[phenixbb] phenix-1.7.2-x refine error

Fri Nov 25 06:06:37 PST 2011

Hi Nat,
Hi Pavel,

With the latest (nightly build 1.7.3) the refinement works again - thanks!

Christoph

Pavel Afonine wrote:
> 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

>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb