Tetherless software stack

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DO NOT REMOVE THESE INSTRUCTIONS

This is a Software Stack page.

This page must be listed at http://tw.rpi.edu/wiki/tw:Labinfo/TW_Server_Administration_Manual
under the notes column for the row associated with this machine.

add any information on this software stack page that is necessary, including but not limited to:
* what is the machine being used for
* when was the last time an update was made on the machine of all installed software (yum update or  apt-get equivalent)
* what services are running on the machine (endpoint, triple store, database, apache, tomcat, etc...)
* if the machine were to go down, what would need to be restarted and whether those services are automatically restarted
** If they are not automatically restarted and need to be, please work with us to get it there.
* anything that has been installed on that machine that wasn't installed originally (if you install it, list it here)
** for example, triple store, sparql endpoint, mysql database, apache, compilers, etc...
* if something needs to be installed, but isn't installed yet, please list that in the second table
* what ports are open to the outside (inside the network and/or outside the network)


List of installed software on the tetherless.rpi.edu system.

tetherless is a Tier 4 (production) machine. Only production systems will be running on this machine. These include:

  • tw semantic media wiki


Contents


Contact

Patrick_West

NOTES

Please read the NOTES section for important information about the machine.

Add /opt/bin to your PATH, /opt/lib to your LD_LIBRARY_PATH, /opt/man to your MANPATH.

Any future applications should be installed in /opt and not /usr or /usr/local. TW will be responsible for whatever is installed in /opt and VCC will be responsible for anything installed in /usr.

It was discovered that /opt, /home, /usr, and virtual memory are all on the root partition, and the root partition filled up rather quickly. The way the machine was set up, there was a different, much larger partition at /ext. So we did the following:

  • Created a /ext/opt directory with a sym link from /opt to /ext/opt
  • Created a /ext/project directory with a sym link from /project to /ext/project
  • Created the directory /project/src for production prep. So there is a /project/src/pwest, /project/src/zednik, /project/src/csc, etc...
  • Created production project directories under /project for any production quality software to be located. For example, /project/vsto (if there was a need for one)

System Configuration Settings

  • CentOS 5.3 x86_64
  • Last updated December 07, 2010

Firewall

The firewall settings can be modified by a user with root privileges by running the system-config-securitylevel utillity.

tetherless is currently set to allow incoming connections on the following ports:
21, used by sshd
1111, used by Virtuoso
80, apache httpd
443, apache httpd secure connection

Currently installed on tetherless

Software Package Version Installed in Maintainer Notes
GNU Compiler Collection (gcc) 4.1.2 (20071124) /usr VCC
Sun Java JDK 1.6.0 update10 /opt/jdk/jdk1.6.0_10 TW #Java JDK 1.6.0_10 Notes
Jena TDB 0.7.2 /opt/TDB/TDB-0.7.2 TW #TDB 0.7.2 Notes
perl 5.8.8 /usr VCC
python 2.4.3 /usr VCC
python 2.5.4 /opt/python/python-2.5.4 TW
php 5.1.6, php-mysql, php-mbstring, php-mcrypt installed /usr VCC
ImageMagick 6.2.8.0 /usr VCC installed via yum
Tcl/Tk 8.4.13 /usr VCC installed via yum
screen 4.00.03 /usr VCC Installed via yum
Virtuoso 5.0.10 /opt/virtuoso/virtuoso-5.0.10 TW #Virtuoso 5.0.10 Notes
mysql 5.0.45 /usr VCC
phpMyAdmin 2.11.11.3 /opt/tw/htdocs TW This version works with the current version of php. Updated Feb 16, 2011
MediaWiki Installation 1.15.0 /opt/tw/htdocs TW Information about MediaWiki installation and extensions installed can be found below
Apache Web Server - httpd 2.2.3 /usr/sbin/httpd - /etc/httpd/ VCC Upgraded March 10, 2010
Joseki 3.4.1 /ext/local/Joseki-3.4.1 TW

Still need to install these software packages

Software Package Version Install in Maintainer Dependencies


TW Web Site on Tetherless

The Tetherless World Constellation Web Site (Semantic Media Wiki) has been moved over from iw.rpi.edu (machine) to tetherless.rpi.edu (machine). Included in the move were tw.rpi.edu, tw.rpi.edu/portal, tw.rpi.edu/internal, Jim's course wiki, and various other wikis. This is a direct move from iw.rpi.edu machine.

