<div class="gmail_quote"><div>I thought I am the only one have this problem. </div><div><br></div><div>I have encountered the same problem with the newest version of phenix.</div><div><br></div><div>My installation is on MacOS X 10.6.8. </div>
<div><br></div><div>If more information needed, I am happy to provide.</div><div><br></div><div><br></div><div>Traceback (most recent call last):</div><div> File "/usr/local/phenix-1.8-1069/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/refine.py", line 11, in <module></div>
<div> command_line.run(command_name="phenix.refine", args=sys.argv[1:])</div><div> File "/usr/local/phenix-1.8-1069/phenix/phenix/refinement/command_line.py", line 146, in run</div><div> call_back_handler=call_back_handler)</div>
<div> File "/usr/local/phenix-1.8-1069/phenix/phenix/refinement/driver.py", line 1510, in run</div><div> ncs_manager = self.ncs_manager)</div><div> File "/usr/local/phenix-1.8-1069/phenix/phenix/refinement/strategies.py", line 575, in refinement_machine</div>
<div> log=log)</div><div> File "/usr/local/phenix-1.8-1069/cctbx_project/mmtbx/torsion_restraints/torsion_ncs.py", line 884, in fix_rotamer_outliers</div><div> monitor_clashscore=False)</div><div> File "/usr/local/phenix-1.8-1069/cctbx_project/mmtbx/refinement/real_space.py", line 336, in refine</div>
<div> geometry_restraints_manager = geo_box)</div><div> File "/usr/local/phenix-1.8-1069/cctbx_project/mmtbx/refinement/real_space.py", line 250, in __init__</div><div> lbfgs_exception_handling_params = lbfgs_exception_handling_params)</div>
<div> File "/usr/local/phenix-1.8-1069/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 137, in __init__</div><div> exception_handling_params=lbfgs_exception_handling_params)</div><div> File "/usr/local/phenix-1.8-1069/cctbx_project/scitbx/lbfgs/__init__.py", line 258, in run</div>
<div> log)</div><div> File "/usr/local/phenix-1.8-1069/cctbx_project/scitbx/lbfgs/__init__.py", line 126, in run_c_plus_plus</div><div> f, g = target_evaluator.compute_functional_and_gradients()</div><div>
File "/usr/local/phenix-1.8-1069/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 193, in compute_functional_and_gradients</div><div> compute_gradients=True)</div><div> File "/usr/local/phenix-1.8-1069/cctbx_project/cctbx/geometry_restraints/manager.py", line 716, in energies_sites</div>
<div> flags=flags, sites_cart=sites_cart, site_labels=site_labels)</div><div> File "/usr/local/phenix-1.8-1069/cctbx_project/cctbx/geometry_restraints/manager.py", line 650, in pair_proxies</div><div> min_cubicle_edge=self.min_cubicle_edge)</div>
<div> File "/usr/local/phenix-1.8-1069/cctbx_project/cctbx/geometry_restraints/__init__.py", line 1295, in __init__</div><div> shell_asu_tables=shell_asu_tables)</div><div>RuntimeError: Estimated memory allocation for cubicles exceeds max_number_of_bytes:</div>
<div> This may be due to unreasonable parameters:</div><div> cubicle_edge=5</div><div> space_span=(2696.14,2555.98,2650.54)</div><div> n_cubicles=(540,512,531)</div><div> max_number_of_bytes=1073741824</div><div>
<br></div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Message: 1<br>
Date: Mon, 11 Jun 2012 11:44:07 -0700<br>
From: Nathaniel Echols <<a href="mailto:nechols@lbl.gov">nechols@lbl.gov</a>><br>
To: PHENIX user mailing list <<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>><br>
Subject: Re: [phenixbb] runtime error in phenix.refine<br>
Message-ID:<br>
<CALeAa1PBCCzKPJTMoDsFbsZMSO=<a href="mailto:SMB_19ns%2BmfvC3HozuUcBaQ@mail.gmail.com">SMB_19ns+mfvC3HozuUcBaQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset=ISO-8859-1<br>
<br>
On Sun, Jun 10, 2012 at 10:04 AM, Eugene Valkov <<a href="mailto:eugene.valkov@gmail.com">eugene.valkov@gmail.com</a>> wrote:<br>
> I'm encountering the following during the second macro-cycle in<br>
> phenix.refine in latest 1.8-1069 dev build for Linux 64-bit:<br>
><br>
> RuntimeError: Excessive number of cubicles:<br>
> ?This may be due to unreasonable parameters:<br>
> ? ?cubicle_edge=5<br>
> ? ?space_span=(8467.78,8440.85,8372.67)<br>
> ? ?n_cubicles=(1694,1689,1675)<br>
> ? ?max_number_of_bytes=101542821888<br>
><br>
> Any thoughts/suggestions much appreciated.<br>
<br>
If I'm interpreting the code correctly, this means that the number of<br>
cubicles will lead to an integer format overflow - which I find hard<br>
to believe if you're using a 64-bit system. Could you please send me<br>
the rest of the error message, along with the output of the command<br>
"boost_adaptbx.show_platform_info"?<br>
<br>
thanks,<br>
Nat<br>
<br><br></blockquote></div><div><br></div>-- <br>
<p></p><p>***************************************************</p><p>Charles Chen</p><p>Research Associate</p><p>University of Pittsburgh School of Medicine</p><p>Department of Anesthesiology</p><p>******************************************************</p>
<p></p><br>