Troubleshooting guide for Mercury-Inova consoles running VnmrJ 2.2D

1. Communication problems between the host and console computers.

Typical symptoms: status window displays “Inactive” or displays “Interactive” and won’t exit

Causes: the software on one end or the other has stopped running.

Cures: restart the workstation end first. Exit VnmrJ, open a shell, type two times:

su acqproc

Restart VnmrJ.

If this does not solve the problem, exit Vnmrj.  On an Inova console, open the left console door.  In the center section of the rack, there is a row of circuit boards.  The left-most board has some Ethernet cables connected to it, and at the top of the board, there is a silver tab with the label "MME" (the board is recessed and you may need to bend down to be able to read it).  On the Mercury consoles, this board is around the back (the side that does not have the smoked glass door).  There is a small reset button on the front of the board which can be labeled either "RESET" or "RST" depending on the model; it can be either white or red.   Push that button, and wait about 90 seconds.  If you have a Linux shell open on the computer, ideally you will get a broadcast message that says "Console at XXX MHz ready." Restart VnmrJ.

Occasionally,  there may be a problem with the reboot, for example, there is a repeated error message saying "Automation card has NOT booted in console."  If so, reboot the console again.  You may have to do another round of su acqproc, or even reboot the host workstation in order to clear all errors and restore the communication between the host workstation and console.

2. A messy exit from VnmrJ leaves an experiment locked.

Typical symptoms: on startup, software attempts to enter experiment 0, and displays error messages like “Variable dn not defined.”

Causes: the folder /home/(user)/vnmrsys contains a file called lock_n.primary (where n is an integer) left over from a previous session, which the new session cannot delete.

Cure: Exit VnmrJ. Open a shell and type

cd vnmrsys

ls (you should see one or more file names starting with lock)

rm lock*

Then restart VnmrJ.

3. Poor resolution.

Typical symptoms: broad, asymmetric, or distorted peak shapes.

Causes: homogeneity controls misset. Unsuitable sample

Cures: reload default shims. On the VnmrJ command line, type




Often this will cause the lock level to jump much higher. Shim from there. If the poor resolution came after gradient shimming, and you intend to gradient shim again, do it from the gradient shim setup program so you can observe what happens with each iteration of shimming. The calculated field profile should get flatter with each iteration. If it appears to be getting worse, stop gradient shimming, reload default shims again, then hand shim or investigate what is making the sample unsuitable for gradient shimming.

If reloading default shims does not help, pull out the sample and examine it for problems such as the sample is too short, the position is incorrect, undissolved solids or paramagnetic substances are present, or it does not contain a deuterated solvent. Check a reference sample’s resolution. If default shims do not produce good results with a reference sample, contact staff.

4. Cannot find lock.

Causes: many.

Cures: reload default shims as in #3, and try to lock again. If a student’s sample won’t lock, try a reference sample. If that won’t lock, view the lock scan and make sure a signal is visible. If not, treat it like a host-console communication problem as described in #1. If there is at least noise in the display when the lock gain is turned up high, verify proper lock phase (about 160 degrees) and z0 (about 1100 for D2O). If none of those things help, call staff.

5. Nothing prints.

Causes: printers are misset in VnmrJ, printer driver software problems, printer hardware problems.

Cures: check the printer display for hardware problems such as a paper jam, out of paper, or toner cartridge issue. If these are found, correct them.

Open a shell and type

lpstat –t

Normal output is a list of printers, their availability, and their status. If there are many unprinted jobs, it may be best to delete them all and start over.

You can cancel all of your own print jobs by typing

cancel printjob1 printjob2 etc.

It is faster to cut and paste the names of the unprinted jobs on to the command line than to type them.  Use the left mouse button to highlight the name of a print job, then click the middle mouse button to paste it on to the command line, with names separated by spaces.  (This cut and paste method works for any text strings in a Linux shell.)

If there are unprinted jobs belonging to other users, the root password is needed to delete them all.

If the lpstat listing contains only two lines, the printer spooler may need to be restarted. Open a shell, then type


Check which print queues are selected in VnmrJ—under the File Menu, select Printers. The plotter should be set to ljplotter and the printer to ljprinter. If these are not correct, change them and click Close.

If none of these things helps, call staff.

6. Someone has forgotten to log out, and the screen is locked; or the colors look really strange on the display.

Typing Ctrl-Alt-Backspace will shut down and restart the graphics display; any current user is logged out.  This should also fix color problems--however you may need to do it twice.  If possible, exit VnmrJ before doing this (obviously you can't if the screen is locked), and verify the instrument is idle--if you zap an acquisition in progress this way, it may result in strange instrument behavior, plus it may antagonize the person whose experiment was running.  It is easy to tell if the Inova consoles are running because lights on the status panel will be blinking every 1-2 seconds.  For the Mercury consoles, if you look at the front panel (the smoked glass side), there will also be green lights blinking when an acquisition is in progress.  If an experiment is running and you believe it is your time on the instrument, try to contact the person who is logged in first.  If the instrument is idle and it is your turn, it is OK to apply the Ctrl-Alt-Backspace cure.

7. Screen is dark.

Make sure the computer and monitor are turned on.

If wiggling the mouse and typing keys does not wake it up, press the power button once to send the computer to a power off state. Wait for that to complete, then press the power button to boot back up. You do not need the root password to restart the computer this way.

Dave 4/16/09