I have tried everything and finally decided to ask. A genepop file with 7000 loci runs smoothly without any problem on any setting for all 4 populations, but when I select 2 populations to run them pairwise, it starts, runs and stops at the end of the second (light blue color) simulations step, I waited several hours multiple times with different files, it looks like still running but it basically freezes. I tried it on 2 different computers, one of them 16GB ram with 8 cores, the other is 4GB ram with 4 cores. I am using the current jnlp Lositan version on Windows with 32 bit Java.
However when I used the old exe Lositan version on an old computer, the same thing was working last year. I dont have that computer anymore so I need to solve it with the current Lositan version. Can you think of any way to get around this?