Hi, how long does it take to reproduce this problem in your case? So far I have examples that take forever before they crash. So if yours takes a few minutes I would be very interested to have it for debugging. Also, Jeff is going to try something else that may eliminate this problem. Thanks, Pavel On 6/14/12 7:10 AM, CPMAS Chen wrote:

I thought I am the only one have this problem.

I have encountered the same problem with the newest version of phenix.

My installation is on MacOS X 10.6.8.

If more information needed, I am happy to provide.

Traceback (most recent call last): File "/usr/local/phenix-1.8-1069/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.8-1069/phenix/phenix/refinement/command_line.py", line 146, in run call_back_handler=call_back_handler) File "/usr/local/phenix-1.8-1069/phenix/phenix/refinement/driver.py", line 1510, in run ncs_manager = self.ncs_manager) File "/usr/local/phenix-1.8-1069/phenix/phenix/refinement/strategies.py", line 575, in refinement_machine log=log) File "/usr/local/phenix-1.8-1069/cctbx_project/mmtbx/torsion_restraints/torsion_ncs.py", line 884, in fix_rotamer_outliers monitor_clashscore=False) File "/usr/local/phenix-1.8-1069/cctbx_project/mmtbx/refinement/real_space.py", line 336, in refine geometry_restraints_manager = geo_box) File "/usr/local/phenix-1.8-1069/cctbx_project/mmtbx/refinement/real_space.py", line 250, in __init__ lbfgs_exception_handling_params = lbfgs_exception_handling_params) File "/usr/local/phenix-1.8-1069/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 137, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/usr/local/phenix-1.8-1069/cctbx_project/scitbx/lbfgs/__init__.py", line 258, in run log) File "/usr/local/phenix-1.8-1069/cctbx_project/scitbx/lbfgs/__init__.py", line 126, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/usr/local/phenix-1.8-1069/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 193, in compute_functional_and_gradients compute_gradients=True) File "/usr/local/phenix-1.8-1069/cctbx_project/cctbx/geometry_restraints/manager.py", line 716, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/usr/local/phenix-1.8-1069/cctbx_project/cctbx/geometry_restraints/manager.py", line 650, in pair_proxies min_cubicle_edge=self.min_cubicle_edge) File "/usr/local/phenix-1.8-1069/cctbx_project/cctbx/geometry_restraints/__init__.py", line 1295, in __init__ shell_asu_tables=shell_asu_tables) RuntimeError: Estimated memory allocation for cubicles exceeds max_number_of_bytes: This may be due to unreasonable parameters: cubicle_edge=5 space_span=(2696.14,2555.98,2650.54) n_cubicles=(540,512,531) max_number_of_bytes=1073741824

Message: 1 Date: Mon, 11 Jun 2012 11:44:07 -0700 From: Nathaniel Echols mailto:[email protected]> To: PHENIX user mailing list mailto:[email protected]> Subject: Re: [phenixbb] runtime error in phenix.refine Message-ID: mailto:SMB_19ns%[email protected]> Content-Type: text/plain; charset=ISO-8859-1

On Sun, Jun 10, 2012 at 10:04 AM, Eugene Valkov mailto:[email protected]> wrote: > I'm encountering the following during the second macro-cycle in > phenix.refine in latest 1.8-1069 dev build for Linux 64-bit: > > RuntimeError: Excessive number of cubicles: > ?This may be due to unreasonable parameters: > ? ?cubicle_edge=5 > ? ?space_span=(8467.78,8440.85,8372.67) > ? ?n_cubicles=(1694,1689,1675) > ? ?max_number_of_bytes=101542821888 > > Any thoughts/suggestions much appreciated.

If I'm interpreting the code correctly, this means that the number of cubicles will lead to an integer format overflow - which I find hard to believe if you're using a 64-bit system. Could you please send me the rest of the error message, along with the output of the command "boost_adaptbx.show_platform_info"?

thanks, Nat

--

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Charles Chen

Research Associate

University of Pittsburgh School of Medicine

Department of Anesthesiology

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