[phenixbb] Rebuild fails in Rosetta-MR

Rhys Grinter rhys.grinter at monash.edu
Mon Feb 22 18:04:25 PST 2016


Hi All,

Thanks for all the help guys, recompiling Rosetta as Nigel suggested seems
to have fixed the problem.
That said I haven't run Rosetta-MR before and while it's using all my CPU
(MacBook Pro i7 2.8GHz 4(+4 HT)) it it's telling me an awful lot. I assume
it's running but the logfile isn't very verbose? What kind of run times am
I looking at for this sort of machine?

Thanks again,

Rhys

On 23 February 2016 at 05:56, Nigel Moriarty <nwmoriarty at lbl.gov> wrote:

> 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
>> > _______________________________________________
>> > phenixbb mailing list
>> > 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
>> 1 Cyclotron Road
>> BLDG 33R0345
>> Berkeley, CA 94720, USA.
>>
>> Executive Assistant: Louise Benvenue [ LBenvenue at lbl.gov ][
>> 1-510-495-2506 ]
>> --
>>
>>
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>
>


-- 
Dr Rhys Grinter
Sir Henry Wellcome Fellow
Monash University
+61 (0)3 9902 9213
+61 (0)403 896 767
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