Installation VNMRJ 1.1D/VNMRJ 2.1B on Sun Blade 1500 (9/21/07)

(this file is saved in microsoft word version, --Emory Server/NMR\NMR_Center\NMR_Doc )

#uname –a

SUN OS snap-ii 5.8 Generic_108528-29 sun 4u sparc SUNW , Sun-Blade-1500

Solaris 8 is installed on this machine.

Re-install everything: SUN OS 8 and VNMRJ 1.1D ------ to work with Mercury 300.

Login as root:

#/usr/sbin/psrinfo –v check the speed of processor and version.

#shutdown –y –g0 –i0 or stop A; or power down/up then press stop A

Come down to ok prompt.

Insert CD “Solaris 8 software 2/04 1 of 2 Part # 705-0852-10” (We have this one)

Note: SOLARIS 8 SOFTWARE 2/02 or older version ---- will not work on Blade 1500.

Error message:

Boot: can not open kernel /sparcv9/unix:

Enter file name /kernel/sparcv9/unix:

Problem: For SUN Blade 1500 should use Solaris HW 5/03 or later version. The above 2/02 will not work. Change to a newer version of Solaris 8 5/03 or, 2/04.

Ok> printenv or help to display some information of SUN computer settings.

OK>Setenv auto-boot false

OK> help

Ok> boot cdrom

The screen will go blank then loading some files, stopped

1024 Mb installed

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.

Loading /platform/SUNW, Sun-blade-1500-s/ufsboot

Loading /plateform/sun4u/ufsboot

SunOS release 5.8 version Generic 108528-29 64 bit

.

.

After boot up on CD, There are two questions for the language selection:

• Select English for both questions. It will restart again and become openwin enviroment.
• Read and then click Continue

• Networked YES
• use DHCP? NO

DHCP ---- (Dynamic Host Configuration Protocol (DHCP) is a network protocol that enables a DHCP server to automatically assign an IP address to an individual computer's TCP/IP stack software. DHCP assigns a number dynamically from a defined range of numbers (i.e., a scope) configured for a given network.

Client computers configured to use DHCP for IP assignment do not need to have a statically assigned IP address. In addition, they generally do not need to have addresses configured for DNS servers or WINS servers, as these are also set by the DHCP server.

• primary network interface: on board beg0, 2 nd card: hme0 Note: beg0 is on board for internet,
• host name: m300.chem.emory.edu
• IP: 170.140.188.74
• System part of subnet: yes.
• 255.255.252.0
• Enable IPv6 NO
• It takes few minutes and show the selections If OK, click continue.
• select NO for keyberos security
• Name server: NO
• Geographic region: united State, Eastern
• Local time: after that it takes for few minutes.
• Initial installation. (Erase all the data on the disk)
• Entire distribution plus OEM support
• total 114469 MB à
• customize the partition,

/ 1000mb swap (double the ram) 2mb /var 24 /opt 50 /usr 50 /export/home rest of the disk space available detailed see the menual from Ken

• Answer few questions and select auto-reboot. It will start to copy files to the disk.
• After reboot; input the root passwd.
• huangpujiang
• It will ask to install CD 2/2 and then skip other CD installations.
• Click Reboot now. After reboot.
• Install Sun Patches: Login as root. Insert “Solaris Patches for Solaris 7,8,9,” from Varian. Part number: 01-910699-03 June 16, 2004
• #cd cdrom ---à Solaris patches à load.patches
• Answer two yes, after the patches installed, reboot computer.
• Login as root to install VNMRJ

Insert VNMRJ 1.1D June 21, 2004 Part number: 01-907388-03

• login as root, open a terminal
• #cd /cdrom/cdrom0
• #ls there are few files in the directory: acc code load.nmr vnmrj vnmrrev
• #./load.nmr
• Select Mercury Plus to be installed (there are less selection). For INOVA, select inova, there are more selections. It takes about 5 minutes. After this step, install the VNMRJ patches.
• Click “DONE” and read the message on the terminal window:

If you system is a spectrometer:

• Exit all vnmr/Vnmrj program.
• Run /vnmr/bin/setacq

On all other systems:

• Run /vnmr/bin/makeuser for everyuser
• In the VNMRJ interface from utilities à systemsettings click System Config to setup printers etc.
• Use vnmrj adm to update users and add printers

