wiza, see zaxo's first response, I think he hit it on the head. You're calling system with only one argument and the shell is mangling it. Try again with
      system("svm_classify","skereigenout.dat","svmmodel.mod");
and see if that works for you. You can also capture the return value of the system call as others have pointed out if you have any more troubles, but that also depends on if you wrote your C program to generate understandable error codes.