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Full Discussion: Bash while read line
Top Forums Shell Programming and Scripting Bash while read line Post 302910489 by chrisjorg on Thursday 24th of July 2014 07:44:14 PM
Old 07-24-2014
Bash while read line

I have a script batch_vmdgenpqr.sh which has a problem:


Code:
#!/bin/bash
while read line
do
      vmd.sh -dispdev text -e vmdgenpqr.tcl -args $line
done<file


The do line calls another program, VMD (called by vmd.sh) and it requires the values from $line, but this is not recognised by vmd. I'm not asking anyone to comment on VMD but is BASH passing on the correct variable?

Code:
[user]$ ./batch_vmdgenpqr.sh 
Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
Info) http://www.ks.uiuc.edu/Research/vmd/                         
Info) Email questions and bug reports to vmd@ks.uiuc.edu           
Info) Please include this reference in published work using VMD:   
Info)    Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual   
Info)    Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 32 CPUs detected.
Info) Free system memory: 126641MB (98%)
Info) Creating CUDA device pool and initializing hardware...
CUDA error: invalid device symbol, CUDAClearDevice.cu line 62
Info) Detected 1 available CUDA accelerator:
Info) [0] Quadro K5000        8 SM_3.0 @ 0.71 GHz, 4.0GB RAM, KTO, OIO, ZCP
Info) Dynamically loaded 2 plugins in directory:
Info) /opt/vmd-1.9.1/plugins/LINUXAMD64/molfile
can't read "line": no such variable


Last edited by Don Cragun; 07-24-2014 at 08:56 PM.. Reason: Add missing ending CODE tag.
 

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source(n)						       Tcl Built-In Commands							 source(n)

__________________________________________________________________________________________________________________________________________________

NAME
source - Evaluate a file or resource as a Tcl script SYNOPSIS
source fileName source -encoding encodingName fileName | _________________________________________________________________ DESCRIPTION
This command takes the contents of the specified file or resource and passes it to the Tcl interpreter as a text script. The return value from source is the return value of the last command executed in the script. If an error occurs in evaluating the contents of the script then the source command will return that error. If a return command is invoked from within the script then the remainder of the file will be skipped and the source command will return normally with the result from the return command. The end-of-file character for files is "32" (^Z) for all platforms. The source command will read files up to this character. This restriction does not exist for the read or gets commands, allowing for files containing code and data segments (scripted documents). If you require a "^Z" in code for string comparison, you can use "32" or "u001a", which will be safely substituted by the Tcl interpreter into "^Z". The -encoding option is used to specify the encoding of the data stored in fileName. When the -encoding option is omitted, the system | encoding is assumed. EXAMPLE
Run the script in the file foo.tcl and then the script in the file bar.tcl: source foo.tcl source bar.tcl Alternatively: foreach scriptFile {foo.tcl bar.tcl} { source $scriptFile } SEE ALSO
file(n), cd(n), encoding(n), info(n) KEYWORDS
file, script Tcl source(n)
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