Scanco User Instructions

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OpenVMS

OpenVMS (informally known as VMS) is a high-end computer server operating system with reliable, multitasking, real-time and batch processing. OpenVMS supports computer clustering via a LAN, enabling computers to share resources such as processors and disks to balance workload efficiently.


Session Manager

The session manager automatically starts after a user logs in locally. For remote sessions, the session manager can be started with the command $ vue .



Session Here you will find an option to "End Session", which you should do when you are finished using a workstation. You can click "Work in Progress..." when you have to leave in the middle of a session without logging out but showing a work in progress screen to other users to prevent interference.

Views (directory shortcuts) The session manager is a graphical user interface that can be used to navigate directories (left side of session manager) and open files (right side of session manager). There are shortcuts to key directories under "Views". Single-click on a directory to list its subdirectories and files. Double-click on a file to open it.

Commands and Utilities Under commands you will find tools such as copy, delete, and rename; however, it is much more practical to do these sorts of operations from a DEC terminal.

Applications Under applications you can launch various applications including:

  • DECterm: opens a DEC terminal
  • MICROCT: opens the micro-ct control panel (buttons for Scanco Medical programs)
  • Mozilla/Netscape: opens a web browser
  • XV: opens a screen capture program


DEC Terminal and Digital Command Language (DCL)

This is a DEC terminal: Commands issued in a DEC terminal are DCL commands.


What is a symbol DCL can store information such as strings or integers in "symbols". DCL can also manipulate these symbols to create other symbols. Symbols are primarily used to define short strings that replace long commands, perform certain calculations and replacements within DCL procedures, hold status information. 

$ UR == "SET DEFAULT DISK4:[BONELAB.PROJECTS]"	!A short hand to change locations to the project disk.
$ UR :== SET DEFAULT DISK4:[BONELAB.PROJECTS]	!Another way to define the symbol without quotations.
$ x == 3	                                !Store the value 3 in the symbol x.
$ SHOW SYMBOL x                                 !Displays the value of the specified symbol, x.
$ DELETE/SYMBOL/GLOBAL x                        !Deletes the specified symbol, x.

Selected symbols on the Scanco system: 

$ UD	                                        !Changes to the data directory.
$ UR	                                        !Changes to the projects directory.
$ DISKS	                                        !Shows the current disk usage.
$ DEC                                           !Opens a new DEC terminal.
$ EVE file.txt                                  !Opens the file in the text editor.
$ AIX file.aim                                  !Shows the processing log for an aim file. 
$ AIX -L file.aimThe                            !"-L" is used to show the full log.
$ QUE	                                        !Shows all entries in the queue.
$ GS file.ps or file.pdf                        !Opens *.ps and *.pdf files in GhostScript.
$ CTHEADER file.isq or file.rsq                 !Shows scan information for an *.isq or *.rsq file.

What is a logical Logical names are strings, like symbols, but can be passed into programs whereas symbols can usually only be interpreted by the command line interpreter. For example, if the logical name UD was defined to be DISK2:[XTREMECT2.DATA] then UD: could be used as a substitute when entering the path to search for files from within a program. 

$ DEFINE UD DISK2:[XTREMECT2.DATA]              !Defines a logical ud to point to the data directory.
$ DEFINE uct_default_isq myfile.isq	        !Defines the default isq file for Scanco Medical programs. The isq filename must contain the full path to the file to be evaluated, whereas the path can be left out if you just want to contour the scan.

