.readPageContent(long,
byte, int) @bci=23, line=788 (Compiled frame)
- com.mckoi.store.LoggingBufferManager$BMPage.initialize() @bci=27,
line=823 (Compiled frame)
- com.mckoi.store.AbstractStore.getAreaHeader(long, long) @bci=9,
line=831 (Compiled frame)
- com.mckoi.store.AbstractStore.free(long) @bci=188, line=1340
(Compiled frame)
- com.mckoi.database.V2MasterTableDataSource.scanForLeaks() @bci=309,
line=794 (Compiled frame)
- com.mckoi.database.V2MasterTableDataSource.open(java.lang.String)
@bci=161, line=406 (Interpreted frame)
- com.mckoi.database.TableDataConglomerate.readVisibleTables()
@bci=192, line=383 (Interpreted frame)
- com.mckoi.database.TableDataConglomerate.open(java.lang.String)
@bci=141, line=1096 (Interpreted frame)
- com.mckoi.database.Database.init() @bci=204, line=1803 (Interpreted
frame)
-

com.mckoi.database.control.DBController.startDatabase(com.mckoi.database.control.DBConfig) @bci=11, line=131 (Interpreted frame)

- org.fao.geonet.util.McKoiDB.start() @bci=12, line=65 (Interpreted
frame)
- org.fao.geonet.activators.McKoiActivator.startup(java.lang.String,
org.jdom.Element) @bci=61, line=54 (Interpreted frame)
- jeeves.server.JeevesEngine.initResources(org.jdom.Element)

@bci=204,

line=373 (Interpreted frame)
- jeeves.server.JeevesEngine.loadConfigFile(java.lang.String,
java.lang.String, jeeves.server.dispatchers.ServiceManager) @bci=226,
line=220 (Interpreted frame)
- jeeves.server.JeevesEngine.init(java.lang.String, java.lang.String,
java.lang.String) @bci=306, line=137 (Interpreted frame)
- jeeves.server.sources.http.JeevesServlet.init() @bci=78, line=66
(Interpreted frame)
- javax.servlet.GenericServlet.init(javax.servlet.ServletConfig)
@bci=6, line=212 (Interpreted frame)
- org.apache.catalina.core.StandardWrapper.loadServlet() @bci=774,
line=1173 (Interpreted frame)
- org.apache.catalina.core.StandardWrapper.load() @bci=2, line=993
(Interpreted frame)

______________________________________________

they suggest me it could be a problem of Geonetwork and in particular
that the Geonetwork DB (McKoy ?) is not starting?
is this correct?

do you have other suggestions?
I hope you can give me some help

many thanks

Ivan

--
Ti prego di cercare di non inviarmi files .dwg, .doc, .xls, .ppt.
Preferisco formati liberi.
Please try to avoid to send me .dwg, .doc, .xls, .ppt files.
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http://en.wikipedia.org/wiki/Open_format

Ivan Marchesini
Perugia (Italy)
Socio fondatore GFOSS "Geospatial Free and Open Source Software" http://www.gfoss.it
e-mail: marchesini@anonymised.com
ivan.marchesini@anonymised.com
fax (home): +39(0)5782830887
jabber: geoivan73@anonymised.com
skype: geoivan73

Richard_Fozzard · April 19, 2010, 11:05pm

Ivan,

We have seen a similar problem running Geonetwork 2.4.2 on Linux RHEL5, Tomcat 5.5, Java 1.6, Oracle. (What version of Geonetwork, OS, and application server are you running?)

When Geonetwork is stopped, delete the entire Lucene index directory: web/geonetwork/WEB-INF/lucene. Sometimes we have seen unending 100% CPU if these files get corrupted somehow. These will get rebuilt when you restart Geonetwork.

I don't know if this is what you are experiencing, but give it a try, and let us know if it helps.

--Rich

ivan marchesini said the following on 04/18/2010 10:19 AM:

Dear Geonetwork users,
I have this problem:

I'm running geonetwork on a JVM version is 1.5.0_06-b05

since this night Geonetwork and Geoserver stopped to run..

I did a lot of things:
stopping catalina killing java processes
removing tomcat lock files
looking if some other process was running on the same port

but nothing!!!

