problems installing Djatoka following the wiki instructions

[Hardy Pottinger]

Hi, I'm following these instructions:

https://wiki.duraspace.org/display/ISLANDORA/Chapter+12+-+Installing+Solution+Pack+Dependencies

and am attempting to install Djatoka. Whenever I go to http://[fedora-server]:8081/adore-djatoka

The LC test image does not load. I'm trying an alternate test image, just to be sure, but every time I try to "Open image in new window" I get "HTTP Status 500", which is fine, but no error shows up in $FEDORA_HOME/tomcat/logs/catalina.out

I'm a bit confused. I've never seen Tomcat throw an error and not put anything in the log file about it, so I'm at a loss for where to go from here, and figured I'd better ask the list, on the off chance I'm just missing something.

[Nelson Hart]

Hi Hardy,

I'm ran into this same problem last week. Check your version of Java installed. I believe Djatoka requires Sun JKD/JRE and not the Open JDK/JRE. I've been meaning to ask someone around the office but haven't gotten to it yet. I still haven't got my setup working.

Cheers,

Nelson

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Nelson Hart
iPad Developer - Islandora / TourPad Project 
Robertson Library
University of Prince Edward Island
nh...@upei.ca

[Pottinger, Hardy J.]

Hi, thanks for the tip, the start script was not explicitly declaring the
path for JAVA_HOME, it is now, but there has been no change in the
behavior I noted before. I can see via PsiProbe that JAVA_HOME is properly
set to: /usr/lib/jvm/java-1.6.0-sun-1.6.0.29/jre which should be golden.
I'm still quite confused that there's no trace of this error in the
catalina.out log file.

Some details on the box I'm using, as it's different than our demo we were
using last week, this is much closer to what we'll be running in
production, so phase 2 of our demo process. The box is running RHEL 5, I'm
using the embedded Tomcat that comes with Fedora 3.5, and am running this
Tomcat as the fedora user with JVC.

--
HARDY POTTINGER <potti...@umsystem.edu>
University of Missouri Library Systems
http://lso.umsystem.edu/~pottingerhj/
https://MOspace.umsystem.edu/
"No matter how far down the wrong road you've gone,
turn back." --Turkish proverb

><mailto:islandora%2Bunsu...@googlegroups.com>.

>
>For more options, visit this group at
>http://groups.google.com/group/islandora?hl=en.
>
>
>
>
>
>
>
>--
>Nelson Hart
>iPad Developer - Islandora / TourPad Project
>Robertson Library
>University of Prince Edward Island
>nh...@upei.ca
>

>--
>You received this message because you are subscribed to the Google Groups
>"islandora" group.

[Jonathan Green]

Is there anything interesting showing up in the djatoka log files?
http://sourceforge.net/apps/mediawiki/djatoka/index.php?title=Logging

By default I believe it will log to the current directory when you started tomcat if you haven't set up a path for logging in the djatoka log4j configuration file.

--
Jonathan Green
DiscoveryGarden Inc. 
Sims Office Suites Building, 3rd Floor, 118 Sydney Street 
Charlottetown, PE C1A 1G4 
902.367.3851 discoverygarden.ca 
jona...@discoverygarden.ca
skype: jonathan.edwards.green

[Pottinger, Hardy J.]

$ cat djatoka.log
2012-04-03/10:14:00.964/CDT [http-8081-3] INFO processingRemoteURI:
http://memory.loc.gov/gmd/gmd433/g4330/g4330/np000066.jp2
2012-04-03/10:15:08.514/CDT [http-8081-3] INFO processingRemoteURI:
http://memory.loc.gov/gmd/gmd3/g3200/g3200/ct000425.jp2

So, it's trying... Just wish I knew more about this mysterious 500 error.

Scanning below, realized I mistyped JVC when I meant JSVC.

--
HARDY POTTINGER <potti...@umsystem.edu>
University of Missouri Library Systems
http://lso.umsystem.edu/~pottingerhj/
https://MOspace.umsystem.edu/

"Debug only code. Comments lie."

On 4/3/12 11:49 AM, "Jonathan Green" <jona...@discoverygarden.ca> wrote:

>Is there anything interesting showing up in the djatoka log files?
>http://sourceforge.net/apps/mediawiki/djatoka/index.php?title=Logging
>
>By default I believe it will log to the current directory when you
>started tomcat if you haven't set up a path for logging in the djatoka
>log4j configuration file.
>
>On Tue, Apr 3, 2012 at 12:31 PM, Pottinger, Hardy J.
><Potti...@umsystem.edu> wrote:
>
>Hi, thanks for the tip, the start script was not explicitly declaring the
>path for JAVA_HOME, it is now, but there has been no change in the
>behavior I noted before. I can see via PsiProbe that JAVA_HOME is properly
>set to: /usr/lib/jvm/java-1.6.0-sun-1.6.0.29/jre which should be golden.
>I'm still quite confused that there's no trace of this error in the
>catalina.out log file.
>
>Some details on the box I'm using, as it's different than our demo we were
>using last week, this is much closer to what we'll be running in
>production, so phase 2 of our demo process. The box is running RHEL 5, I'm
>using the embedded Tomcat that comes with Fedora 3.5, and am running this
>Tomcat as the fedora user with JVC.
>
>--
>HARDY POTTINGER <potti...@umsystem.edu>
>University of Missouri Library Systems
>http://lso.umsystem.edu/~pottingerhj/

><http://lso.umsystem.edu/%7Epottingerhj/>

>><mailto:islandora%2Bunsu...@googlegroups.com
>><mailto:islandora%252Buns...@googlegroups.com>>.

>Jonathan Green
>DiscoveryGarden Inc.
>Sims Office Suites Building, 3rd Floor, 118 Sydney Street
>
>Charlottetown, PE C1A 1G4

>902.367.3851 discoverygarden.ca <http://discoverygarden.ca/>
>jona...@discoverygarden.ca
>skype: jonathan.edwards.green

[Pottinger, Hardy J.]

Aha, progress, I now have an error message and a clue to follow up on. I
turned on DEBUG logging in
$CATALINA_HOME/webapps/adore-djatoka/WEB-INF/classes/log4j.properties, and
now I can see the following in djatoka.log:

2012-04-03/12:45:46.838/CDT [http-8081-1] INFO processingRemoteURI:
http://memory.loc.gov/gmd/gmd3/g3200/g3200/ct000425.jp2
2012-04-03/12:45:56.124/CDT [http-8081-1] DEBUG remoteCacheSize: 1
2012-04-03/12:45:56.126/CDT [http-8081-1] DEBUG
java.lang.UnsatisfiedLinkError: no kdu_jni in java.library.path
2012-04-03/12:46:01.220/CDT [http-8081-1] DEBUG
java.lang.NoClassDefFoundError: Could not initialize class
kdu_jni.Jpx_source

So, clearly the Kakadu dependencies are not getting found.

I'm on the trail now, will post the solution when I find it.

--
HARDY POTTINGER <potti...@umsystem.edu>
University of Missouri Library Systems
http://lso.umsystem.edu/~pottingerhj/
https://MOspace.umsystem.edu/
"Debug only code. Comments lie."

[Nick Ruest]

Do you have these path variables setup?
LD_LIBRARY_PATH or DLD_LIBRARY_PATH
KAKADU_LIBRARY_PATH
KAKADU_HOME

This is what they look like on my machine:
DLD_LIBRARY_PATH=/usr/local/djatoka/lib/Linux-x86-64
KAKADU_LIBRARY_PATH=/usr/local/djatoka/lib/Linux-x86-64
KAKADU_HOME=/usr/local/djatoka/lib/Linux-x86-64

-nruest

[Pottinger, Hardy J.]

Hi, Nick. Yes. I had to hack the env.sh script in $KAKADU_HOME/bin
changing:

DJATOKA_HOME=`pwd`

To:

DJATOKA_HOME=/opt/adore-djatoka-1.1

When I start fedora, here are the JAVA_OPTS that are getting passed:

-Djava.awt.headless=true
-Dkakadu.home=/opt/adore-djatoka-1.1/bin/Linux-x86-32
-Djava.library.path=/opt/adore-djatoka-1.1/lib/Linux-x86-32
-DLD_LIBRARY_PATH=/opt/adore-djatoka-1.1/lib/Linux-x86-32 -Xmx512m
-Djava.awt.headless=true
-Dkakadu.home=/opt/adore-djatoka-1.1/bin/Linux-x86-32
-Djava.library.path=/opt/adore-djatoka-1.1/lib/Linux-x86-32
-DLD_LIBRARY_PATH=/opt/adore-djatoka-1.1/lib/Linux-x86-32 -Xmx1024M
-Xms768M -XX:MaxPermSize=128M -XX:PermSize=32M -XX:+UseParallelGC
-Dfile.encoding=UTF-8 -Dcom.sun.management.jmxremote

Now when I try my test, this is what I see in djatoka.log:

2012-04-03/13:08:19.934/CDT [http-8081-1] INFO processingRemoteURI:
http://memory.loc.gov/gmd/gmd3/g3200/g3200/ct000425.jp2
2012-04-03/13:08:32.952/CDT [http-8081-1] DEBUG remoteCacheSize: 1
2012-04-03/13:08:33.039/CDT [http-8081-1] DEBUG null/kdu_expand -quiet -i
/tmp/cache1354165286829378066425685907.jp2 -o /dev/stdout -reduce 3
-region {0.0,0.0},{0.6476683937823834,0.335401643468053}
2012-04-03/13:08:33.042/CDT [http-8081-1] ERROR java.io.IOException:
Cannot run program "null/kdu_expand" (in directory "null"):
java.io.IOException: error=2, No such file or directory
java.io.IOException: Cannot run program "null/kdu_expand" (in directory
"null"): java.io.IOException: error=2, No such file or directory
at java.lang.ProcessBuilder.start(ProcessBuilder.java:460)
at java.lang.Runtime.exec(Runtime.java:593)
at java.lang.Runtime.exec(Runtime.java:431)
at
gov.lanl.adore.djatoka.kdu.KduExtractExe.process(KduExtractExe.java:229)
at
gov.lanl.adore.djatoka.DjatokaExtractProcessor.extractImage(DjatokaExtractP
rocessor.java:157)
at
gov.lanl.adore.djatoka.DjatokaExtractProcessor.extractImage(DjatokaExtractP
rocessor.java:85)
at
gov.lanl.adore.djatoka.openurl.OpenURLJP2KService.resolve(OpenURLJP2KServic
e.java:255)
at
org.oclc.oomRef.OpenURLRequestProcessorImpl.resolve(OpenURLRequestProcessor
Impl.java:82)
at
gov.lanl.adore.djatoka.openurl.OpenURLServlet.doGet(OpenURLServlet.java:121
)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:617)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applicatio
nFilterChain.java:290)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterC
hain.java:206)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.j
ava:233)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.j
ava:191)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:12
7)
at
com.googlecode.psiprobe.Tomcat60AgentValve.invoke(Tomcat60AgentValve.java:3
0)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:10
2)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.jav
a:109)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:298)
at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:857)
at
org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Htt
p11Protocol.java:588)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489)
at java.lang.Thread.run(Thread.java:662)
Caused by: java.io.IOException: java.io.IOException: error=2, No such file
or directory
at java.lang.UNIXProcess.<init>(UNIXProcess.java:148)
at java.lang.ProcessImpl.start(ProcessImpl.java:65)
at java.lang.ProcessBuilder.start(ProcessBuilder.java:453)
... 23 more

It still looks like a path problem.

