JAMF Archive

BioCompanion as published in 1995
THIS IS THE REFERENCE CODE AS PUBLISHED. 
		Doelz, R.   
		Optimal production of biological documentation: the JAM format.
		Comput. Applic. Biosci. 11, 224-226 (1995).
The version you are currently viewing is the one printed and distributed via the Internet from the server of BioComputing Basel. Version 3.1 of the BioCompanion was published with version 2 of the JAMF software. The server that was indicated in the documentation has ceased to exist.

Version 3.2 of the BioCompanion was not publicly available for free but was shareware that was distributed with GCG's software release 9. For the purpose of enhanced editing, JAMF was partially rewritten and the proprietary version 3.x of JAMF was used from 1996 onwards. The Biocompanion is available in a current version from the publisher . It has significantly changed both in software and content.

JAMF source code

 LATEX version source code

location: Home > Archive > BioCompanion V2.x (1995)

Chapter 3: CommonTechnicalProblemsTroubleShooting

Common Technical Problems: Trouble Shooting

No Response: No Window or Dark Screen

Technical Problems

Configuration Problems

The VMS X-Windows manager has a menu in the 'Options' pull-down which allows you to add the host of interest to your 'authorisation database'. If names do not work, try the IP number instead (e.g., 131.152.8.55).

No or Wrong Response (Setup Worked Before)

Problems on Serial Lines (Modems, etc.)

Problems on Ethernet

Communication Problems on Various Configurations

No Connection to Remote Host

Communication Problems on Various Configurations

Communication Problems on DECnet

The host and/or network might be misconfigured. Check for node reachability of your own node and of the target node in NCP from other nodes with the command

$ mc ncp show node biox

Communication Problems on TCP/IP

The host and/or network might be misconfigured. Check from another host whether you can reach your own node or the target node (e.g., basel.ch.embnet.org) with the appropriate command: 

 
  
UCX:  
$ ucx loop basel.ch.embnet.org  
  
MULTINET:  
$ mu ping basel.ch.embnet.org  
  
ALL, IF AVAILABLE:  
$ ping basel.ch.embnet.org
(kill with <CTRL><Y>)

Connection Problems on X-Windows

As mentioned before , the connection of an X process requires that you permit access to your host. A frequent problem on personal computers is the limitation of the X-server programs (refer to the manual to optimise memory or other resources). Either you need to restart the X-server program or you reboot the personal computer.

If a special program fails, try to open a well-known program (such as a clock or terminal window). Some applications require specific performance features of local displays. Postscript viewers and molecular modelling programs are frequently affected if you work in heterogeneous environments.

No Successful Login

Local Problems on LAT

On terminal servers, it occasionally happens that a previous session is still active and the error message is: 

 
  
- Session limit reached -
In this case, you can log out the server:

local> logout

and proceed as described to log in.

Local Problems on PCs

Personal computers tend to block occasionally if some buffer or memory is temporarily unavailable. To unfreeze the communication, you may need to reboot the computer.

Remote Problems on VMS

There is usually a maximum number of users configured in order to avoid overloading. You may see the error message 

 
	  
Too many users, try again later
During maintenance, system backups and other activities the system is usually not available for user logins. Error messages might look like 
 
  
Logins are currently disabled, try again later

Remote Problems on UNIX

There is usually a maximum number of users configured in order to avoid overloading. You may see the error message 

 
	  
no more processes
During maintenance, system backups and other activities the system is usually not available for user logins. Error messages might look like 
 
  
MAINTENANCE - try again later

Remote Account Problems

If you can connect but you fail to log in, one of the following might apply:

During Session: No or Strange Events

Unknown Terminal

The screen setup should be changed as follows:

$ set term/vt100

Screen Accidentally Locked

If the screen suddenly stops and nothing happens any longer, this may indicate that you accidentally hit <CTRL><S> (screen stop). The screen lock can be removed as follows:

<CTRL><Q>

Screen Occupied by another Program - no Reaction

If the screen becomes inactive and nothing happens any longer, this usually indicates that another program is running. Most programs can be killed as follows:

<CTRL><C>

(merciful) or

<CTRL><Y>

(no mercy)

Screen Occupied by another Program - Takes all Input

If the screen displays all your input without taking any action, another program may be running (e.g., the editor, which is used to modify data files). To exit an editor program, try the following:

<CTRL><Z>

If you see the prompt (*), type 'exit': 

 
  
 * exit

Keys Give Wrong Response

<CURSOR>: In some sessions across the network, the <CURSOR> keys either have no effect at all or result in ^]A or similar. Make sure that you are running the most recent version of the operating system and terminal emulation software. On PCs, the program manual should explain how to use cursor keys. On systems running VMS or UNIX, the terminal setting may be wrong. Some PC terminal emulators are known to have problems with the cursor keys.

