Bulletin 182 - 2008 September 22

1. CSIRO Cluster re-fresh and changeover
   • 1.1 Log-in changes
   • 1.2 Software changes
   • 1.3 Getting old files
   • 1.4 Current status

The refreshed burnet cluster is now available. Now when you connect to 'burnet' you will find your session on burnet-usr.hpsc.csiro.au (the new head node).

The CMIS CM group nodes (blade85-blade110) are still attached to the old system - now burnet-old. There will be a separate transition process for these nodes.

1.1 Log-in changes

With the hardware change, the ssh host key has changed. You may need to remove old entries from .ssh/known_hosts on linux/unix computers that you connect to burnet from. If you use "putty" to connect, click "yes" when asked if you want to replace the cached key.

1.2 Software changes

Software on the refreshed system is listed at: http://intra.hpsc.csiro.au/user/pkginfoweb/ under: "NEW burnet-usr.hpsc.csiro.au - head node"

The system has a completely new set of larger file-systems for storage. The nodes all run the SLES10 operating system and the default version of the intel compilers is now a version 10 release. For MPI users we recommend using OpenMPI, and a recent version, compiled with the intel compilers is available. If you have problems with your own code that are not resolved by recompiling (and using OpenMPI), you should contact so we can help.

1.3 Getting old files

Files from the home area on the old file-system have copied to /system/oldhome during the downtime when no users were active. You can move files to your new home directory with the mv command. You can find the copy of your old home directory at $OLDHOME

Please move rather than copy files as as both areas are in the same file-system so the move operation is just rearranging the directory tree without actual reading or writing of the data in files. It should be very fast.

After October 13th, files remaining in /system/oldhome will be archived. They will still be retrievable but more time will be required if this becomes necessary.

If you have logged in already, the files that you had during the test period will still be present. In this case take care merging in files from the old system.

If you have not logged in yet, you will already have a copy of files and directories starting with '.' and moving files from the old home will over-write them.

To move all files and directories except those starting with a '.' do:

mv $OLDHOME/* $HOME/

To move files and directories starting with '.' do:

mv $OLDHOME/.??* $HOME/

If you happen to have files with names that are just "." and one other character - transfer move those one by one. This is unlikely. You can check with:

ls -al $OLDHOME

If you prefer, you can move only particular files or directories with commands like:

cd $OLDHOME

mv <file1> <file2> <dir1> <dir2> $HOME/

If there are files and directories that you don't need anymore, this would be a good time to delete them. There are backups if you make a mistake, though retrieval will take a little time.

If you also need files from the $DATADIR area, you will need to copy them from the old system which will be available as burnet-old. For example to recursively copy a directory from burnet-old, you could use a command like:

rsync -av burnet-old:$DATADIR/dir1 $DATADIR/

to copy the whole lot do:

rsync -av burnet-old:$DATADIR/. $DATADIR/

The rsync commands can be run again if they get interrupted and will only copy files that have not already been copied.

1.4 Current status

This is a major change and there are a number of known problems that we expect to resolve over the next few days. There will be up-to-date information in the "Message of the Day" which you see on log-in. You can check this at any time on burnet-usr with:

cat /etc/motd         

You can also check the req system for recent reported problems:

http://intra.hpsc.csiro.au/cgi-bin/wreq/req?list-active-1-sort-Req-10-1