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Thanks. Yeah I assumed it was more difficult than it actually was. I'll try to do things the easy way next time.

The line is a filename so I just type
./a.out<<EOF
'20090924_001.nc'
EOF

and it runs. The line from the file doesn't have the quotations so I need to pass them to enable to executable to run....

I am trying a set up a very simple korn shell script. It has 2 basic steps.

Firstly I read the first line of a text file (which is a file name)
Secondly I run a fortran executable using that line...