Infrastructure Progress

Security

• Security Progress

Critical Steps

• 	Debian Package Proxy and Custom Repository for building our own packages (Completed 2008-04-15)
  	Fix sizes of the Partitions on the head node. This will involve making an Image of the Head Node (Completed 2008-06-03)
  	IPoverIB (Completed 2008-05-14)
  	MPI (Completed 2008-05-14)
  	Home directories (NFSv4) (Completed 2008-06-12)
  	Change of all passwords to more secure ones (Completed 2008-06-04)
  	Kerberos Working connections: External -> Biocluster, Biocluster -> Worker Nodes, Worker Nodes -> Worker Nodes; Connections that still do NOT work: Worker Nodes -> Biocluster, External -> Biocluster -> Worker Nodes and all Owl connections. (Completed 2008-06-11)
  	Queuing with Torque. Configured on the clients and the server (Completed 2008-06-13)

Important Steps

• 	BUG Check echo "echo \$PATH" | qsub. /usr/local/bin did not show up on several occasions. (Added 2009-05-30) (fixed 2009-11-19)
  	Must read http://marc.info/?l=linux-kernel&m=123732127919368&w=2 (added 2008-04-09) (Compleated 2009-11-19)
  	Discuss Updating R (and possibly a lot of other software) on Bioweb. (added 2008-12-09)
  	Make the User Guide wiki for Biocluster (qsub, taskset, .forward)
  	Give professor Girke the capability to install R packages on a system-wide level
  	A complete /etc/init.d/biocluster-check-config - script that checks the syntax and some semantics of /etc/biocluster
  	A complete /etc/init.d/biocluster-network-config - script that generates the proper fstab on the head nodes.
  	A complete /etc/init.d/biocluster-fs-config - script that generates the proper fstab on the head nodes.
  	A complete /etc/init.d/biocluster-kerberos-config - script that configures the master and the slave KDCs.
  	A complete /etc/init.d/biocluster-torque - script that start pbs_server and pbs_sched on Biocluster
  	A map of the topology of the networks
  	A documented procedure for reverting the golden and owl images to an earlier state
  	A secondary Kerberos Key Distribution Center (KDC) on Owl
  	A script that adds new users
  	Install Munin system monitoring on Biocluster (added 2008-08-25)
  	Install EMBOSS (added 2008-08-25) (completed 2009-04-14)
  	Upgrade Phred/Phrap/Consed (added 2009-02-23) (completed 2009-03-05)
  	Discuss and install ELAND (added 2008-08-25) (completed 2009-03-13)
  	Test out the reliable NFS problem test (added 2008-09-02) Test script is not good (added 2008-09-29)
  	Set up an HTTP/FTP cache for for the compute nodes to set of common data sources: NCBI, UniProt, etc... (added 2008-04-14)

Useful Steps

• 	qsub available on worker nodes
  	Get NFSv4 to work over Kerberos
  	bashrc separation for workstations, head nodes, and worker nodes
  	Try out the 9000 MTU on campus connections.
  	Kerbrerize SUDO
  	Unify .bash_hisory among the computenodes (added 2008-09-30)
  	Find and promote a tool that shows working directories of running processes (added 2009-04-08)