[phenixbb] error after adp refinement

[Christian Roth]

Hi Nat,

fixed in the latest build.

Thanks a lot and best wishes

Christian

Am Donnerstag 08 März 2012 15:14:25 schrieb 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
> >
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
> 
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