[phenixbb] error generating output file overal_best pdb

Terwilliger, Thomas C terwilliger at lanl.gov
Fri Mar 23 13:03:30 PDT 2012


Hi Andres,

I'm not sure if someone already answered this...but in case they didn't here is my guess.  

This sounds like you may be running on an NFS-mounted disk (i.e., not one on your local computer) and the system was busy and an attempt to write to your disk timed out.  If this is the case, then you might expect to have pretty random problems of this sort.

One possible solution is to change the time-out value in autobuild:

  max_wait_time= 1.0 You can specify the length of time (seconds) to wait
                     when looking for a file. If you have a cluster where jobs
                     do not start right away you may need a longer time to
                     wait. The symptom of too short a wait time is 'File not
                     found'

The default is 1 second...you could try 10 or 20 and see if that makes the problem go away.

All the best,
Tom T
________________________________________
From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Andres PALENCIA [palencia at embl.fr]
Sent: Thursday, March 22, 2012 12:59 PM
To: PHENIX user mailing list
Subject: [phenixbb] error generating output file overal_best pdb

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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