[phenixbb] Autobuild error

Nicholas R Silvaggi silvaggi at uwm.edu
Fri Apr 15 05:37:19 PDT 2011


Dear Phenix Developers,

I have been experiencing problems with autobuild whenever I try to rebuild an MR model or calculate a composite OMIT map. These tasks always end the same way: with "[Errno 5] Input/output error". The failure always happens when the run is basically finished and trying to combine the output from multiple tasks. My first thought was that my hard drive was full or fixing to crash, but these problems happen across several machines and have persisted through multiple official and nightly Phenix releases (currently running 1.7-634). The computers that cannot run autobuild successfully are both core i7-based PCs running Fedora 14 (though these problems also occurred running earlier Fedora versions). My older xeon-based PC runs autobuild without any trouble, which makes me think this a core i7-related problem. I have searched the PhenixBB archive and have not turned up any similar problems - have any other users experienced trouble with Phenix and core i7? Is there a work-around I can use to manually combine the various outputs? The core i7 machines are so much faster, I would really like to solve this problem so that I can stop relying on my aging xeon PC for these long calculations. I have included the end of two log files for reference. Also, autosol runs fine on the core i7 computers and successfully builds wonderful models from my SeMet SAD data. Thank you for Phenix and for any advice you can give.

Best wishes,
Nick Silvaggi

P.S. I apologize if this message appears twice - I sent it once from an address that was not registered with the BB and decided to re-send from a registered address.

Autobuild after MR:
-----------------------------------------------------------------------------------------------------
Standard build in parallel  starting with  refine.pdb_1
This is the first try at building this model
Try:  1 building 1 model
Try:  2 building 1 model
Try:  3 building 1 model
Running up to  3  jobs in parallel... with total of  3  jobs

Splitting work into 3 jobs and running with 3 processors using sh
background=True in /home/nicks/projects/r51/phenix_mr/AutoBuild_run_2_/TEMP0

Starting job 1...Log will be: /home/nicks/projects/r51/phenix_mr/AutoBuild_run_2_/TEMP0/RUN_FILE_1.log
Starting job 2...Log will be: /home/nicks/projects/r51/phenix_mr/AutoBuild_run_2_/TEMP0/RUN_FILE_2.log
Starting job 3...Log will be: /home/nicks/projects/r51/phenix_mr/AutoBuild_run_2_/TEMP0/RUN_FILE_3.log
Collecting all runs now
*************ERROR ENDING *******************

********************************************************************************
Failed to carry out AutoBuild_build_cycle:

[Errno 5] Input/output error
********************************************************************************

*************ERROR ENDING *******************


Calculating SA composite omit map:
-----------------------------------------------------------------------------------------------------
Starting job 34...Log will be: /home/nicks/projects/r51/phenix_mr/AutoBuild_run_3_/TEMP0/RUN_FILE_34.log
Starting job 35...Log will be: /home/nicks/projects/r51/phenix_mr/AutoBuild_run_3_/TEMP0/RUN_FILE_35.log
Starting job 36...Log will be: /home/nicks/projects/r51/phenix_mr/AutoBuild_run_3_/TEMP0/RUN_FILE_36.log
Collecting all runs now
*************ERROR ENDING *******************

********************************************************************************
Failed to carry out AutoBuild_parallel_omit:

[Errno 5] Input/output error
********************************************************************************

*************ERROR ENDING *******************

Nicholas R Silvaggi, Ph.D.
University of Wisconsin, Milwaukee
Department of Chemistry and Biochemistry
3210 North Cramer St
Milwaukee, WI 53211

Office: Chemistry 272B
Phone: 414-229-2647
silvaggi at uwm.edu



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