phenix-1.7.2-x refine error
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
On Thu, Nov 24, 2011 at 9:46 AM, Christoph Parthier
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:
... 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?
Probably neither - you're just running out of memory. My guess is something in the map-related calculations changed between 1.7.1 and 1.7.2 that made it less memory-efficient (I've seen the same error a lot recently). You're using a 32-bit OS, so the maximum amount of memory that Phenix can use is limited to 2GB - if your hardware supports a 64-bit kernel, that may solve the problem. I'd also recommend trying the latest nightly build, which should consume less memory creating maps, although I'm not sure if will help with this specific case. -Nat
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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (3)
-
Christoph Parthier -
Nathaniel Echols -
Pavel Afonine