• Logout root and login as vnmr1 first time there is no passwd
• set the passwd for vnmr1 and login again. Use CDE environment.
• Click more information of the yellow window and then click never register.
• You have go to terminal and type eject to eject the CD.
• Varian Users’ page login: login name: usergroup passwd : vnmrj4me
• Download patches from Varian website. We have Mercury Vx 300. There is another type: Mercury Plus (it is a later model). There are two patches for Mercury Vx on SUN (Solaris) ---- 1.1DallSOLmvx106 (released 2004-10-25)

1.1DpsgSOLmvx905 (released 2006-01-20). This one is required for the system with ProTune accessory. We do not have it!

Note: I installed as Mercury Plus, since there is not VNRMJ VX selection on the VNMRJ 1.1D installation CD. There are only INOVA and Mercury Plus.

Not sure it will work or not.????? At this time.

• Varian Patches have been downloaded and stored in my computer under Varian Documentation directory.
• To install patches, move the original patches file (zipped) into /vnmr/patches
• (login as VNMR1, root doesn’t work) type %./patcheinstall /vnmr/patches/patche_name. It will automatically check and install it.
• After the patched installed, reboot the computer. It is ready for connect to the console.
• Turn off the computer, printer, monitor, then connect all together. Turn on the power. After computer bootup, login as vnmr1.
• cd /vnmr/bin ./setacq select 2 for the connection. Reboot console. Then open vnmrj. It should be in idle mode. If not check the config, it should set to spectrometer. Set frequency, lock reference frequency etc. type su and exit vnmrj and get in again.
• ./makesuacqproc, vnmrj adm to update the vnmr1 account
• ./sudoins to update the links
• Type in the shim values and setup the lock, at this point the instrument should be able to take a proton spectrum.
• If there is no probe file, then we have to add a probe by vnmr1. calibrate the probe by using ethel benzene std.
• Modify the proton stdard files: /vnmr/parlib /parstd by using svp(‘Proton’) and svp(‘H1’). Double check the probe file if there are correct parameters.
• For the first time new account: a. add passwd, readjust windows, setup printers, setup the z0, Lpower, L gain, Lphase and shim etc.
• For the data folder, they could make a new one in the file manager window. Then in the command line: type cd(‘my_data_dir’) to switch to their own file directory. Cd to back to home directory.

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Additional Reading:

Additional Patche information on VNMRJ 1.1D/SUN solaris/Mercury Vx

CHECKSUM Validation for Patch File "1.1DallSOLmvx106.tar.Z": ----------------------------------------------------------------------

1. After downloading the patch file "1.1DallSOLmvx106.tar.Z" and storing it on your Sun workstation, DON'T uncompress and/or extract it, but run the following command PRIOR TO installing the patch: cksum 1.1DallSOLmvx106.tar.Z you should see an output line    2354741764 7657791 1.1DallSOLmvx106.tar.Z where the first number is the checksum for the file, and the second number is the size of the file in bytes. IF EITHER OF THESE TWO VALUES DIFFER FROM THE OUTPUT SHOWN ABOVE, DON'T PROCEED WITH THE INSTALLATION, BUT DOWNLOAD THE PATCH FILE AGAIN, PREFERABLY WITH AN ALTERNATIVE METHOD, then reevaluate the checksum! Login as VNMR1 to patchinstall  There are two version of Mercury system---Vx and Plus. On our VNMRJ 1.1D CD there is only for Mercury Plus. So you have to install the patche for Mercury Plus, otherwise a error message: this patch is not suitable for this kind of console. 1.1DallSOLmvx106.tar.Z--- for Mercury VX console 1.1DallSOLmpl106.tar.Z -----Mercury Plus console   If both numbers are correct you can install the patch, from the directory where the patch is stored, using    /vnmr/bin/patchinstall 1.1DallSOLmvx106.tar.Z #######################################################################  

Patch 1.1DallSOLmvx106.tar.Z fully contains 1.1DallSOLmvx105.tar.Z, i.e., you do not need to install any earlier patches prior to this one - on the other hand, if patch 1.1DallSOLmvx105.tar.Z is installed the new one can be installed on top of the earlier ones.   Patch 1.1DallSOLmvx106.tar.Z fixes one additional bug: After installing VnmrJ 1.1D data may be lost from "~vnmrsys/data/studies", when "Clear Study" from the "Study Options" menu in the StudyQ is selected for the first time in VnmrJ 1.1D. This happens the first time only. Therefore it is not the installation of the software, nor the "makeuser" script, nor the patch installation that deletes the data in "~/vnmrsys/data/studies". See also bug "data_loss.j1101".   Therefore we urge you to BACK UP YOUR DATA BEFORE INSTALLING VnmrJ 1.1D, particularly "~vnmrsys/data/studies" for ALL users.   You must install patch 1.1DallSOLmvx106 or later before running VnmrJ as any user.

