[phenixbb] Segmentation Fault

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Mon Aug 3 10:51:22 PDT 2009

Hi Andrew,

>         I've recently solved a membrane protein structure largely
> with the help of phenix refine. I also have been using the autobuild
> programs recently  for ligand fitting and whatnot.  The program
> during this time has been running flawlessly on my machine (Ubuntu
> 9.04 E8400 3.0ghz etc etc) However this weekend Autobuild and AutoMR
> spontaneously started throwing this error.
> (boost_adaptbx_segmentation_fault_backtrace+0x1f) [0xb7de2e27]

What version of phenix do you have (phenix.version)?

Which phenix installer tar file did you use?

Did that same version work before?

Are you running automatic OS updates?

Do you have a 32-bit or 64-bit OS (uname -m)?

> Memtest 86 says my RAM is good.

Yes, it is almost certainly a software problem, but what exactly is
difficult to know.

> I have reinstalled phenix and
> am still getting the same error. I can't seem to find any other
> information on this error (segmentation faults are tricky I know)
> and am just wondering if anyone else has seen or solved this type of
> problem, thanks for your help.

Could you try installing from sources?
This is not guaranteed to help, and you'll get slower solve and resolve
(gfortran optimizes very poorly), but it would be another data point 
for us.
To get the sources:
Replace the version number with the one you have already.
You will need the password again (which has just changed; you probably have
to re-request).
Don't forget to add --nproc=8 or similar to the ./install command, to
speed up the installation.


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