Package Specific Notes

Java JDK 1.6.0_10 Notes

Java JDK 1.6.0 update 10 has been installed to /opt/jdk/jdk1.6.0_10. The standard java executables in /usr/bin (jar, jarsigner, java, javac, javadoc, and javah) are actually symbolic links to entries in /etc/alternatives, which themselves are symbolic links to the java install bin executables. I changed the /etc/alternative links to point to the executables in /opt/jdk/jdk1.6.0_10/bin.

TDB 0.7.2 Notes

set the environment variable TDBROOT to /opt/TDB/TDB-0.7.2 and add $TDBROOT/bin to your PATH.

Virtuoso 5.0.10 Notes

Virtuoso was configured pre-compile with the following command:

./configure CFLAGS="-O2 -m64" '--prefix=/opt/virtuoso/virtuoso-5.0.10' '--enable-perl' '--enable-python' \
'--enable-imagemagick=/usr' '--with-jdk4=/opt/jdk/jdk1.6.0_10'


The configuration script printed the following summary: 

Virtuoso Open Source Edition 5.0.10 configuration summary
=========================================================

Installation variables
  layout                  default
  prefix                  /opt/virtuoso/virtuoso-5.0.10
  exec_prefix             ${prefix}

Installation paths
  programs                ${exec_prefix}/bin
  include files           ${prefix}/include
  libraries               ${exec_prefix}/lib
  manual pages            ${datarootdir}/man
  vad packages            ${datarootdir}/virtuoso/vad
  database                ${prefix}/var/lib/virtuoso/db
  hosting                 ${exec_prefix}/lib/virtuoso/hosting

Options
  BUILD_OPTS               xml ssl ldap imsg pldebug pthreads

`make check` failed with virtuoso the first time I ran it, with an error connection to localhost:1111. I opened that port on the firewall and re-ran make check, which succeeded, so I have decided to leave that port open on the firewall for now (it is not publicly available).

Live TW Web Site Installation

Patrick West, 16 March 2010 (EDT)

tw.rpi.edu Path: /opt/tw/htdocs/html/tw.rpi.edu/wiki.tw Weblog Path: /opt/tw/htdocs/html/tw.rpi.edu/weblog

Wiki Prototype Installation

Baojie 19:59, 2 September 2009 (EDT)

Path: /opt/tw/htdocs/html/tw.rpi.edu/wiki.new

Backups of Tetherless

Currently, backups are done on tetherless using EZ Snapshot. This was installed and configured by VCC.

Directories being backed up:

  • /ext

Backups occur every 2 days and last 5 hours.

A backup check is run every 2 days, sending an email to westp@rpi.edu if there is a problem. /ext/opt/backups/bin/backup_check.sh. Since the backups run every 2 days and 5 hours, due to the 5 hour duration, the check will fail once a week. If it fails twice in a row then there is actually a problem

Databases being backed up:

  • All databases are being backed up, every Sunday at 12:00 am via a cron for user root that runs /ext/opt/backups/bin/dbdump-cron.sh. The backups are made to /ext/opt/backups/mysqldb. This directory is backed up as part of the EZ Snapshot backup.

Instructions on backups and restore:

To check status of backups, run these commands 

% sudo dsmc query file
% sudo dsmc query schedule
% ps -eaf | grep dsmc | grep -v grep

The first command displays the list of files recently backed up and when they were backed up. The second command displays the schedule of backups, which currently is every 12 hours. The third makes sure that the backups are actually running. If it isn't running, it needs to be restarted as follows: 

% sudo /etc/init.d/tsm start

This writes to the log file /var/log/adsm.log. Check this log to make sure that it actually starts properly.


SPARQL Endpoint information 

DO NOT DELETE THESE INSTRUCTIONS

This section belongs on this Software Stack page because it hosts at least one SPARQL endpoint.

This section must describe the following:
1) The SPARQL service URL(s) (e.g., http://logd.tw.rpi.edu:8890/sparql)
2) The service implementation(s) (e.g., Virtuoso, TDB+Joseki, ARC2, AllegroGraph)
3) The directory location(s) for each endpoint software installed
4) How the endpoint(s) can be restarted
5) Whether or not the installation follows the guidance provided at How to install a critical process The Right Way

This Software Stack page must be listed on the SPARQL endpoint coordination page
Retrieved from "http://tw.rpi.edu/wiki/Tetherless_software_stack"
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