  -----------------------------------------------------------------------

This patch 1.1DallSOLmvx105.tar.Z fixes a certain number of bugs for the VnmrJ 1.1D release. Patch 102, 103, and 104 were internal patches only. Patch 1.1DallSOLmvx105.tar.Z fully contains the 1.1DallSOLmvx101.tar.Z patch.   This patch contains a fix to the walkup macro (see bug "nightq.j1101" below). It is recommended that you check your crontab if you used automation with the night queue, to remove crontab entries for the nightQ. See 'man crontab' for details.   The additional bugs fixed are:   aipdeleterois.d1101 Doesn't delete all ROIs annotations.d1101 Preview shows frames annotations.d1110 Menu in editor gives incorrect suggestion ("$vi") annotations.d1114 Orientation annotation seem to be wrong for coronals fixpar.j1105 Does not set "dgroup" for "ref1" properly ghmqctoxy.j1101     Macro aborts because it cannot retrieve "twpr_cf" image_display.d1104 No way to sort on slice order image_display.d1105 "aipWindowSplit" index error layout.d1104 "Auto" sometimes goofy (improved) locator.d1118 "rfcoil" not recognized nightq.j1101 Walkup nightQ may start twice panels.d1107 Wrong if parameter doesn't exist proton.d1103 Incorrect default values in parameter set protocols.d1107 "Create new protocol" may have bad parameter protocols.d1108 Doesn't deal well with spaces pulsetool.d1101 Will not start with VnmrJ running qtune.j1104     "qtune" shows just a noisy line at the bottom recon.d1103 Problems when installing patch 1.bDallSOLall102 recon.d1104 Some gems images are split when arraying slices recon_all.d1109 Doesn't work with "fract_ky" for multi-slice/shot rf_coil.d1102 User has to change RF coil after loading new scan save_data_setup.j1101 Displays wrong path for saved data studyq.d1105 Error "sqval[0]: index out of bounds" studyq.d1117 comments on nodes in SQ don't match comment in data vnmrj.d1109 Accelerator keys "g[n]" and "[n]f" not working     fsems       tep not shown in panel        power and gss may get calculated incorrectly        because of a limitation in imprep (pi,pipat        disabled; ir not allowed)        pulse patten not checked fse3d       show profile sets nv, nv2 to zero.        tep not implemented        waveform timings not taken into account in the sequence        crusher pulses not used in sequence prescan       cannot write to pulsecal file prescan_power     cannot acquire a profile print images     printing images in landscape mode        printing to other then default printer semsdw       diffusion scheme may not be displayed        (diffscheme parameter created)   This patch 1.1DallSOLmvx101.tar.Z is fixes a certain number of bugs for the VnmrJ 1.1D release. Some have been reported as bugs, others are improvements over existing features.   This patch contains fixes to password protected files for the "Imaging_Sequences" option. After loading the patch, to load type: /vnmr/bin/load.pwd passwd Imaging_Sequences.pwd where "passwd" is the same as when loading VnmrJ 1.1D   imaging.d1106 "Copy image" always copies into next available imaging.d1107 "Delete image" should update ReviewQ imaging.d1112 "sort by slice" fails when frames are not "1-(n)" imaging.d1108 The button "Delete Selected" should update ReviewQ layout.d1107 Menu doesn't change frame layout layout.d1108 Menu can only sort group by scan layout.d1109 ### In saving, name of layout shouldn't be entry field parameter_popup.d1101 Too wide plan.d1114 "Plan" button changes plan recon_all.d1109 Doesn't work with "fract_ky" for multi-slice/shot recon_all.d1111 Problem with arrayed "fsems" data with zero-filling recon_all.d1112 Header info wrong for arrayed experiments review_queue.d1108 String/real conflict when loading review_queue.d1107 ### "frames" should always be showing roi.d1113 No "displayed" option in the Current viewport vnmrj.d1110 Using "Delete" key causes core dump       procproc     Fixes a core dump setparams     write format refers to $s instead of %s vwacq       Under some circomstances an 18 element array would        not complete, 17 an 19 were ok. This fix also        improves downloading time for waveforms. vwauto       occasionally get "MSR not booted" msg vnmrj.jar Vnmrbg Vnmr   Under Imaging planning would slow down        ft and ft2d now set procdim, even in background AT300       small bug fix SQ Comments comments on nodes in SQ don't match comment in data     Additiona Reading:

