[phenixbb] RuntimeError: Not enough memory for cubicles:
Nathaniel Echols
NEchols at lbl.gov
Thu Feb 26 18:08:37 PST 2009
The ordered_solvent option is probably okay, but the peak/hole search
is turned off by default in the current release (1.4-3). Try
upgrading and see if that fixes the problem.
thanks,
Nat
On Feb 26, 2009, at 6:01 PM, Gino Cingolani wrote:
> Hi,
>
> I'm refining a huge structure with ~13,000 residues in the
> asymmetric unit.
> I started a massive job with the following inputs:
>
> phenix.refine data.mtz model.pdb
> ordered_solvent=true
> strategy=individual_sites+group_adp+tls
> tls_group_selections.params
> main.ncs=true
> main.number_of_macro_cycles=10
>
> After >24 h the Rfree had dropped from 45% to 33%, but at the very
> end,
> just before outputting the refined pdb model, Phenix died with the
> following
> error message:
>
>
> ############################################################
> Hello all========== residual map mFobs-DFmodel: highest peaks and
> deepst
> holes =========
> ----------peaks----------
>
> Traceback (most recent call last):
> File "/usr/local/phenix-1.3-final/phenix/phenix/command_line/
> refine.py",
> line 5, in <module>
> command_line.run(command_name="phenix.refine", args=sys.argv[1:])
> File
> "/usr/local/phenix-1.3-final/phenix/phenix/refinement/
> command_line.py", line
> 89, in run
> call_back_after_monitor_collect=call_back_after_monitor_collect)
> File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/
> driver.py",
> line 1081, in run
> call_back_after_monitor_collect = call_back_after_monitor_collect)
> File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/
> strategies.py",
> line 724, in refinement_machine
> fmodels=fmodels, model=model, log=log)
> File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/
> strategies.py",
> line 752, in highest_peaks_and_deepest_holes_in_residual_map
> log = log)
> File "/usr/local/phenix-1.3-final/mmtbx/mmtbx/find_peaks.py", line
> 210, in
> show_highest_peaks_and_deepest_holes
> log = log)
> File "/usr/local/phenix-1.3-final/mmtbx/mmtbx/find_peaks.py", line
> 117, in
> __init__
> map = fft_map_data).all(max_clusters = max_number_of_peaks)
> File "/usr/local/phenix-1.3-final/cctbx/cctbx/maptbx/__init__.py",
> line
> 196, in peak_search
> max_clusters=parameters.max_clusters())
> File "/usr/local/phenix-1.3-final/cctbx/cctbx/maptbx/__init__.py",
> line
> 303, in __init__
> general_positions_only=self._general_positions_only)
> File "/usr/local/phenix-1.3-final/cctbx/cctbx/crystal/__init__.py",
> line
> 477, in site_cluster_analysis
> cubicle_epsilon=cubicle_epsilon)
> RuntimeError: Not enough memory for cubicles:
> This may be due to unreasonable parameters:
> cubicle_edge=0.7
> space_span=(293.298,92.903,214.527)
> n_cubicles=(419,133,307)
> max_number_of_bytes=1724676096
>
>
> ######################################################
>
> Any suggestion on what to do?
> As invididual refinement modules (e.g. regular rigid body
> refinemnet, SA,
> energy minimization, TLS, etc)
> run OK, is the problem coming from the "ordered_solvent=true"
> command?
> Thanks in advance!
>
>
> Gino Cingolani, Ph.D.
>
> ***********************************************************
> Gino Cingolani, Ph.D.
> Assistant Professor
> Dept. of Biochemistry and Molecular Biology
> SUNY Upstate Medical University
> 750 E. Adams Street, Syracuse, NY, 13210
> Tel. (315) 464 8744
> Fax. (315) 464 8750
> Email: cingolag at upstate.edu
> ***********************************************************
> "Nati non foste per viver come bruti, ma per seguir virtute e
> conoscenza"
> ("You were not born to live like brutes, but to follow virtue and
> knowledge")
> Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)
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-------------------
Nathaniel Echols
Lawrence Berkeley Lab
510-486-5136
NEchols at lbl.gov
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