--

HARDY POTTINGER <potti...@umsystem.edu>
University of Missouri Library Systems
http://lso.umsystem.edu/~pottingerhj/
https://MOspace.umsystem.edu/

"I think I like disruptive technology because
it makes the whole world a bit fuzzy, my
normal state of mind."
-- Robert Llewellyn (aka Kryten)

[Pottinger, Hardy J.]

Yep, this is definitely a problem with the env.sh script in
$KAKADU_HOME/bin. I've modified it as per the instructions on the wiki,
and it does look like LD_LIBRARY_PATH is getting set, however, from
djatoka.log, it's clearly not getting that environment variable:

2012-04-03/15:11:42.688/CDT [http-8081-1] DEBUG envParams:
LD_LIBRARY_PATH=null | null/kdu_expand

Looking for ideas for things to try next.

--
HARDY POTTINGER <potti...@umsystem.edu>
University of Missouri Library Systems
http://lso.umsystem.edu/~pottingerhj/
https://MOspace.umsystem.edu/

"I am always doing that which I cannot do, in order that I may learn how
to do it." --Pablo Picasso

[Pottinger, Hardy J.]

I think I'm on to something. I searched LD_LIB_PATH to find out more about
what it was I was monkeying with, and found this article:

http://linuxmafia.com/faq/Admin/ld-lib-path.html

And their recommendation is to *never* use this environment variable. The
top reason is probably applicable to my situation:

LD_LIBRARY_PATH is used in preference to any run time or default system
linker path. If (God forbid) you had it set to something like
/dcs/spod/baduser/lib, if there was a hacked version of libc in that
directory (for example) your account could be compromised. It is for this
reason that set-uid programs completely ignore LD_LIBRARY_PATH

I am using JSVC to run tomcat as the fedora user. I think that probably
makes jsvc a set-uid program. Which would seem to indicate that no matter
how I attempt to set LD_LIBRARY_PATH, the variable will be dropped when
jsvc starts up.

Back to the drawing board here.

--
HARDY POTTINGER <potti...@umsystem.edu>
University of Missouri Library Systems
http://lso.umsystem.edu/~pottingerhj/
https://MOspace.umsystem.edu/

"Look for the answer inside your question." --Rumi

[Jonathan Green]

Did you add the env.sh to your tomcat start up script? If so, you might want to do an echo at the end of the tomcat start up script and make sure LD_LIBRARY_PATH is setup there.

jona...@discoverygarden.ca
skype: jonathan.edwards.green

[Pottinger, Hardy J.]

Hi, I have sourced the env.sh script in my start script, however, as previously indicated, I am using the jsvc tomcat wrapper to handle running tomcat as the fedora user. It looks like jsvc drops LD_LIBRARY_PATH as a security measure (see previous message in this thread for details). I am going to rework my start script to not use jsvc and see where that gets me. I think I would prefer to figure out why Djatoka is using LD_LIBRARY_PATH, but first I want to be sure everything is working with just the normal tomcat start script.

--Hardy

Sent from my iPad

On Apr 3, 2012, at 6:07 PM, "Jonathan Green" <jona...@discoverygarden.ca<mailto:jona...@discoverygarden.ca>> wrote:

Did you add the env.sh to your tomcat start up script? If so, you might want to do an echo at the end of the tomcat start up script and make sure LD_LIBRARY_PATH is setup there.

On Tue, Apr 3, 2012 at 5:45 PM, Pottinger, Hardy J. <<mailto:Potti...@umsystem.edu>Potti...@umsystem.edu<mailto:Potti...@umsystem.edu>> wrote:
Yep, this is definitely a problem with the env.sh script in
$KAKADU_HOME/bin. I've modified it as per the instructions on the wiki,
and it does look like LD_LIBRARY_PATH is getting set, however, from
djatoka.log, it's clearly not getting that environment variable:

2012-04-03/15<tel:2012-04-03%2F15>:11:42.688/CDT [http-8081-1] DEBUG envParams:
LD_LIBRARY_PATH=null | null/kdu_expand

Looking for ideas for things to try next.

--
HARDY POTTINGER <<mailto:potti...@umsystem.edu>potti...@umsystem.edu<mailto:potti...@umsystem.edu>>

University of Missouri Library Systems

<http://lso.umsystem.edu/%7Epottingerhj/>http://lso.umsystem.edu/~pottingerhj/
<https://MOspace.umsystem.edu/>https://MOspace.umsystem.edu/

"I am always doing that which I cannot do, in order that I may learn how
to do it." --Pablo Picasso

On 4/3/12 2:07 PM, "Pottinger, Hardy J." <<mailto:Potti...@umsystem.edu>Potti...@umsystem.edu<mailto:Potti...@umsystem.edu>> wrote:

>Hi, Nick. Yes. I had to hack the env.sh script in $KAKADU_HOME/bin
>changing:
>
>DJATOKA_HOME=`pwd`
>
>To:
>
>DJATOKA_HOME=/opt/adore-djatoka-1.1
>
>When I start fedora, here are the JAVA_OPTS that are getting passed:
>
>-Djava.awt.headless=true
>-Dkakadu.home=/opt/adore-djatoka-1.1/bin/Linux-x86-32
>-Djava.library.path=/opt/adore-djatoka-1.1/lib/Linux-x86-32
>-DLD_LIBRARY_PATH=/opt/adore-djatoka-1.1/lib/Linux-x86-32 -Xmx512m
>-Djava.awt.headless=true
>-Dkakadu.home=/opt/adore-djatoka-1.1/bin/Linux-x86-32
>-Djava.library.path=/opt/adore-djatoka-1.1/lib/Linux-x86-32
>-DLD_LIBRARY_PATH=/opt/adore-djatoka-1.1/lib/Linux-x86-32 -Xmx1024M
>-Xms768M -XX:MaxPermSize=128M -XX:PermSize=32M -XX:+UseParallelGC
>-Dfile.encoding=UTF-8 -Dcom.sun.management.jmxremote
>
>
>Now when I try my test, this is what I see in djatoka.log:
>

>2012-04-03/13<tel:2012-04-03%2F13>:08:19.934/CDT [http-8081-1] INFO processingRemoteURI:
><http://memory.loc.gov/gmd/gmd3/g3200/g3200/ct000425.jp2>http://memory.loc.gov/gmd/gmd3/g3200/g3200/ct000425.jp2
>2012-04-03/13<tel:2012-04-03%2F13>:08:32.952/CDT [http-8081-1] DEBUG remoteCacheSize: 1
>2012-04-03/13<tel:2012-04-03%2F13>:08:33.039/CDT [http-8081-1] DEBUG null/kdu_expand -quiet -i

>/tmp/cache1354165286829378066425685907.jp2 -o /dev/stdout -reduce 3
>-region {0.0,0.0},{0.6476683937823834,0.335401643468053}

>2012-04-03/13<tel:2012-04-03%2F13>:08:33.042/CDT [http-8081-1] ERROR java.io.IOException:

>HARDY POTTINGER <<mailto:potti...@umsystem.edu>potti...@umsystem.edu<mailto:potti...@umsystem.edu>>

>University of Missouri Library Systems

><http://lso.umsystem.edu/%7Epottingerhj/>http://lso.umsystem.edu/~pottingerhj/
><https://MOspace.umsystem.edu/>https://MOspace.umsystem.edu/

>"I think I like disruptive technology because
>it makes the whole world a bit fuzzy, my
>normal state of mind."
>-- Robert Llewellyn (aka Kryten)
>
>
>
>
>
>On 4/3/12 1:37 PM, "Nick Ruest" <<mailto:rue...@gmail.com>rue...@gmail.com<mailto:rue...@gmail.com>> wrote:
>
>>Do you have these path variables setup?
>>LD_LIBRARY_PATH or DLD_LIBRARY_PATH
>>KAKADU_LIBRARY_PATH
>>KAKADU_HOME
>>
>>This is what they look like on my machine:
>>DLD_LIBRARY_PATH=/usr/local/djatoka/lib/Linux-x86-64
>>KAKADU_LIBRARY_PATH=/usr/local/djatoka/lib/Linux-x86-64
>>KAKADU_HOME=/usr/local/djatoka/lib/Linux-x86-64
>>
>>-nruest
>>
>>On 12-04-03 02:29 PM, Pottinger, Hardy J. wrote:
>>> Aha, progress, I now have an error message and a clue to follow up on.
>>>I
>>> turned on DEBUG logging in
>>> $CATALINA_HOME/webapps/adore-djatoka/WEB-INF/classes/log4j.properties,
>>>and
>>> now I can see the following in djatoka.log:
>>>

>>> 2012-04-03/12<tel:2012-04-03%2F12>:45:46.838/CDT [http-8081-1] INFO processingRemoteURI:
>>> <http://memory.loc.gov/gmd/gmd3/g3200/g3200/ct000425.jp2> http://memory.loc.gov/gmd/gmd3/g3200/g3200/ct000425.jp2
>>> 2012-04-03/12<tel:2012-04-03%2F12>:45:56.124/CDT [http-8081-1] DEBUG remoteCacheSize: 1
>>> 2012-04-03/12<tel:2012-04-03%2F12>:45:56.126/CDT [http-8081-1] DEBUG

>>> java.lang.UnsatisfiedLinkError: no kdu_jni in java.library.path

>>> 2012-04-03/12<tel:2012-04-03%2F12>:46:01.220/CDT [http-8081-1] DEBUG

>>> java.lang.NoClassDefFoundError: Could not initialize class
>>> kdu_jni.Jpx_source
>>>
>>> So, clearly the Kakadu dependencies are not getting found.
>>>
>>> I'm on the trail now, will post the solution when I find it.
>>>
>>>
>>> --

>>> HARDY POTTINGER<<mailto:potti...@umsystem.edu>potti...@umsystem.edu<mailto:potti...@umsystem.edu>>

>>> University of Missouri Library Systems

>>> <http://lso.umsystem.edu/%7Epottingerhj/> http://lso.umsystem.edu/~pottingerhj/
>>> <https://MOspace.umsystem.edu/> https://MOspace.umsystem.edu/

>>> "Debug only code. Comments lie."
>>>
>>>
>>>
>>>
>>>

>>> On 4/3/12 12:01 PM, "Pottinger, Hardy J."<<mailto:Potti...@umsystem.edu>Potti...@umsystem.edu<mailto:Potti...@umsystem.edu>>
>>>wrote:
>>>
>>>> $ cat djatoka.log
>>>> 2012-04-03/10<tel:2012-04-03%2F10>:14:00.964/CDT [http-8081-3] INFO processingRemoteURI:
>>>> <http://memory.loc.gov/gmd/gmd433/g4330/g4330/np000066.jp2> http://memory.loc.gov/gmd/gmd433/g4330/g4330/np000066.jp2
>>>> 2012-04-03/10<tel:2012-04-03%2F10>:15:08.514/CDT [http-8081-3] INFO processingRemoteURI:
>>>> <http://memory.loc.gov/gmd/gmd3/g3200/g3200/ct000425.jp2> http://memory.loc.gov/gmd/gmd3/g3200/g3200/ct000425.jp2

>>>>
>>>> So, it's trying... Just wish I knew more about this mysterious 500
>>>>error.
>>>>
>>>> Scanning below, realized I mistyped JVC when I meant JSVC.
>>>>
>>>>
>>>> --

>>>> HARDY POTTINGER<<mailto:potti...@umsystem.edu>potti...@umsystem.edu<mailto:potti...@umsystem.edu>>

>>>> University of Missouri Library Systems

>>>> <http://lso.umsystem.edu/%7Epottingerhj/> http://lso.umsystem.edu/~pottingerhj/
>>>> <https://MOspace.umsystem.edu/> https://MOspace.umsystem.edu/

>>>> "Debug only code. Comments lie."
>>>>
>>>>
>>>>
>>>>
>>>>

>>>> On 4/3/12 11:49 AM, "Jonathan Green"<<mailto:jona...@discoverygarden.ca>jona...@discoverygarden.ca<mailto:jona...@discoverygarden.ca>>

>>>>wrote:
>>>>
>>>>> Is there anything interesting showing up in the djatoka log files?

