[phenixbb] Rebuild fails in Rosetta-MR

[Nigel Moriarty]

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 : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Mon, Feb 22, 2016 at 10:33 AM, Paul Adams <pdadams at lbl.gov> 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 <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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> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
> > Unsubscribe: phenixbb-leave at phenix-online.org
>
> --
> 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
>
> Lawrence Berkeley Laboratory
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> BLDG 33R0345
> Berkeley, CA 94720, USA.
>
> Executive Assistant: Louise Benvenue [ LBenvenue at lbl.gov ][ 1-510-495-2506
> ]
> --
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