Problem installing dvn on Debian

[ofu...@gmail.com]

Hi,
I could start glassfish, but when I start installation dvn, I get the following errors:

Stopping glassfish...
CLI306 Warning - The server located at /usr/local/glassfish3/glassfish/domains/domain1 is not running.
Command stop-domain executed successfully.

Starting glassfish.
Waiting for domain1 to start ........Error starting domain domain1.
The server exited prematurely with exit code 0.
Before it died, it produced the following output:

Listening for transport dt_socket at address: 9009
Launching GlassFish on Felix platform
Feb 03, 2014 2:14:48 PM BundleProvisioner update
INFO: Updated bundle 102 from /usr/local/glassfish3/glassfish/modules/web-core.jar
Can't load log handler "com.sun.enterprise.server.logging.GFFileHandler"
java.lang.ClassNotFoundException: com.sun.enterprise.server.logging.GFFileHandler
java.lang.ClassNotFoundException: com.sun.enterprise.server.logging.GFFileHandler
        at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
        at java.util.logging.LogManager$4.run(LogManager.java:784)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.util.logging.LogManager.loadLoggerHandlers(LogManager.java:778)
        at java.util.logging.LogManager.initializeGlobalHandlers(LogManager.java:1350)
        at java.util.logging.LogManager.access$1500(LogManager.java:148)
        at java.util.logging.LogManager$RootLogger.getHandlers(LogManager.java:1433)
        at com.sun.enterprise.server.logging.LogManagerService.postConstruct(LogManagerService.java:325)
        at com.sun.hk2.component.AbstractCreatorImpl.inject(AbstractCreatorImpl.java:131)
        at com.sun.hk2.component.ConstructorCreator.initialize(ConstructorCreator.java:91)
        at com.sun.hk2.component.AbstractCreatorImpl.get(AbstractCreatorImpl.java:82)
        at com.sun.hk2.component.SingletonInhabitant.get(SingletonInhabitant.java:67)
        at com.sun.hk2.component.EventPublishingInhabitant.get(EventPublishingInhabitant.java:139)
        at com.sun.hk2.component.AbstractInhabitantImpl.get(AbstractInhabitantImpl.java:78)
        at com.sun.enterprise.v3.server.AppServerStartup.run(AppServerStartup.java:229)
        at com.sun.enterprise.v3.server.AppServerStartup.doStart(AppServerStartup.java:145)
        at com.sun.enterprise.v3.server.AppServerStartup.start(AppServerStartup.java:136)
        at com.sun.enterprise.glassfish.bootstrap.GlassFishImpl.start(GlassFishImpl.java:79)
        at com.sun.enterprise.glassfish.bootstrap.GlassFishDecorator.start(GlassFishDecorator.java:63)
        at com.sun.enterprise.glassfish.bootstrap.osgi.OSGiGlassFishImpl.start(OSGiGlassFishImpl.java:69)
        at com.sun.enterprise.glassfish.bootstrap.GlassFishMain$Launcher.launch(GlassFishMain.java:117)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at com.sun.enterprise.glassfish.bootstrap.GlassFishMain.main(GlassFishMain.java:97)
        at com.sun.enterprise.glassfish.bootstrap.ASMain.main(ASMain.java:55)
[#|2014-02-03T14:14:50.830+0100|INFO|glassfish3.1.2|com.sun.enterprise.server.logging.GFFileHandler|_ThreadID=1;_ThreadName=main;|Running GlassFish Version: GlassFish Server Open Source Edition 3.1.2 (build 23)|#]

[#|2014-02-03T14:14:51.819+0100|INFO|glassfish3.1.2|javax.enterprise.system.core.com.sun.enterprise.v3.services.impl|_ThreadID=35;_ThreadName=Grizzly-kernel-thread(4);|Grizzly Framework 1.9.46 started in: 107ms - bound to [0.0.0.0:443]|#]

[#|2014-02-03T14:14:51.822+0100|INFO|glassfish3.1.2|javax.enterprise.system.core.com.sun.enterprise.v3.services.impl|_ThreadID=48;_ThreadName=Grizzly-kernel-thread(4);|Grizzly Framework 1.9.46 started in: 5ms - bound to [0.0.0.0:4848]|#]

[#|2014-02-03T14:14:51.837+0100|INFO|glassfish3.1.2|javax.enterprise.system.core.com.sun.enterprise.v3.services.impl|_ThreadID=51;_ThreadName=Grizzly-kernel-thread(1);|Grizzly Framework 1.9.46 started in: 6ms - bound to [0.0.0.0:3700]|#]

