[phenixbb] install Rosetta for use in Phenix fails

[Billy Poon]

Hi Aaron,

Are you running rosetta.build_phenix_interface in a shell with
administrative privileges (i.e. "sudo -i")? Because Phenix is in
/Applications and Rosetta is in /usr/local, the command needs
administrative privileges to write in those directories.

Also, I am current testing newer versions of Rosetta since Rosetta 3.9
seems to have some problems on macOS. I'll update this thread and the
documentation once we've settled on a version.

--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
Web: https://phenix-online.org


On Tue, Aug 21, 2018 at 1:45 AM Aaron Oakley <aarono at uow.edu.au> wrote:

> I have repeatedly tried to install Rosetta for use in Phenix with zero
> success.
>
> System: macOS 10.13.6
> Phenix version: phenix-1.14rc1-3177
> Rosetta version: 3.9 (rosetta_src_2018.09.60072_bundle)
>
> Relevant environmental variables:
>
>
>
>
>
>
> *ROSETTA3_DB=/usr/local/rosetta_src_2018.09.60072_bundle/main/database
> ROSETTA_TOOLS=/usr/local/rosetta_src_2018.09.60072_bundle/tools
> ROSETTA3=/usr/local/rosetta_src_2018.09.60072_bundle/main/source
> PHENIX=/Applications/phenix-1.14rc1-3177 PHENIX_VERSION=1.14rc1-3177
> PHENIX_ROSETTA_PATH=/usr/local/rosetta_src_2018.09.60072_bundle*
>
> *rosetta.build_phenix_interface* —seemed— to work OK.
>
> However...
>
> *rosetta.run_tests* fails with
>
> DEBUG dumping error message
> ERROR: Rosetta exited with status 1
> stderr output:
> BACKTRACE:
> 0   libcore.3.dylib                     0x0000000114b0e4e6
> print_backtrace(char const*) + 54
>
> …40 lines of traceback crap…
>
> Traceback (most recent call last):
>   File
> "/Applications/phenix-1.14rc1-3177/build/../modules/phenix/phenix/command_line/rosetta_refine.py",
> line 307, in <module>
>     run(sys.argv[1:], create_dir=True)
>   File
> "/Applications/phenix-1.14rc1-3177/build/../modules/phenix/phenix/command_line/rosetta_refine.py",
> line 191, in run
>     debug=params.output.debug)
>   File
> "/Applications/phenix-1.14rc1-3177/modules/phenix/phenix/rosetta/refine.py",
> line 313, in __init__
>     self.run_jobs()
>   File
> "/Applications/phenix-1.14rc1-3177/modules/phenix/phenix/rosetta/refine.py",
> line 388, in run_jobs
>     check_result(result)
>   File
> "/Applications/phenix-1.14rc1-3177/modules/phenix/phenix/rosetta/refine.py",
> line 379, in check_result
>     raise RuntimeError("Aborted due to error in job %d." % result.job_id)
> RuntimeError: Aborted due to error in job 1.
>
>
> Any ideas?
>
> Aaron Oakley
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