Solaris Patches:

VNMRJ ----Solaris Patches for Solaris 7,8,9 with VNMRJ 1.1D June 21, 2004

Part No. 01-910699-03

#cd cdrom/cdrom0

#./load.patches it will start to install the patches on the CD.

Before you install VnmrJ, there are Solaris patches that are necessary for proper VnmrJ and

VNMR operation. For example, Solaris patch 108940-24 handles core dumps. In Solaris 9

patch 111649-03 (which is not supplied with VnmrJ) might be needed for the firmware for

the Toshiba SD-M1401 DVD-ROM drive. We recommend that you load patches now.

Patches are on the VnmrJ Solaris Patches CD-ROM.

Make sure that your system has the latest Solaris patches. In the patch number, the two

digits after the dash are the patch version number. Each patch has a README file that

provides specific information about the patch.

For the latest information about Solaris patches, visit the SunSolve Online Web site:

http://sunsolve.sun.com

You can also check the Sun patch FTP server:

ftp://sunsolve.sun.com/pub/patches/

Or you can visit the Varian NMR User Page at http:/www.varianinc.com. Click on

NMR in the list of Scientific Instruments, then click on User Page in the Quick Links

section.

Preparing for Patch Installation

Before you begin installing patches, make sure the following conditions are true:

Chapter 3. Solaris Patch Installation and Error Messages

38 Solaris Installation and Administration 01-999270-00 A0604

• You are logged in as single user (boot -s).

• VnmrJ is not running.

• No users are logged on to your system (use the who command to verify this condition).

• The NMR console is idle.

If you are not sure which version of Solaris you are using, enter the command showrev.

If the command shows SunOS 5.8, your system is running Solaris 8; similarly, SunOS

5.7 is Solaris 7.

Even within a given Solaris release, there can be newer versions that automatically include

and install many patches, including those required by VnmrJ. To check whether a particular

patch (for example, 108940-24) is already installed, use the following command (no output

means that the patch is not installed):

showrev -p | grep 108940-24

In addition to individual patches, Sun also offers entire clusters of recommended patches,

such as 2.8_Recommended.tar.Z (typically files of 20 to 30 MB after compression),

that permit bringing your Solaris installation to the latest level. Note, however, that the

installation of patch clusters requires extra disk space. If don’t have at least 36 MB of free

space in/var (/var/sadm), you can handle this problem four ways:

• Install patches one by one using the patchadd command.

• Use the -B option while invoking patchadd. This option directs patchadd to save

the backout data to the user-specified file system.

• Generate additional disk space by deleting files that are not needed.

• Override the saving of the old files by using the -d (do not save) option when running

patchadd. This method eliminates the possibility of restoring files to previous

versions.

Also see the manual page for the patchadd command:

man patchadd

Installation of a Solaris patch cluster takes one to two hours.

Installing Solaris Patches

To install Solaris patches, do the following:

1. Enter su to become root.

2. Enter init 0.

3. Enter boot -s in order to boot up in the single user mode.

4. Enter the following:

# ps -ef | grep vold

If no results are shown , ?????:

# /etc/init.d/volmgt start

5. Insert patch CD, and enter the following in a terminal window:

# cd /cdrom/cdrom0

# ./load.patches

6. You are asked to confirm the installation of patches. Type y to install all patches or

n to skip patch installation.

If you select y, the appropriate patches for Solaris are installed.

3.2 Error Messages

01-999270-00 A0604 Solaris Installation and Administration 39

7. Eject the CD and reboot the computer:

# eject cdrom

# reboot