[phenixbb] phenixbb Digest, Vol 79, Issue 4

[Pavel Afonine]

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 <nechols at lbl.gov <mailto:nechols at lbl.gov>>
>     To: PHENIX user mailing list <phenixbb at phenix-online.org
>     <mailto:phenixbb at phenix-online.org>>
>     Subject: Re: [phenixbb] runtime error in phenix.refine
>     Message-ID:
>     <CALeAa1PBCCzKPJTMoDsFbsZMSO=SMB_19ns+mfvC3HozuUcBaQ at mail.gmail.com <mailto:SMB_19ns%2BmfvC3HozuUcBaQ at mail.gmail.com>>
>     Content-Type: text/plain; charset=ISO-8859-1
>
>     On Sun, Jun 10, 2012 at 10:04 AM, Eugene Valkov
>     <eugene.valkov at gmail.com <mailto:eugene.valkov at gmail.com>> 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
>
>
>
> -- 
>
> ***************************************************
>
> Charles Chen
>
> Research Associate
>
> University of Pittsburgh School of Medicine
>
> Department of Anesthesiology
>
> ******************************************************
>
>
>
>
> _______________________________________________
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> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

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