The problem is the compilation stage. What standalone basically does to support multiple runs, is that it generates the whole network code over and over again for each run (one reason is that external constants are hardcoded into the code, so to take this into account we have to write the code again). For complex networks this means that there is a potentially huge number of code files that need to be compiled. This not only takes a long time, but depending on the compiler and OS it can also simply run into a “command line too long issue”. Finally, on linux we run make -j, which means that it uses independent parallel processes to compile all the source files. If there are many of them, this can take a lot of memory and make things crash. I would therefore consider changing the devices.cpp_standalone.extra_make_args_unix preference to something like ['-j', '8'] (for 8 processes, adapt this to the number of processors on your machine). I thought we had already changed this, but apparently not…
Finally, there’s a much faster technique where you only compile a single code and then change parameters “under the hood”, but this approach is not yet exposed by Brian. If you are interested in that approach you should have a look at this gist.