[phenixbb] rosetta refine error message

[Nigel Moriarty]

Georg

We got you error message via the GUI bug system and I'm working with others
to get this bug solved. Can you send me (directly) the input files so I can
double check that we have solved it?

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Mon, Dec 7, 2015 at 12:40 PM, Georg Mlynek <georg.mlynek at univie.ac.at>
wrote:

> Dear Phenix/Rosetta Developers, we get following error message when
> running rosetta.refine on ubuntu 14.04 and on scientic linux 6.0.
>
>
>
> untimeError : Aborted due to error in job 1.
> Traceback:
>   File
>
> "/home/xsoft/phenix-dev-2247/modules/cctbx_project/libtbx/runtime_utils.py",
> line 179, in run
>     return_value = self.target()
>
>   File
>
> "/home/xsoft/phenix-dev-2247/modules/cctbx_project/libtbx/runtime_utils.py",
> line 74, in __call__
>     result = self.run()
>
>   File
>
> "/home/xsoft/phenix-dev-2247/modules/phenix/phenix/command_line/rosetta_refine.py",
> line 300, in run
>     return run(args=list(self.args))
>
>   File
>
> "/home/xsoft/phenix-dev-2247/modules/phenix/phenix/command_line/rosetta_refine.py",
> line 189, in run
>     debug=params.output.debug)
>
>   File
> "/home/xsoft/phenix-dev-2247/modules/phenix/phenix/rosetta/refine.py",
> line 313, in __init__
>     self.run_jobs()
>
>   File
> "/home/xsoft/phenix-dev-2247/modules/phenix/phenix/rosetta/refine.py",
> line 397, in run_jobs
>     check_result(result)
>
>   File
> "/home/xsoft/phenix-dev-2247/modules/phenix/phenix/rosetta/refine.py",
> line 379, in check_result
>     raise RuntimeError("Aborted due to error in job %d." % result.job_id)
>
>
>
> Platform info:
> __FILE__ =
>
> /home/builder/slave/phenix-nightly-intel-linux-2_6-x86_64-centos6/modules/cctbx_project/boost_adaptbx/meta_ext.cpp
> __DATE__ = Dec  3 2015
> __TIME__ = 23:02:36
> __TIMESTAMP__ = Tue Sep  1 10:03:35 2015
> __x86_64__
> __linux
> __GNUC__ = 4
> __GNUC_MINOR__ = 4
> __GNUC_PATCHLEVEL__ = 7
> boost::python::cxxabi_cxa_demangle_is_broken(): false
> __GXX_WEAK__ = 1
> __LP64__ = 1
> __VERSION__ = 4.4.7 20120313 (Red Hat 4.4.7-4)
> FE_INEXACT = 32
> FE_DIVBYZERO = 4
> FE_UNDERFLOW = 16
> FE_OVERFLOW = 8
> FE_INVALID = 1
> FE_ALL_EXCEPT = 61
> __SSE2__ = 1
> BOOST_LIB_VERSION = 1_55
> PY_VERSION = 2.7.8
> 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
> gnu libc version: 2.12
> BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED_LONG
> boost/TAG: 86799
> os.name: posix
> sys.platform: linux2
> sys.byteorder: little
> platform.platform():
> Linux-2.6.32-573.7.1.el6.x86_64-x86_64-with-redhat-6.7-Santiago
> platform.architecture(): ('64bit', 'ELF')
> floating_point_exceptions.division_by_zero_trapped: False
> floating_point_exceptions.invalid_trapped: False
> floating_point_exceptions.overflow_trapped: False
> number of processors: 24
> Memory total:  76,158,160,896
> Memory free:   60,290,256,896
> 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
>
>
> Many thanks in advance, Georg.
>
>
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