Problem with multiple threads need some advise

[PATTON, BILLY \(SBCSI\)]

I have to create dependencies for almost 11,000 files. 
I have c,c++,pro-c, cobol, pro-cobol, rql and sql.  The
cobol and [sr]ql use a home grown script to trace down the dependencies.
But I use makedepend for the c,c++,pro-c.  It apparently opens the file
for writing.  Nothing else can get to it and I don't know how to make 
it wait.  Running serially would take too long.

Any suggestions on how to get around this problem?