Re: [phenixbb] phenixbb Digest, Vol 79, Issue 4

14 Jun 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 mailto:[email protected]>
    To: PHENIX user mailing list mailto:[email protected]>
    Subject: Re: [phenixbb] runtime error in phenix.refine
    Message-ID:
    mailto:SMB_19ns%[email protected]>
    Content-Type: text/plain; charset=ISO-8859-1
On Sun, Jun 10, 2012 at 10:04 AM, Eugene Valkov
    mailto:[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
--
***************************************************
Charles Chen
Research Associate
University of Pittsburgh School of Medicine
Department of Anesthesiology
******************************************************
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Re: [phenixbb] phenixbb Digest, Vol 79, Issue 4

Pavel Afonine