[phenixbb] phenixbb Digest, Vol 79, Issue 4
Pavel Afonine
pafonine at lbl.gov
Thu Jun 14 08:24:44 PDT 2012
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
>
> ******************************************************
>
>
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
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