>>>>> <http://sourceforge.net/apps/mediawiki/djatoka/index.php?title=Logging> http://sourceforge.net/apps/mediawiki/djatoka/index.php?title=Logging

>>>>> HARDY POTTINGER<<mailto:potti...@umsystem.edu>potti...@umsystem.edu<mailto:potti...@umsystem.edu>>

>>>>> University of Missouri Library Systems

>>>>> <http://lso.umsystem.edu/%7Epottingerhj/> http://lso.umsystem.edu/~pottingerhj/
>>>>> <<http://lso.umsystem.edu/%7Epottingerhj/>http://lso.umsystem.edu/%7Epottingerhj/>
>>>>> <https://MOspace.umsystem.edu/> https://MOspace.umsystem.edu/

>>>>> "No matter how far down the wrong road you've gone,
>>>>> turn back." --Turkish proverb
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On 4/2/12 5:35 PM, "Nelson Hart"<<mailto:nh...@upei.ca>nh...@upei.ca<mailto:nh...@upei.ca>> wrote:
>>>>>
>>>>>> Hi Hardy,
>>>>>> I'm ran into this same problem last week. Check your version of Java
>>>>>> installed. I believe Djatoka requires Sun JKD/JRE and not the Open
>>>>>> JDK/JRE. I've been meaning to ask someone around the office but
>>>>>>haven't
>>>>>> gotten to it yet. I still haven't got my setup working.
>>>>>>
>>>>>> Cheers,
>>>>>> Nelson
>>>>>>
>>>>>> On Mon, Apr 2, 2012 at 7:22 PM, Hardy Pottinger
>>>>>> <<mailto:potti...@umsystem.edu>potti...@umsystem.edu<mailto:potti...@umsystem.edu>> wrote:
>>>>>>
>>>>>> Hi, I'm following these instructions:
>>>>>>

>>>>>><https://wiki.duraspace.org/display/ISLANDORA/Chapter+12+-+Installing+>https://wiki.duraspace.org/display/ISLANDORA/Chapter+12+-+Installing+

>>>>>>S
>>>>>>ol
>>>>>> u
>>>>>> t
>>>>>> ion+Pack+Dependencies
>>>>>>
>>>>>>
>>>>>> and am attempting to install Djatoka. Whenever I go to

>>>>>> <http://[fedora-server]:8081/adore-djatoka> http://[fedora-server]:8081/adore-djatoka

>>>>>>
>>>>>> The LC test image does not load. I'm trying an alternate test image,
>>>>>> just
>>>>>> to be sure, but every time I try to "Open image in new window" I get
>>>>>> "HTTP Status 500", which is fine, but no error shows up in
>>>>>> $FEDORA_HOME/tomcat/logs/catalina.out
>>>>>>
>>>>>> I'm a bit confused. I've never seen Tomcat throw an error and not
>>>>>>put
>>>>>> anything in the log file about it, so I'm at a loss for where to go
>>>>>>from
>>>>>> here, and figured I'd better ask the list, on the off chance I'm
>>>>>>just
>>>>>> missing something.
>>>>>>
>>>>>> --
>>>>>> You received this message because you are subscribed to the Google
>>>>>> Groups
>>>>>> "islandora" group.
>>>>>> To view this discussion on the web visit

>>>>>> <https://groups.google.com/d/msg/islandora/-/NCbu9A3D9gsJ> https://groups.google.com/d/msg/islandora/-/NCbu9A3D9gsJ.
>>>>>>
>>>>>> To post to this group, send email to <mailto:isla...@googlegroups.com> isla...@googlegroups.com<mailto:isla...@googlegroups.com>.

>>>>>> To unsubscribe from this group, send email to

>>>>>> <mailto:islandora%2Bunsu...@googlegroups.com> islandora+...@googlegroups.com<mailto:islandora+...@googlegroups.com>
>>>>>> <mailto:islandora%2Bunsu...@googlegroups.com<mailto:islandora%252Buns...@googlegroups.com>>
>>>>>
>>>>>> <mailto:islandora%2Bunsu...@googlegroups.com<mailto:islandora%252Buns...@googlegroups.com>
>>>>>> <mailto:islandora%252Buns...@googlegroups.com<mailto:islandora%25252Bun...@googlegroups.com>>>.

>>>>>>
>>>>>> For more options, visit this group at

>>>>>> <http://groups.google.com/group/islandora?hl=en> http://groups.google.com/group/islandora?hl=en.

>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Nelson Hart
>>>>>> iPad Developer - Islandora / TourPad Project
>>>>>> Robertson Library
>>>>>> University of Prince Edward Island

>>>>>> <mailto:nh...@upei.ca> nh...@upei.ca<mailto:nh...@upei.ca>

>>>>>>
>>>>>> --
>>>>>> You received this message because you are subscribed to the Google
>>>>>> Groups
>>>>>> "islandora" group.

>>>>>> To post to this group, send email to <mailto:isla...@googlegroups.com> isla...@googlegroups.com<mailto:isla...@googlegroups.com>.

>>>>>> To unsubscribe from this group, send email to

>>>>>> <mailto:islandora%2Bunsu...@googlegroups.com> islandora+...@googlegroups.com<mailto:islandora+...@googlegroups.com>

>>>>>> <mailto:islandora%2Bunsu...@googlegroups.com<mailto:islandora%252Buns...@googlegroups.com>>.
>>>>>>
>>>>>> For more options, visit this group at

>>>>>> <http://groups.google.com/group/islandora?hl=en> http://groups.google.com/group/islandora?hl=en.

>>>>> --
>>>>> You received this message because you are subscribed to the Google
>>>>>Groups
>>>>> "islandora" group.

>>>>> To post to this group, send email to <mailto:isla...@googlegroups.com> isla...@googlegroups.com<mailto:isla...@googlegroups.com>.

>>>>> To unsubscribe from this group, send email to

>>>>> <mailto:islandora%2Bunsu...@googlegroups.com> islandora+...@googlegroups.com<mailto:islandora+...@googlegroups.com>

>>>>> <mailto:islandora%2Bunsu...@googlegroups.com<mailto:islandora%252Buns...@googlegroups.com>>.
>>>>> For more options, visit this group at

>>>>> <http://groups.google.com/group/islandora?hl=en> http://groups.google.com/group/islandora?hl=en.

>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Jonathan Green
>>>>> DiscoveryGarden Inc.
>>>>> Sims Office Suites Building, 3rd Floor, 118 Sydney Street
>>>>>
>>>>> Charlottetown, PE C1A 1G4

>>>>> 902.367.3851<tel:902.367.3851> <http://discoverygarden.ca> discoverygarden.ca<http://discoverygarden.ca><<http://discoverygarden.ca/>http://discoverygarden.ca/>
>>>>> <mailto:jona...@discoverygarden.ca> jona...@discoverygarden.ca<mailto:jona...@discoverygarden.ca>

>>>>> skype: jonathan.edwards.green
>>>>>
>>>>>
>>>>> --
>>>>> You received this message because you are subscribed to the Google
>>>>>Groups
>>>>> "islandora" group.

>>>>> To post to this group, send email to <mailto:isla...@googlegroups.com> isla...@googlegroups.com<mailto:isla...@googlegroups.com>.

>>>>> To unsubscribe from this group, send email to

>>>>> <mailto:islandora%2Bunsu...@googlegroups.com> islandora+...@googlegroups.com<mailto:islandora+...@googlegroups.com>.

>>>>>
>>>>> For more options, visit this group at

>>>>> <http://groups.google.com/group/islandora?hl=en> http://groups.google.com/group/islandora?hl=en.

>>>> --
>>>> You received this message because you are subscribed to the Google
>>>>Groups
>>>> "islandora" group.

>>>> To post to this group, send email to <mailto:isla...@googlegroups.com> isla...@googlegroups.com<mailto:isla...@googlegroups.com>.

>>>> To unsubscribe from this group, send email to

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>>>> For more options, visit this group at

>>>> <http://groups.google.com/group/islandora?hl=en> http://groups.google.com/group/islandora?hl=en.

>>>>
>>
>>--
>>You received this message because you are subscribed to the Google Groups
>>"islandora" group.

>>To post to this group, send email to <mailto:isla...@googlegroups.com> isla...@googlegroups.com<mailto:isla...@googlegroups.com>.

>>To unsubscribe from this group, send email to

>><mailto:islandora%2Bunsu...@googlegroups.com>islandora+...@googlegroups.com<mailto:islandora+...@googlegroups.com>.

>>For more options, visit this group at

>><http://groups.google.com/group/islandora?hl=en>http://groups.google.com/group/islandora?hl=en.

>>
>
>--
>You received this message because you are subscribed to the Google Groups
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--
Jonathan Green
DiscoveryGarden Inc.
Sims Office Suites Building, 3rd Floor, 118 Sydney Street
Charlottetown, PE C1A 1G4

902.367.3851 <http://discoverygarden.ca/> discoverygarden.ca<http://discoverygarden.ca>
<mailto:jona...@discoverygarden.ca>jona...@discoverygarden.ca<mailto:jona...@discoverygarden.ca>
skype: jonathan.edwards.green

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[Jonathan Green]

Sorry. It takes me awhile for me to process my email queue, and I missed your second message. The reason Djatoka wants the LD_LIBRARY_PATH to be set it its calling some JNI libraries which reference djatokas native shared object libraries. Some possible work arounds:

1. Set java.library.path system property (this may or may not work depending how the JNI dependencies)
2. Put symlinks to the shared object files from djatoka into a folder that is on the default library path, usually the /usr/lib or /lib folders
   

To post to this group, send email to isla...@googlegroups.com.

To unsubscribe from this group, send email to islandora+...@googlegroups.com.

For more options, visit this group at http://groups.google.com/group/islandora?hl=en.

