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

[Pavel Afonine]

Hi Robert,

if this error occurs in the latest available nightly build then please 
send me input files and briefly describe steps that lead to the crash. 
-Thanks!
Pavel

On 11/15/21 13:04, Robert Munoz wrote:
> 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 <http://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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