[phenixbb] error generating output file overal_best pdb

Nathaniel Echols nechols at lbl.gov
Thu Mar 22 12:02:31 PDT 2012


This isn't AutoBuild failing - it's the GUI choking when it tries to
update the job status.  (AutoBuild could still be okay, but I can't
tell from this message.)  The error seems to be indicating that your
home directory is no longer readable, which is bizarre; it could be an
NFS error.  What happens when you run this command?

ls -l /user/palencia

thanks,
Nat

On Thu, Mar 22, 2012 at 11:59 AM, Andres PALENCIA <palencia at embl.fr> wrote:
> Dear Phenix users,
>
> I have been running Phenix_Autobuild successfully for the last houra. The
> program generates the corresponding Autobuild_run_** folders as usually,
> however I got an error message when the program was trying to generate the
> overal_best.pdb file after the Autobuild cycle 3.
>
> I copy below the error message that I got, thank you in advance for any
> help:
>
>
> OSError : [Errno 2] No such file or directory: '/user/palencia'
>
> Traceback (most recent call last):
>  File
> "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/phenix/wxGUI2/Home/Jobs.py",
> line 170, in OnTimer
>    self.project.refresh_detached_jobs()
>  File
> "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/phenix/wxGUI2/Tracking.py",
> line 72, in refresh_detached_jobs
>    tmp_dir = self.get_tmp_dir()
>  File
> "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/phenix/phenix/tracking/project.py",
> line 97, in get_tmp_dir
>    os.makedirs(tmp_dir)
>  File
> "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py",
> line 150, in makedirs
>    makedirs(head, mode)
>  File
> "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py",
> line 150, in makedirs
>    makedirs(head, mode)
>  File
> "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py",
> line 150, in makedirs
>    makedirs(head, mode)
>  File
> "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py",
> line 150, in makedirs
>    makedirs(head, mode)
>  File
> "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py",
> line 150, in makedirs
>    makedirs(head, mode)
>  File
> "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py",
> line 150, in makedirs
>    makedirs(head, mode)
>  File
> "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py",
> line 157, in makedirs
>    mkdir(name, mode)
> OSError: [Errno 2] No such file or directory: '/user/palencia'
>
>
>
> Platform info:
> __FILE__ =
> /net/anaconda/scratch1/phenix/phenix-1.7.3-928/cctbx_project/boost_adaptbx/meta_ext.cpp
> __DATE__ = Dec  6 2011
> __TIME__ = 04:18:10
> __x86_64__
> __linux
> __GNUC__ = 3
> __GNUC_MINOR__ = 4
> __GNUC_PATCHLEVEL__ = 2
> boost::python::cxxabi_cxa_demangle_is_broken(): false
> __GXX_WEAK__ = 1
> __LP64__ = 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
> __SSE2__ = 1
> 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) = 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: 2.5
> BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED_LONG
> os.name: posix
> sys.platform: linux2
> sys.byteorder: little
> platform.platform(): Linux-2.6.18-238.9.1.el5-x86_64-with-redhat-5.7-Final
> 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:  25,263,722,496
> Memory free:   20,157,317,120
> 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 = Ã…
>
> _______________________________________________
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