Selected logical on the micro-CT system: 

COM                    !Logical pointing to the commands directory IDISK1:[XTREMECT2.COMMANDS]
UD                     !Logical pointing to the data directory DISK2:[XTREMECT2.DATA]
UD6                    !Logical pointing to the data directory DISK6:[XTREMECT2.DATA]
UR                     !Logical pointing to the projects directory DISK4:[BONELAB.PROJECTS]
UE                     !Logical pointing to the evaluation script directory MICROCT_ROOT:[EVAL]
UU                     !Logical pointing to the templates directory MICROCT_ROOT:[UIL]
UCT_RESULTS            !Logical pointing to the results directory MICROCT_USER:[RESULTS]

How to copy and paste using the mouse In the DEC terminal, you can highlight text by holding down and moving the mouse. Highlighted text can be pasted into applications or in the terminal using the middle mouse button. You can also highlight files in the Session Manager and paste the filename (with its full path) using the middle mouse button.

List of common commands

$ DEC	                                        !Open a new DEC terminal
$ VUE	                                        !Start the session manager. Press enter after to regain prompt.
$ UCT	                                        !Open the micro-CT control panel.
$ UCT_SAMPLE	                                !Start µCT Samples.
$ UCT_MEASUREMENT	                        !Start µCT Tomography.
$ UCT_EVALUATION	                        !Start µCT Evaluation Program.
$ UCT_3D	                                !Start µCT Ray.
$ UCT_BACKUP	                                !Start µCT Disk-Utility.
$ CD UD	                                        !Change location to the data directory.
$ CD UR	                                        !Change location to the projects directory.
$ CD SYS$SCRATCH	                        !Change location to the scratch directory.
$ CD UCT_RESULTS	                        !Change location to the results directory.
$ DIR UE	                                !List files in the evaluation directory.
$ DIR UU	                                !List files in the templates directory.
$ DIR COM	                                !List files in the commands directory.
$ DIR/SIZE/GRAND_TOTAL [.SUBDIR...]	        !List the total size of all files in the SUBDIR directory. The "..." indicates to do so recursively (i.e., counting all files in all subdirectories).
$ UCT_LIST	                                !Extract results from the database.
$ AIX -L	                                !View the header of an AIM file.
$ CTHEADER	                                !View the header of an RSQ or ISQ file.
$ DISKS		                                !Show the current disk usage (all hard drives).
$ @COM:DISK_MOUNTIES.COM	                !Run the disk_mounties.com script from the commands directory, which will give disk usage information on all scans stored on the data disk.
$ LOGOUT	                                !End a session. For remote sessions, logout from the main (initial) login terminal.
$ EVE	                                        !Start the text editor.

For remote sessions, once started the text editor, press Ctrl-B to bring up a command line at the bottom of the screen.

Command: @eveconfig

This will set backspace to delete normally. Ctrl-X cut Ctrl-C copy Ctrl-V paste Ctrl-S save file Ctrl-L learn command Ctrl-F find next Ctrl-Q quit Ctrl-O open Ctrl-space to select


How to move to a different directory Use the SET DEFAULT command. You can use an absolute directory path or a relative directory path. 

$ SET DEFAULT disk:[dir.subdir]	                !Moves to specified path.
$ SET DEFAULT [.subdir]		                !Moves one level into subdirectory subdir.

Use the CD (i.e., change directory) command (this calls the script $ @SCOM:CD.COM). 

$ CD subdir	                                !Moves into subdirectory subdir.
$ CD subdir1 subdir2	                        !Moves into subdirectory subdir1, then into subdir2.
$ CD ..		                                !Moves up one level (i.e., out of one directory).

How to list the files in a directory Use the DIRECTORY command, which may be abbreviated to DIR. 

$ DIR		                         !List everything in the current directory.
$ DIR disk:[dir.subdir]		         !Lists everything in the specified directory.
$ DIR/COL=1 *.aim	                 !Lists all files with the extension .aim in a single column.
$ DIR/SINCE=TODAY		         !Lists all files created today.
$ HELP DIR	                         !More information on the DIRECTORY command.

How to copy files Use the COPY or BACKUP command. 