I have noted that, looking at "top" results, the cpu usage was really
hight
It seems there are some processes that use a lot of cpu

  PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+
COMMAND 4600 root 20 0 2488m 143m 39m R 109 0.8 480:35.39 java

In the list of Geoerver Italian Users, someone suggest me to try to
execute some java diagnostic tools.
In particular, looking at the output of jstack:
________________________________________________--


Thread 4600: (state = IN_NATIVE)
- java.io.RandomAccessFile.readBytes(byte, int, int) @bci=0


(Compiled


frame; information may be imprecise)
- java.io.RandomAccessFile.read(byte, int, int) @bci=4, line=315
(Compiled frame)
- com.mckoi.store.JournalledSystem$Resource.read(long, byte, int)
@bci=341, line=1546 (Compiled frame)
- com.mckoi.store.LoggingBufferManager$BMPage.readPageContent(long,
byte, int) @bci=23, line=788 (Compiled frame)
- com.mckoi.store.LoggingBufferManager$BMPage.initialize() @bci=27,
line=823 (Compiled frame)
- com.mckoi.store.AbstractStore.getAreaHeader(long, long) @bci=9,
line=831 (Compiled frame)
- com.mckoi.store.AbstractStore.free(long) @bci=188, line=1340
(Compiled frame)
- com.mckoi.database.V2MasterTableDataSource.scanForLeaks() @bci=309,
line=794 (Compiled frame)
- com.mckoi.database.V2MasterTableDataSource.open(java.lang.String)
@bci=161, line=406 (Interpreted frame)
- com.mckoi.database.TableDataConglomerate.readVisibleTables()
@bci=192, line=383 (Interpreted frame)
- com.mckoi.database.TableDataConglomerate.open(java.lang.String)
@bci=141, line=1096 (Interpreted frame)
- com.mckoi.database.Database.init() @bci=204, line=1803 (Interpreted
frame)
-

com.mckoi.database.control.DBController.startDatabase(com.mckoi.database.control.DBConfig) @bci=11, line=131 (Interpreted frame)


- org.fao.geonet.util.McKoiDB.start() @bci=12, line=65 (Interpreted
frame)
- org.fao.geonet.activators.McKoiActivator.startup(java.lang.String,
org.jdom.Element) @bci=61, line=54 (Interpreted frame)
- jeeves.server.JeevesEngine.initResources(org.jdom.Element)


@bci=204,


line=373 (Interpreted frame)
- jeeves.server.JeevesEngine.loadConfigFile(java.lang.String,
java.lang.String, jeeves.server.dispatchers.ServiceManager) @bci=226,
line=220 (Interpreted frame)
- jeeves.server.JeevesEngine.init(java.lang.String, java.lang.String,
java.lang.String) @bci=306, line=137 (Interpreted frame)
- jeeves.server.sources.http.JeevesServlet.init() @bci=78, line=66
(Interpreted frame)
- javax.servlet.GenericServlet.init(javax.servlet.ServletConfig)
@bci=6, line=212 (Interpreted frame)
- org.apache.catalina.core.StandardWrapper.loadServlet() @bci=774,
line=1173 (Interpreted frame)
- org.apache.catalina.core.StandardWrapper.load() @bci=2, line=993
(Interpreted frame)


______________________________________________

they suggest me it could be a problem of Geonetwork and in particular
that the Geonetwork DB (McKoy ?) is not starting?
is this correct?

do you have other suggestions?
I hope you can give me some help

many thanks

Ivan

  ------------------------------------------------------------------------

------------------------------------------------------------------------------
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
------------------------------------------------------------------------

_______________________________________________
GeoNetwork-users mailing list
GeoNetwork-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/geonetwork-users
GeoNetwork OpenSource is maintained at http://sourceforge.net/projects/geonetwork

Ivan_Marchesini3 · April 20, 2010, 9:12am

Dear Rich,
thank you very much
the problem was exactly that

I'm running Fedora Core 8, Geonetwork 2.4 beta (I think.. because I
didn't installed it), tomcat 6, java 1.5

I have installed another tomcat and moved the old geonetwork dir inside
the new webapp dir

then I removed the lucene folder as you suggest.

geonetwork now is up!!!!

the only problem is that it seems that all the tumbnails are not
available...

any suggestion about that problem??

thank you very much

Il giorno lun, 19/04/2010 alle 17.05 -0600, Richard Fozzard ha scritto:

Ivan,

We have seen a similar problem running Geonetwork 2.4.2 on Linux
RHEL5, Tomcat 5.5, Java 1.6, Oracle. (What version of Geonetwork, OS,
and application server are you running?)

When Geonetwork is stopped, delete the entire Lucene index directory:
web/geonetwork/WEB-INF/lucene. Sometimes we have seen unending 100%
CPU if these files get corrupted somehow. These will get rebuilt when
you restart Geonetwork.

I don't know if this is what you are experiencing, but give it a try,
and let us know if it helps.

