I am compiling and running two versions of a program in two different folders. I made changes to the second version and it wouldn't run correctly (it runs for days instead of about 2 minutes), so started using diff to find any differences between the makefile, C files, input files, configuration files and run scripts and changing them until there were no differences. When I did this diff said that the two executable differ, even though the same compiler and options are used (no difference in make files).
After all of this the first version runs fine still, and the second version doesn't. I even went through and checked the all the file sizes and permissions and they all match. I don't understand how everything can be the same, yet they compile and run differently.
The program is a scientific software running in a linux environment (CentOS) and I am trying to make modifications to it.
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