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