[phenixbb] error after adp refinement

[Nathaniel Echols]

Please update to the latest nightly build (1000!) - I think either
Pavel or I fixed this a few weeks ago.  (But if not, let us know
ASAP.)

-Nat

On Thu, Mar 8, 2012 at 5:37 AM, Christian Roth
<christian.roth at bbz.uni-leipzig.de> wrote:
> 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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