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Full Discussion: Bash while read line
Top Forums Shell Programming and Scripting Bash while read line Post 302910491 by chrisjorg on Thursday 24th of July 2014 08:09:05 PM
Old 07-24-2014
First line in file "file" is PA2_2_f1010 so it is echoing correctly.


What VMD wants is the value of a variable $line which contains the first line of the file "file", namely PA2_2_f1010..

but I tried running with $line and just line, no difference.


Code:
[user]$ ./batch_vmdgenpqr.sh 
line: PA2_2_f1010
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: 111420MB (86%)
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
Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
Info) Exiting normally.
invalid command name "PA2_2_f1043"

 

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ATF-SH(1)						    BSD General Commands Manual 						 ATF-SH(1)

NAME
atf-sh [-s shell] -- interpreter for shell-based test programs SYNOPSIS
atf-sh script DESCRIPTION
atf-sh is an interpreter that runs the test program given in script after loading the atf-sh(3) library. atf-sh is not a real interpreter though: it is just a wrapper around the system-wide shell defined by ATF_SHELL. atf-sh executes the inter- preter, loads the atf-sh(3) library and then runs the script. You must consider atf-sh to be a POSIX shell by default and thus should not use any non-standard extensions. The following options are available: -s shell Specifies the shell to use instead of the value provided by ATF_SHELL. ENVIRONMENT
ATF_LIBEXECDIR Overrides the builtin directory where atf-sh is located. Should not be overridden other than for testing purposes. ATF_PKGDATADIR Overrides the builtin directory where libatf-sh.subr is located. Should not be overridden other than for testing purposes. ATF_SHELL Path to the system shell to be used in the generated scripts. Scripts must not rely on this variable being set to select a specific interpreter. EXAMPLES
Scripts using atf-sh(3) should start with: #! /usr/bin/env atf-sh Alternatively, if you want to explicitly choose a shell interpreter, you cannot rely on env(1) to find atf-sh. Instead, you have to hardcode the path to atf-sh in the script and then use the -s option afterwards as a single parameter: #! /path/to/bin/atf-sh -s/bin/bash ENVIRONMENT
ATF_SHELL Path to the system shell to be used in the generated scripts. SEE ALSO
atf-sh(3) BSD
September 27, 2014 BSD
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