Philip Pemberton wrote about Xilinx ISE:
It's a pain to make it work on Linux x64. The 64-bit version of ISE
doesn't work in any usable fashion -- PlanAhead and PACE are
broken-by-design (segfault on start), and firing up the Constraints
Editor is a great way to bring it down hard and fast.
I've had 64-bit ISE 10.x, 11.x, and 12.x working on Fedora 12, 13, and
14 without the problems you describe. Presumably this works because
RHEL5, which Xilinx supports, is closely related to Fedora. What
distribution are you using? You might want to try Centos 5, which is
essentially identical to RHEL5.
Eric