Bash script not running properly, but same command of script runs properly when manually ran in terminal

Question

I have a bash script for reading data and creating images of it. I use a bash script for each file number(100-150) in a for loop to create the images for each of them.

#!/bin/bash

echo "PATH = $PATH";
echo "SHELL = $SHELL";

directory="../run-folders/Gritschneder_et_al_2009/3D_stirMin\=2_stirMax\=20_solWeight\=0.5/Ionization\ Data/dbl_files"        

Resolution=100

for i in `seq 100 150`;
    do

        echo ./surf $directory $i $Resolution $Resolution $Resolution   
    done    


for j in `seq 100 150`;
    do
            python plotsurfdens.py $directory $j $Resolution 
    done    

rm -rf $directory/*.txt

When I run the script it produces the following message from the executable "surf" where I have checked if the number of arguments is as expected by :-

if(argc!=6)   //TO check if no of arguments correct
    cout<<"Usage : ./read filedirectory fileno N[X] N[Y] N[Z]"<<endl;

This should not be happening as the number of arguments passed is 6 in the script. Also when I echo the command of running "surf" and copy the printed command,it works. Which means that when I manually type the command I give as a line in a script, it works but not in the script. Why is this happening? Thanks in advance :)

Always quote your variables unless you have a good reason not to. — Barmar
– Barmar, Commented Jun 11, 2018 at 16:26

Barmar · Accepted Answer · 2018-06-11 16:28:13Z

1

Escapes are not processed when expanding a variable value. Take the backslashes out of the directory assignment, and quote the variable when you use it.

#!/bin/bash

echo "PATH = $PATH";
echo "SHELL = $SHELL";

directory="../run-folders/Gritschneder_et_al_2009/3D_stirMin=2_stirMax=20_solWeight=0.5/Ionization Data/dbl_files"        

Resolution=100

for i in `seq 100 150`;
    do

        echo ./surf "$directory" $i $Resolution $Resolution $Resolution   
    done    


for j in `seq 100 150`;
    do
            python plotsurfdens.py "$directory" $j $Resolution 
    done    

rm -rf "$directory"/*.txt

answered Jun 11, 2018 at 16:28

Barmar

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2 Comments

Shyam Harimohan Menon Over a year ago

Yes this solved the problem, thanks a lot!! Also is it not necessary to quote the integer variable I pass $Resolution ? Or is quoting only necessary for strings that I pass. ( I realise bash does not have data types but I'm just indicating the general type that the data has by saying string or integer).

Barmar Over a year ago

I generally recommend quoting all variables to be safe, but if you know that a variable can never contain special characters it OK to use it unquoted.

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