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<p>Hi Rob,</p>
<p><br>
</p>
<p>I'll give it a try.</p>
<p><br>
</p>
<p>Best wishes,<br>
Reza</p>
<div id="Signature">
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<br>
Reza Khayat, PhD
<div>Assistant Professor </div>
<div>City College of New York</div>
<div>Department of Chemistry</div>
<div>New York, NY 10031</div>
</div>
</div>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" color="#000000" face="Calibri, sans-serif"><b>From:</b> Dr. Robert Oeffner <rdo20@cam.ac.uk><br>
<b>Sent:</b> Wednesday, November 23, 2016 9:24 AM<br>
<b>To:</b> Reza Khayat; phenixbb@phenix-online.org<br>
<b>Subject:</b> Re: [phenixbb] Crashing Phenix during MRage</font>
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<div>Dear professor Reza,</div>
<div> </div>
<div>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?</div>
<div> </div>
<div> </div>
<div>Regards,</div>
<div> </div>
<div>Rob</div>
<div style="font-size:12pt; font-family:'Calibri'; color:#000000">-- <br>
Robert Oeffner, Ph.D.<br>
Research Associate, The Read Group<br>
Department of Haematology,<br>
Cambridge Institute for Medical Research<br>
University of Cambridge<br>
Cambridge Biomedical Campus<br>
Wellcome Trust/MRC Building<br>
Hills Road<br>
Cambridge CB2 0XY<br>
<br>
www.cimr.cam.ac.uk/investigators/read/index.html<br>
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<div style=""><b>From:</b> <a title="rkhayat@ccny.cuny.edu">Reza Khayat</a> </div>
<div><b>Sent:</b> Wednesday, November 23, 2016 2:05 PM</div>
<div><b>To:</b> <a title="phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
</div>
<div><b>Subject:</b> [phenixbb] Crashing Phenix during MRage</div>
</div>
</div>
<div> </div>
</div>
<div style="font-size:small; text-decoration:none; font-family:"Calibri"; font-weight:normal; color:#000000; font-style:normal; display:inline">
<p>Hi,</p>
<p> </p>
<p>MRage stops running after sometime with the following error:</p>
<p> </p>
<p>===========================================<br>
</p>
<p>Process Process-1:29434:<br>
Traceback (most recent call last):<br>
File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap<br>
self.run()<br>
File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 114, in run<br>
self._target(*self._args, **self._kwargs)<br>
File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/engine.py", line 175, in mpjob_run<br>
result = calculation.run()<br>
File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/calculation.py", line 138, in run<br>
assert len( raw ) == 1<br>
AssertionError<br>
Process Process-1:29436:<br>
Traceback (most recent call last):<br>
File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap<br>
self.run()<br>
File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 114, in run<br>
self._target(*self._args, **self._kwargs)<br>
File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/engine.py", line 175, in mpjob_run<br>
result = calculation.run()<br>
File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/calculation.py", line 138, in run<br>
assert len( raw ) == 1<br>
AssertionError<br>
Process Process-1:29438:<br>
Traceback (most recent call last):<br>
File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap<br>
self.run()<br>
File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 114, in run<br>
self._target(*self._args, **self._kwargs)<br>
File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/engine.py", line 175, in mpjob_run<br>
result = calculation.run()<br>
File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/calculation.py", line 138, in run<br>
assert len( raw ) == 1<br>
AssertionError<br>
Process Process-1:29440:<br>
Traceback (most recent call last):<br>
File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap<br>
self.run()<br>
File "/opt/X-tal_suite/phenix-1.10.1-2155/base/lib/python2.7/multiprocessing/process.py", line 114, in run<br>
self._target(*self._args, **self._kwargs)<br>
File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/engine.py", line 175, in mpjob_run<br>
result = calculation.run()<br>
File "/opt/X-tal_suite/phenix-1.10.1-2155/modules/phaser/phaser/pipeline/calculation.py", line 138, in run<br>
assert len( raw ) == 1<br>
AssertionError<br>
<br>
<br>
<br>
<br>
** (gedit:5901): WARNING **: Couldn't connect to accessibility bus: Failed to connect to socket /tmp/dbus-pJCFNfwEtI: Connection refused<br>
<br>
(gedit:5901): GLib-GIO-ERROR **: No GSettings schemas are installed on the system<br>
</p>
<p>==============================================================================</p>
<p> </p>
<p>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.
</p>
<p> </p>
<p>Best wishes,<br>
Reza<br>
</p>
<p> </p>
<div id="Signature">
<div name="divtagdefaultwrapper" style="font-family:calibri,arial,helvetica,sans-serif; margin:0px">
Reza Khayat, PhD
<div>Assistant Professor </div>
<div>City College of New York</div>
<div>Department of Chemistry</div>
<div>New York, NY 10031</div>
</div>
</div>
<p> </p>
<p></p>
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