[phenixbb] phenix and PAE kernels

Nathaniel Echols NEchols at lbl.gov
Fri Jun 12 10:07:32 PDT 2009

On Jun 12, 2009, at 6:45 AM, nick at silvaggi.com wrote:
> Sorry if this is a naive question, but is there a known bug with
> phenix (or python?) on PAE kernels? I have looked on
> phenix-online.org, but did not find anything. This problem is
> independent of the phenix version (I have tried 1.4-92, 1.4-3, 1.3,
> and several releases of cci_apps) and occurs with almost all of the
> programs (most fail in the cci_apps test_apps script). The problem
> appears to be specific to the PAE kernels, since the same programs run
> fine in the non-PAE counterparts. I am running Fedora 10 with kernel
> versions and Phenix
> programs fail under both PAE kernels, but are fine under the non-PAE
> kernels. Thanks in advance for any help you can provide.
> OverflowError: long int too large to convert

I believe we've seen this error before with a pharma user, but we  
weren't able to get much detail about the system - in retrospect, it  
was probably a PAE kernel as well.  Anyway, it's some kind of binary  
incompatability, so the best solution in this case is probably to  
compile from source.  (I'll send you the link for that separately.)

One question: is the PAE kernel the default or did you have to custom- 
compile it?  I wasn't familiar with the term until now, and I haven't  
seen a kernel with that extension before.  What is the result when you  
enter the command 'uname -a'?


Nathaniel Echols
Lawrence Berkeley Lab
NEchols at lbl.gov

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