Bash while read line Post: 302910489

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

07-24-2014

Registered User

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.

chrisjorg

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shells

shells(4)							   File Formats 							 shells(4)

NAME

       shells - shell database

SYNOPSIS

       /etc/shells

DESCRIPTION

       The shells file contains a list of the shells on the system. Applications use this file to determine whether a shell is valid. See getuser-
       shell(3C). For each shell a single line should be present, consisting of the shell's path, relative to root.

       A hash mark (#) indicates the beginning of a comment; subsequent characters up to the end of the line are not interpreted by  the  routines
       which search the file. Blank lines are also ignored.

       The following default shells are used by utilities: /bin/bash, /bin/csh, /bin/jsh, /bin/ksh, /bin/ksh93, /bin/pfcsh, /bin/pfksh, /bin/pfsh,
       /bin/sh, /bin/tcsh, /bin/zsh, /sbin/jsh, /sbin/sh, /usr/bin/bash, /usr/bin/csh, /usr/bin/jsh, /usr/bin/ksh, /usr/bin/ksh93, /usr/bin/pfcsh,
       /usr/bin/pfksh, /usr/bin/pfsh, and /usr/bin/sh, /usr/bin/tcsh, /usr/bin/zsh, and /usr/sfw/bin/zsh. /etc/shells overrides the default list.

       Invalid shells in /etc/shells could cause unexpected behavior, such as being unable to log in by way of ftp(1).

FILES

       /etc/shells    list of shells on system

SEE ALSO

       vipw(1B), ftpd(1M), sendmail(1M), getusershell(3C), aliases(4)

SunOS 5.11							    20 Nov 2007 							 shells(4)