[phenixbb] Phenix crashes during refinement of a large structure

[Nathaniel Echols]

Sorry, the CCP4 installation is obviously conflicting here - try this instead:

$PHENIX/build/$PHENIX_MTYPE/bin/boost_adaptbx.show_platform_info

(You might want to switch the order in which you source the Phenix and
CCP4 setup scripts in your .cshrc or .bashrc or equivalent, so it
defaults to using the Phenix commands.)

-Nat

On Fri, May 18, 2012 at 2:34 PM, Gino Cingolani
<Gino.Cingolani at jefferson.edu> wrote:
> Thanks Nat, here is the output
>
> *******************************************************************************
> Traceback (most recent call last):
>  File "/usr/local/ccp4-6.1.13/lib/cctbx/cctbx_sources/boost_adaptbx/boost/command_line/show_platform_info.py", line 3, in <module>
>    import boost.python
>  File "/usr/local/ccp4-6.1.13/lib/cctbx/cctbx_sources/boost_adaptbx/boost/python.py", line 45, in <module>
>    ext = import_ext("boost_python_meta_ext")
>  File "/usr/local/ccp4-6.1.13/lib/cctbx/cctbx_sources/boost_adaptbx/boost/python.py", line 24, in import_ext
>    + ["  "+p for p in sys.path]))
> ImportError: __import__("boost_python_meta_ext"): /usr/local/ccp4-6.1.13/src/phaser/phaser-2.1.4/build/intel-linux/lib/boost_python_meta_ext.so: wrong ELF class: ELFCLASS32
>  sys.path:
>    /usr/local/ccp4-6.1.13/lib/cctbx/cctbx_sources/boost_adaptbx/boost/command_line
>    /usr/local/ccp4-6.1.13/lib/cctbx/cctbx_sources/mmtbx
>    /usr/local/ccp4-6.1.13/lib/cctbx/cctbx_sources/iotbx
>    /usr/local/ccp4-6.1.13/lib/cctbx/cctbx_sources/PyCifRW
>    /usr/local/ccp4-6.1.13/src/phaser/source/phaser
>    /usr/local/ccp4-6.1.13/lib/cctbx/cctbx_sources/cctbx
>    /usr/local/ccp4-6.1.13/lib/cctbx/cctbx_sources/scitbx
>    /usr/local/ccp4-6.1.13/lib/cctbx/cctbx_sources/boost_adaptbx
>    /usr/local/ccp4-6.1.13/lib/cctbx/cctbx_sources/libtbx
>    /usr/local/ccp4-6.1.13/src/phaser/phaser-2.1.4/build/intel-linux/lib
>    /usr/local/ccp4-6.1.13/share/python
>    /home/gino/XTAL/F1/Eps-S65D/nREF
>    /usr/lib/python2.7
>    /usr/lib/python2.7/plat-linux2
>    /usr/lib/python2.7/lib-tk
>    /usr/lib/python2.7/lib-old
>    /usr/lib/python2.7/lib-dynload
>    /usr/local/lib/python2.7/dist-packages
>    /usr/lib/python2.7/dist-packages
>    /usr/lib/python2.7/dist-packages/PIL
>    /usr/lib/pymodules/python2.7/gtk-2.0
>    /usr/lib/python2.7/dist-packages/gst-0.10
>    /usr/lib/python2.7/dist-packages/gtk-2.0
>    /usr/lib/pymodules/python2.7
>    /usr/lib/pymodules/python2.7/ubuntuone-client
>    /usr/lib/pymodules/python2.7/libubuntuone
>    /usr/lib/pymodules/python2.7/ubuntuone-storage-protocol
>    /usr/lib/pymodules/python2.7/ubuntuone-control-panel
>
> Gino
>
> ******************************************************************************
> Gino Cingolani, Ph.D.
> Associate Professor
> Thomas Jefferson University
> Dept. of Biochemistry & Molecular Biology
> 233 South 10th Street - Room 826
> Philadelphia PA 19107
> Office (215) 503 4573
> Lab    (215) 503 4595
> Fax    (215) 923 2117
> E-mail:   gino.cingolani at jefferson.edu
> Website:  http://www.cingolanilab.org
> ******************************************************************************
> "Nati non foste per viver come bruti, ma per seguir virtute e canoscenza"
> ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno,  XXVI, vv. 119-120)
>
>
> ________________________________________
> From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Nathaniel Echols [nechols at lbl.gov]
> Sent: Friday, May 18, 2012 5:18 PM
> To: PHENIX user mailing list
> Subject: Re: [phenixbb] Phenix crashes during refinement of a large structure
>
> On Fri, May 18, 2012 at 2:12 PM, Gino Cingolani
> <Gino.Cingolani at jefferson.edu> wrote:
>> PHENIX keeps crashing while refining a large structure (>18,000 residues/asym unit).
>> Can anybody make sense of the following error message (see below)?
>> ...
>>  File "/usr/local/phenix-1.7.3-928/cctbx_project/libtbx/subprocess_with_fixes.py", line 1015, in _execute_child
>>    self.pid = os.fork()
>
> It's a memory error - the stage at which it crashes is running
> phenix.clashscore (which has been used internally by phenix.refine
> since version 1.7.2).  Unfortunately there's no way around this other
> than installing more memory and/or upgrading to a 64-bit OS.  What is
> the output of boost_adaptbx.show_platform_info?
>
> -Nat
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