Notes on Topspin on AV800

Notes on Topspin

These are some quick hints to deal with Topspin on the 600, 700 and 800 spectrometers. Much more detail is given in the Linux Installation Guide, available under Help in Topspin, especially Part III, Tips, Tricks & Trouble Shooting:

To start Topspin under CentOS 5 or 7 either:
- double-click desktop icon. A shell should open in which Topspin is started.
- open a shell and type "topspin"
If you have problems starting Topspin:
- find the shell where Topspin was attempting to start and see if there is any useful information i.e. flexlm license problem.
- make sure there are no shells open where starting Topspin was attempted but failed and are now in a "hung" state i.e. have not returned to the command prompt. Either click in the shell and hit enter to terminate the Topspin attempt, type Control C in the shell until the command prompt returns or kill the shell via the shell X button
- in a shell type ps -ef|grep topspin
  If any process running, do kill -9 <first process number>
  and then repeat ps -ef|grep topspin to ensure all process are gone. If not, repeat the "kill"
If in Topspin you have any errors or problems with acquistion, including wobb/atma/atmm, the first thing to do is the "ii" (initialize interface) command in a data set. This will initialize all the hardware for acquisition i.e. do everything but start acquiring. (Note that after the power to the spectrometer has been switched off, ii gives a number of warnings about resetting devices. It is a good idea to then repeat ii a second time to see that none of the warnings reappear). If ii gives any errors, do not attempt to proceed further until these are resolved. Steps with may resolve the errors, in order of increasing severity, are:
- exit and restart Topspin. (Wait 10 seconds before restarting, so that all Topspin processes have properly terminated).
- make sure "spect" is alive - see 4) below
- shutdown and reboot spect - see later. Restart Topspin and retry ii.
- shutdown spect, power off/on the AQS rack (switch at top of the AQS rack in left cabinet), reboot spect -see later. Restart Topspin and retry ii.
Spect - the following applies only to the Av II console used on the 600. It is no longer possible to do this on Avance III consoles.
Spect refers to the CPU board in the AQS rack (left-most board) which controls all communication between the user/pc host computer/Topspin interface and the acquisition hardware. It is actually called the CCU (communication control board) and is a diskless workstation that boots a version of Unix, referred to as "diskless" software in the XWINNMR/Topspin installations, from the host computer disk that is mounted via NFS and the second ethernet card in the PC.
For spect to boot, the host PC must be up and running, NFS running and configured, and the diskless software and various services installed. Booting is initiated by pressing the red reset button on the CCU board and should take about 1-2 minutes. Booting should cause considerable activity on the CCU board LEDS. With successful booting, it is possible to "ping spect" and "telnet spect". Note that the simplest way to check that spect is alive and booted is to "telnet spect", and just observing that you get a login prompt, at which point you would just kill this shell without proceeding with the login. The only reasons to ever complete the login ( as root with no password) is to run some test programs or to shut down spect. Note that as with all Unix systems, it is important to shutdown the operating system before powering off the AQS rack by telneting in and typing "init 0" and waiting for shutdown to finish. Also note that if there are problems booting spect, it is possible to monitor the boot process via an rs323 connection and the unix command "cu -lttyS1" (might be ttyS0, the "connected" message should appear) in a shell.

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