Re: [phenixbb] Rebuild fails in Rosetta-MR

Rhys I can't speak to this exact dynamic library problem being wholly Rosetta's fault as I've seen this error in other situations with binaries being mismatched. This is a problem with your machine not being able to run the Rosetta binaries. You may have to fix the libraries on your machine or move to a machine that has the correct libraries. I am updating the docs but you should download Phenix dev-2313 and the Rosetta 2016.02 build. Follow the instructions for installing Rosetta refine (which will compile Rosetta so the source bundle is fine). This is more than what is required for MR-Rosetta but it is required for Rosetta refine which you may want in the future. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Mon, Feb 22, 2016 at 10:33 AM, Paul Adams wrote:

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 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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

-- 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

Building 33, Room 347 Building 80, Room 247 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul

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