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    Hi,<br>
    <br>
    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. <br>
    <br>
    Also, Jeff is going to try something else that may eliminate this
    problem.<br>
    <br>
    Thanks,<br>
    Pavel<br>
    <br>
    On 6/14/12 7:10 AM, CPMAS Chen wrote:
    <blockquote
cite="mid:CAAU4GKaK4x=6s+BnhuK+YBFuarPPKVzWuecbSjAWrHbrYDcQcw@mail.gmail.com"
      type="cite">
      <div class="gmail_quote">
        <div>I thought I am the only one have this problem.&nbsp;</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.&nbsp;</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>&nbsp; File
          "/usr/local/phenix-1.8-1069/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/refine.py",
          line 11, in &lt;module&gt;</div>
        <div>&nbsp; &nbsp; command_line.run(command_name="phenix.refine",
          args=sys.argv[1:])</div>
        <div>&nbsp; File
          "/usr/local/phenix-1.8-1069/phenix/phenix/refinement/command_line.py",
          line 146, in run</div>
        <div>&nbsp; &nbsp; call_back_handler=call_back_handler)</div>
        <div>&nbsp; File
          "/usr/local/phenix-1.8-1069/phenix/phenix/refinement/driver.py",
          line 1510, in run</div>
        <div>&nbsp; &nbsp; ncs_manager &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; = self.ncs_manager)</div>
        <div>&nbsp; File
          "/usr/local/phenix-1.8-1069/phenix/phenix/refinement/strategies.py",
          line 575, in refinement_machine</div>
        <div>&nbsp; &nbsp; log=log)</div>
        <div>&nbsp; File
          "/usr/local/phenix-1.8-1069/cctbx_project/mmtbx/torsion_restraints/torsion_ncs.py",
          line 884, in fix_rotamer_outliers</div>
        <div>&nbsp; &nbsp; monitor_clashscore=False)</div>
        <div>&nbsp; File
          "/usr/local/phenix-1.8-1069/cctbx_project/mmtbx/refinement/real_space.py",
          line 336, in refine</div>
        <div>&nbsp; &nbsp; geometry_restraints_manager = geo_box)</div>
        <div>&nbsp; File
          "/usr/local/phenix-1.8-1069/cctbx_project/mmtbx/refinement/real_space.py",
          line 250, in __init__</div>
        <div>&nbsp; &nbsp; lbfgs_exception_handling_params =
          lbfgs_exception_handling_params)</div>
        <div>&nbsp; File
          "/usr/local/phenix-1.8-1069/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py",
          line 137, in __init__</div>
        <div>&nbsp; &nbsp;
          exception_handling_params=lbfgs_exception_handling_params)</div>
        <div>&nbsp; File
          "/usr/local/phenix-1.8-1069/cctbx_project/scitbx/lbfgs/__init__.py",
          line 258, in run</div>
        <div>&nbsp; &nbsp; log)</div>
        <div>&nbsp; File
          "/usr/local/phenix-1.8-1069/cctbx_project/scitbx/lbfgs/__init__.py",
          line 126, in run_c_plus_plus</div>
        <div>&nbsp; &nbsp; f, g =
          target_evaluator.compute_functional_and_gradients()</div>
        <div>
          &nbsp; 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>&nbsp; &nbsp; compute_gradients=True)</div>
        <div>&nbsp; File
          "/usr/local/phenix-1.8-1069/cctbx_project/cctbx/geometry_restraints/manager.py",
          line 716, in energies_sites</div>
        <div>&nbsp; &nbsp; flags=flags, sites_cart=sites_cart,
          site_labels=site_labels)</div>
        <div>&nbsp; File
          "/usr/local/phenix-1.8-1069/cctbx_project/cctbx/geometry_restraints/manager.py",
          line 650, in pair_proxies</div>
        <div>&nbsp; &nbsp; min_cubicle_edge=self.min_cubicle_edge)</div>
        <div>&nbsp; File
          "/usr/local/phenix-1.8-1069/cctbx_project/cctbx/geometry_restraints/__init__.py",
          line 1295, in __init__</div>
        <div>&nbsp; &nbsp; shell_asu_tables=shell_asu_tables)</div>
        <div>RuntimeError: Estimated memory allocation for cubicles
          exceeds max_number_of_bytes:</div>
        <div>&nbsp; This may be due to unreasonable parameters:</div>
        <div>&nbsp; &nbsp; cubicle_edge=5</div>
        <div>&nbsp; &nbsp; space_span=(2696.14,2555.98,2650.54)</div>
        <div>&nbsp; &nbsp; n_cubicles=(540,512,531)</div>
        <div>&nbsp; &nbsp; max_number_of_bytes=1073741824</div>
        <div>
          <br>
        </div>
        <div><br>
        </div>
        <div>&nbsp;</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 &lt;<a moz-do-not-send="true"
            href="mailto:nechols@lbl.gov">nechols@lbl.gov</a>&gt;<br>
          To: PHENIX user mailing list &lt;<a moz-do-not-send="true"
            href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>&gt;<br>
          Subject: Re: [phenixbb] runtime error in phenix.refine<br>
          Message-ID:<br>
          &nbsp; &nbsp; &nbsp; &nbsp;&lt;CALeAa1PBCCzKPJTMoDsFbsZMSO=<a
            moz-do-not-send="true"
            href="mailto:SMB_19ns%2BmfvC3HozuUcBaQ@mail.gmail.com">SMB_19ns+mfvC3HozuUcBaQ@mail.gmail.com</a>&gt;<br>
          Content-Type: text/plain; charset=ISO-8859-1<br>
          <br>
          On Sun, Jun 10, 2012 at 10:04 AM, Eugene Valkov &lt;<a
            moz-do-not-send="true" href="mailto:eugene.valkov@gmail.com">eugene.valkov@gmail.com</a>&gt;
          wrote:<br>
          &gt; I'm encountering the following during the second
          macro-cycle in<br>
          &gt; phenix.refine in latest 1.8-1069 dev build for Linux
          64-bit:<br>
          &gt;<br>
          &gt; RuntimeError: Excessive number of cubicles:<br>
          &gt; ?This may be due to unreasonable parameters:<br>
          &gt; ? ?cubicle_edge=5<br>
          &gt; ? ?space_span=(8467.78,8440.85,8372.67)<br>
          &gt; ? ?n_cubicles=(1694,1689,1675)<br>
          &gt; ? ?max_number_of_bytes=101542821888<br>
          &gt;<br>
          &gt; 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. &nbsp;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>Charles Chen</p>
      <p>Research Associate</p>
      <p>University of Pittsburgh School of Medicine</p>
      <p>Department of Anesthesiology</p>
      <p>******************************************************</p>
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