Linux installation on DELL 380N with SATA internal hardisk.

 

NMR Software Note (7/27/07)

 

Name

OS

NMR OP

Version

Compute

Note

INOVA600

Solaris 8

VNMR

6.1C

Ultra10

 

INOVA400

Solaris 8

VNMR

6.1C

Ultra 5

 

Unity600

Solaris 7

VNMR

6.1C

Ultra 5

 

Mercury300

Solaris 7

VNMR

6.1C

Ultra 5

 

Unity400

Solaris 6

VNMR

6.1c

Ultra 1

 

VNMRS

Linux 4ws

VNMRJ

2.1B

Dell 380N

 

Roll400

Linux 4ws

VNMRJ

2.1B

Dell 380N

 

Avance600

 

 

 

 

 

 

 

 

 

 

 

FOB M400

Linus 4 ws

VNMRJ

1.1D

Dell 370N

 

AIG V400

Linux 4ws

VNMRJ

2.1B

Dell 380N

 

Phar M400

Solaris 9

VNMRJ

1.1D

Blade1500

 

Reddy M300

Solaris 7

VNMR

6.1B

Ultra 5

 

WW M300

Solaris 6

VNMR

6.1C

Ultra 5

 

 

1/7/2007

Paralell saved in X:\NMR_Center\NMR_Doc\NMR_software

Temp working file on desktop---office PC

Linux installation on DELL 380N with SATA internal hardisk.

Use 10 CDs set for 64BITs operation system. Supplement for Dell 380N, VNMRJ2.1B and patch: 2.1BallANYvnm109.tar.Z.

 

Power on the PC, press F2 to set boot sequence on CDROM. And select drive à Set to combination.

  1. Insert the first CD and exit save. At the prompt boot :
  2. press return at prompt
  3. After few minutes, a window will pop up click next, to skip the test and select English for both questions.
  4. Click automatically partition, Click YES for the following question (Erase data…)
  5. Select remove all partition on this system. It should have only one hard disk. It is check on the hard drive in the computer. Click Next and click YES on the next question.
  6. High light the partition and click delete to delete all partitions, until say free disk space. Until /dev/had free 78167
  7. click new to create a new partition.
  8. /boot 300 MB
  9. / 10000 MB
  10. swap 12000MB ( It should be larger than the RAM 1G on board)
  11. /home fill to maximum allowable size 55859mb
  12. Click next. No change on this page, click next
  13. If there are two Ethernet cards installed: The one build-in for console (Eth1). Select active on boot, select the eth1 and click Edit. Leave the eth0 un-edited
  14. De-select DHCP and input the IP address 172.16.0.11 and 255.255.255.0 to communicate with console. Click OK. For the internet: Select eth1. Select active on boot, and Select on DHCP or get an IP and netmask.
  15. Select hostname: vnmrs400 click next
  16. Click no firewall. Do not change others on this page
  17. Select English, Next
  18. Select Eastern time zoon, Next
  19. root passwd: varian1.
  20. Select custom package installation, on the next page, move down and select everything. Note: it needs 5 CDs 1 st CD 12 mins; 2 nd 20 mins 3 rd CD 30 mins; 4 th CD 25mins; 5 th CD 15 mins. And then back to 1 st CD. 2 mins.
  21. It start installation: 11:30 for the first CD and finished at 1:10pm. Click reboot. The system will be rebooted.
  22. After reboot. The screen in color at the top 1/3 area. Have to do the following:

 

 

 

 

 

Turn off the computer and turn on again, at the Linux graphic window press return, it will stop boot up.

High light the first line:

Red Hat Enterprise Linux Ws (2.6.9 – 5. Elsmp

 

Pre the “a” key and wait for the following line to be displayed:

Grap append>ro root=/dev/VolGroup00/LogVoL00 rhgb quiet

It could be different:

Grap append>ro root ………… rhgb quiet

 

Add an “-s” at the end of the line:

 

Grap append>ro root=/dev/VolGroup00/LogVoL00 rhgb quiet -s

 

Make sure there is space between quiet and –s. Then press Enter.

Inert the Supplement for Dell 380N CD, supplied by Varian into the CDROM.

This CD should come with VNMRJ2.1B package.

 

Few minus, a prompt will be displayed:

Sh -3.00#

 

Type the following:

 

Sh -3.00#mount /dev/cdrom /media

Mount block device /dev/cdrom is write-protected mounting is ready

 

Sh -3.00#cd /media

Sh -3.00# ls ----- list the CD

Sh -3.00# ./pkgsetup

 

It will install the package (patches), it takes about 7 minutes.

After finish the installation, it will return to the prompt sh -3.00#

Type following:

cd

umount

eject -----eject CD

reboot ------- reboot the computer again.

After the reboot.

 

  1. The window display: Welcome, click Next to setup the Linux
  2. License agreement YES and Next
  3. Date and Time
  4. Display: click configure to select Dell and 1901FD (Digital)
  5. Resolution: 1280x1024
  6. color depth: millions of colors. Then Next
  7. Select “Tell me why I need to …..” Next
  8. Not register now, Next
  9. System User: user01, Shaoxiong wu varian1
  10. No additional CD Next
  11. Finish up. Next, system will be rebooted. To the login prompt:
  12. Login as root varian1. Check the following: Applications à Sytem settings à network. Check the eth1 for the console, hostname r400 172.16.0.1 255.255.255.0 and eth0 for the network 170.140.242.11, 255.255.255..0, 170.140.242.2. quit.

