These are pages for docking.org sysadmins. This is a starting point and central node for anyone who wants to install, run and manage a docking.org site locally. Sysadmin pages are *only* relevant if you have sudo on a docking.org type cluster. For other roles, see here. Once the docking lab has been set up , it must be maintained. This guide covers the events we could think of that may occur after you have a computational pharmacology lab up and running.

For security reasons, documents pertaining to authentication and access are kept in google docs

Google Docs docs

• Lab Software Status
• Lab IP addresses
• Sysadmin Secrets

Access requests to sysadmins.

There are two kinds of maintenance, reactive and pro-active. Pro-active maintenance is classified temporally, reactive is always in the present.

Pro-active

• Periodic system maintenance
• Backups
• Security review
• Software upgrades

Reactive

• Create a new user
• Retire a user
• RAID disk failure

System down/hung/crashed/offline

This section has two parts. In the first, Diagnosis, we enumerate the possible problems and what the symptoms might look like. In the second part, we rehearse scenarios of how to proceed. There are so many different kinds of failure that it is difficult to anticipate every one. Still, we have tried to write down the most common failure modes and sensible ways to proceed.

Diagnosis

• system up but df hangs -> disk is off, hung, or unmounted. Solution ->
• cannot ping head node.
• no home directory
• web server down or does not respond
• jobs don't start in queuing system
• disk full
• kernel panic

Scenarios

• Install new software by request

After power failure

• check that mailman came back up properly
• Cluster 0 - check that XML RPC services came back up properly
• check on pipeline pilot server back up correctly.

When someone leaves the lab

• back up their data or move to proust as appropriate
• reduce disk footprint as much as possible
• offer them portable USB disks for backups

• Add new hardware to the cluster

Procedures

• How to run backups
• How to restore
• How to set up a new computer
• Monthly tasks
• Security

Updating Software

• Delphi
• AMSOL
• DOCK
• dockenv
• mol2db
• molinspiration
• OpenEye
• Cactvs
• Daylight
• Marvin/JChem

Troubleshooting Services

• MySQL
• Perl
• Apache, mod_perl
• Python
• Mailman
• condor
• sendmail