[phenixbb] Crashing Phenix during MRage

[Dr. Robert Oeffner]

Dear professor Reza,

Sorry for the problems you’re having with MRage. If it wasn’t for the issues you’re having installing the latest official phenix release I was gonna suggest you try running MRage with that. Much has changed in the underlying code. Have you tried the centos6 installer version instead?


Regards,

Rob
-- 
Robert Oeffner, Ph.D.
Research Associate, The Read Group
Department of Haematology,
Cambridge Institute for Medical Research
University of Cambridge
Cambridge Biomedical Campus
Wellcome Trust/MRC Building
Hills Road
Cambridge CB2 0XY

www.cimr.cam.ac.uk/investigators/read/index.html

From: Reza Khayat 
Sent: Wednesday, November 23, 2016 2:05 PM
To: phenixbb at phenix-online.org 
Subject: [phenixbb] Crashing Phenix during MRage

Hi,



MRage stops running after sometime with the following error:



===========================================


Process Process-1:29434:
Traceback (most recent call last):
  File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
    self.run()
  File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 114, in run
    self._target(*self._args, **self._kwargs)
  File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/engine.py", line 175, in mpjob_run
    result = calculation.run()
  File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/calculation.py", line 138, in run
    assert len( raw ) == 1
AssertionError
Process Process-1:29436:
Traceback (most recent call last):
  File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
    self.run()
  File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 114, in run
    self._target(*self._args, **self._kwargs)
  File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/engine.py", line 175, in mpjob_run
    result = calculation.run()
  File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/calculation.py", line 138, in run
    assert len( raw ) == 1
AssertionError
Process Process-1:29438:
Traceback (most recent call last):
  File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
    self.run()
  File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 114, in run
    self._target(*self._args, **self._kwargs)
  File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/engine.py", line 175, in mpjob_run
    result = calculation.run()
  File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/calculation.py", line 138, in run
    assert len( raw ) == 1
AssertionError
Process Process-1:29440:
Traceback (most recent call last):
  File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
    self.run()
  File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 114, in run
    self._target(*self._args, **self._kwargs)
  File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/engine.py", line 175, in mpjob_run
    result = calculation.run()
  File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/calculation.py", line 138, in run
    assert len( raw ) == 1
AssertionError




** (gedit:5901): WARNING **: Couldn't connect to accessibility bus: Failed to connect to socket /tmp/dbus-pJCFNfwEtI: Connection refused

(gedit:5901): GLib-GIO-ERROR **: No GSettings schemas are installed on the system


==============================================================================



The system is a Debian 8 (Jessie), and I'm using 40 threads for the job. Also, I'm using X11 forwarding for the GUI. Any help is appreciated. 



Best wishes,
Reza




Reza Khayat, PhD 
Assistant Professor 
City College of New York
Department of Chemistry
New York, NY 10031




--------------------------------------------------------------------------------
_______________________________________________
phenixbb mailing list
phenixbb at phenix-online.org
http://phenix-online.org/mailman/listinfo/phenixbb
Unsubscribe: phenixbb-leave at phenix-online.org
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20161123/b7977c3c/attachment.htm>