[phenixbb] autoBuild error, OSError: [Errno 12] Cannot allocate memory

luzuok luzuokun at 126.com
Fri May 6 19:44:00 PDT 2016


Hello,

The autobuild had been running for almost 2 hours in my Desktop, but it suddenly stopped and  posed an error message as indicated below. Is this caused by my insufficient memory?

Best wishes!
Luzuokun

Splitting work into 4 jobs and running with 2 processors using sh
background=True in /home/lu/Documents/StructurePro/why/P43212/AutoBuild_run_2_/TEMP0

Starting job 1...Log will be: /home/lu/Documents/StructurePro/why/P43212/AutoBuild_run_2_/TEMP0/RUN_FILE_4.log
Starting job 2...Log will be: /home/lu/Documents/StructurePro/why/P43212/AutoBuild_run_2_/TEMP0/RUN_FILE_5.log
Starting job 3...Log will be: /home/lu/Documents/StructurePro/why/P43212/AutoBuild_run_2_/TEMP0/RUN_FILE_6.log
Starting job 4...Log will be: /home/lu/Documents/StructurePro/why/P43212/AutoBuild_run_2_/TEMP0/RUN_FILE_7.log
Traceback (most recent call last):
  File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/autosol/AutoBaseExtend.py", line 987, in DoNextMethod
    self.CarryOutBest()     # to be obtained after it is finished
  File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/autosol/AutoBaseExtend.py", line 2147, in CarryOutBest
    getattr(self,str(self.application_method))()  # call this fn
  File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/wizards/AutoBuild.py", line 2372, in AutoBuild_build_cycle
    self.AutoBuild_rebuild_cycle_run()
  File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/wizards/AutoBuild.py", line 4714, in AutoBuild_rebuild_cycle_run
    always_reuse_model=always_reuse_model)
  File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/wizards/AutoBuild.py", line 7589, in AutoBuild_build_refine
    mtz_file=mtz_file,mtz_ref_file=mtz_ref_file)
  File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/wizards/AutoBuild.py", line 7833, in run_standard_build_in_parallel
    r.run(out=sys.stdout)
  File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/autosol/run_group_of_wizards.py", line 294, in run
    self.start_run(run_file,last=is_last)
  File "/usr/local/phenix-1.10.1-2155/modules/phenix/phenix/autosol/run_group_of_wizards.py", line 604, in start_run
    cmd+" "+self.add_double_quote(run_file,escape_space=False))
  File "/usr/local/phenix-1.10.1-2155/modules/cctbx_project/libtbx/easy_run.py", line 160, in __init__
    close_fds=not subprocess.mswindows)
  File "/usr/local/phenix-1.10.1-2155/base/lib/python2.7/subprocess.py", line 710, in __init__
    errread, errwrite)
  File "/usr/local/phenix-1.10.1-2155/base/lib/python2.7/subprocess.py", line 1223, in _execute_child
    self.pid = os.fork()
OSError: [Errno 12] Cannot allocate memory






--

卢作焜
南开大学新生物站A202


Lu Zuokun, Ph.D. Candidate
College of Life Science, Nankai University
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