From Andrew.Waight@med.nyu.edu Mon Aug 3 09:30:12 2009 From: "Waight, Andrew" To: phenixbb@phenix-online.org Subject: [phenixbb] Segmentation Fault Date: Mon, 03 Aug 2009 12:30:21 -0400 Message-ID: <3760BF13083CBF4F94D34D000ACFB3AB4120B2ED@MSGWSDCPMB04.nyumc.org> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============4038730070619283316==" --===============4038730070619283316== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Hello All, I've recently solved a membrane protein structure largely with the he= lp of phenix refine. I also have been using the autobuild programs recently = for ligand fitting and whatnot. The program during this time has been runnin= g flawlessly on my machine (Ubuntu 9.04 E8400 3.0ghz etc etc) However this we= ekend Autobuild and AutoMR spontaneously started throwing this error. (boost_adaptbx_segmentation_fault_backtrace+0x1f) [0xb7de2e27] Segmentation fault (Python and libc call stacks above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical. Memtest 86 says my RAM is good. I have reinstalled phenix and am still gettin= g the same error. I can't seem to find any other information on this error (s= egmentation faults are tricky I know) and am just wondering if anyone else ha= s seen or solved this type of problem, thanks for your help. Andrew Waight Wang Lab Skirball Institut= e of Biomolecular Medicine NYU school of med= icine ------------------------------------------------------------
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From rwgk@cci.lbl.gov Mon Aug  3 10:51:22 2009
From: "Ralf W. Grosse-Kunstleve" 
To: phenixbb@phenix-online.org
Subject: Re: [phenixbb] Segmentation Fault
Date: Mon, 03 Aug 2009 10:51:22 -0700
Message-ID: <200908031751.n73HpMLg005976@cci.lbl.gov>
In-Reply-To: <3760BF13083CBF4F94D34D000ACFB3AB4120B2ED@MSGWSDCPMB04.nyumc.org>
MIME-Version: 1.0
Content-Type: multipart/mixed; boundary="===============1044292023403929218=="

--===============1044292023403929218==
Content-Type: text/plain; charset="utf-8"
Content-Transfer-Encoding: quoted-printable

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=20
for us.
To get the sources:
  https://www.phenix-online.org/download/phenix/nightly/?version=3D1.4-129&sh=
ow_source=3D1
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=3D8 or similar to the ./install command, to
speed up the installation.

Ralf

--===============1044292023403929218==--


From Andrew.Waight@med.nyu.edu Thu Aug  6 09:07:28 2009
From: "Waight, Andrew" 
To: phenixbb@phenix-online.org
Subject: Re: [phenixbb] Segmentation Fault [SOLVED]
Date: Thu, 06 Aug 2009 12:07:23 -0400
Message-ID: <3760BF13083CBF4F94D34D000ACFB3AB4120B2F0@MSGWSDCPMB04.nyumc.org>
In-Reply-To: <200908031751.n73HpMLg005976@cci.lbl.gov>
MIME-Version: 1.0
Content-Type: multipart/mixed; boundary="===============5075059230436779018=="

--===============5075059230436779018==
Content-Type: text/plain; charset="utf-8"
Content-Transfer-Encoding: quoted-printable

Thanks for your help Ralf,

               Just to close out this issue, after trying everything suggeste=
d... reinstalls etc etc, and trying to track down the call backs for approxim=
ately 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 pr=
ocesses worked fine). Anyway I apologize that the solution was so embarrassin=
gly simple.=20

                                      Drew Waight

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

-----Original Message-----
From: phenixbb-bounces(a)phenix-online.org [mailto:phenixbb-bounces(a)phenix-=
online.org] On Behalf Of Ralf W. Grosse-Kunstleve
Sent: Monday, August 03, 2009 10:51 AM
To: phenixbb(a)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=20
for us.
To get the sources:
  https://www.phenix-online.org/download/phenix/nightly/?version=3D1.4-129&sh=
ow_source=3D1
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=3D8 or similar to the ./install command, to
speed up the installation.

Ralf
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From NEchols@lbl.gov Thu Aug  6 09:33:57 2009
From: Nathaniel Echols 
To: phenixbb@phenix-online.org
Subject: Re: [phenixbb] Segmentation Fault [SOLVED]
Date: Thu, 06 Aug 2009 09:33:55 -0700
Message-ID: 
In-Reply-To: <3760BF13083CBF4F94D34D000ACFB3AB4120B2F0@MSGWSDCPMB04.nyumc.org>
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> 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?


I'm not sure if I understand the question, but you should be able to  
turn off building in AutoMR, and run AutoBuild through the new GUI  
afterwards.  The replacement for the AutoMR GUI should be available  
sometime next month, I hope.

--------------------
Nathaniel Echols
Lawrence Berkeley Lab
510-486-5136
NEchols(a)lbl.gov






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