 

  1. Insert VNMRJ2.1B CD, open terminal and type: #mount /dev/cdrom /media
  2. cd /media #ls should list all the vnmrJ files
  3. #./load.nmr Starting the vnmrj installation program Make sure use the correct CD (vnmrj for INOVA syste, vnmrj for vnmrs system etc.) double check the top of the window. Then click install. It take about 10 -15 min. then click done.
  4. #cd / #umount /media #eject the CD.
  5. reboot (logout the linux and select reboot)

 

  1. login as vnmr1 (no passwd at first time, open shell and create the passwd varian1).

 

  1. Install vnmrj patches: it could be downloaded from Varian website(usergroup, vnmrj4me) The patch: 2.1BallANYvnm109.tar.Z is required for new VNMRS system. We have a CD for it.

 

  1. In the shell, login as root (su, root passwd) at the prompt # mount /dev/cdrom /dedia (mount the patch CD).

 

  1. #cd /media; # ls There is a patch for the system. Move it to the folder in vnmr1.

 

  1. #./vnmr/bin/patchinstall /home/vnmr1/2.1BallANYvnm109.tar.Z: Installing Patches 2.1BallANY ….. passwd: varian1, select yes. It will take few minutes.

 

  1. Make su acqproc: #./vnmr/bin/makesuacqproc

 

  1. Setup the system configure: $vnmrj (it will take for 30 seconds comeup): Edit à System Settings à Select Standard, Gradient Z, Save system file. Click system configure, Select the items as described in the console data sheet: Very important is the lock frequency. It should be recorded on the book. Save the file.

 

  1. #cd /vnmr/bin #./setacq It will take several minutes to download 9 files. You need root passwd to do that. If completed, “starting communication”

 

  1. Add new users: $vnmrj adm (if it is not work, after type the new user name, then the window freezed), you should quit and do the following: login as root: #./vnmr/bin/sudoins. If the user is added correctly, there is a message: new user so so saved.

 

  1. Go to User update, to update the user, by select the user and move it to the right site of the window. Then click update.

 

  1. Add a printer: management à printers à Use the following name: hp_ploter and hp_printer (printer uses portrait format; plotter uses landscape formate). Select laserjet300 for printer and laserject300R for the plotter. It will work for printon dgs printoff.

 

 

 

 

 

 

 

NMR Software Note (7/27/07)

 

Name

OS

NMR OP

Version

Compute

Note

INOVA600

Solaris 8

VNMR

6.1C

Ultra10

 

INOVA400

Solaris 8

VNMR

6.1C

Ultra 5

 

Unity600

Solaris 7

VNMR

6.1C

Ultra 5

 

Mercury300

Solaris 7

VNMR

6.1C

Ultra 5

 

Unity400

Solaris 6

VNMR

6.1c

Ultra 1

 

VNMRS

Linux 4ws

VNMRJ

2.1B

Dell 380N

 

Roll400

Linux 4ws

VNMRJ

2.1B

Dell 380N

 

Avance600

 

 

 

 

 

 

 

 

 

 

 

FOB M400

Linus 4 ws

VNMRJ

1.1D

Dell 370N

 

AIG V400

Linux 4ws

VNMRJ

2.1B

Dell 380N

 

Phar M400

Solaris 9

VNMRJ

1.1D

Blade1500

 

Reddy M300

Solaris 7

VNMR

6.1B

Ultra 5

 

WW M300

Solaris 6

VNMR

6.1C

Ultra 5

 

Huarui Q300

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

After loading VNMRJ 1.1D (100%) on the SUN

------If your system is a spectrometer, Exit all VNMR /VNMRJ programs Run /vnmr/bin/setacq as root

 

------ On all systems, run /vnmr/bin/makeuser for everyuser to update user files. You can use VNMRJ adm for this, Config user - à Users à Update Users.

 

------ In the VNMRJ interface from utilities à system settings à click system config à to set all system parameters.

 

Uname –a to check the current version of linux installed on the computer.

Printon iconfig(‘display’) printoff to print configuration file on the instrument.

