Re: [phenixbb] Crashing Phenix during MRage

Hi Rob, The download version of centos6 gives me the same problems. Can I run MRage from the command line if I have a PHIL file that was generated by the GUI? I successfully used phenix.10-2155 GUI to run the toxd tutorial with the MRage package. I retrieved the PHIL file (mr_pipeline_13.eff) used by MRage in the .phenix directory. However, the suggested syntax does not appear to start the program. phenix.mrage -i mr_pipeline_13.eff The program just sits there and using the top command does not indicate that anything is running. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031 ________________________________ From: [email protected] on behalf of Reza Khayat Sent: Wednesday, November 23, 2016 9:28 AM To: Dr. Robert Oeffner; [email protected] Subject: Re: [phenixbb] Crashing Phenix during MRage Hi Rob, I'll give it a try. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031 ________________________________ From: Dr. Robert Oeffner Sent: Wednesday, November 23, 2016 9:24 AM To: Reza Khayat; [email protected] Subject: Re: [phenixbb] Crashing Phenix during MRage 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: [email protected] 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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]