$ COPY file1.ext disk:[dir.subdir1]file2.ext          !Make a copy of file1.ext to another location and call it file2.ext
$ COPY *.aim;* disk:[dir.subdir1]	              !Copy all .aim files (including all versions) to another location keeping the same name.
$ BACKUP/VERIFY [.subdir1...]*.*;* [.subdir2...]      !Copy the entire directory SUBDIR1, including all subdirectories and files, into SUBDIR2.
$ BACKUP/VERIFY [.subdir1...]*.*;* []subdir1.sav/SAVE !Copy the entire directory SUBDIR1, including all subdirectories and files, into a save set. The save set could be transferred and unpacked on another OpenVMS machine.
$ HELP COPY		                              !More information on the COPY command.
$ HELP BACKUP		                              !More information on the BACKUP command.

How to delete files Use the DELETE command, which may be abbreviated to DEL. 

$ DEL myfile.txt;	                        !Delete the most recent version of myfile.txt.
$ DEL myfile.txt;*	                        !Delete all versions of myfile.txt.
$ HELP DELETE		                        !More information on the DELETE command.

Warning: Extreme caution! 

$ DEL *.*;*	                                !Delete everything in the current directory!


How to delete directories Use the DL command (this calls the script $ @SCOM:DL.COM), but first remove all files from the directory. 

$ DEL subdir.dir;	                        !Deletes subdir.dir with confirmation.

Warning: Extreme caution! 

$ DEL [.subdir...]*.*;*                         !Deletes all files in subdir. CAREFUL!!!

Use the DELETE command, but first remove all files from the directory and set file protections to enable deletion of the directory. 

$ DEL [.subdir...]*.*;*                         !Deletes all files in subdir. CAREFUL!!!
$ SET FILE/PROTECTION=O:RWED subdir.dir         !Changes protections so you can delete the subdirectory subdir.dir.  O is short for OWNER and RWED refers to Read, Write, Edit, Delete.
$ DEL subdir.dir;                               !Deletes the subdirectory.

How to delete older versions of files Use the PURGE command. Warning: Extreme caution! 

$ PURGE	                                        !Removes older versions of all files in the directory! CAREFUL!!!!
$ PURGE myfile.aim                              !Removes older versions of myfile.aim.
$ PURGE /KEEP=3                                 !Removes all but the three most recent versions of all files.
$ HELP PURGE	                                !More information on the PURGE command.

How to rename files and directories Use the RENAME command. 

$ SET FILE/PROTECTION=O:RWED olddir.dir         !Sets protections so you can rename the directory.
$ RENAME oldfile.ext newfile.ext                !Renames oldfile.ext to newfile.ext.

How to create a directory Use the CREATE/DIR command. 

$ CREATE/DIR [.subdir]	                        !Creates a subdirectory named subdir.dir in the current directory.
$ CREATE/DIR disk:[dir.subdir]	                !Creates the subdirectory subdir at the specified path.

How to FTP files Use the FTP command. 

$ FTP 136.159.74.231	                        !Connect to an FTP Server. Need to input user name and password.	
FTP> bin	                                !Set transfer mode to binary (.aim, .gobj, .isq, and most file types).
FTP> ascii	                                !Set transfer mode to ascii (.txt, .log, .com files).
FTP> mput *.aim	                                !Put all files with the .aim extension on the FTP server (mput = multiple put).
FTP> mget *.aim	                                !Get all files with the .aim extension from the FTP server (mput = multiple get).
FTP> quit	                                !Disconnect from the FTP Server.

How to check the queue Use the SHOW QUEUE command, which may be abbreviated to SH QUE. 

$ SHOW QUEUE	                                !Shows all the queues, there are many!
$ SH QUE *FAST	                                !Shows all queues whose names end with "fast", these are used for evaluations.
$ SH QUE *SLOW                                  !Shows all queues whose names end with "slow", these are used for reconstructions.
$ SH QUE *FAST/ALL	                        !By default you are only shown queue entries for the user you are logged in as. To show jobs for all users, use the /ALL qualifier.
$ SH QUE *FAST/BY=EXE/ALL	                !Show only jobs that are currently executing for all users.