--

Jonathan Green
DiscoveryGarden Inc. 
Sims Office Suites Building, 3rd Floor, 118 Sydney Street 
Charlottetown, PE C1A 1G4 

902.367.3851 discoverygarden.ca 
jona...@discoverygarden.ca
skype: jonathan.edwards.green

[Pottinger, Hardy J.]

I thought I'd just give an update. I haven't made any progress on getting
Djatoka to run alongside Fedora Commons in our JSVC-wrapped tomcat
instance.

WARNING: lots and lots of debug output below, sorry for the wall of text.

Here's the debug output from djatoka.log when I attempt to use the Djatoka
OpenURL Demo:

2012-04-05/13:56:32.562/CDT [http-8081-1] DEBUG envParams:
LD_LIBRARY_PATH=null | null/kdu_expand
2012-04-05/13:56:32.568/CDT [http-8081-1] INFO processingRemoteURI:
http://memory.loc.gov/gmd/gmd3/g3200/g3200/ct000425.jp2
2012-04-05/13:56:45.932/CDT [http-8081-1] DEBUG remoteCacheSize: 1
2012-04-05/13:56:45.943/CDT [http-8081-1] DEBUG null/kdu_expand -quiet -i
/tmp/cache1354165284219469834668641784.jp2 -o /dev/stdout -reduce 3
-region {0.0,0.0},{0.6476683937823834,0.335401643468053}
2012-04-05/13:56:45.946/CDT [http-8081-1] ERROR java.io.IOException:

Cannot run program "null/kdu_expand" (in directory "null"):
java.io.IOException: error=2, No such file or directory
java.io.IOException: Cannot run program "null/kdu_expand" (in directory
"null"): java.io.IOException: error=2, No such file or directory
at java.lang.ProcessBuilder.start(ProcessBuilder.java:460)
at java.lang.Runtime.exec(Runtime.java:593)
at java.lang.Runtime.exec(Runtime.java:431)
at
gov.lanl.adore.djatoka.kdu.KduExtractExe.process(KduExtractExe.java:229)
at

gov.lanl.adore.djatoka.DjatokaExtractProcessor.extractImage(DjatokaExtractP
rocessor.java:157)
at
gov.lanl.adore.djatoka.DjatokaExtractProcessor.extractImage(DjatokaExtractP
rocessor.java:85)
at
gov.lanl.adore.djatoka.openurl.OpenURLJP2KService.resolve(OpenURLJP2KServic
e.java:255)
at
org.oclc.oomRef.OpenURLRequestProcessorImpl.resolve(OpenURLRequestProcessor
Impl.java:82)
at
gov.lanl.adore.djatoka.openurl.OpenURLServlet.doGet(OpenURLServlet.java:121

)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:617)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
at

org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applicatio
nFilterChain.java:290)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterC
hain.java:206)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.j
ava:233)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.j
ava:191)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:12

7)
at
com.googlecode.psiprobe.Tomcat60AgentValve.invoke(Tomcat60AgentValve.java:3
0)
at

org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:10
2)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.jav
a:109)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:298)
at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:857)
at
org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Htt

p11Protocol.java:588)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489)
at java.lang.Thread.run(Thread.java:662)
Caused by: java.io.IOException: java.io.IOException: error=2, No such file
or directory
at java.lang.UNIXProcess.<init>(UNIXProcess.java:148)
at java.lang.ProcessImpl.start(ProcessImpl.java:65)
at java.lang.ProcessBuilder.start(ProcessBuilder.java:453)
... 23 more

2012-04-05/13:56:45.947/CDT [http-8081-1] DEBUG cacheSize: 1
2012-04-05/13:56:45.947/CDT [http-8081-1] DEBUG makingTile:
/var/djatokacache/cache1834139402-5425033306250233200.jpg 0 params:
{"reduce": "3", "level": "3", "region": "0,0,500,500", "rotate": "0",
"scalingFactor": "1.0", "scalingDims": "", "compLayer": "0" }

The pertinent part is:

2012-04-05/13:56:45.946/CDT [http-8081-1] ERROR java.io.IOException:

Cannot run program "null/kdu_expand" (in directory "null"):
java.io.IOException: error=2, No such file or directory
java.io.IOException: Cannot run program "null/kdu_expand" (in directory
"null"):

However, from the debug output from JSVC startup, I can confirm the
LD_LIBRARY_PATH environment variable is getting passed:

sudo service fedora restart

-Xmx512m -Djava.awt.headless=true
-Dkakadu.home=/opt/adore-djatoka-1.1/bin/Linux-x86-32
-Djava.library.path=/opt/adore-djatoka-1.1/lib/Linux-x86-32
-DLD_LIBRARY_PATH=/opt/adore-djatoka-1.1/lib/Linux-x86-32 -Xmx1024M
-Xms768M -XX:MaxPermSize=128M -XX:PermSize=32M -XX:+UseParallelGC
-Dfile.encoding=UTF-8 -Dcom.sun.management.jmxremote

Stopping Fedora's Tomcat with PID 20498...
Stopping jsvc.exec: [ OK ]
05/04/2012 13:53:23 21200 jsvc debug: +-- DUMPING PARSED COMMAND LINE
ARGUMENTS --------------
05/04/2012 13:53:23 21200 jsvc debug: | Detach: True
05/04/2012 13:53:23 21200 jsvc debug: | Show Version: No
05/04/2012 13:53:23 21200 jsvc debug: | Show Help: No
05/04/2012 13:53:23 21200 jsvc debug: | Check Only: Disabled
05/04/2012 13:53:23 21200 jsvc debug: | Stop: False
05/04/2012 13:53:23 21200 jsvc debug: | Wait: 0
05/04/2012 13:53:23 21200 jsvc debug: | Run as service: No
05/04/2012 13:53:23 21200 jsvc debug: | Install service: No
05/04/2012 13:53:23 21200 jsvc debug: | Remove service: No
05/04/2012 13:53:23 21200 jsvc debug: | JVM Name: "null"
05/04/2012 13:53:23 21200 jsvc debug: | Java Home:
"/etc/alternatives/java_sdk_sun"
05/04/2012 13:53:23 21200 jsvc debug: | PID File:
"/home/fedora/fedora/tomcat/temp/fedora-tomcat-jsvc.pid"
05/04/2012 13:53:23 21200 jsvc debug: | User Name: "fedora"
05/04/2012 13:53:23 21200 jsvc debug: | Extra Options: 4
05/04/2012 13:53:23 21200 jsvc debug: |
"-Dcatalina.home=/home/fedora/fedora/tomcat"
05/04/2012 13:53:23 21200 jsvc debug: |
"-Dcatalina.base=/home/fedora/fedora/tomcat"
05/04/2012 13:53:23 21200 jsvc debug: |
"-Djava.library.path=/opt/adore-djatoka-1.1/lib/Linux-x86-32"
05/04/2012 13:53:23 21200 jsvc debug: |
"-Djava.class.path=/etc/alternatives/java_sdk_sun/lib/tools.jar:/home/fedor
a/fedora/tomcat/bin/commons-daemon.jar:/home/fedora/fedora/tomcat/bin/boots
trap.jar"
05/04/2012 13:53:23 21200 jsvc debug: | Class Invoked:
"org.apache.catalina.startup.Bootstrap"
05/04/2012 13:53:23 21200 jsvc debug: | Class Arguments: 0
05/04/2012 13:53:23 21200 jsvc debug:
+-------------------------------------------------------
05/04/2012 13:53:23 21201 jsvc debug: user changed to 'fedora'
05/04/2012 13:53:23 21200 jsvc debug: User 'fedora' validated
05/04/2012 13:53:23 21200 jsvc debug: Attempting to locate Java Home in
/etc/alternatives/java_sdk_sun
05/04/2012 13:53:23 21200 jsvc debug: Attempting to locate VM
configuration file /etc/alternatives/java_sdk_sun/jre/lib/jvm.cfg
05/04/2012 13:53:23 21200 jsvc debug: Attempting to locate VM
configuration file /etc/alternatives/java_sdk_sun/lib/jvm.cfg
05/04/2012 13:53:23 21200 jsvc debug: Attempting to locate VM
configuration file /etc/alternatives/java_sdk_sun/jre/lib/i386/jvm.cfg
05/04/2012 13:53:23 21200 jsvc debug: Found VM configuration file at
/etc/alternatives/java_sdk_sun/jre/lib/i386/jvm.cfg
05/04/2012 13:53:23 21200 jsvc debug: Found VM client definition in
configuration
05/04/2012 13:53:23 21200 jsvc debug: Checking library
/etc/alternatives/java_sdk_sun/jre/lib/i386/client/libjvm.so
05/04/2012 13:53:23 21200 jsvc debug: Found VM server definition in
configuration
05/04/2012 13:53:23 21200 jsvc debug: Checking library
/etc/alternatives/java_sdk_sun/jre/lib/i386/server/libjvm.so
05/04/2012 13:53:23 21200 jsvc debug: Found VM hotspot definition in
configuration
05/04/2012 13:53:23 21200 jsvc debug: Checking library
/etc/alternatives/java_sdk_sun/jre/lib/i386/hotspot/libjvm.so
05/04/2012 13:53:23 21200 jsvc debug: Checking library
/etc/alternatives/java_sdk_sun/lib/i386/hotspot/libjvm.so
05/04/2012 13:53:23 21200 jsvc debug: Cannot locate library for VM hotspot
(skipping)
05/04/2012 13:53:23 21200 jsvc debug: Found VM classic definition in
configuration
05/04/2012 13:53:23 21200 jsvc debug: Checking library
/etc/alternatives/java_sdk_sun/jre/lib/i386/classic/libjvm.so
05/04/2012 13:53:23 21200 jsvc debug: Checking library
/etc/alternatives/java_sdk_sun/lib/i386/classic/libjvm.so
05/04/2012 13:53:23 21200 jsvc debug: Cannot locate library for VM classic
(skipping)
05/04/2012 13:53:23 21200 jsvc debug: Found VM native definition in
configuration
05/04/2012 13:53:23 21200 jsvc debug: Checking library
/etc/alternatives/java_sdk_sun/jre/lib/i386/native/libjvm.so
05/04/2012 13:53:23 21200 jsvc debug: Checking library
/etc/alternatives/java_sdk_sun/lib/i386/native/libjvm.so
05/04/2012 13:53:23 21200 jsvc debug: Cannot locate library for VM native
(skipping)
05/04/2012 13:53:23 21200 jsvc debug: Found VM green definition in
configuration
05/04/2012 13:53:23 21200 jsvc debug: Checking library
/etc/alternatives/java_sdk_sun/jre/lib/i386/green/libjvm.so
05/04/2012 13:53:23 21200 jsvc debug: Checking library
/etc/alternatives/java_sdk_sun/lib/i386/green/libjvm.so
05/04/2012 13:53:23 21200 jsvc debug: Cannot locate library for VM green
(skipping)
05/04/2012 13:53:23 21200 jsvc debug: Java Home located in
/etc/alternatives/java_sdk_sun
05/04/2012 13:53:23 21200 jsvc debug: +-- DUMPING JAVA HOME STRUCTURE
------------------------
05/04/2012 13:53:23 21200 jsvc debug: | Java Home:
"/etc/alternatives/java_sdk_sun"
05/04/2012 13:53:23 21200 jsvc debug: | Java VM Config.:
"/etc/alternatives/java_sdk_sun/jre/lib/i386/jvm.cfg"
05/04/2012 13:53:23 21200 jsvc debug: | Found JVMs: 2
05/04/2012 13:53:23 21200 jsvc debug: | JVM Name: "client"
05/04/2012 13:53:23 21200 jsvc debug: |
"/etc/alternatives/java_sdk_sun/jre/lib/i386/client/libjvm.so"
05/04/2012 13:53:23 21200 jsvc debug: | JVM Name: "server"
05/04/2012 13:53:23 21200 jsvc debug: |
"/etc/alternatives/java_sdk_sun/jre/lib/i386/server/libjvm.so"
05/04/2012 13:53:23 21200 jsvc debug:
+-------------------------------------------------------
05/04/2012 13:53:23 21200 jsvc debug: Using default JVM in
/etc/alternatives/java_sdk_sun/jre/lib/i386/client/libjvm.so
05/04/2012 13:53:23 21200 jsvc debug: Invoking w/
LD_LIBRARY_PATH=/opt/adore-djatoka-1.1/lib/Linux-x86-32:/etc/alternatives/j
ava_sdk_sun/jre/lib/i386/client:/etc/alternatives/java_sdk_sun/jre/lib/i386
05/04/2012 13:53:23 21200 jsvc.exec debug: +-- DUMPING PARSED COMMAND LINE
ARGUMENTS --------------
05/04/2012 13:53:23 21200 jsvc.exec debug: | Detach: True
05/04/2012 13:53:23 21200 jsvc.exec debug: | Show Version: No
05/04/2012 13:53:23 21200 jsvc.exec debug: | Show Help: No
05/04/2012 13:53:23 21200 jsvc.exec debug: | Check Only: Disabled
05/04/2012 13:53:23 21200 jsvc.exec debug: | Stop: False
05/04/2012 13:53:23 21200 jsvc.exec debug: | Wait: 0
05/04/2012 13:53:23 21200 jsvc.exec debug: | Run as service: No
05/04/2012 13:53:23 21200 jsvc.exec debug: | Install service: No
05/04/2012 13:53:23 21200 jsvc.exec debug: | Remove service: No
05/04/2012 13:53:23 21200 jsvc.exec debug: | JVM Name: "null"
05/04/2012 13:53:23 21200 jsvc.exec debug: | Java Home:
"/etc/alternatives/java_sdk_sun"
05/04/2012 13:53:23 21200 jsvc.exec debug: | PID File:
"/home/fedora/fedora/tomcat/temp/fedora-tomcat-jsvc.pid"
05/04/2012 13:53:23 21200 jsvc.exec debug: | User Name: "fedora"
05/04/2012 13:53:23 21200 jsvc.exec debug: | Extra Options: 4
05/04/2012 13:53:23 21200 jsvc.exec debug: |
"-Dcatalina.home=/home/fedora/fedora/tomcat"
05/04/2012 13:53:23 21200 jsvc.exec debug: |
"-Dcatalina.base=/home/fedora/fedora/tomcat"
05/04/2012 13:53:23 21200 jsvc.exec debug: |
"-Djava.library.path=/opt/adore-djatoka-1.1/lib/Linux-x86-32"
05/04/2012 13:53:23 21200 jsvc.exec debug: |
"-Djava.class.path=/etc/alternatives/java_sdk_sun/lib/tools.jar:/home/fedor
a/fedora/tomcat/bin/commons-daemon.jar:/home/fedora/fedora/tomcat/bin/boots
trap.jar"
05/04/2012 13:53:23 21200 jsvc.exec debug: | Class Invoked:
"org.apache.catalina.startup.Bootstrap"
05/04/2012 13:53:23 21200 jsvc.exec debug: | Class Arguments: 0
05/04/2012 13:53:23 21200 jsvc.exec debug:
+-------------------------------------------------------
05/04/2012 13:53:23 21202 jsvc.exec debug: user changed to 'fedora'
05/04/2012 13:53:23 21200 jsvc.exec debug: User 'fedora' validated
05/04/2012 13:53:23 21200 jsvc.exec debug: Attempting to locate Java Home
in /etc/alternatives/java_sdk_sun
05/04/2012 13:53:23 21200 jsvc.exec debug: Attempting to locate VM
configuration file /etc/alternatives/java_sdk_sun/jre/lib/jvm.cfg
05/04/2012 13:53:23 21200 jsvc.exec debug: Attempting to locate VM
configuration file /etc/alternatives/java_sdk_sun/lib/jvm.cfg
05/04/2012 13:53:23 21200 jsvc.exec debug: Attempting to locate VM
configuration file /etc/alternatives/java_sdk_sun/jre/lib/i386/jvm.cfg
05/04/2012 13:53:23 21200 jsvc.exec debug: Found VM configuration file at
/etc/alternatives/java_sdk_sun/jre/lib/i386/jvm.cfg
05/04/2012 13:53:23 21200 jsvc.exec debug: Found VM client definition in
configuration
05/04/2012 13:53:23 21200 jsvc.exec debug: Checking library
/etc/alternatives/java_sdk_sun/jre/lib/i386/client/libjvm.so
05/04/2012 13:53:23 21200 jsvc.exec debug: Found VM server definition in
configuration
05/04/2012 13:53:23 21200 jsvc.exec debug: Checking library
/etc/alternatives/java_sdk_sun/jre/lib/i386/server/libjvm.so
05/04/2012 13:53:23 21200 jsvc.exec debug: Found VM hotspot definition in
configuration
05/04/2012 13:53:23 21200 jsvc.exec debug: Checking library
/etc/alternatives/java_sdk_sun/jre/lib/i386/hotspot/libjvm.so
05/04/2012 13:53:23 21200 jsvc.exec debug: Checking library
/etc/alternatives/java_sdk_sun/lib/i386/hotspot/libjvm.so
05/04/2012 13:53:23 21200 jsvc.exec debug: Cannot locate library for VM
hotspot (skipping)
05/04/2012 13:53:23 21200 jsvc.exec debug: Found VM classic definition in
configuration
05/04/2012 13:53:23 21200 jsvc.exec debug: Checking library
/etc/alternatives/java_sdk_sun/jre/lib/i386/classic/libjvm.so
05/04/2012 13:53:23 21200 jsvc.exec debug: Checking library
/etc/alternatives/java_sdk_sun/lib/i386/classic/libjvm.so
05/04/2012 13:53:23 21200 jsvc.exec debug: Cannot locate library for VM
classic (skipping)
05/04/2012 13:53:23 21200 jsvc.exec debug: Found VM native definition in
configuration
05/04/2012 13:53:23 21200 jsvc.exec debug: Checking library
/etc/alternatives/java_sdk_sun/jre/lib/i386/native/libjvm.so
05/04/2012 13:53:23 21200 jsvc.exec debug: Checking library
/etc/alternatives/java_sdk_sun/lib/i386/native/libjvm.so
05/04/2012 13:53:23 21200 jsvc.exec debug: Cannot locate library for VM
native (skipping)
05/04/2012 13:53:23 21200 jsvc.exec debug: Found VM green definition in
configuration
05/04/2012 13:53:23 21200 jsvc.exec debug: Checking library
/etc/alternatives/java_sdk_sun/jre/lib/i386/green/libjvm.so
05/04/2012 13:53:23 21200 jsvc.exec debug: Checking library
/etc/alternatives/java_sdk_sun/lib/i386/green/libjvm.so
05/04/2012 13:53:23 21200 jsvc.exec debug: Cannot locate library for VM
green (skipping)
05/04/2012 13:53:23 21200 jsvc.exec debug: Java Home located in
/etc/alternatives/java_sdk_sun
05/04/2012 13:53:23 21200 jsvc.exec debug: +-- DUMPING JAVA HOME STRUCTURE
------------------------
05/04/2012 13:53:23 21200 jsvc.exec debug: | Java Home:
"/etc/alternatives/java_sdk_sun"
05/04/2012 13:53:23 21200 jsvc.exec debug: | Java VM Config.:
"/etc/alternatives/java_sdk_sun/jre/lib/i386/jvm.cfg"
05/04/2012 13:53:23 21200 jsvc.exec debug: | Found JVMs: 2
05/04/2012 13:53:23 21200 jsvc.exec debug: | JVM Name: "client"
05/04/2012 13:53:23 21200 jsvc.exec debug: |
"/etc/alternatives/java_sdk_sun/jre/lib/i386/client/libjvm.so"
05/04/2012 13:53:23 21200 jsvc.exec debug: | JVM Name: "server"
05/04/2012 13:53:23 21200 jsvc.exec debug: |
"/etc/alternatives/java_sdk_sun/jre/lib/i386/server/libjvm.so"
05/04/2012 13:53:23 21200 jsvc.exec debug:
+-------------------------------------------------------
05/04/2012 13:53:23 21200 jsvc.exec debug: Running w/
LD_LIBRARY_PATH=/opt/adore-djatoka-1.1/lib/Linux-x86-32:/etc/alternatives/j
ava_sdk_sun/jre/lib/i386/client:/etc/alternatives/java_sdk_sun/jre/lib/i386
05/04/2012 13:53:23 21203 jsvc.exec debug: redirecting stdout to
/home/fedora/fedora/tomcat/logs/catalina.out and stderr to &1
Starting jsvc.exec [ OK ]
Fedora's Tomcat running with PID 21204

At this point all I can do is scratch my head, and proceed with deploying
an instance of Fedora that does not make use of the JSVC wrapper.

If anyone has wrestled with these issues, and won, I'd love to hear about
it. Thanks!

--
HARDY POTTINGER <potti...@umsystem.edu>

University of Missouri Library Systems

http://lso.umsystem.edu/~pottingerhj/

https://MOspace.umsystem.edu/
"I am always doing that which I cannot do, in order that I may learn how
to do it." --Pablo Picasso

On 4/3/12 9:17 PM, "Jonathan Green" <jona...@discoverygarden.ca> wrote:

>Sorry. It takes me awhile for me to process my email queue, and I missed
>your second message. The reason Djatoka wants the LD_LIBRARY_PATH to be
>set it its calling some JNI libraries which reference djatokas native
>shared object libraries. Some possible work arounds:
>

>1. Set java.library.path system property (this may or may not work

>depending how the JNI dependencies)

>2. Put symlinks to the shared object files from djatoka into a folder

>that is on the default library path, usually the /usr/lib or /lib folders
>
>
>On Tue, Apr 3, 2012 at 11:00 PM, Pottinger, Hardy J.
><Potti...@umsystem.edu> wrote:
>
>Hi, I have sourced the env.sh script in my start script, however, as
>previously indicated, I am using the jsvc tomcat wrapper to handle
>running tomcat as the fedora user. It looks like jsvc drops
>LD_LIBRARY_PATH as a security measure (see previous message in this
>thread for details). I am going to rework my start script to not use jsvc
>and see where that gets me. I think I would prefer to figure out why
>Djatoka is using LD_LIBRARY_PATH, but first I want to be sure everything
>is working with just the normal tomcat start script.
>
>--Hardy
>
>Sent from my iPad
>
>On Apr 3, 2012, at 6:07 PM, "Jonathan Green"
><jona...@discoverygarden.ca<mailto:jona...@discoverygarden.ca>> wrote:
>
>Did you add the env.sh to your tomcat start up script? If so, you might
>want to do an echo at the end of the tomcat start up script and make sure
>LD_LIBRARY_PATH is setup there.
>
>
>On Tue, Apr 3, 2012 at 5:45 PM, Pottinger, Hardy J.

