DIP2000
user manual
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Installation of software for the DIP2000 system
Most of the DIP software installation and setup requires root
privileges to implement. As such, special care should be taken to follow
the directions carefully and avoid typos. A complete system backup before
proceeding is recommended. Communication between the host computer and
the DIP controller (interface) occurs over two lines; A serial
line communication protocol (called the LINEEYE) carries all commands and
responses between the computers. A dedicated
ethernet line
is used for transport of the spiral images to the host computer where they
are converted to cartesian coordinate images for viewing and analysis.
The DIP operating software must be placed on a locally mounted disk to operate properly. Do not use NFS mounted disks for data transfer. Data disks may of course be NFS exported to other computers for ease of data processing.
Under the directory xdip here will be three directories env, Xdipsys and Xmxpsys installed in the first step. These three directories must be placed in the same directory and all ownership will be given to the new user, xdip. In the Xdipsys directory all programs and files are stored to operate the DIP2000 image plate. The /bin directory has all the programs, the /conf directory has all the configuration files (e.g. for DIP2020 or DIP2030, with or without kappa goniostat) and the data directory contains the files that are used to convert the spiral images to cartesian files. The Xmxpsys directory contains general programs like the xpress program itself, the communication program between the DIP and its controller and the program that pops up the icons and windows. Approximate disk space necessary for each directory:
Xdipsys: 120 MBytes
Xmxpsys: 10 MBytes
xdip: 40 Mbytes for additional files
Installing the software for the first time
From the desktop toolbox, select System, Security and access control,
User manager. Click Add.
Fill in the login name : xdip and long name DIP2000 system. Click OK.
Next, fill in the relevant items in the user manager window like the
primary group (ie. user).
Set the home directory to the absolute path of the xdip directory (ie.
/usr/people/xdip).
Add a password.
Select tcsh as the Irix shell.
Press OK to accept he values and close the user manager window.
Installation of the software can be done by reading the tar file from tape (e.g /dev/nrtape or /dev/rmt/tps0d7nrns) to disk. At least 200 MB should be available on the disk.
Login as xdip and set the default directory to /usr/people/xdip. Load the software from the DAT tape with the tar command. If the DAT tape unit is the only unit on the machine, this can be done with a simple
tar xv
If there are more tape units attached to the computer, find out the number of the SCSI port of the DAT tape (in the following example 7) and then read the software from tape with the following tar command :
tar xvf /dev/rmt/tps0d7nrns
(x stands for extract, v for verbose and f indicates that the name of the device will follow). If there is only a DAT tape on another system, then you can load the system remotely e.g. as follows:
sh remotehost '(dd if=/dev/mt/tps0d2ns)' tar xvfBp -
This only works if the file /.rhosts contains the name of the remote machine.
This should load all the DIP2000 software in the xdip directory. Uncompress any compressed files (*.Z) in directory /usr/people/xdip/Xdipsys/data :
cd Xdipsys/data
uncompress *.Z
If there is no file CorrectData, copy the file CorrectData_old to Correctdata :
cp CorrectData_old Correctdata
3. Installing the X11 optional fonts
The xpress software needs the optional fonts of X11. These can be loaded from the CD-rom containing the Irix operating system.
From the toolchest go to System, then to Software manager. The software
should be read from /CDROM/dist. Press Customize installation. Click the
envelop to the left of X11 execution environment. Go down with the dragging
bar on the right of the window and look for X11 optional fonts & (for
Irix 6.3) X11 optional type 1 fonts. Select these two and click Start to
start the installation of the software.
4. Setting serial port communications
The following instructions should be performed as root!!
The serial port has to be set for communications with the controller. To assign ttyd1 (the serial port) do the following : Using the Toolchest go to SystemManager --> Tools --> System admin. tools --> Port setup and set the serial port 1 (/dev/ttyd1) to "off" or "available".
Then change the privileges of ttyd1:
cd /dev
chmod a+r ttyd1
5. Setting the X11 operating environment
Check the file /var/X11/xdm/Xservers.
If the option "-bs" is specified, edit the file to remove it.
6. Configuring the xdip user environment
Copy the files and directories which are in the directory env to the
login directory.
The following lines should at least be present in the .cshrc file in
the xdip directory.
setenv MXPHOME $HOME/Xmxpsys
setenv DIPHOME $HOME/Xdipsys
setenv XPRESSHOME $HOME/Xmxpsys
setenv LD_LIBRARY_PATH $DIPHOME/xv-lib
setenv EXTRASMENU $LD_LIBRARY_PATH/.text_extras_menu
set path = (~/bin $DIPHOME/bin $MXPHOME/bin $path)
setenv LINEEYE ON
xset fp= /usr/lib/X11/fonts/75dpi/, /usr/lib/X11/fonts/100dpi/
, /usr/lib/X11/fonts/misc/
From the directory where the DIP software has been installed ownership of all the DIP software and directories should be given to user xdip using e.g.:
cd /usr/people
chown -R xdip.user xdip
Before beginning the user will require the following pieces of information; the ip address and name to be assigned to the host computer and the ip address of the default gateway. The system administrator should be able to provide these. In the example given below, the host computer is assigned as NONIUS_DIP with ip address 133.50.21.67. The default gateway is 133.50.21.1. These should be changed to reflect the individual user's setup.
The DIP images are rather large so it is recommended that two ethernet
cards be installed in the computer. The first for standard internet access
and the second dedicated to transferring the DIP images. This requires
special setups for both cards while isolating the DIP communications on
the second. Routing must be set properly to ensure proper operation of
the DIP. Confirm proper hardware installation using the hinv command. An
entry for ec0 and ec1 indicate the presence of two ethernet ports.
