[phenixbb] phenix.refine crashed

[Jianghai Zhu]

Hi,

In my refinement phenix.refine crashed with the following errors.

================================ xyz refinement  
===============================

Traceback (most recent call last):
   File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/command_line/ 
refine.py", line 5, in <module>
     command_line.run(command_name="phenix.refine", args=sys.argv[1:])
   File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/ 
command_line.py", line 78, in run
     call_back_after_monitor_collect=call_back_after_monitor_collect)
   File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/ 
driver.py", line 1310, in run
     log                     = log)
   File "/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/ 
strategies.py", line 733, in refinement_machine
     h_params                 = h_params)
   File "/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/refinement/ 
minimization.py", line 136, in __init__
     ignore_line_search_failed_step_at_lower_bound = True))
   File "/nfs/home/jzhu/cci_apps_sources/scitbx/scitbx/lbfgs.py",  
line 242, in run
     log)
   File "/nfs/home/jzhu/cci_apps_sources/scitbx/scitbx/lbfgs.py",  
line 121, in run_c_plus_plus
     f, g = target_evaluator.compute_functional_and_gradients()
   File "/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/refinement/ 
minimization.py", line 369, in compute_functional_and_gradients
     u_iso_refinable_params = u_iso_refinable_params)
   File "/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/refinement/ 
minimization.py", line 224, in compute_target
     sf_v3d_sel = sf_v3d.set_selected(self.hd_selection, [0,0,0])
RuntimeError: scitbx Internal Error: /net/sharptail/scratch1/rwgk/ 
auto_build/sources/scitbx/include/scitbx/array_family/boost_python/ 
flex_wrapper.h(473): SCITBX_ASSERT(a.accessor() == flags.accessor())  
failure.


What happened here?  Thanks.

Jianghai

+++++++++++++++++++++++++++++++
Jianghai Zhu, Ph.D
CBR Institute for Biomedical Research
Department of Pathology
Harvard Medical School
200 Longwood Ave., Boston, MA 02115
Ph: 617-278-3211
Fx: 618-278-3232
+++++++++++++++++++++++++++++++



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