><<mailto:Potti...@umsystem.edu>Potti...@umsystem.edu<mailto:Pottinge

>r...@umsystem.edu>> wrote:
>
>Yep, this is definitely a problem with the env.sh script in
>$KAKADU_HOME/bin. I've modified it as per the instructions on the wiki,
>and it does look like LD_LIBRARY_PATH is getting set, however, from
>djatoka.log, it's clearly not getting that environment variable:
>
>

>2012-04-03/15 <tel:2012-04-03%2F15><tel:2012-04-03%2F15>:11:42.688/CDT

>[http-8081-1] DEBUG envParams:
>LD_LIBRARY_PATH=null | null/kdu_expand
>
>Looking for ideas for things to try next.
>
>--
>
>HARDY POTTINGER

><<mailto:potti...@umsystem.edu>potti...@umsystem.edu<mailto:pottinge
>r...@umsystem.edu>>

>University of Missouri Library Systems
>
><http://lso.umsystem.edu/%7Epottingerhj/>http://lso.umsystem.edu/~pottinge

>rhj/ <http://lso.umsystem.edu/%7Epottingerhj/>
>
><https://MOspace.umsystem.edu/>https://MOspace.umsystem.edu/

>"I am always doing that which I cannot do, in order that I may learn how
>to do it." --Pablo Picasso
>
>
>
>
>
>
>On 4/3/12 2:07 PM, "Pottinger, Hardy J."

><<mailto:Potti...@umsystem.edu>Potti...@umsystem.edu<mailto:Pottinge

>r...@umsystem.edu>> wrote:
>
>>Hi, Nick. Yes. I had to hack the env.sh script in $KAKADU_HOME/bin
>>changing:
>>
>>DJATOKA_HOME=`pwd`
>>
>>To:
>>
>>DJATOKA_HOME=/opt/adore-djatoka-1.1
>>
>>When I start fedora, here are the JAVA_OPTS that are getting passed:
>>
>>-Djava.awt.headless=true
>>-Dkakadu.home=/opt/adore-djatoka-1.1/bin/Linux-x86-32
>>-Djava.library.path=/opt/adore-djatoka-1.1/lib/Linux-x86-32
>>-DLD_LIBRARY_PATH=/opt/adore-djatoka-1.1/lib/Linux-x86-32 -Xmx512m
>>-Djava.awt.headless=true
>>-Dkakadu.home=/opt/adore-djatoka-1.1/bin/Linux-x86-32
>>-Djava.library.path=/opt/adore-djatoka-1.1/lib/Linux-x86-32
>>-DLD_LIBRARY_PATH=/opt/adore-djatoka-1.1/lib/Linux-x86-32 -Xmx1024M
>>-Xms768M -XX:MaxPermSize=128M -XX:PermSize=32M -XX:+UseParallelGC
>>-Dfile.encoding=UTF-8 -Dcom.sun.management.jmxremote
>>
>>
>>Now when I try my test, this is what I see in djatoka.log:
>>
>

>>2012-04-03/13 <tel:2012-04-03%2F13><tel:2012-04-03%2F13>:08:19.934/CDT

>>[http-8081-1] INFO processingRemoteURI:
>><http://memory.loc.gov/gmd/gmd3/g3200/g3200/ct000425.jp2>http://memory.lo
>>c.gov/gmd/gmd3/g3200/g3200/ct000425.jp2
>

>>2012-04-03/13 <tel:2012-04-03%2F13><tel:2012-04-03%2F13>:08:32.952/CDT
>>[http-8081-1] DEBUG remoteCacheSize: 1
>>2012-04-03/13 <tel:2012-04-03%2F13><tel:2012-04-03%2F13>:08:33.039/CDT

>>[http-8081-1] DEBUG null/kdu_expand -quiet -i
>>/tmp/cache1354165286829378066425685907.jp2 -o /dev/stdout -reduce 3
>>-region {0.0,0.0},{0.6476683937823834,0.335401643468053}
>

>>2012-04-03/13 <tel:2012-04-03%2F13><tel:2012-04-03%2F13>:08:33.042/CDT

>>[http-8081-1] ERROR java.io.IOException:
>>Cannot run program "null/kdu_expand" (in directory "null"):
>>java.io.IOException: error=2, No such file or directory
>>java.io.IOException: Cannot run program "null/kdu_expand" (in directory
>>"null"): java.io.IOException: error=2, No such file or directory
>> at java.lang.ProcessBuilder.start(ProcessBuilder.java:460)
>> at java.lang.Runtime.exec(Runtime.java:593)
>> at java.lang.Runtime.exec(Runtime.java:431)
>> at
>>gov.lanl.adore.djatoka.kdu.KduExtractExe.process(KduExtractExe.java:229)
>> at

>>gov.lanl.adore.djatoka.DjatokaExtractProcessor.extractImage(DjatokaExtrac
>>t
>>P
>>rocessor.java:157)
>> at
>>gov.lanl.adore.djatoka.DjatokaExtractProcessor.extractImage(DjatokaExtrac
>>t
>>P
>>rocessor.java:85)
>> at
>>gov.lanl.adore.djatoka.openurl.OpenURLJP2KService.resolve(OpenURLJP2KServ
>>i
>>c
>>e.java:255)
>> at
>>org.oclc.oomRef.OpenURLRequestProcessorImpl.resolve(OpenURLRequestProcess
>>o

>>r
>>Impl.java:82)
>> at
>>gov.lanl.adore.djatoka.openurl.OpenURLServlet.doGet(OpenURLServlet.java:1
>>2
>>1
>>)
>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:617)
>> at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
>> at

>>org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applicat
>>i
>>o
>>nFilterChain.java:290)
>> at
>>org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilte
>>r
>>C
>>hain.java:206)
>> at
>>org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve
>>.
>>j
>>ava:233)
>> at
>>org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve
>>.

>>j
>>ava:191)
>> at
>>org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:
>>1
>>2
>>7)
>> at
>>com.googlecode.psiprobe.Tomcat60AgentValve.invoke(Tomcat60AgentValve.java
>>:
>>3
>>0)
>> at
>>org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:
>>1
>>0
>>2)
>> at
>>org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.j
>>a
>>v
>>a:109)
>> at

>>org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:29
>>8
>>)
>> at
>>org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:857
>>)
>> at
>>org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(H
>>t

>>t
>>p11Protocol.java:588)
>> at
>>org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489)
>> at java.lang.Thread.run(Thread.java:662)
>>Caused by: java.io.IOException: java.io.IOException: error=2, No such
>>file
>>or directory
>> at java.lang.UNIXProcess.<init>(UNIXProcess.java:148)
>> at java.lang.ProcessImpl.start(ProcessImpl.java:65)
>> at java.lang.ProcessBuilder.start(ProcessBuilder.java:453)
>> ... 23 more
>>
>>
>>It still looks like a path problem.
>>
>>
>>--
>>
>
>
>>HARDY POTTINGER

>><<mailto:potti...@umsystem.edu>potti...@umsystem.edu<mailto:potting
>>er...@umsystem.edu>>

>>University of Missouri Library Systems
>
>><http://lso.umsystem.edu/%7Epottingerhj/>http://lso.umsystem.edu/~potting

>>erhj/ <http://lso.umsystem.edu/%7Epottingerhj/>
>
>><https://MOspace.umsystem.edu/>https://MOspace.umsystem.edu/

>>"I think I like disruptive technology because
>>it makes the whole world a bit fuzzy, my
>>normal state of mind."
>>-- Robert Llewellyn (aka Kryten)
>>
>>
>>
>>
>>
>
>>On 4/3/12 1:37 PM, "Nick Ruest"
>><<mailto:rue...@gmail.com>rue...@gmail.com<mailto:rue...@gmail.com>>
>>wrote:
>
>>
>>>Do you have these path variables setup?
>>>LD_LIBRARY_PATH or DLD_LIBRARY_PATH
>>>KAKADU_LIBRARY_PATH
>>>KAKADU_HOME
>>>
>>>This is what they look like on my machine:
>>>DLD_LIBRARY_PATH=/usr/local/djatoka/lib/Linux-x86-64
>>>KAKADU_LIBRARY_PATH=/usr/local/djatoka/lib/Linux-x86-64
>>>KAKADU_HOME=/usr/local/djatoka/lib/Linux-x86-64
>>>
>>>-nruest
>>>
>>>On 12-04-03 02:29 PM, Pottinger, Hardy J. wrote:
>>>> Aha, progress, I now have an error message and a clue to follow up on.
>>>>I
>>>> turned on DEBUG logging in
>>>> $CATALINA_HOME/webapps/adore-djatoka/WEB-INF/classes/log4j.properties,
>>>>and
>>>> now I can see the following in djatoka.log:
>>>>
>
>>>> 2012-04-03/12

>>>><tel:2012-04-03%2F12><tel:2012-04-03%2F12>:45:46.838/CDT [http-8081-1]

>>>>INFO processingRemoteURI:
>>>> <http://memory.loc.gov/gmd/gmd3/g3200/g3200/ct000425.jp2>
>>>>http://memory.loc.gov/gmd/gmd3/g3200/g3200/ct000425.jp2
>
>>>> 2012-04-03/12

>>>><tel:2012-04-03%2F12><tel:2012-04-03%2F12>:45:56.124/CDT [http-8081-1]
>>>>DEBUG remoteCacheSize: 1
>>>> 2012-04-03/12
>>>><tel:2012-04-03%2F12><tel:2012-04-03%2F12>:45:56.126/CDT [http-8081-1]

>>>>DEBUG
>>>> java.lang.UnsatisfiedLinkError: no kdu_jni in java.library.path
>
>>>> 2012-04-03/12

>>>><tel:2012-04-03%2F12><tel:2012-04-03%2F12>:46:01.220/CDT [http-8081-1]

>>>>DEBUG
>>>> java.lang.NoClassDefFoundError: Could not initialize class
>>>> kdu_jni.Jpx_source
>>>>
>>>> So, clearly the Kakadu dependencies are not getting found.
>>>>
>>>> I'm on the trail now, will post the solution when I find it.
>>>>
>>>>
>>>> --
>
>>>> HARDY
>>>>POTTINGER<<mailto:potti...@umsystem.edu>potti...@umsystem.edu<mai

>>>>lto:potti...@umsystem.edu>>
>>>> University of Missouri Library Systems
>
>>>> <http://lso.umsystem.edu/%7Epottingerhj/>
>>>>http://lso.umsystem.edu/~pottingerhj/
>>>><http://lso.umsystem.edu/%7Epottingerhj/>
>

