Indeed. It sounds like a problem within the program. Something's causing a file descriptor to not be opened, and the program isn't performing sufficient error-checking. Cuz I know one can open file descriptors at will!
To elaborate a bit more... The program "strace" is invaluable for finding out what a program is doing (or failing to do). If you strace your program's execution (and the failure is happening early enough) then you can probably find out which fopen() is failing and why.
Like I said, this may be due to a VE issue (too many FDs open already, out of memory while reading file, etc) or may be something about the program itself.
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