--Rich

ivan marchesini said the following on 04/18/2010 10:19 AM:
> Dear Geonetwork users,
> I have this problem:
>
> I'm running geonetwork on a JVM version is 1.5.0_06-b05
>
> since this night Geonetwork and Geoserver stopped to run..
>
> I did a lot of things:
> stopping catalina
> killing java processes
> removing tomcat lock files
> looking if some other process was running on the same port
>
> but nothing!!!
>
> I have noted that, looking at "top" results, the cpu usage was really
> hight
> It seems there are some processes that use a lot of cpu
>
> PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+
> COMMAND
> 4600 root 20 0 2488m 143m 39m R 109 0.8 480:35.39 java
>
> In the list of Geoerver Italian Users, someone suggest me to try to
> execute some java diagnostic tools.
> In particular, looking at the output of jstack:
> ________________________________________________--
>
> > Thread 4600: (state = IN_NATIVE)
> > - java.io.RandomAccessFile.readBytes(byte, int, int) @bci=0
> >
> (Compiled
>
> > frame; information may be imprecise)
> > - java.io.RandomAccessFile.read(byte, int, int) @bci=4, line=315
> > (Compiled frame)
> > - com.mckoi.store.JournalledSystem$Resource.read(long, byte, int)
> > @bci=341, line=1546 (Compiled frame)
> > - com.mckoi.store.LoggingBufferManager$BMPage.readPageContent(long,
> > byte, int) @bci=23, line=788 (Compiled frame)
> > - com.mckoi.store.LoggingBufferManager$BMPage.initialize() @bci=27,
> > line=823 (Compiled frame)
> > - com.mckoi.store.AbstractStore.getAreaHeader(long, long) @bci=9,
> > line=831 (Compiled frame)
> > - com.mckoi.store.AbstractStore.free(long) @bci=188, line=1340
> > (Compiled frame)
> > - com.mckoi.database.V2MasterTableDataSource.scanForLeaks() @bci=309,
> > line=794 (Compiled frame)
> > - com.mckoi.database.V2MasterTableDataSource.open(java.lang.String)
> > @bci=161, line=406 (Interpreted frame)
> > - com.mckoi.database.TableDataConglomerate.readVisibleTables()
> > @bci=192, line=383 (Interpreted frame)
> > - com.mckoi.database.TableDataConglomerate.open(java.lang.String)
> > @bci=141, line=1096 (Interpreted frame)
> > - com.mckoi.database.Database.init() @bci=204, line=1803 (Interpreted
> > frame)
> > -
> >
> >
> com.mckoi.database.control.DBController.startDatabase(com.mckoi.database.control.DBConfig) @bci=11, line=131 (Interpreted frame)
>
> > - org.fao.geonet.util.McKoiDB.start() @bci=12, line=65 (Interpreted
> > frame)
> > - org.fao.geonet.activators.McKoiActivator.startup(java.lang.String,
> > org.jdom.Element) @bci=61, line=54 (Interpreted frame)
> > - jeeves.server.JeevesEngine.initResources(org.jdom.Element)
> >
> @bci=204,
>
> > line=373 (Interpreted frame)
> > - jeeves.server.JeevesEngine.loadConfigFile(java.lang.String,
> > java.lang.String, jeeves.server.dispatchers.ServiceManager) @bci=226,
> > line=220 (Interpreted frame)
> > - jeeves.server.JeevesEngine.init(java.lang.String, java.lang.String,
> > java.lang.String) @bci=306, line=137 (Interpreted frame)
> > - jeeves.server.sources.http.JeevesServlet.init() @bci=78, line=66
> > (Interpreted frame)
> > - javax.servlet.GenericServlet.init(javax.servlet.ServletConfig)
> > @bci=6, line=212 (Interpreted frame)
> > - org.apache.catalina.core.StandardWrapper.loadServlet() @bci=774,
> > line=1173 (Interpreted frame)
> > - org.apache.catalina.core.StandardWrapper.load() @bci=2, line=993
> > (Interpreted frame)
> >
> ______________________________________________
>
> they suggest me it could be a problem of Geonetwork and in particular
> that the Geonetwork DB (McKoy ?) is not starting?
> is this correct?
>
> do you have other suggestions?
> I hope you can give me some help
>
> many thanks
>
> Ivan
>
>
>
>
>
>
>
>
>
> ____________________________________________________________________
>
> ------------------------------------------------------------------------------
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
>
> ____________________________________________________________________
>
> _______________________________________________
> GeoNetwork-users mailing list
> GeoNetwork-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/geonetwork-users
> GeoNetwork OpenSource is maintained at http://sourceforge.net/projects/geonetwork
>

--
Ti prego di cercare di non inviarmi files .dwg, .doc, .xls, .ppt.
Preferisco formati liberi.
Please try to avoid to send me .dwg, .doc, .xls, .ppt files.
I prefer free formats.
http://it.wikipedia.org/wiki/Formato_aperto
http://en.wikipedia.org/wiki/Open_format

Ivan Marchesini
Perugia (Italy)
Socio fondatore GFOSS "Geospatial Free and Open Source Software" http://www.gfoss.it
e-mail: marchesini@anonymised.com
ivan.marchesini@anonymised.com
fax (home): +39(0)5782830887
jabber: geoivan73@anonymised.com
skype: geoivan73