I ran my app twice (in the VS ide). The first time it took 33seconds. I decommented obj.save which calls a lot of code and it took 87seconds. Thats some slow serialization code! I suspect two problems. The first is i do the below
template<class T> void Save_IntX(ostream& o, T v){ o.write((char*)&v,sizeof(T)); }
I call this templates hundreds of thousands of times (well maybe not that much). Does each .write() use a lock that may be slowing it down? maybe i can use a memory steam which doesnt require a lock and dump that instead? Which ostream may i use that doesnt lock and perhaps depends that its only used in a single thread?
The other suspected problem is i use dynamic_cast a lot. But i am unsure if i can work around this.
Here is a quick profiling session after converting it to use fopen instead of ostream. I wonder why i dont see the majority of my functions in this list but as you can see write is still taking the longest. Note: i just realize my output file is half a gig. oops. Maybe that is why.

I’m glad you got it figured out, but the next time you do profiling, you might want to consider a few points:
The VS profiler in sampling mode does not sample during I/O or any other time your program is blocked, so it’s only really useful for CPU-bound profiling. For example, if it says a routine has 80% inclusive time, but the app is actually computing only 10% of the time, that 80% is really only 8%. Because of this, for any non-CPU-bound work, you need to use the profiler’s instrumentation mode.
Assuming you did that, of all those columns of data, the one that matters is “Inclusive %”, because that is the routine’s true cost, in the sense that if it could be avoided, that is how much the overall time would be reduced.
Of all those rows of data, the ones likely to matter are the ones containing your routines, because your routines are the only ones you can do anything about. It looks like “Unknown Frames” are maybe your code, if your code is compiled without debugging info. In general, it’s a good idea to profile with debugging info, make it fast, and then remove the debugging info.