[phenixbb] Submitting SLURM jobs through PHENIX GUI

Thomas Cleveland thomas.cleveland at gmail.com
Fri Oct 26 10:51:21 PDT 2018


Hi all,

Has anyone gotten SLURM job submission to work through the PHENIX GUI?

Under Preferences/Processes, I set Queueing system to SLURM with queue
submit comand "sbatch." The job does indeed submit to the queue, and I can
see it in the listing using the "squeue" command. However, there is quickly
an error, "OSError : [Errno 2] No such file or directory:
'/home/clevelandt/data/MX/181016_P1_merge/phenix/.phenix/tmp/10.libtbx_info.LOCK'".

I've attached the full error log. Basically the program is looking for a
lock file that isn't there. I'm not sure why it's not there. All compute
nodes should have access to this directory, and there is no caching of any
kind, so any files placed there should immediately be accessible.

I can manually submit e.g. phenix.refine jobs to the queue using the
command line and everything works fine. It would be really nice to have it
through the GUI though.

Thanks for any help,
Tom
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OSError : [Errno 2] No such file or directory: '/home/clevelandt/data/MX/181016_P1_merge/phenix/.phenix/tmp/10.libtbx_info.LOCK'
Traceback:
  File "/ibbr/phenix-1.14-3228/modules/cctbx_project/libtbx/runtime_utils.py", line 179, in run
    return_value = self.target()

  File "/ibbr/phenix-1.14-3228/modules/cctbx_project/libtbx/runtime_utils.py", line 74, in __call__
    result = self.run()

  File "/ibbr/phenix-1.14-3228/modules/phenix/phenix/refinement/runtime.py", line 79, in run
    refine_object = self._run(args, callback)

  File "/ibbr/phenix-1.14-3228/modules/phenix/phenix/refinement/runtime.py", line 92, in _run
    call_back_handler=callback)

  File "/ibbr/phenix-1.14-3228/modules/phenix/phenix/refinement/command_line.py", line 152, in run
    call_back_handler=call_back_handler)

  File "/ibbr/phenix-1.14-3228/modules/phenix/phenix/refinement/driver.py", line 1169, in run
    call_back_handler       = call_back_handler).result

  File "/ibbr/phenix-1.14-3228/modules/phenix/phenix/refinement/strategies.py", line 132, in __init__
    monitors.collect(step = "0    :", model = self.model, fmodels = self.fmodels)

  File "/ibbr/phenix-1.14-3228/modules/cctbx_project/mmtbx/refinement/__init__.py", line 47, in collect
    rigid_body_shift_accumulator = rigid_body_shift_accumulator)

  File "/ibbr/phenix-1.14-3228/modules/cctbx_project/mmtbx/refinement/print_statistics.py", line 215, in collect
    self.call_back(model, fmodel, method=step)

  File "/ibbr/phenix-1.14-3228/modules/cctbx_project/mmtbx/refinement/print_statistics.py", line 219, in call_back
    self.call_back_handler(self, model, fmodel, method)

  File "/ibbr/phenix-1.14-3228/modules/phenix/phenix/refinement/runtime.py", line 170, in __call__
    accumulate=True)

  File "/ibbr/phenix-1.14-3228/modules/cctbx_project/libtbx/callbacks.py", line 93, in __call__
    cached=cached)

  File "/ibbr/phenix-1.14-3228/modules/cctbx_project/libtbx/runtime_utils.py", line 205, in callback_wrapper
    cached=cached))

  File "/ibbr/phenix-1.14-3228/modules/cctbx_project/libtbx/runtime_utils.py", line 250, in callback_other
    os.remove(self.info_lock)



Platform info:
__FILE__ = /home/builder/slave/phenix-nightly-intel-linux-2_6-x86_64-centos6/modules/cctbx_project/boost_adaptbx/meta_ext.cpp
__DATE__ = Aug 11 2018
__TIME__ = 00:48:19
__TIMESTAMP__ = Mon May 14 23:23:22 2018
__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 4.4.7-18)
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_63
PY_VERSION = 2.7.15
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
_OPENMP = 200805
gnu libc version: 2.17
BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED_LONG
boost/TAG: None
os.name: posix
sys.platform: linux2
sys.byteorder: little
platform.platform(): Linux-3.10.0-693.21.1.el7.x86_64-x86_64-with-centos-7.4.1708-Core
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: 32
Memory total:  134,928,052,224
Memory free:    90,739,843,072
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


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