[phenixbb] Error: "cannot allocate memory"

[Tanner, John J.]

We also received these errors for large unit cells with high resolution diffraction.  We solved the problem by installing more memory and using 64 bit architecture.


John J. Tanner
Professor of Biochemistry and Chemistry
University of Missouri-Columbia
125 Chemistry Building
Columbia, MO 65211
Phone: 573-884-1280
Fax: 573-882-2754
Email: tannerjj at missouri.edu<mailto:tannerjj at missouri.edu>
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html

On Aug 19, 2014, at 12:15 PM, sujata halder <halder.sujata at gmail.com<mailto:halder.sujata at gmail.com>>
 wrote:

Hi,

I am trying to refine a protein with 60 chains (a T=1 virus; 5-3-2 symmetry) and each chain has 520 amino acids. I am using version 1.9 (Release tag: 1692). The job stopped midway and gave the error below followed by "Cannot allocate memory". I have run a similar job (i.e using a similar sized protein) before on an older version (version 1.7) and that worked.
Looking at the error I can't really figure out if the problem is related to installation or a missing module or something different about the code.

I can share my input and output files off-list.

Here is the error:


====================== XYZ individual (reciprocal space) ======================

    R-FACTORS           RMSD     CLASH  RAMA  ROTA CBET WEIGHT    TARGETS
 work  free  delta  bonds  angl                                  data   restr
28.80 29.29   0.49  0.016   1.6   11.9   0.8   7.4   60   none  0.093 160.8996
Traceback (most recent call last):
  File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6-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-1.9-1692/phenix/phenix/refinement/command_line.py", line 163, in run
    call_back_handler=call_back_handler)
  File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/driver.py", line 1577, in run
    reference_model_manager = self.reference_model_manager).result
  File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/strategies.py", line 183, in __init__
    ion_placement_manager = ion_placement_manager)
  File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/macro_cycle.py", line 114, in __init__
    self.call(self.xyzrec,   "XYZ individual (reciprocal space)")
  File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/macro_cycle.py", line 142, in call
    func(prefix = prefix)
  File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/macro_cycle.py", line 374, in xyzrec
    prefix         = prefix)
  File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/xyz_reciprocal_space.py", line 204, in __init__
    call_back=(len(trial_weights)==1))
  File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/xyz_reciprocal_space.py", line 314, in try_weight
    result = self.show(weight=wt, print_stats=print_stats, call_back=call_back)
  File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/xyz_reciprocal_space.py", line 365, in show
    molprobity_scores = self.main.use_molprobity)
  File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/model.py", line 1341, in geometry_statistics
    molprobity_scores  = molprobity_scores)
  File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/model_statistics.py", line 99, in __init__
    self.clashscore = clashscore(pdb_hierarchy=pdb_hierarchy).get_clashscore()
  File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/validation/clashscore.py", line 133, in __init__
    verbose=verbose)
  File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/validation/clashscore.py", line 257, in __init__
    self.run_probe_clashscore(self.h_pdb_string)
  File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/validation/clashscore.py", line 341, in run_probe_clashscore
    stdin_lines=pdb_string).raise_if_errors().stdout_lines
  File "/usr/local/phenix-1.9-1692/cctbx_project/libtbx/easy_run.py", line 158, in __init__
    close_fds=not subprocess.mswindows)
  File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6-x86_64/base/lib/python2.7/subprocess.py", line 709, in __init__
    errread, errwrite)
  File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6-x86_64/base/lib/python2.7/subprocess.py", line 1222, in _execute_child
    self.pid = os.fork()
OSError: [Errno 12] Cannot allocate memory
-------------------------------------------------------------------------------------------------------------

Thanks,
Sujata
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