[phenixbb] phenix-1.7.2-x refine error

Pavel Afonine pafonine at lbl.gov
Thu Nov 24 16:21:29 PST 2011


Hi Christoph,

yes, most likely your computer runs out of memory when phenix.refine 
creates 2mFo-Fc "missing-Fobs-filled" map 
(http://www.phenix-online.org/papers/dz5186_reprint.pdf). This is 
because when it restores missing Fobs as DFc it excludes unreliably 
defined model parts based on computing map CC. And map CC requires 
calculating two maps.

Try latest PHENIX to see if that works (Nat recently did a change that 
should help to reduce memory consumption at this step):

http://www.phenix-online.org/download/nightly_builds.cgi

or disable calculation of "missing-Fobs-filled" map.

Pavel


On 11/24/11 9:46 AM, Christoph Parthier wrote:
> Dear Phenix developers,
>
> Using the current phenix version, refinements of a 'certain structure' 
> always stop with the error message quoted below, while the refinement 
> of other 'similar structures' work flawlessly.
>
> In the error case the three scheduled macrocycles of refinement seem 
> to finish (the refined PDB is there) but at there seems to be problem 
> in finishing the job - the output MTZ file has zero byte length and 
> the last line in refine.log is:
>
> ============================== Exporting results 
> ==============================
>
>
>
> This occurs with several 1.7.2-x versions of phenix, I'm not sure 
> about 1.7.1-x. Interestingly, the 'problem structure' can be refined 
> without problems using the same input files in phenix-1.7-650.
>
> Any idea whether this is due to an installation problem or a bug?
>
> Thanks,
> Christoph
>
> Here's the error message:
>
>
> MemoryError :
> Traceback:
>   File "/cryst/phenix-1.7.2-869/cctbx_project/libtbx/thread_utils.py", 
> line 229, in run
>     return_value = self._target(self._args, self._kwargs, self._c)
>
>   File 
> "/cryst/phenix-1.7.2-869/cctbx_project/libtbx/runtime_utils.py", line 
> 72, in __call__
>     result = self.target()
>
>   File "/cryst/phenix-1.7.2-869/phenix/phenix/refinement/runtime.py", 
> line 67, in __call__
>     call_back_handler=callback)
>
>   File 
> "/cryst/phenix-1.7.2-869/phenix/phenix/refinement/command_line.py", 
> line 115, in run
>     map_manger.write_files()
>
>   File "/cryst/phenix-1.7.2-869/phenix/phenix/refinement/driver.py", 
> line 1535, in write_files
>     map_coeff_dataset=self.write_mtz_file(),
>
>   File "/cryst/phenix-1.7.2-869/phenix/phenix/refinement/driver.py", 
> line 1524, in write_mtz_file
>     params = self.map_params.map_coefficients)
>
>   File "/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/maps/__init__.py", 
> line 502, in __init__
>     coeffs = map_coefficients_from_fmodel(fmodel = fmodel, params = mcp)
>
>   File "/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/maps/__init__.py", 
> line 353, in map_coefficients_from_fmodel
>     fill_mode          = "dfmodel")
>
>   File "/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/f_model.py", line 
> 1887, in electron_density_map
>     fill_mode              = fill_mode)
>
>   File "/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/map_tools.py", 
> line 114, in __init__
>     update_scaling = update_scaling)
>
>   File "/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/f_model.py", line 
> 1663, in fill_missing_f_obs
>     fmodel=self, fill_mode=fill_mode, update_scaling=update_scaling)
>
>   File 
> "/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/missing_reflections_handler.py", 
> line 131, in fill_missing_f_obs
>     fmodel = select_by_map_cc(fmodel = fmodel.deep_copy()))
>
>   File 
> "/cryst/phenix-1.7.2-869/cctbx_project/mmtbx/missing_reflections_handler.py", 
> line 85, in select_by_map_cc
>     fourier_coefficients = coeffs)
>
>   File 
> "/cryst/phenix-1.7.2-869/cctbx_project/cctbx/miller/__init__.py", line 
> 3688, in __init__
>     conjugate_flag=True)
>
>
>
> Platform info:
> __FILE__ = 
> /net/longnose/scratch2/phenix/phenix-1.7.2-869/cctbx_project/boost_adaptbx/meta_ext.cpp
> __DATE__ = Sep 23 2011
> __TIME__ = 00:13:14
> __i386__
> __linux
> __GNUC__ = 3
> __GNUC_MINOR__ = 4
> __GNUC_PATCHLEVEL__ = 2
> boost::python::cxxabi_cxa_demangle_is_broken(): false
> __GXX_WEAK__ = 1
> __VERSION__ = 3.4.2 20041017 (Red Hat 3.4.2-6.fc3)
> FE_INEXACT = 32
> FE_DIVBYZERO = 4
> FE_UNDERFLOW = 16
> FE_OVERFLOW = 8
> FE_INVALID = 1
> FE_ALL_EXCEPT = 61
> BOOST_LIB_VERSION = 1_48
> PY_VERSION = 2.7.2
> PYTHON_API_VERSION = 1013
> sizeof(bool) = 1
> sizeof(short) = 2
> sizeof(int) = 4
> sizeof(long) = 4
> sizeof(std::size_t) = 4
> sizeof(void*) = 4
> sizeof(long long) = 8
> sizeof(float) = 4
> sizeof(double) = 8
> sizeof(long double) = 12
> sizeof(boost::int32_t) = 4
> sizeof(boost::uint32_t) = 4
> sizeof(wchar_t) = 4
> __PTRDIFF_TYPE__
> Py_USING_UNICODE
> sizeof(PY_UNICODE_TYPE) = 2
> gnu libc version: 2.6.1
> BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED
> os.name: posix
> sys.platform: linux2
> sys.byteorder: little
> platform.platform(): 
> Linux-2.6.22.13-GOLIAT-0.3-bigsmp-i686-with-SuSE-10.3-i586
> platform.architecture(): ('32bit', 'ELF')
> floating_point_exceptions.division_by_zero_trapped: False
> floating_point_exceptions.invalid_trapped: False
> floating_point_exceptions.overflow_trapped: False
> number of processors: 8
> Memory total:  4,238,028,800
> Memory free:   3,715,174,400
> import thread: OK
> "hello" = ['h', 'e', 'l', 'l', 'o']
> u"hello" = ['h', '\x00', 'e', '\x00', 'l', '\x00', 'l', '\x00', 'o', 
> '\x00']
> u"\u00C5" = ['\xc5', '\x00'] as utf-8 = ['\xc3', '\x85']
> LATIN CAPITAL LETTER A WITH RING ABOVE = Ã

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