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I don't know if this will help, but I just encountered the same problem running SETI on FreeBSD 7.0-RELEASE with BOINC 6.2.14 (bleeding edge). The WUs would run normally until fraction done was equal to 1.000000 and then they would swap out and hang. Once both running WUs finished (dual CPU), BOINC would not start any further WUs unless I GUIed it and suspended the two hangs that just occurred. Even then they wouldn't finish up and transmit, and I eventually got a queue full of duds. A ps -A command would show 8 threads for two WUs while the processes were running, two of which were getting large amounts of CPU. All thread names ended with the characters LINUX-GNU.
I fixed the problem by doing a make deinstall on the BOINC client port, then a MAKE CONFIG to uncheck the "download LINUX work units" option, and a MAKE INSTALL again. Now I have just two fine and dandy threads with names ending in portbld-freebsd that seem to be doing their job. When I restarted the system, the duds quickly finished up and transmitted back to STARFLEET COMMAND and I got more queued-up work. If it doesn't hang again overnight, I'm going to go buy a quad core CPU and go to WARP 2.
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