[phenixbb] Phenix bug report [robertm at lbl.gov - Mon Jun 22 19:42:79 2021]

[Robert Munoz]

User name: Robert Munoz
  E-mail address: robertm at lbl.gov
  Version: 1.18.2-3874
  Platform: mac-intel-osx-x86_64
  Comments: Trying to refinement using locscale out map

  Traceback:
RuntimeError : cctbx Internal Error:
/Users/builder/slave/phenix-nightly-mac-intel-osx-x86_64/modules/cctbx_project/cctbx/maptbx/resolution.h(38):
CCTBX_ASSERT(sum_all != 0.) failure.
Traceback:
  File
"/Applications/phenix-1.18.2-3874/modules/cctbx_project/libtbx/runtime_utils.py",
line 181, in run
    return_value = self.target()

  File
"/Applications/phenix-1.18.2-3874/modules/cctbx_project/libtbx/runtime_utils.py",
line 76, in __call__
    result = self.run()

  File
"/Applications/phenix-1.18.2-3874/modules/phenix/phenix/command_line/real_space_refine.py",
line 908, in run
    self.result = run(args=self.args, validated=True, log=sys.stdout)

  File
"/Applications/phenix-1.18.2-3874/modules/phenix/phenix/command_line/real_space_refine.py",
line 581, in __init__
    self.caller(func = self.initialize,       prefix="Initialize")

  File
"/Applications/phenix-1.18.2-3874/modules/phenix/phenix/command_line/real_space_refine.py",
line 619, in caller
    status = func(prefix=prefix, **kwargs)

  File
"/Applications/phenix-1.18.2-3874/modules/phenix/phenix/command_line/real_space_refine.py",
line 696, in initialize
    self.inputs = self.process_inputs()

  File
"/Applications/phenix-1.18.2-3874/modules/phenix/phenix/command_line/real_space_refine.py",
line 675, in process_inputs
    return process_inputs_stage_1(process_inputs_stage_0_object=pis_0,
log=self.log)

  File
"/Applications/phenix-1.18.2-3874/modules/phenix/phenix/command_line/real_space_refine.py",
line 403, in process_inputs_stage_1
    crystal_symmetry = model.crystal_symmetry()).result.d99

  File
"/Applications/phenix-1.18.2-3874/modules/cctbx_project/cctbx/maptbx/__init__.py",
line 117, in __init__
    d_max      = self.d_max)



  Platform info:
  __FILE__ =
/Users/builder/slave/phenix-nightly-mac-intel-osx-x86_64/modules/cctbx_project/boost_adaptbx/meta_ext.cpp
__DATE__ = May 17 2020
__TIME__ = 22:35:27
__TIMESTAMP__ = Thu Feb 27 10:57:04 2020
__x86_64__
__APPLE_CC__ = 6000
__GNUC__ = 4
__GNUC_MINOR__ = 2
__GNUC_PATCHLEVEL__ = 1
__clang__
__clang_major__ = 11
__clang_minor__ = 0
__clang_patchlevel__ = 0
__clang_version__ = 11.0.0 (clang-1100.0.33.17)
__llvm__
__GXX_WEAK__ = 1
__LP64__ = 1
__VERSION__ = 4.2.1 Compatible Apple LLVM 11.0.0 (clang-1100.0.33.17)
FE_INEXACT = 32
FE_DIVBYZERO = 4
FE_UNDERFLOW = 16
FE_OVERFLOW = 8
FE_INVALID = 1
FE_ALL_EXCEPT = 63
__SSE2__ = 1
BOOST_LIB_VERSION = 1_63
PY_VERSION = 2.7.15
PYTHON_API_VERSION = 1013
sizeof(bool) = 1
sizeof(short) = 2
sizeof(int) = 4
sizeof(long) = 8
sizeof(std::size_t) = 8
sizeof(void*) = 8
sizeof(long long) = 8
sizeof(float) = 4
sizeof(double) = 8
sizeof(long double) = 16
sizeof(boost::int32_t) = 4
sizeof(boost::uint32_t) = 4
sizeof(wchar_t) = 4
__PTRDIFF_TYPE__
Py_USING_UNICODE
sizeof(PY_UNICODE_TYPE) = 2
BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED_LONG
boost/TAG: None
os.name: posix
sys.platform: darwin
sys.byteorder: little
platform.platform(): Darwin-17.7.0-x86_64-i386-64bit
platform.architecture(): ('64bit', '')
floating_point_exceptions.division_by_zero_trapped: False
floating_point_exceptions.invalid_trapped: False
floating_point_exceptions.overflow_trapped: False
number of processors: 4
Memory total:  17,179,869,184
Memory free:          unknown
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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