In HL3D I have seen very small opens between the polygon which you can look for with the check connection command. In 9.3 based on the HL Advanced Solver technology we don't see this effect. That's why I recommend this one. The difference in run time is rather large. Even if I don't know what machine or cluster you use I tend to say that 5minutes also with adaptive frequency sweep (reduction of frequencies) is too short when the same 3D area takes in HL 9.3 roughly 1 hour. Again, without seeing it is a bit difficult to judge. Just shoot me an email with the data and I'll have a look at it (rocco_gruschwitz@mentor.com).
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