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: [email protected] 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: [email protected] [[email protected]] on behalf of Nathaniel Echols [[email protected]] 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 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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

that makes sense, Thank-you! 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: [email protected] 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: [email protected] [[email protected]] on behalf of Nathaniel Echols [[email protected]] Sent: Friday, May 18, 2012 5:39 PM To: PHENIX user mailing list Subject: Re: [phenixbb] Phenix crashes during refinement of a large structure 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 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: [email protected] 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: [email protected] [[email protected]] on behalf of Nathaniel Echols [[email protected]] 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 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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb