Re: [phenixbb] rosetta_mr autobuild failure - typo fixed
Hi all,
I wanted to use the rebuilding feature of Rosetta to help improve the
R-fators of MR solution in a new space group. I'm using Phenix 1.7.1-743 w/ Rosetta 3.2 on MAC OSX 10.5.8
installation was succesful, so after editing my .profile to include
export PHENIX_ROSETTA_PATH=/usr/local/bin/rosetta, I tried to run the following tests:
1. phenix_regression.wizards.test_command_line_rosetta_quick_tests
test_set_up
2. phenix_regression.wizards.test_command_line_rosetta test_mr_rosetta
3. phenix_regression.wizards.test_command_line_rosetta_quick_tests
While the first was successful (ALL COMMAND_LINE TEST OK), the second
reported the following error:
Error: test_command_line_rosetta failed
Upon subsequently running the test_mr_rosetta.com script created in the
subdirectory, the following error was reported:
coords1.ali coords1.pdb fobs.mtz mr_rosetta_quick.eff perfect.mtz seq.dat test3.gz test9.gz test_mr_rosetta.com test_mr_rosetta.log Sorry: mr_rosetta failed...
********************************************************************************
Sorry, a subprocess has failed...
END OF LOG FILE /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_RESCORE_MR_1/RUN_FILE_1.log
:
SYMMETRY FROM INPUT SOLUTION: CRYST1 25.000 25.000 25.000 90.00
100.00 90.00 P 1 21 1
Scoring the model /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/AutoMR_run_1_/coord_mr.1.pdb
Relaxing model at 3.0 A, generating and scoring 1 relaxed models
Error message:
child process stderr output: command: 'sh /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_RESCORE_MR_1/RUN_1/RESCORE_MR_1/WORK_1/run_relax.sh' /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_RESCORE_MR_1/RUN_1/RESCORE_MR_1/WORK_1/run_relax.sh: line 3: 11915 Trace/BPT trap /usr/local/bin/rosetta/rosetta_source/bin/mr_protocols.default.macosgccrelease
@relax.flags > relax.log 2>&1
Failed to run RELAX
******************* ERROR ENDING *************** Failed to run RELAX ...see log file in /usr/local/bin/rosetta/test_mr_rosetta/MR_ROSETTA_1/GROUP_OF_RESCORE_MR_1/RUN_1/RESCORE_MR_1/WORK_1/relax.log
******************* ERROR ENDING ***************
The resulting log file showed the following:
dyld: Library not loaded: /Applications/rosetta3.2_bundles/rosetta_source/build/src/release/macos/10.5/64/x86/gcc/libdevel.dylib Referenced from: /usr/local/bin/rosetta/rosetta_source/bin/mr_protocols.default.macosgccrelease Reason: image not found
phenix_regression.wizards.test_command_line_rosetta_quick_tests failed with the following:
Running test_autobuild FALED TO RUN: test_autobuild ************************************************************** Error: test_command_line_rosetta_quick_test failed
After running the resulting test_autobuild.com script, the log file showed:
S_COORD_0001_ed_0005_ed.pdb averaged_map_coeffs.mtz coords1.pdb fobs.mtz relax.pkl seq.dat test_autobuild.com test_autobuild.log Sorry: Failed to run autobuild ERROR MESSAGE: Sorry the file /net/sigma/raid1/scratch1/terwill/misc/mr_rosetta/coords1_data.mtz seems not to exist? ( key = input_data_file)
The last error message was particularly confusing as that directory indeed does not exist on my machine, put was rather the directory path given as an example in the documentation.
I have two hunches for what could be going wrong, but I unsure how to fix either:
1. In the phenix documentation it says if using a mac, I might have to download some patches, but I could not find any on the Rosetta dowload
2. The documentation also stipulates to specify a proxy server if
behind a firewall using
export HTTP_PROXY=proxyout.mydomain.edu:8080 I am behind a firewall, but on my machine there is no proxy server
Hi again Joe, Typo below (csh vs bash) fixed in this version of the message. -Tom Hi Joe, I'm sorry for the problems in running mr_rosetta! Getting the set up to work is appearing to be a bit of a challenge, particularly on a mac. So the first problem is this: "dyld: Library not loaded: /Applications/rosetta3.2_bundles/rosetta_source/build/src/release/macos/10.5/64/x86/gcc/libdevel.dylib Referenced from: /usr/local/bin/rosetta/rosetta_source/bin/mr_protocols.default.macosgccrelease Reason: image not found" In the cases that have come up so far, there have been two problems. Here are the solutions to those two problems: 1. The installation of Rosetta cannot be moved after it is compiled. This is because the path to the libraries (as in the error message above) is compiled into Rosetta. So...if you moved this installation around at all, try remaking the installation and keeping it in its original location. 2. In some cases the path to the libraries can be conflicting between PHENIX and some other definition on your system. In this case you can try the following shell command (before running phenix.mr_rosetta): with csh: setenv PHENIX_TRUST_OTHER_ENV 1 or with bash or sh: export PHENIX_TRUST_OTHER_ENV=1 Hopefully...one of those will fix this problem. Now the second problem...I am not sure what the actual error is in this one. The error message you got is not helpful as you say because it refers to a file path on the machine where I created the test. That path does not actually have to exist however (I just ran the test on another machine that is not connected to that directory and it runs fine). This means there is some other problem that is the real one. (I will get rid of this error message so this won't happen in the future). Can you try this: 1. reproduce the problem: phenix_regression.wizards.test_command_line_rosetta_quick_tests \ test_autobuild 2. have a look at the log files: cat run.log # if not empty, may give a big clue more test_autobuild_current.log # look at end of this file for clues 3. the test_autobuild_current.log log file may refer to a sub-process where the actual problem occurs: Log file for autobuilding will be: /Users/terwill/unix/misc/junk/test_autobuild/WORK_1/autobuild.log in this case that autobuild log file, and files in WORK_1/AutoBuild_run_1_/TEMP0 may give additional clues. Let me know what this shows! All the best, Tom T page ;(. listed under system prefernces-->advanced-->proxies. I can access my machine using a vpn, but don't know how to tell rosetta to do the same.
Thanks for all your help in advance and sorry that this is so long
winded ;)
Cheers,
Joe
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Thomas C. Terwilliger