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 <[email protected]>
To: PHENIX user mailing list <[email protected]>
Subject: Re: [phenixbb] runtime error in phenix.refine
Message-ID:
<CALeAa1PBCCzKPJTMoDsFbsZMSO=[email protected]>
Content-Type: text/plain; charset=ISO-8859-1

On Sun, Jun 10, 2012 at 10:04 AM, Eugene Valkov <[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