[#|2014-02-03T14:14:51.844+0100|INFO|glassfish3.1.2|javax.enterprise.system.core.com.sun.enterprise.v3.services.impl|_ThreadID=54;_ThreadName=Grizzly-kernel-thread(1);|Grizzly Framework 1.9.46 started in: 1ms - bound to [0.0.0.0:7676]|#]

[#|2014-02-03T14:14:51.991+0100|INFO|glassfish3.1.2|javax.enterprise.system.core.com.sun.enterprise.v3.admin.adapter|_ThreadID=1;_ThreadName=main;|The Admin Console is already installed, but not yet loaded.|#]

[#|2014-02-03T14:14:52.274+0100|INFO|glassfish3.1.2|javax.enterprise.system.container.web.com.sun.enterprise.web|_ThreadID=1;_ThreadName=main;|WEB0169: Created HTTP listener [http-listener-1] on host/port [0.0.0.0:80]|#]

[#|2014-02-03T14:14:52.300+0100|INFO|glassfish3.1.2|javax.enterprise.system.container.web.com.sun.enterprise.web|_ThreadID=1;_ThreadName=main;|WEB0169: Created HTTP listener [http-listener-2] on host/port [0.0.0.0:443]|#]

[#|2014-02-03T14:14:52.317+0100|INFO|glassfish3.1.2|javax.enterprise.system.container.web.com.sun.enterprise.web|_ThreadID=1;_ThreadName=main;|WEB0169: Created HTTP listener [admin-listener] on host/port [0.0.0.0:4848]|#]

[#|2014-02-03T14:14:52.384+0100|INFO|glassfish3.1.2|javax.enterprise.system.container.web.com.sun.enterprise.web|_ThreadID=1;_ThreadName=main;|WEB0171: Created virtual server [server]|#]

[#|2014-02-03T14:14:52.393+0100|INFO|glassfish3.1.2|javax.enterprise.system.container.web.com.sun.enterprise.web|_ThreadID=1;_ThreadName=main;|WEB0171: Created virtual server [__asadmin]|#]

[#|2014-02-03T14:14:53.023+0100|INFO|glassfish3.1.2|javax.enterprise.system.container.web.com.sun.enterprise.web|_ThreadID=1;_ThreadName=main;|WEB0172: Virtual server [server] loaded default web module []|#]

[#|2014-02-03T14:14:54.241+0100|INFO|glassfish3.1.2|javax.enterprise.system.core.com.sun.enterprise.v3.services.impl|_ThreadID=1;_ThreadName=main;|core.start_container_done|#]

[#|2014-02-03T14:14:54.265+0100|INFO|glassfish3.1.2|org.glassfish.ha.store.spi.BackingStoreFactoryRegistry|_ThreadID=1;_ThreadName=main;|Registered org.glassfish.ha.store.adapter.cache.ShoalBackingStoreProxy for persistence-type = replicated in BackingStoreFactoryRegistry|#]

[#|2014-02-03T14:14:54.339+0100|INFO|glassfish3.1.2|javax.enterprise.system.core.com.sun.enterprise.v3.server|_ThreadID=1;_ThreadName=main;|GlassFish Server Open Source Edition 3.1.2 (23) startup time : Felix (2,998ms), startup services(3,972ms), total(6,970ms)|#]

[#|2014-02-03T14:14:54.339+0100|SEVERE|glassfish3.1.2|javax.enterprise.system.core.com.sun.enterprise.v3.server|_ThreadID=1;_ThreadName=main;|Shutting down v3 due to startup exception : No free port within range: 80=com.sun.enterprise.v3.services.impl.monitor.MonitorableSelectorHandler@6d2db501|#]

[#|2014-02-03T14:14:54.372+0100|INFO|glassfish3.1.2|javax.enterprise.system.tools.admin.com.sun.enterprise.v3.admin|_ThreadID=64;_ThreadName=Thread-40;|Server shutdown initiated|#]

[#|2014-02-03T14:14:54.373+0100|INFO|glassfish3.1.2|javax.enterprise.system.core.com.sun.enterprise.v3.server|_ThreadID=64;_ThreadName=Thread-40;|Already stopped, so just returning|#]


Command start-domain failed.
Could not start glassfish!
(exit code: 0)

[Philip Durbin]

Interesting. Are you saying you can start and stop Glassfish just fine
before you attempt to install DVN? And that once you install DVN,
Glassfish will no longer start? This seems strange...

