[phenixbb] Segmentation Fault [SOLVED]

Waight, Andrew Andrew.Waight at med.nyu.edu
Thu Aug 6 09:07:23 PDT 2009

Thanks for your help Ralf,

               Just to close out this issue, after trying everything suggested... reinstalls etc etc, and trying to track down the call backs for approximately two days, I fixed the problem. I simply dialed back the overclock on my rig a little (duh) I guess phenix just taxes the cpu a little bit more than all my other stress tests (overnight ray traces and other dual 99% CPU o/n processes worked fine). Anyway I apologize that the solution was so embarrassingly simple. 

                                      Drew Waight

P.S. I like the new interface exhibited in the nightly builds, but does one need to manually configure an AutoBuild through the deprecated GUI (or command line) following an AutoMR run?

-----Original Message-----
From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Ralf W. Grosse-Kunstleve
Sent: Monday, August 03, 2009 10:51 AM
To: phenixbb at phenix-online.org
Subject: Re: [phenixbb] Segmentation Fault

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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