>>>> <https://MOspace.umsystem.edu/> https://MOspace.umsystem.edu/
>>>> "Debug only code. Comments lie."
>>>>
>>>>
>>>>
>>>>
>>>>
>
>>>> On 4/3/12 12:01 PM, "Pottinger, Hardy
>>>>J."<<mailto:Potti...@umsystem.edu>Potti...@umsystem.edu<mailto:Po

>>>>ttin...@umsystem.edu>>

>
>>>>wrote:
>>>>
>>>>> $ cat djatoka.log
>>>>> 2012-04-03/10

>>>>><tel:2012-04-03%2F10><tel:2012-04-03%2F10>:14:00.964/CDT

>>>>>[http-8081-3] INFO processingRemoteURI:
>>>>> <http://memory.loc.gov/gmd/gmd433/g4330/g4330/np000066.jp2>
>>>>>http://memory.loc.gov/gmd/gmd433/g4330/g4330/np000066.jp2
>
>>>>> 2012-04-03/10

>>>>><tel:2012-04-03%2F10><tel:2012-04-03%2F10>:15:08.514/CDT

>>>>>[http-8081-3] INFO processingRemoteURI:
>>>>> <http://memory.loc.gov/gmd/gmd3/g3200/g3200/ct000425.jp2>
>>>>>http://memory.loc.gov/gmd/gmd3/g3200/g3200/ct000425.jp2
>>>>>
>>>>> So, it's trying... Just wish I knew more about this mysterious 500
>>>>>error.
>>>>>
>>>>> Scanning below, realized I mistyped JVC when I meant JSVC.
>>>>>
>>>>>
>>>>> --
>
>>>>> HARDY
>>>>>POTTINGER<<mailto:potti...@umsystem.edu>potti...@umsystem.edu<ma

>>>>>ilto:potti...@umsystem.edu>>
>>>>> University of Missouri Library Systems
>
>>>>> <http://lso.umsystem.edu/%7Epottingerhj/>
>>>>>http://lso.umsystem.edu/~pottingerhj/
>>>>><http://lso.umsystem.edu/%7Epottingerhj/>
>

>>>>> <https://MOspace.umsystem.edu/> https://MOspace.umsystem.edu/
>>>>> "Debug only code. Comments lie."
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>
>>>>> On 4/3/12 11:49 AM, "Jonathan
>>>>>Green"<<mailto:jona...@discoverygarden.ca>jona...@discoverygarden.ca
>>>>><mailto:jona...@discoverygarden.ca>>
>>>>>wrote:
>>>>>
>>>>>> Is there anything interesting showing up in the djatoka log files?
>
>>>>>>
>>>>>><http://sourceforge.net/apps/mediawiki/djatoka/index.php?title=Loggin
>>>>>>g>
>>>>>>http://sourceforge.net/apps/mediawiki/djatoka/index.php?title=Logging
>>>>>>
>>>>>> By default I believe it will log to the current directory when you
>>>>>> started tomcat if you haven't set up a path for logging in the
>>>>>>djatoka
>>>>>> log4j configuration file.
>>>>>>
>>>>>> On Tue, Apr 3, 2012 at 12:31 PM, Pottinger, Hardy J.
>
>>>>>>
>>>>>><<mailto:Potti...@umsystem.edu>Potti...@umsystem.edu<mailto:Pot

>>>>>><<http://lso.umsystem.edu/%7Epottingerhj/>http://lso.umsystem.edu/%7E

>>>>>>pottingerhj/>
>
>>>>>> <https://MOspace.umsystem.edu/> https://MOspace.umsystem.edu/
>>>>>> "No matter how far down the wrong road you've gone,
>>>>>> turn back." --Turkish proverb
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>
>>>>>> On 4/2/12 5:35 PM, "Nelson
>>>>>>Hart"<<mailto:nh...@upei.ca>nh...@upei.ca<mailto:nh...@upei.ca>>
>>>>>>wrote:
>
>>>>>>
>>>>>>> Hi Hardy,
>>>>>>> I'm ran into this same problem last week. Check your version of
>>>>>>>Java
>>>>>>> installed. I believe Djatoka requires Sun JKD/JRE and not the Open
>>>>>>> JDK/JRE. I've been meaning to ask someone around the office but
>>>>>>>haven't
>>>>>>> gotten to it yet. I still haven't got my setup working.
>>>>>>>
>>>>>>> Cheers,
>>>>>>> Nelson
>>>>>>>
>>>>>>> On Mon, Apr 2, 2012 at 7:22 PM, Hardy Pottinger
>
>>>>>>>
>>>>>>><<mailto:potti...@umsystem.edu>potti...@umsystem.edu<mailto:po

>>>>>>><mailto:islandora%252Buns...@googlegroups.com>>
>>>>>>>islandora+...@googlegroups.com
>>>>>>><mailto:islandora%2Bunsu...@googlegroups.com><mailto:islandora+u
>>>>>>>nsubs...@googlegroups.com
>>>>>>><mailto:islandora%2Bunsu...@googlegroups.com>>

>
>>>>>>> <mailto:islandora%2Bunsu...@googlegroups.com
>>>>>>><mailto:islandora%252Buns...@googlegroups.com><mailto:islandora

>>>>>>>%252Buns...@googlegroups.com
>>>>>>><mailto:islandora%25252Bun...@googlegroups.com>>>

>
>>>>>>
>>>>>>> <mailto:islandora%2Bunsu...@googlegroups.com
>>>>>>><mailto:islandora%252Buns...@googlegroups.com><mailto:islandora

>>>>>>>%252Buns...@googlegroups.com
>>>>>>><mailto:islandora%25252Bun...@googlegroups.com>>
>
>>>>>>> <mailto:islandora%252Buns...@googlegroups.com
>>>>>>><mailto:islandora%25252Bun...@googlegroups.com><mailto:islando
>>>>>>>ra%25252Bun...@googlegroups.com
>>>>>>><mailto:islandora%2525252Bu...@googlegroups.com>>>>.

>>>>>>>
>>>>>>> For more options, visit this group at
>
>>>>>>> <http://groups.google.com/group/islandora?hl=en>
>>>>>>>http://groups.google.com/group/islandora?hl=en.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Nelson Hart
>>>>>>> iPad Developer - Islandora / TourPad Project
>>>>>>> Robertson Library
>>>>>>> University of Prince Edward Island
>
>>>>>>> <mailto:nh...@upei.ca> nh...@upei.ca<mailto:nh...@upei.ca>
>>>>>>>
>>>>>>> --
>>>>>>> You received this message because you are subscribed to the Google
>>>>>>> Groups
>>>>>>> "islandora" group.
>
>>>>>>> To post to this group, send email to
>>>>>>><mailto:isla...@googlegroups.com>
>>>>>>>isla...@googlegroups.com<mailto:isla...@googlegroups.com>.
>>>>>>> To unsubscribe from this group, send email to
>
>>>>>>> <mailto:islandora%2Bunsu...@googlegroups.com

>>>>>>><mailto:islandora%252Buns...@googlegroups.com>>
>>>>>>>islandora+...@googlegroups.com
>>>>>>><mailto:islandora%2Bunsu...@googlegroups.com><mailto:islandora+u
>>>>>>>nsubs...@googlegroups.com
>>>>>>><mailto:islandora%2Bunsu...@googlegroups.com>>

>>>>>>> <mailto:islandora%2Bunsu...@googlegroups.com
>>>>>>><mailto:islandora%252Buns...@googlegroups.com><mailto:islandora

>>>>>>>%252Buns...@googlegroups.com

>>>>>>><mailto:islandora%25252Bun...@googlegroups.com>>>.
>
>>>>>>>
>>>>>>> For more options, visit this group at
>
>>>>>>> <http://groups.google.com/group/islandora?hl=en>
>>>>>>>http://groups.google.com/group/islandora?hl=en.
>>>>>> --

>>>>>> You received this message because you are subscribed to the Google
>>>>>>Groups
>>>>>> "islandora" group.
>
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[Ryan Gjerde]

Hello Hardy, et al.

I hate to poke such a long-dormant thread, but in recently setting up a test Islandora instance, I've found myself stuck at the same point - namely, Djatoka is reporting that LD_LIBRARY_PATH=null (djatoka.log pasted in below).  I've found a number of other threads that have gotten me this far... creating symbolic links to the Djatoka library files was helpful, but corresponding symlinks to to kdu_compress and kdu_expand in /usr/local/bin do not seem to allow Djatoka to execute them.  I'm curious if anyone has discovered a solution.

Here are some of the relevant system info:

Ubuntu 13.10

Java 1.7.0_51

Fedora 3.7 (using bundled Tomcat)

Djatoka 1.1

djatoka.log output:

2014-04-01/15:17:06.822/CDT [main] DEBUG envParams: LD_LIBRARY_PATH=null | null/kdu_compress

2014-04-01/15:20:28.597/CDT [http-8080-1] DEBUG envParams: LD_LIBRARY_PATH=null | null/kdu_expand

2014-04-01/15:20:28.606/CDT [http-8080-1] INFO  processingRemoteURI: http://memory.loc.gov/gmd/gmd433/g4330/g4330/np000066.jp2

2014-04-01/15:20:38.156/CDT [http-8080-1] DEBUG remoteCacheSize: 1

2014-04-01/15:20:38.166/CDT [http-8080-1] DEBUG null/kdu_expand -quiet -i /usr/local/fedora/tomcat/temp/cache9865356473297583089356120902.jp2 -o /dev/stdout -reduce 3 -region {0.0,0.0},{1.122334455667789,0.9086778736937755} 

2014-04-01/15:20:38.169/CDT [http-8080-1] ERROR java.io.IOException: Cannot run program "null/kdu_expand" (in directory "null"): error=2, No such file or directory

java.io.IOException: Cannot run program "null/kdu_expand" (in directory "null"): error=2, No such file or directory

at java.lang.ProcessBuilder.start(ProcessBuilder.java:1041)

at java.lang.Runtime.exec(Runtime.java:617)

at java.lang.Runtime.exec(Runtime.java:450)

at gov.lanl.adore.djatoka.kdu.KduExtractExe.process(KduExtractExe.java:229)

at gov.lanl.adore.djatoka.DjatokaExtractProcessor.extractImage(DjatokaExtractProcessor.java:205)

at gov.lanl.adore.djatoka.DjatokaExtractProcessor.extractImage(DjatokaExtractProcessor.java:129)

at gov.lanl.adore.djatoka.openurl.OpenURLJP2KService.resolve(OpenURLJP2KService.java:234)

at org.oclc.oomRef.OpenURLRequestProcessorImpl.resolve(OpenURLRequestProcessorImpl.java:82)

at gov.lanl.adore.djatoka.openurl.OpenURLServlet.doGet(OpenURLServlet.java:121)

at javax.servlet.http.HttpServlet.service(HttpServlet.java:617)

at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)

at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)

at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)

at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)

at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)

at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)

at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)

at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:293)

at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:859)

at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:602)

at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489)

at java.lang.Thread.run(Thread.java:744)

Caused by: java.io.IOException: error=2, No such file or directory

at java.lang.UNIXProcess.forkAndExec(Native Method)

at java.lang.UNIXProcess.<init>(UNIXProcess.java:135)

at java.lang.ProcessImpl.start(ProcessImpl.java:130)

at java.lang.ProcessBuilder.start(ProcessBuilder.java:1022)

... 22 more

[Nick Ruest]

Hi Ryan-

I have created this file '/etc/ld.so.conf.d/djatoka.conf' and it
contains one line, '/usr/local/djatoka/lib/Linux-x86-64/'.

