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Like CDT, Photran compiles a program by running a makefile. So, Photran doesn't have to know how to run the compiler, it just has to know how to run "make". However, if you select the "managed build" option, Photran will try to write a makefile for you. Managed build works for simple Fortran programs, but not complex ones. Managed build depends on the compiler, so each compiler supported by Photran needs a customized managed build plugin. I don't know whether the problem you are reporting is due to managed build in general, or just the adaptation to the ifort compiler, but it is definitely a problem with managed build. The workaround is always to write your own makefile.
I don't have a good feeling for the limits of managed build. I haven't seen a document that explains it. In my experience, it is pretty easy to run into the limits. So, we don't use managed build very much, but just write our own makefiles.
-Ralph Johnson