[phenixbb] rosetta_mr autobuild failure

Thomas C. Terwilliger terwilliger at lanl.gov
Thu Jun 2 06:55:52 PDT 2011 

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 bash or sh:

     setenv PHENIX_TRUST_OTHER_ENV 1

or with csh:

      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



>>
>> 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
>> page ;(.
>>
>> 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 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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>>

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