Phenix dev-2247 fails to start
Dear developers, I am now having some troubles initiating the most updated nightly built dev-2247. I have to use this version because it is supposed to have a bug fixed based on my bug report in November. My machine is running Debian 7 with kernel version 3.2.0-4-amd64. And the pheinx installation file I downloaded is the 64 bit linux version for CentOS 5. The symptom is that after I called phenix from a terminal window, there is an error message saying "local 'en_GB' cannot be set" (which is always the case and which does not seem to matter). After that, phenix GUI did not start at all, but ps command shows two python2.7 processes running. Running phenix from command line seems to work fine. Before switching to this version I was running the stable version 1.10.1-2155, and have no problem. Is there any simple fix? If not, I will probably just stick to the command line version for the moment. Thanks a lot, Chen
Hi Chen,
It looks like en_GB is associated with English (Great Britain). I'm not
sure why that would cause the GUI to not work. What is the output from
typing "locale" at a terminal? A possible fix would be to set the LC_ALL
environment variable to "C". For C shells, you would type "setenv LC_ALL C"
and for bash, the command would be "export LC_ALL=C".
Let me know if that doesn't solve the problem. Thanks!
--
Billy K. Poon
Research Scientist
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
Web: https://phenix-online.org
On Sun, Dec 6, 2015 at 7:25 PM, Chen Zhao
Dear developers,
I am now having some troubles initiating the most updated nightly built dev-2247. I have to use this version because it is supposed to have a bug fixed based on my bug report in November. My machine is running Debian 7 with kernel version 3.2.0-4-amd64. And the pheinx installation file I downloaded is the 64 bit linux version for CentOS 5. The symptom is that after I called phenix from a terminal window, there is an error message saying "local 'en_GB' cannot be set" (which is always the case and which does not seem to matter). After that, phenix GUI did not start at all, but ps command shows two python2.7 processes running. Running phenix from command line seems to work fine. Before switching to this version I was running the stable version 1.10.1-2155, and have no problem.
Is there any simple fix? If not, I will probably just stick to the command line version for the moment.
Thanks a lot, Chen
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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.
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 : [email protected]
Fax : 510-486-5909 Web : CCI.LBL.gov
On Mon, Dec 7, 2015 at 12:40 PM, Georg Mlynek
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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participants (4)
-
Billy Poon -
Chen Zhao -
Georg Mlynek -
Nigel Moriarty