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Dataverse Network Application User Guide Inputs (My Experience) *In progress*

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shubster edited this page Mar 5, 2013 · 5 revisions

DISCLAIMER: These are my installation notes for Dataverse Network Application and in no way official, for official installation guide, please refer to- http://guides.thedata.org/book/installers-guides link.

The prerequisites, i.e. glassfish 3.1.2, postgreSQL, R and Rserve (Optional) and setting up the system configuration.

Each dependency (pre-requisite) has to be configured in a specific way so that the DVN installation script can run without any errors.

Configuration of all pre-requisites can be seen from the http://guides.thedata.org/book/installers-guides link.

Bugs which i found:

  1. Glassfish was not able to install at first. It was giving some incompatibility with java error. Able to solve by uninstalling the incorrect version and installing the correct version.

  2. Installation of postgresql was simple and easy. Just followed the steps given in the installer’s guide. However changing the “var/lib/pgsql/data/pg_hba.conf” file was a little tricky. There were some errors in the installer’s guide as well. Had to use and learn “VIM editor” to make changes to the configuration file. Details of the change can be seen from - http://guides.thedata.org/book/2b-postgresql” link.

  3. Installation of R and Rserve was straighforwad. Followed the installation guide.

  4. System configuration was plain and easy. Opened the ports needed to be opened.

  5. Now, the main part is running the installer. For the first time, the installer script asks for the confirmation of these settings in yes or no –

  • Internet Address of your host: localhost.localdomain
  • Glassfish Directory: /usr/local/glassfish3
  • SMTP (mail) server to relay notification messages: localhost
  • Postgres Server: localhost
  • Postgres Server Port: 5432
  • Name of the Postgres Database: dvnDb
  • Name of the Postgres User: dvnApp
  • Postgres user password: secret
  • Rserve Server: localhost
  • Rserve Server Port: 6311
  • Rserve User Name: rserve
  • Rserve User Password: rserve

After that the first error I got was EJB error-

  • ejbtimer.sql: No such file or directory
  • Could not create EJB timer entry in the database!
  • (command: /usr/bin/psql -d dvnDb -f ejbtimer.sql)
  • (psql exit code: 256)
  • Please consult the installation manual and/or
  • seek support from the DVN team.

I think it "couldn't change directory" because I unpacked the files as a normal user (kakra) in my homedir, and then it tried to setuid to postgres to read the files, which it didn't have permission to. Possible fix might be to read in the files as the running user, and feed them to the privilege-separated command via STDIN.

I fixed by changing the directory where I unzipped dvn-install from/desktop to /tmp directory as i read about it from here - https://redmine.hmdc.harvard.edu/issues/1931

Now, After this when I tried to run the script, it gave me the error that the script has already made a DB, so I have to delete the previous DB first or change the DB name in the script.

I deleted the DB by these lines-

  • “Su postgres
  • dropdb dvnDb“

and I got rid of that error.

Now, after that, I got glassfish configuration error which was –

  • Checking your Glassfish installation...
  • Invalid Glassfish directory /usr/local/glassfish3!
  • Enter the root directory of your Glassfish installation:
  • (Or ctrl-C to exit the installer): /root/glassfish3
  • OK!
  • Setting the heap limit for Glassfish to 562MB.
  • You may need to adjust this setting to better suit
  • your system.
  • Press any key to continue...
  • Writing glassfish configuration file (domain.xml)... done.
  • Insecure dependency in system while running with -T switch at ./install line 721

I got rid of the error by uninstalling and installing the glassfish server again in /usr/local/glassish3directory, it wasn’t mentioned in the installer’s guide as to in which directory it should be stored but I figured out that it might be the incorrect directory probem. After debugging that error, I ran the installer script again and it ran successfully-

  • Starting glassfish, again:
  • Waiting for domain1 to start ...............................................................................................................
  • Successfully started the domain : domain1
  • domain Location: /usr/local/glassfish3/glassfish/domains/domain1
  • Log File: /usr/local/glassfish3/glassfish/domains/domain1/logs/server.log
  • Admin Port: 4848
  • Debugging is enabled. The debugging port is: 9009
  • Command start-domain executed successfully.
  • You should now have a running DVN instance;
  • Please go to the application at the following URL:
  • and log in by using "networkAdmin" as both the user name
  • and password. Click the "networkAdmin" link on the right side
  • Of the main screen, then click "Update Account". Change this
  • default password and default e-mail address.
  • Finally, checking if Rserve is running and accessible...
  • Could not establish connection to localhost
  • on port 6311, the address you provided
  • for your R server.
  • DVN can function without a working R server, but
  • much of the functionality concerning running statistics
  • and analysis on quantitative data will not be available.
  • Please consult the "Installing R" section in the Installers guide
  • for more info.
  • [root@localhost dvninstall]#

I followed the http://localhost.localdomain/dvn ( can be different for you) and i was able to access the newly created DVN network on the local host.

You can Mail me at - "[email protected]" if there are any mistakes in the above notes.

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