[phenixbb] Rebuild fails in Rosetta-MR

Paul Adams pdadams at lbl.gov
Mon Feb 22 10:33:03 PST 2016


If I remember correctly (quite possibly not), this is to do with a newer binary being run on a older version of the OS. Is this possible? We are in the process of updating the Rosetta/Phenix installation instructions, so it might be that compiling Rosetta with Phenix might fix the problem (but does require a compiler). Nigel might have some thoughts. 

> On Feb 22, 2016, at 6:13 AM, Rhys Grinter <rhys.grinter at MONASH.EDU> wrote:
> 
> Dear all,
> 
> I'm currently trying to improve an model for a difficult MR problem using Rosetta-MR,
> 
> When the program gets to the Rebuild stage it fails with the following message:
> Error message:
> 
> child process stderr output:
> 
>   command: 'sh  .../MR_ROSETTA_17/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_4/WORK_1/run_rebuild.sh"'
> 
>   .../MR_ROSETTA_17/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_4/WORK_1/run_rebuild.sh: line 5:  8996 Trace/BPT trap: 5       "/Applications/Rosetta/main/source/bin/mr_protocols.macosclangrelease" @"rebuild.flags" > "rebuild.log" 2>&1
> 
> Failed to run REBUILD
> 
> Sorry: Failed to run REBUILD...see log file in .../MR_ROSETTA_17/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_4/WORK_1/rebuild.log
> 
> Sorry: mr_rosetta failed...
> 
> Sorry routine failed
> 
> Please see log file for full error message
> 
> 
> In the rebuild logfile:
> 
> dyld: lazy symbol binding failed: Symbol not found: ___sincos_stret
>   Referenced from: /Applications/Rosetta/main/source/bin/mr_protocols.macosclangrelease
>   Expected in: /usr/lib/libSystem.B.dylib
> 
> dyld: Symbol not found: ___sincos_stret
>   Referenced from: /Applications/Rosetta/main/source/bin/mr_protocols.macosclangrelease
>   Expected in: /usr/lib/libSystem.B.dylib
> 
> Has anyones experienced this error?
> 
> Cheers,
> 
> Rhys
> 
> -- 
> Dr Rhys Grinter
> Sir Henry Wellcome Fellow
> Monash University
> +61 (0)3 9902 9213
> +61 (0)403 896 767
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-- 
Paul Adams
Interim Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab
Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
Laboratory Research Manager, ENIGMA Science Focus Area

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