Then select ec1 and fill in according to the following example :
Name : gate-NONIUS_DIP
IP address : 192.168.200.10
Netmask : 0xffffff00
Click Apply to confirm the input and proceed as follows :
2. Add the following entry to the file /etc/services.
#
# DIP image data transfer port
#
MAC_SV 2051/tcp
3. Edit the file /etc/sys_id to reflect the chosen name of the host computer (ie. NONIUS_DIP)
4. Edit the file /etc/hosts to include the following:
#
# IP address-hostname database
#
127.0.0.1 Localhost
#
133.50.21.67 NONIUS_DIP #primary port ec0
:
:
192.168.200.10 gate-NONIUS_DIP #secondary port (ec1)
192.168.200.11 DIP-Controller #DIP-2000
In this example, the ip address of the host computer (NONIUS_DIP) is 133.50.21.67. The addresses assigned to ec1 and the DIP-Controller are a dedicated network. These addresses are the default addresses set by the factory in the DIP-Controller. If you wish to use different addresses you will have to change these values in the DIP controller using the program dipebterm.
5. Edit the file /etc/config/ifconfig-1.options to look like:
netmask 0xffff0000 broadcast 133.50.255.255
Edit the file /etc/config/ifconfig-2.options to look like:
netmask 0xffffff00 broadcast 192.168.200.255
The first two values of the ip address in ifconfig-1.options should
match that of the given ip address of the system. The last two positions
should be 255. The netmask should be that of the local network, this may
be 0xfffff00
6. Execute the command
/etc/chkconfig routed off
This turns off the static routing (system default is on)
7. Edit the file /etc/config/routed.options to contain the options -q and -h e.g.
-qh
The system default is -h
8. Edit the file /var/sysgen/master.d/bsd This file may have be write
protected, before editing change the permissions using
chmod +w /var/sysgen/master.d/bsd
The file contains a line
int ipforwarding = 1;
this should be changed to
int ipforwarding = 0;
Under Irix 6.3 this has been changed and ipforwarding has been made tunable. To change this value do the following :
% systune -i
systune-> net_ip
group : net_ip (dynamically changeable)
ipforwarding = 1 (0x1)
ipfilterd_interactive_behavior = 1 (0x1)
icmp_dropredirects = 0 (0x0)
systune ->
systune -> ipforwarding 0
ipforwarding = 1 (0x1)
Do you really want to change ipforwarding to 0 (0x0) (y/n)
y
systune ->
systune -> net_ip
group : net_ip (dynamically changeable)
ipforwarding = 0 (0x0)
ipfilterd_interactive_behavior = 1 (0x1)
icmp_dropredirects = 0 (0x0)
systune -> quit
Reconfigure the kernel using
/etc/autoconfig
and reboot the system.
To properly setup the primary ethernet card (ec0) a default gateway setting must be input. For this you will require the default gateway ip address. (In this example, 133.50.21.1). Edit the file /etc/init.d/network.local to contain
/usr/etc/route add default 133.50.21.1 0
Link this file to the computer's startup procedure using the command
ln -s /etc/init.d/network.local /etc/rc2.d/S31network
Reboot the computer. After reboot, proper ethernet setup should be checked using the following commands:
/usr/etc/ifconfig ec0
should return the following:
ec0: flags=c63<UP.BROADCAST.NOTRAILERS.RUNNING.FILTMULTI.MULTICAST>
inet 133.50.21.67 netmask 0xffff0000 broadcast 133.50.255.255
And
/usr/etc/ifconfig ec1
should return the following:
ec1: flags=163<UP.BROADCAST.NOTRAILERS.RUNNING.FILTMULTI.MULTICAST>
inet 192.168.200.10 netmask 0xffffff00 broadcast 192.168.200.255
Lastly,
/etc/chkconfig -s
confirms that static routing has been turned off:
Flag State
:
routed off
:
8. Final configuration of the DIP
The rest of the configuration can be done as user xdip. Logout from root and login as xdip. The first time you login the system a desktop environment setup window will appear. Click okay to create a new desktop environment. Check the following:
1. Check the contents of the file Xdipsys/conf/*.CNF to insure the following
values are set correctly:
co_tail.dtype
| ADC type in the controller | dual 12bit | dual 16bit |
| Value to be set | 21 | 321 |
recsize and rdcyc
| Read-out speed |
|
high speed | |
| IP diameter | 20[cm] | 30[cm] | 30[cm] |
| recsize | 15700 | 18800 | 2048 |
| rdcyc | 1250 | 1500 | 13770 |
2. For kappa-gonio equipped system, machine description file(Xdipsys/conf/DIPTYPE)
should be edited or copied. There are files DIPTYPE_DIP2000L and DIPTYPE_DIP2000R
in that directory which are standard model files for left or right handed
systems, respectively.
The DIP control program can now be started by typing
% xpress
If there is an indication (fixed to the machine) for zero point correction value to the reading arm or IP exchange arm, that value must be entered in the Setup window before the first time operation then execute a setup start with correction:"Yes" mode.
Successful software installation is confirmed by capturing an image
form the DIP and writing it to the computer disk.
Installing
an upgrade of the xpress software
In the case of a software upgrade care should be taken not to overwrite files. The following files should be saved before starting the installation :
$DIPHOME/data/CorrectData
$DIPHOME/data/DIP_ZERO_COMP (if present)
$MXPHOME/data/Status
Check your .cshrc for the meaning of the alias $DIPHOME and $MXPHOME
Assuming that the serial line connection and the X11 optional fonts
have been loaded, install the software following points 2,
5,
6,
7
and 8