[phenixbb] error after adp refinement
Christian Roth
christian.roth at bbz.uni-leipzig.de
Thu Mar 8 04:37:12 PST 2012
Dear Phenix Team,
I started a refinement with anisotropic adp and weight optimization and
directly after the optimization step an error appeared which never appeared
befor for me.
The previous steps of mask optimization and xyz refinement worked well.
Best Regards
Christian
AssertionError :
Traceback:
File "/userdata-2/christian/phenix-
dev-979/cctbx_project/libtbx/thread_utils.py", line 229, in run
return_value = self._target(self._args, self._kwargs, self._c)
File "/userdata-2/christian/phenix-
dev-979/cctbx_project/libtbx/runtime_utils.py", line 72, in __call__
result = self.target()
File "/userdata-2/christian/phenix-
dev-979/phenix/phenix/refinement/runtime.py", line 68, in __call__
call_back_handler=callback)
File "/userdata-2/christian/phenix-
dev-979/phenix/phenix/refinement/command_line.py", line 97, in run
call_back_handler=call_back_handler)
File "/userdata-2/christian/phenix-
dev-979/phenix/phenix/refinement/driver.py", line 1494, in run
ncs_manager = self.ncs_manager)
File "/userdata-2/christian/phenix-
dev-979/phenix/phenix/refinement/strategies.py", line 1046, in
refinement_machine
h_params = h_params)
File "/userdata-2/christian/phenix-
dev-979/cctbx_project/mmtbx/refinement/adp_refinement.py", line 212, in __init__
nproc = nproc)
File "/userdata-2/christian/phenix-
dev-979/cctbx_project/mmtbx/refinement/adp_refinement.py", line 389, in __init__
compute_gradients=False).target_work())
Platform info:
__FILE__ = /net/longnose/scratch2/phenix/phenix-
dev-979/cctbx_project/boost_adaptbx/meta_ext.cpp
__DATE__ = Feb 7 2012
__TIME__ = 02:05:24
__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: 2.10.1
BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED
os.name: posix
sys.platform: linux2
sys.byteorder: little
platform.platform(): Linux-2.6.31-23-generic-pae-i686-with-debian-squeeze-sid
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: 25,405,636,608
Memory free: 20,305,633,280
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 = Å
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