We have more experience with Red Hat than Debian. Do you think you
could try an installation on CentOS 6.x first? Also, can you please
email us at sup...@thedata.org if you continue to have trouble so we
can track this internally with a ticket number? I'm sorry to hear
you're having trouble but we're happy to help!

Thanks,

Phil

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Philip Durbin
Software Developer for http://thedata.org
http://www.iq.harvard.edu/people/philip-durbin

[Philip Durbin]

A sharp-eyed developer a couple doors down from me noticed this in the
log output you provided:

"No free port within range: 80"

Could you please confirm that there is nothing running on port 80
before Glassfish attempts to start? I often use `lsof -i` to check
what's running on various ports.

Thanks,

Phil

[Philip Durbin]

Oh, one other quick thing... if you have any Debian-specific notes you
think might be helpful to others, please consider adding them to our
wiki! Here's a link: https://github.com/IQSS/dvn/wiki

Phil

On Mon, Feb 3, 2014 at 10:04 AM, Philip Durbin

[ofu...@gmail.com]

Hi,
I have checked and there is nothing running on port 80. See the attached file isof.text.

Thanks

- Ofuuzo

>> email to dataverse-community+unsub...@googlegroups.com.

[Philip Durbin]

Hmm, can you please check if apache2 is running/listening on port 80?
Check this out from your lsof output:

COMMAND PID USER FD TYPE DEVICE SIZE/OFF NODE NAME
apache2 2715 www-data 3u IPv4 5679 0t0 TCP *:http (LISTEN)

On CentOS, when I run `lsof -i -P` it converts the name (http) to the
port (80) in the output.

Phil

>> >> email to dataverse-commu...@googlegroups.com.

>> >> For more options, visit https://groups.google.com/groups/opt_out.
>> >
>> >
>> >
>> > --
>> > Philip Durbin
>> > Software Developer for http://thedata.org
>> > http://www.iq.harvard.edu/people/philip-durbin
>>
>>
>>
>> --
>> Philip Durbin
>> Software Developer for http://thedata.org
>> http://www.iq.harvard.edu/people/philip-durbin
>

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[ofu...@gmail.com]

Hi,
I stopped/disable apache process from running on port 80 and the dvn installation went fine.
 Thanks to those that helped trying to solve the problem.

Ofuuzo

[Philip Durbin]

Great! I just used the new* "mark as complete" button in Google
Groups. If you have any more trouble, please either start a new thread
or remind me to click "Unmark as complete". :)

Happy Dataversing!

Phil

* https://groups.google.com/d/msg/dataverse-community/gJVRWDB1Zak/psm2YhSr-DgJ

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[david reinstein]

I'm at Essex University. Working with the Data Archive and ESSExLab and setting up a Dataverse installation. 

We are planning to run it on Debian 64bit version 6.x.

 I was wondering if you had any particular tips on Debian installation, perhaps that came out of this conversation.  We checked the Wiki but couldn't find anything.

Thanks!

-David (and Tudor)

[Condon, Kevin]

David,

Thanks for the question, unfortunately Phil and others most likely to answer your question are out of the office this week. 

Ofuuzo or anyone else on the list, do you have any recommendations? We typically install on Redhat platforms and don't have much insight for Debian installations.

Thanks for any help,

Kevin

[david reinstein]

We are still trying to do this but having this same problem. Can someone please advise?

" Glassfish is unable to load GFFileHandler because it cannot find GFFileHandler class (code). Glassfish cannot resolve the class name GFFileHandler. "

How can we make glassfish  load GFFileHandler. 

Can you give us the posgres configuration files (postgresql.conf, pg_hba.conf) to see if it is a configuration issue?

Thanks,

David

[Philip Durbin]

Hi David,

I'm hoping the community can jump in Debian or Ubuntu experience because I'm much more familiar with CentOS.

I went ahead and filed an issue for this in our Dataverse 4.0 code base (*not* DVN 3.x which we are not working on every day): https://github.com/IQSS/dataverse/issues/1059

In our Vagrant config you can now specify the operating system, and `export OPERATING_SYSTEM=debian` before `vagrant up` currently gives you Debian 7.3 from http://puppet-vagrant-boxes.puppetlabs.com

I need to focus on our next Dataverse 4.0 milestone but the next step from here would be get the installer script to make fewer assumptions about CentOS: https://github.com/IQSS/dataverse/tree/master/scripts/installer

That installer script configures Glassfish with a series of asadmin commands at https://github.com/IQSS/dataverse/blob/master/scripts/installer/glassfish-setup.sh

Within Vagrant (where I don't worry about security), this is PostgreSQL config I use: https://github.com/IQSS/dataverse/blob/master/conf/vagrant/var/lib/pgsql/data/pg_hba.conf

I'm sorry that I don't have time to work on this more but I hope these pointers help!

Phil

p.s. Output from a Vagrant session. Next step is to work on the installer.

murphy:dataverse pdurbin$ export OPERATING_SYSTEM=debian
murphy:dataverse pdurbin$ vagrant ssh
WARNING: Debian specified. Here be dragons! https://github.com/IQSS/dataverse/issues/1059
MAIL_SERVER environment variable not specified. Using localhost by default.
To specify it in bash: export MAIL_SERVER=localhost
Linux vagrant 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64

The programs included with the Debian GNU/Linux system are free software;
the exact distribution terms for each program are described in the
individual files in /usr/share/doc/*/copyright.

Debian GNU/Linux comes with ABSOLUTELY NO WARRANTY, to the extent
permitted by applicable law.
Last login: Wed Feb  5 12:49:09 2014 from 10.0.2.2
vagrant@vagrant:~$ sudo -i
root@vagrant:~# cd /usr/local
root@vagrant:/usr/local# cp /downloads/glassfish-4.0.zip .
root@vagrant:/usr/local# apt-get install unzip
root@vagrant:/usr/local# unzip -q glassfish-4.0.zip
root@vagrant:/usr/local# apt-get install openjdk-7-jre
root@vagrant:/usr/local# /usr/local/glassfish4/glassfish/bin/asadmin start-domain
Waiting for domain1 to start ...........
Successfully started the domain : domain1
domain  Location: /usr/local/glassfish4/glassfish/domains/domain1
Log File: /usr/local/glassfish4/glassfish/domains/domain1/logs/server.log
Admin Port: 4848
Command start-domain executed successfully.
root@vagrant:/usr/local# /usr/local/glassfish4/glassfish/bin/asadmin deploy /dataverse/target/dataverse-4.0.war
remote failure: Error occurred during deployment: Exception while preparing the app : Invalid resource : jdbc/VDCNetDS__pm. Please see server.log for more details.
Command deploy failed.

 

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[HAMMA RAHMA]

Howdy,

I want to install dataverse software on debian linux ,how shall  i proceed

[Don Sizemore]

I want to install dataverse software on debian linux ,how shall  i proceed

Hello,

It isn't very thoroughly tested, but if you're just getting started, you can install the most recent (5.7) version of Dataverse using the Debian 11 branch of Dataverse-Ansible:

https://github.com/GlobalDataverseCommunityConsortium/dataverse-ansible/tree/debian_11

You could test it in Vagrant with:

VAGRANT_VAGRANTFILE=Vagrantfile.debian11 vagrant up

Don

[HAMMA RAHMA]

Hello Don,

Thanks a lot for replying,although i think i might need more details on how to use the

dataverse-ansible

cause i runned this cmd

─$ ansible-playbook --connection=local -v -i dataverse/inventory dataverse/dataverse.pb -e dataverse/defaults/main.yml                                              5 ⨯
No config file found; using defaults
ERROR! couldn't resolve module/action 'alternatives'. This often indicates a misspelling, missing collection, or incorrect module path.

The error appears to be in '/home/hamma/dataverse/tasks/dataverse-prereqs.yml': line 81, column 3, but may
be elsewhere in the file depending on the exact syntax problem.

The offending line appears to be:


- name: Dataverse installer calls /usr/bin/python explicitly
  ^ here
                

i understood that it doesn't get the alternatives word but i don't know how to proceed

cordially thanks for ur help

[Dominik Wasielewski]

Hi Don,

i have exact the same behavior when trying to install dataverse via. the ansible script with the same result that you get. Did you get to solve the problem?

[Don Sizemore]

Hello,

I merged my Debian 11 branch a few weeks ago. What version of Debian are you using (11?), and what version of Ansible? Do you have a current version of dataverse-ansible?

It may just want quotes around those forward-slashes.

Don

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