[phenixbb] Phenix crashes during refinement of a large structure

[Gino Cingolani]

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
_______________________________________________
phenixbb mailing list
phenixbb at phenix-online.org
http://phenix-online.org/mailman/listinfo/phenixbb