echo $PHENIX_ROSETTA_PATH
/usr/local/rosetta/rosetta-2018.33.60351
which rosetta.run_tests
/usr/local/phenix/phenix-dev-3283/build/bin/rosetta.run_tests
rosetta.run_tests
(...)
End of input processing
Traceback (most recent call last):
File "/usr/local/phenix/phenix-dev-3283/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 304, in <module>
run(sys.argv[1:], create_dir=True)
File "/usr/local/phenix/phenix-dev-3283/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 143, in run
Hi again, the missing $PHENIX_ROSETTA_PATH/main/source/bin error I reported below can be fixed by redefining these variables in the shell where one runs rosetta.run_tests:
export PHENIX_ROSETTA_PATH=/usr/local/rosetta/rosetta-2018.33.60351
export ROSETTA_BIN=$PHENIX_ROSETTA_PATH/main/source/bin
export ROSETTA3_DB=$PHENIX_ROSETTA_PATH/main/database
and then re-running rosetta.run_tests.
However, I then get yet another error from Rosetta… will report off-list as that is probably related to my specific installation.
Best, Luca
Begin forwarded message:
From: Luca Jovine mailto:[email protected]>
Subject: Re: [phenixbb] Rosetta installation problems (II)
Date: 7 October 2018 at 11:43:24 CEST
To: Billy Poon mailto:[email protected]>
Cc: PHENIX user mailing list mailto:[email protected]>
On 6 Oct 2018, at 21:45, Billy Poon mailto:[email protected]> wrote:
Hi Luca,
Please try the latest version of Rosetta 3.10. There was a bug with macOS 10.13.6 that is fixed. I have tested Rosetta 3.10 on macOS 10.13.6 and Xcode 10. The rosetta.run_tests step completes without using massive amounts of memory. Also, if you use the GUI for phenix.rosetta_refine, please use the latest nightly build, dev-3283. There was a bug where the final R-values are not stored, which caused the GUI to crash.
--
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.orghttps://phenix-online.org/
Hi Billy,
Thanks for the follow-up, I tried and confirm that the combination of Rosetta 3.10 + PHENIX dev-3283 indeed works fine on Mac OS 10.13.6.
However, I then tried the same on ubuntu (16.04) and in this case I got the following:
scripts_cmd = phenix.rosetta.refine.find_scripts_command()
File "/usr/local/phenix/phenix-dev-3283/modules/phenix/phenix/rosetta/refine.py", line 26, in find_scripts_command
return find_rosetta_command("rosetta_scripts.python.", **kwds)
File "/usr/local/phenix/phenix-dev-3283/modules/phenix/phenix/rosetta/refine.py", line 50, in find_rosetta_command
rosetta_cmd = search_path(rosetta_bin)
File "/usr/local/phenix/phenix-dev-3283/modules/phenix/phenix/rosetta/refine.py", line 31, in search_path
for node in os.listdir(path) :
OSError: [Errno 2] No such file or directory: '$PHENIX_ROSETTA_PATH/main/source/bin'
...but directory $PHENIX_ROSETTA_PATH/main/source/bin does exist, and it’s populated:
ls -l $PHENIX_ROSETTA_PATH/main/source/bin
total 2292
lrwxrwxrwx 1 luca luca 92 Oct 7 10:29 AbinitioRelax.default.linuxgccrelease -> ../build/src/release/linux/4.15/64/x86/gcc/5.4/default/AbinitioRelax.default.linuxgccrelease
(...)
lrwxrwxrwx 1 luca luca 101 Oct 7 10:54 zinc_statistic_generator.python.linuxgccrelease -> ../build/src/release/linux/4.15/64/x86/gcc/5.4/python/zinc_statistic_generator.python.linuxgccrelease
Do you have any idea of why this happens?
Thanks again,
Luca
