[phenixbb] RuntimeError: Not enough memory for cubicles:

Pavel Afonine PAfonine at lbl.gov
Thu Feb 26 18:53:44 PST 2009


Hi Gino,

sorry for the problem. Please use the latest version of PHENIX:
http://www.phenix-online.org/download/

As already suggested, try setting (this is the default in the latest 
version):
show_residual_map_peaks_and_holes=False
this most likely will help.

If not, to further reduce the memory consumption try using these 
parameters all at once:

refinement {
 output {
   write_maps = False
 }
 electron_density_maps {
   grid_resolution_factor = 1/3.
 }
 main {
   show_residual_map_peaks_and_holes = False
 }
 ordered_solvent {
   correct_drifted_waters = False
 }
 peak_search {
   resolution_factor = 1./3.
 }
 mask {
   grid_step_factor = 3.0
 }
}

The word "cubicles" tells me that this is not a memory problem though... 
Anyway, setting "show_residual_map_peaks_and_holes=False" or using the 
latest version should help. But it will actually hide the problem. If 
you want us to debug it and so prevent it in future, we will need to 
have the data, model and the exact command you used.

Pavel.


On 2/26/09 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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>   



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