The biggest performance issue Clojure has, which isn't mentioned in the article and is fundamentally unsolvable, is that it misses the CPU cache - a lot.
The data structure that drives the immutable variables, the Hash-Array Mapped Trie, is efficient in terms of time- and space- complexity, but it's incredibly CPU cache-unfriendly because by nature it's fragmented - it's not contiguous in RAM. Any operation on a HAMT will be steeped in cache misses, which slows you down by a factor of hundreds to thousands. The longer the trie has been around, the more fragmented it is likely to become. Looping over a HAMT is slower than looping over an array by two or three orders of magnitude.
I don't think there is really a solution to that. It's inherent. Clojure will always be slow, because it's not cache friendly. The architecture of your computer means you physically can't speed it up without sacrificing immutability.
The data structure that drives the immutable variables, the Hash-Array Mapped Trie, is efficient in terms of time- and space- complexity, but it's incredibly CPU cache-unfriendly because by nature it's fragmented - it's not contiguous in RAM. Any operation on a HAMT will be steeped in cache misses, which slows you down by a factor of hundreds to thousands. The longer the trie has been around, the more fragmented it is likely to become. Looping over a HAMT is slower than looping over an array by two or three orders of magnitude.
I don't think there is really a solution to that. It's inherent. Clojure will always be slow, because it's not cache friendly. The architecture of your computer means you physically can't speed it up without sacrificing immutability.