To make things even stranger, I tried running the binary distribution of cci_apps on another machine with a PAE kernel and it works! Here is the uname output: Linux fluffy.bu.edu 2.6.27.21-170.2.56.fc10.i686.PAE #1 SMP Mon Mar 23 23:24:26 EDT 2009 i686 i686 i386 GNU/Linux Now, phenix fails under this same kernel on *my* machine, but on fluffy here it works fine. The only thing I can think of is that the problem is due to the hardware differences between the two: Fluffy has 2 quad core Xeons with DDR2 (I think) and my machine has Core i7 with DDR3. I don't know if this bit of detail helps or not, but there it is. I will try recompiling on my core i7 box this evening and let you know how it turns out. Cheers, Nick Ralf W. Grosse-Kunstleve wrote:
Sorry if this is a naive question, but is there a known bug with phenix (or python?) on PAE kernels?
Thanks for the "PAE" clue! This finally sheds some light on the strange error you get, which I've seen a few times before. In my experience, even compiling from sources (including Python) doesn't help. I'm guessing the error will need to be fixed in Python. This may not happen quickly. Can you reboot your system without PAE? Starting with Fedora 11, which just came out this week, 64-bit kernels are the default even on 32-bit machines. IMO that's the best way forward. (The Fedora 11 system we have has been stable for the few days it is up and runs all the phenix tests without problems.)
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