 

 

VNMRS -------

  1. Same as INOVA system: RF amps, PFG amps, PTS (diff adapter board), Lock transceiver, attenuator board, all preamps --- different housing)
  2. Different from INOVA system: Ref Gen ( 2 or more, use 80 MHz), trnasmitters with finer phase shifts, 28/40 shim supply, 14 shims with different jumpers, dual mixer (controls gain)
  3. Swappable parts in the same VNMR system: Generic controllers, RFIFs, transmitters, LB directional couplers from 300 – 900 MHz. HB directional couples from 400 – 900 MHz.
  4. Swappable parts between VNMRS system (300 – 900 MHz): All RF CC boards except lock transceiver ( OK for same frequency instrument). All digital controllers; Pneumatics router parts; NSR board, GS relays; power suplly, shims; accessories PFG, VT; pneumatics router unit.
  5. Non-swappable parts: among different frequency VNMR systems: lock transceiver, HB preamps, PTS, RF amps, Lock diplexor (200-400 & 500-900 versions)

 

VNMRS ---- VT Control Note:

  1. Presure Sensor: A 20 psi presure sensor is on the “purge” regulator. This regulator must be set to > 20 PSI or the VT heater shuts off --- à a red LED on the VT unit turns on regardless of the “setup/run” switch position.
  2. During normal VT operation, this switch must be in the “RUN” position. If the probe sir goes out or the VT connect pops off the probe, this will trigger a pneumatic fault so that the VT heater shuts off and prevents the probe from over heat. If VT is not being used, the switch position does not matter. Howere, if VT is used and the switch is not in the “RUN” position, the probe will not be protected if the gas goes off or something wrong.

 

 

VNMRS ---- Maintenance Kit: #0191663500 (Diagnostic “tip” cable, RF extender board, adapters. The tip cable is a RS-232 null modem cable, it is needed for tip hardwaire or to initialize a controller. Detailed information the training manual from Ken.

 

VNMRS ---- Setting Presure Regulators and flow meters:

  1. Filter Regulator at the wall: not exceed 100 PSI, but no less than 60 psi (Opt. 80 psi).
  2. The upper barrel regulator 40 – 55 PSI ----just enough to eject sample. Too much will cause spin problem.
  3. The Purge Regulator > 20 PSI (Opt 30 PSI) ------ It is used to aupply purge gas to the shim coil @ ca 4 – 5 LPM and the probe @ ca 10 – 15 LPM.
  4. The anti-vibration leg regulator is set to 60 – 80 PSI. Low filed need only one, high field uses all three.
  5. Set the pre-reg as low as possible & maintain VT air flow then set temp regulator at 5 PSI lower. Example: set pre-reg to 60 PSI and then set the temp regulator to 55 PSI.
  6. When using an FTS, the bleed valves inside the router must be adjusted: Open the bleed gas regulator (located inside of the pneumatic router) approx 1 full turn from fully closed position. This should cause a small amount of VT gas to flow in the bleed gas line ----- disconnect the output line, one should be able to hear the gas hissing). With the VT setup for high temperature operation, the main VT gas flow will go directly to the probe. This small amount of bleed gas will be routed to the pre-conditioner unit (FTS) input.
  7. Bearing air adjustment: Place the Pneumatic router outside of 5 Gauss line to prevent spin instabilities. Liqbear = 0 to 65534 (fully open). The different values of liqbear drive the valve with vary voltages at J6 on the Current Driver Board. The default is 41000. Set vtairflow to 10 (probe dependent parameter).
  8. To clear a Pneumatics Fault Error:
    1. Clear Flashing led by flipping the switch to “setup” then “run”.
    2. Ensure input purge regulator pressure is > 20PSI.
    3. Set VT airflow > 7 to ensure flow ball is in the green led zoon.
    4. Press “Reset Pneumatic Fault button in VNMRJ.
    5. Press VT reset button in VNMRJ.
    6. Press Regulate temp in VNMRJ
    7. su.

VNMRS ----- Probe Tuning

  1. The tune meter sensitivity is dependent on the RF amp output. It should be measuring about 8 – 10 dBm at the probe.
  2. When the probe is tuned very well, the meter does not read Zero, it should be between 40 -50 units. Reason: VNMRS lost about 10 dB signal on directional coupler compairing with INOVA system. VNMRS increase a gain (10) on the NSR interface board to get the same level to tune the probe. Unfortunately, this will increase the ground noise level too.
  3. Tune Box attn switches: VNMRS uses 0 -9 in 5 dB steps; (INOVA uses 0 – 8 in 10 dB steps with 9 is a duplicate of 8, in other words, 8 = 9 on the attn switches)
  4. If tuning a LB or HB with the tether box: #1 is always HB, #2 is always LB whatever the setting tn=C13 or tn=H1; as well as dn=C13 or dn =H1.

VNMRS ----- Setacq: Re-install any controller, or replace a new controller, re-run setacq to ensure it has the latest firmware in flash.

 

VNMRS ---- Software Tips:

  1. Flat baselines: Use the macro ‘setlp0’: Phase the spectrum, type setlp0, and re-acquire a spectrum. This macro adjusts ‘ddrtc’ so that there is zero first order phase correction (lp0=0), retype setlp0 only if change sw or at (acquisition time). In INOVA system we use crof2 and calfa to do this, change the rof2 and alfa)
  2. Pwx calibration now uses pwxlvl1 or pwxlvl2 for power, Use the pwxcal in /vnmr/maclib (not in our install CD).

 

 

 
 ! 

Varian Software Update 9/9/2008 rem Ipsum

Current Varian deliver Dell 390N for VNMRS system

with VNMRJ 2.2C on Linux ws5.

SUN Blade 1500 with Solaris 8 or 9 works with Mercury Plus with VNMRJ 1.1D, patches

1.1DallSOLmpl106.tar.Z