<HTML><HEAD>
<META content="text/html; charset=iso-8859-1" http-equiv=Content-Type>
<STYLE style="DISPLAY: none" type=text/css><!--P{margin-top:0;margin-bottom:0;} p
{margin-top:0;
margin-bottom:0}--></STYLE>
</HEAD>
<BODY
style="FONT-SIZE: 12pt; FONT-FAMILY: Calibri,Arial,Helvetica,sans-serif; COLOR: #000000; BACKGROUND-COLOR: #ffffff"
dir=ltr>
<DIV dir=ltr>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: 'Calibri'; COLOR: #000000">
<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>
<DIV
style='FONT-SIZE: small; TEXT-DECORATION: none; FONT-FAMILY: "Calibri"; FONT-WEIGHT: normal; COLOR: #000000; FONT-STYLE: normal; DISPLAY: inline'></DIV>
<DIV style="FONT: 10pt tahoma">
<DIV style="BACKGROUND: #f5f5f5">
<DIV style="font-color: black"><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 style="FONT-FAMILY: calibri,arial,helvetica,sans-serif; MARGIN: 0px"
name="divtagdefaultwrapper">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>
<HR>
_______________________________________________<BR>phenixbb mailing
list<BR>phenixbb@phenix-online.org<BR>http://phenix-online.org/mailman/listinfo/phenixbb<BR>Unsubscribe:
phenixbb-leave@phenix-online.org</DIV></DIV></DIV></BODY></HTML>