<DELETE>: In some sessions across the network, the delete key may produce ^? (or similar) or jump to the beginning of the line. Make sure that you are running the most recent version of the operating system and terminal emulation software. On PCs, the program manual should explain how to use <ERASE> and <BACKSPACE> keys instead of <DELETE>. On systems running VMS or UNIX, <CTRL><H> might work as well. Try to use the <DELETE> key in the numeric key block if available.

National Character Set

National character sets are a notorious source of oddities. E.g., the pipe symbol (|) is difficult to find on Swiss keyboards and occasionally prints as national u(umlaut) on Swiss screens. Depending on your terminal or terminal emulator, there are ways around this by setting the communication line to eight bit. Other solutions include the re-mapping of the keyboard, but this should be left to system specialists.

WORKAROUND

Due some technical problems with localised keyboards it might be difficult for you to display the characters "{" and "}" by typing the corresponding characters on the keyboard. The only option to survive is to find the character elsewhere and transfer it. E.g., use the command 'genhelp distances example' and use the COPY option of your terminal or terminal emulator to take the {*} into the Paste buffer. PASTE the resulting keystrokes where appropriate.

Need to Delete 'lock'-File

In some cases, the software you want to use does not work because a previous session is still active or has been terminated abnormally. Programs like 'nn' or 'seqed' are known to create so-called 'lock'-files which need to be removed in order to restart a session. Refer to section "File Handling Commands" in order to delete such a file.

Problems Caused by User

Quota Exceeded

Occasionally, software fails to run when some limit granted to you is reached (error message is "quota exceeded"). Most frequently, the software you want to use does not work because it wants to create files. File creation requires disk space, and on most systems this disk space is limited. The error messages vary - sometimes nothing happens at all, or the message "disk quota exceeded" shows up. The GCG software reports "write error to logical device...". You can look at your disk quota with the command:

$ show quota 

 
User [BIO,DOELZ]has 3108 blocks used, 1892 available, of   
5000 authorised and permitted overdraft of 30 blocks on D$BIO
If your quota is exceeded, you need to delete files. Refer to the section "File Handling Commands" for details on how to do this.

Need to Stop a Previous Session

In some cases (e.g., the electronic mail program 'EAN' on VMS), the software you want to use does not work because a previous session is still active. Abandoning a session as described in sections "Emergency Break" can create such a lost session. To stop a session, determine the PID (process identification) number which uniquely identifies your lost session and stop this process from another session. Your most recent (i.e., your currently active) session will have a higher PID number than the earlier session(s). The PID is a hexadecimal number. You can check your sessions with the command:

$ show user doelz/full 

 
      VAX/VMS User Processes at 8-JUN-1994 21:34:56.34      
Total number of users = 1,  number of processes = 2   
Username  Node   Process Name    PID     Terminal   
DOELZ      YOGI  doelz 1       2021268B  TNA105:    
            (Host: biomac.bioz.unibas.ch Port: 26993 )   
DOELZ      YOGI  doelz 2       20210485  TNA114:                
            (Host: biomac.bioz.unibas.ch Port: 60209 )
To kill a session, type

$ stop/id=2021268B

Need to Stop a Print Session

In some cases (e.g., GCG's plotting software), printing fails to proceed as desired due to some misconfiguration. Abandoning a session as described in sections "Emergency Break" cannot stop such a print job. To stop a print job, determine the "entry" number which uniquely identifies your (lost) print job and stop this process from your interactive session. Your most recent (i.e., your last submitted) print job will have a higher "entry" number than the earlier jobs. Further, a print job title is given frequently. If you started a print job (as described in section "File Handling" ) by 

 
  
$ print/queue=bioprint test.seq
you can inquire about its status with

$ sh entry 

 
  Entry  Jobname         Username     Blocks  Status  
  -----  -------         --------     ------  ------  
      7  HSCAM           DOELZ             9  Printing  
         On busy terminal queue $BIOZ23_PRINT
To stop the print job, use the "entry" number (7 in this example) and type 
 
$ delete/entry=7
Make sure that your job is deleted by listing the print queue again.

JAM produced file: COMMON3.HTML as [next page] , or [overview] , or [table of contents]