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@lbl.gov>
To: PHENIX user mailing list <phenixbb@phenix-online.org>
Subject: Re: [phenixbb] runtime error in phenix.refine
Message-ID:
<CALeAa1PBCCzKPJTMoDsFbsZMSO=SMB_19ns+mfvC3HozuUcBaQ@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
On Sun, Jun 10, 2012 at 10:04 AM, Eugene Valkov <eugene.valkov@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