How to get information and manage jobs in the queue Use the SHOW ENTRY command to obtain information about batch jobs in the queues. 

$ SHOW ENTRY	                                !Shows all the batch jobs for your user, there may be lots!
$ SHOW ENTRY 251	                        !Shows information for batch job number 251.
$ SHOW ENTRY 251/FULL                           !Shows detailed information for batch job number 251.
$ SHOW ENTRY/ALL                                !Shows all the batch jobs for all users.

Use the DELETE/ENTRY and SET ENTRY commands to manage a batch job. 

$ DELETE/ENTRY 251                              !Deletes batch job number 251.
$ SET ENTRY 251/PRIORITY=50                     !Changes the priority of batch job number 251. Default priority is 100 for all jobs, max is 200.
$ SET ENTRY 251/REQUEUE=SCEVAL_FAST             !Moves entry 251 to queue sceval_fast. Note, the job cannot be executing to do this.
$ SET ENTRY 251/AFTER=TOMORROW                  !Holds entry 251 until the following day (midnight).
$ HELP SET ENTRY                                !More information on the SET ENTRY command.

Helpful VMS commands

  • Directory listing
$ dir /size=all /grand_total [...] 
$ dir [...*.aim]
  • Delete
$ delete *.aim;*
$ dl *.aim
  • Delete a directory that is full. CAUTION!
$ SET FILE/PROT=O:RWED [.SUBDIR...]*.*;*
$ DELETE [.SUBDIR...]*.*;*                  ! Repeat until no error messages appear.  Each iteration gets rid of more sub directories.
$ SET FILE/PROT=O:RWED SUBDIR.DIR
$ DELETE SUBDIR.DIR;

or 

$ dl disk2:[microct.projects...]*.dir     ! A for all; do until sub-dirs are gone
$ dl subdir.dir
$ @scom:dl.com subdir.dir

If the file cannot be deleted to due a permission error 

$ purge 12_RAD_FX.AIM
%PURGE-W-FILNOTPUR, error deleting DISK4:[BONELAB.PROJECTS.MULTILOAD.CAMOS]12_RAD_FX.AIM;1
-RMS-E-FLK, file currently locked by another user

Do the following: 

$ set ho 0  ! log in as calibration
$ spb 
$ del DISK4:[BONELAB.PROJECTS.MULTILOAD.CAMOS]12_RAD_FX.AIM;1
$ logout

If that still doesn't work, then maybe you need to kill a process first: 

$ show device  disk4 /file   ! shows all the files currently involved in a process
$ set ho 0     ! log in as 'system'
$ stop /id=2081F1EC
$ del DISK4:[BONELAB.PROJECTS.MULTILOAD.CAMOS]12_RAD_FX.AIM;1
$ logout
  • Copy

As user system you can copy files between accounts (e.g., microct and devel). There is no need to set user/priv=bypass as this is set by default as user system.

If you want to copy between two users (i.e. normal users, not calibration or system), then you can only write on the user directories for which you are logged in. So, if you want to copy files from account xtremect2 to microct, you need to log into microct account and copy the file from xtremect2 to microct

If you want to use the backup command for copying multiple subdirectories with the three dots (e.g., disk2:[microct.data.00000034...]) then you HAVE to put an /owner=devel at the end: 

$ backup/log disk2:[microct.data.00000034...] -
        disk2:[devel.data.00000034...]/own=devel
  • UNIX filenames on VMS with multiple '.'

The directory names would have been cvs-1.11.21.dir on Linux. However VMS doesn't allow more than 1 . in the name. If you enter 

$ set process/parse=extended

in a terminal you'll be able to access these files. You could consider renaming them i.e. cvs-1_11_21.dir.

  • Change hosts
$ mcr latcp show service *   ! and if it shows you SCTHIN:
$ set host scthin ! or
$ set host scthin/lat
  • Send a message
$ reply/all "hello there"
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