My symlinks for kdu_compress is:

/usr/bin/kdu_compress -> /extra/djatoka/bin/Linux-x86-64/kdu_compress

Let me know that helps out.

cheers!

-nruest

On 14-04-01 05:31 PM, Ryan Gjerde wrote:
> Hello Hardy, et al.
>
> I hate to poke such a long-dormant thread, but in recently setting up a
> test Islandora instance, I've found myself stuck at the same point -
> namely, Djatoka is reporting that LD_LIBRARY_PATH=null (djatoka.log
> pasted in below). I've found a number of other threads that have gotten
> me this far... creating symbolic links to the Djatoka library files was
> helpful, but corresponding symlinks to to kdu_compress and kdu_expand in
> /usr/local/bin do not seem to allow Djatoka to execute them. I'm
> curious if anyone has discovered a solution.
>
> Here are some of the relevant system info:
> Ubuntu 13.10
> Java 1.7.0_51
> Fedora 3.7 (using bundled Tomcat)
> Djatoka 1.1
>

> *djatoka.log output:*

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[Ryan Gjerde]

Thanks, Nick,

  I had found one of your previous comments which had suggested creating the conf file, and implementing that resolved the issue of "kdu_jni" not being found. I had similar symlinks to yours set up too, however my guess is there is something in my version of djatoka that will only look at $KAKADU_HOME to create the path to those commands.

  What finally worked for me this morning is I declared $DJATOKA_HOME, $KAKADU_HOME, $LD_LIBRARY_PATH in my bash profile, and also added the JAVA_OPTS string from Djatoka's env.sh to the existing JAVA_OPTS in my profile.  I don't know if this will have unexpected consequences down the road, but it allowed the Djatoka demo to work...

  After doing all of that, here's what my djatoka.log looked like

Ryan

djatoka.log:

2014-04-02/08:34:13.192/CDT [main] DEBUG envParams: LD_LIBRARY_PATH=/opt/adore-djatoka-1.1/lib/Linux-x86-64 | /usr/opt/adore-djatoka-1.1/bin/Linux-x86-64/kdu_compress

2014-04-02/08:37:21.377/CDT [http-8080-1] DEBUG envParams: LD_LIBRARY_PATH=/opt/adore-djatoka-1.1/lib/Linux-x86-64 | /opt/adore-djatoka-1.1/bin/Linux-x86-64/kdu_expand

2014-04-02/08:37:21.388/CDT [http-8080-1] INFO  processingRemoteURI: http://memory.loc.gov/gmd/gmd433/g4330/g4330/np000066.jp2

2014-04-02/08:37:31.490/CDT [http-8080-1] DEBUG remoteCacheSize: 1

2014-04-02/08:37:31.500/CDT [http-8080-1] DEBUG /opt/adore-djatoka-1.1/bin/Linux-x86-64/kdu_expand -quiet -i /usr/local/fedora/tomcat/temp/cache9865356473616744008367810959.jp2 -o /dev/stdout -reduce 3 -region {0.0,0.0},{1.122334455667789,0.9086778736937755} 

[Peter Murray]

Djatoka can be a source of pain in an Islandora installation.  Has anyone looked at one of the other servers that serves up IIIF like IIPImage Server? (http://iiif.io/apps-demos.html).

Peter

--
Peter Murray
Assistant Director, Technology Services Development
LYRASIS
Peter....@lyrasis.org
+1 678-235-2955
800.999.8558 x2955

[Nick Ruest]

+1

Would it be worth creating a Jira ticket? It would at least guarantee a
committers call discussion.

-nruest

On 14-04-02 07:32 PM, Peter Murray wrote:
> Djatoka can be a source of pain in an Islandora installation. Has
> anyone looked at one of the other servers that serves up IIIF like
> IIPImage Server? (http://iiif.io/apps-demos.html).
>
>
> Peter
>
> On Apr 2, 2014, at 10:09 AM, Ryan Gjerde <gjer...@luther.edu

> <mailto:gjer...@luther.edu>> wrote:
>> Thanks, Nick,
>> I had found one of your previous comments which had suggested
>> creating the conf file, and implementing that resolved the issue of
>> "kdu_jni" not being found. I had similar symlinks to yours set up too,
>> however my guess is there is something in my version of djatoka that
>> will only look at $KAKADU_HOME to create the path to those commands.
>>
>> What finally worked for me this morning is I declared $DJATOKA_HOME,
>> $KAKADU_HOME, $LD_LIBRARY_PATH in my bash profile, and also added the
>> JAVA_OPTS string from Djatoka's env.sh to the existing JAVA_OPTS in my
>> profile. I don't know if this will have unexpected consequences down
>> the road, but it allowed the Djatoka demo to work...
>>
>> After doing all of that, here's what my djatoka.log looked like
>>
>> Ryan

>> *
>> *
>> *djatoka.log:*

> Peter....@lyrasis.org <mailto:Peter....@lyrasis.org>
> +1 678-235-2955
> 800.999.8558 x2955
>
>

[Peter Murray]

Maybe, except that it might be a short discussion if no one else has investigated the possibility. :-)


Peter

On Apr 3, 2014, at 8:01 AM, Nick Ruest <rue...@gmail.com> wrote:
>
> +1
>
> Would it be worth creating a Jira ticket? It would at least guarantee a committers call discussion.
>
> -nruest
>
> On 14-04-02 07:32 PM, Peter Murray wrote:
>> Djatoka can be a source of pain in an Islandora installation. Has
>> anyone looked at one of the other servers that serves up IIIF like
>> IIPImage Server? (http://iiif.io/apps-demos.html).
>>
>>
>> Peter

--
Peter Murray
Assistant Director, Technology Services Development
LYRASIS
Peter....@lyrasis.org

+1 678-235-2955
800.999.8558 x2955

[Pottinger, Hardy J.]

It is *always* worth creating a Jira ticket. Especially to clarify a pain point in the installation process.

--Hardy

Sent from my iPad

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[Nick Ruest]

Done!

https://jira.duraspace.org/browse/ISLANDORA-961

[Bridger Dyson-Smith]

Hi all, 

I too would like to apologize for adding to this thread, but we are experiencing a similar issue with our Djatoka install. We have explicitly stated $DJATOKA_HOME, $KAKADU_HOME, $LD_LIBRARY_PATH, and $JAVA_OPTS [1] in /etc/profile.d/fedora.sh but we continue to get the following error message:

2014-08-22/14:13:19.534/EDT [http-8080-3] DEBUG null/kdu_expand -quiet -i /vhosts/fedora/tomcat/temp/cache986535647595606520958519023.jp2 -o /dev/stdout -reduce 3 -region {0.0,0.0},{1.122334455667789,0.9086778736937755}

2014-08-22/14:13:19.537/EDT [http-8080-3] ERROR java.io.IOException: Cannot run program "null/kdu_expand" (in directory "null"): error=2, No such file or directory

java.io.IOException: Cannot run program "null/kdu_expand" (in directory "null"): error=2, No such file or directory

Thank you for any suggestions or guidance you can provide.

Best,
Bridger

[1] As well as /etc/ld.so.conf.d/kakadu.conf.

    

[1] We've installed via the Islandora Large Image Solution Pack and via the instructions on the wiki

[p37]

Hi,

   As my colleague, Bridger, said we have been having djatoka issues for a while and I meant to post our solution earlier but have been busy trying to get our install online. 

  Over the last year or so I have installed islandora on various servers for testing and about half the time djatoka would work.  Last month I thought I had finally found a solution when I found the "adore.sh" in the large solution pack.  It worked great.  Then In a meeting I demostrated it and of course it didn't work....  we were getting the error Bridger describes above.

  I finally traced what was happening with enviroment variables by using different users and the env command.  I found that on some of our servers we are setting the JAVA_OPTS in /etc/profile.d or elsewhere to handle other conditions or applications.  The djatoka install expects to set those itself and depending on which user and which enviroment you run the tomcat startup.sh with, the JAVA_OPTS either change completely or do not change.

  Inside the djatoka env.sh, it sets the DJATOKA_HOME and the KAKADU_HOME and other lib paths that it needs to run.  At one point we had it reading in the JAVA_OPTS and then adding on what it wanted also, but that didn't work as everytime you restarted tomcat the JAVA_OPTS string would have another copy of everything added to it.

 What we finally did is take the JAVA_OPTS that djatoka wanted to add in and put those in ONE place in profile.d, then remove any JAVA_OPTS setting in the djatoka env.sh.

 There were other little things to deal with, like the directory name.  having a symlink from adore-djatoka-1.1 to adore-djatoka seems to help a lot.

  And also ignoring trying to set up the kakadu binaries (that are newer than the ones that come with djatoka), elsewhere and confusing the KAKADU_HOME setting.
 

 I hope some of that may help someone.  We hope to join the effort to make the iipsrv a choice for image server as we have been using it with other programs for a while.

Thanks to this list and the people at Islandora, you all are very helpful!

( OR2013, icamp and the Gahan house were great!)

Paul C

Knoxville, TN

[Eddie Rubeiz]

Hi all,

If you follow the instructions at https://wiki.duraspace.org/display/ISLANDORA/Djatoka verbatim, you might end up with a $CATALINA_HOME/bin/startup.sh script that invokes exec "$PRGDIR"/"$EXECUTABLE" start "$@" twice. This is not good, and for me it caused the problem Hardy describes (the error message no kdu_jni in java.library.path, and large images getting displayed as a large black rectangle).

What the instructions say:

At the very end of the file, insert the following:

. /opt/adore-djatoka-1.1/bin/env.sh

export JAVA_OPTS

echo $JAVA_OPTS

exec "$PRGDIR"/"$EXECUTABLE" start "$@"

What I think the instructions should say:

Right before the last line of the file, "exec "$PRGDIR"/"$EXECUTABLE" start "$@", insert the following three lines:

. /opt/adore-djatoka-1.1/bin/env.sh

export JAVA_OPTS

echo $JAVA_OPTS

If, after you follow the instructions in the wiki, your startup.sh contains two lines that read "exec "$PRGDIR"/"$EXECUTABLE" start "$@", please try commenting out the first of these and restarting Tomcat. Fixed the problem for me.

P.S. I don't have time to retrace my steps right now, but if what I allege is correct -- someone please update the documentation.

Best,

Eddie Rubeiz

Digital Repository Applications Developer

Drexel University Libraries

[click...@gmail.com]

Hi all,

our problem was in $CATALINA_HOME/bin/setenv.sh. Use JAVA_OPTS="$JAVA_OPTS ..." if you use any.

Kind regards,

Alen