[phenixbb] Rosetta installation problems

Billy Poon BKPoon at lbl.gov
Mon Oct 8 09:38:09 PDT 2018


Hi Simone,

With later compilers (GCC >= 5.1), you need to add the site.settings file
from https://www.phenix-online.org/documentation/extras/site.settings. That
adds a flag that correctly links Phenix and Rosetta.

--
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 Mon, Oct 8, 2018 at 3:15 AM Simone Pellegrino <simonpelle81 at gmail.com>
wrote:

> Hi Andy and Nigel,
>
> I started from scratch again and did the following.
>
> 1) I installed latest CentOS6 phenix and installed onto an Ubuntu 18.04
> system.
> 2) I downloaded Rosetta 2018.31 and compiled by running the scons.py code.
> 3) Then I followed the instructions form Nigel and compiled the interface
> between phenix and Rosetta by doing all the steps as written in the
> installation procedure.
> 4) Still having the same issue.
>
> Any clue about what am I doing wrong please?
> Many thanks
> Best
> Simone
>
>
> Il giorno sab 6 ott 2018 alle ore 19:59 Andy Watkins <
> andy.watkins2 at gmail.com> ha scritto:
>
>> That seems like an issue unrelated to rosetta_refine per se but instead
>> related to your Rosetta configuration in general. I don't know much about
>> rosetta_refine, but does it use any scripts from the Rosetta tools
>> repository, or could you be invoking a test that uses some of those scripts?
>>
>> parse_tag is a Python component that's invoked by some of the python
>> scripts in ERRASER, for example, and if it can't find it then it means that
>> Rosetta/tools/rna_tools/bin isn't on your $PYTHONPATH.
>>
>> On Sat, Oct 6, 2018 at 11:50 AM Simone Pellegrino <simonpelle81 at gmail.com>
>> wrote:
>>
>>> Hi Nigel,
>>>
>>> to install Phenix I followed the recommended procedure as specified in
>>> the online manual.
>>> Then to install Rosetta I finally followed one of the response on the
>>> Rosetta forum (can't remember now the exact thread)
>>>  and I came to this last error of the
>>>
>>> ImportError: No module named parse_tag
>>>
>>> Many thnaks for your help.
>>> Best
>>> Simone
>>>
>>>
>>> Il giorno sab 6 ott 2018 alle ore 17:41 Nigel Moriarty <
>>> nwmoriarty at lbl.gov> ha scritto:
>>>
>>>> This looks very strange. The error is in the file in the installer
>>>> directories. This should not be the case. Can you provide more details on
>>>> what you did to install Phenix etc.
>>>>
>>>> Cheers
>>>>
>>>> Nigel
>>>>
>>>> ---
>>>> Nigel W. Moriarty
>>>> Building 33R0349, Molecular Biophysics and Integrated Bioimaging
>>>> Lawrence Berkeley National Laboratory
>>>> Berkeley, CA 94720-8235
>>>> Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
>>>> Fax   : 510-486-5909       Web  : CCI.LBL.gov
>>>>
>>>>
>>>> On Sat, Oct 6, 2018 at 4:15 AM Simone Pellegrino <
>>>> simonpelle81 at gmail.com> wrote:
>>>>
>>>>> Dear all,
>>>>>
>>>>> I encounter a problem running the rosetta.run_tests after having
>>>>> compiled rosetta for interfacing with phenix. I have the following error:
>>>>>
>>>>>
>>>>> DEBUG dumping error message
>>>>> ERROR: Rosetta exited with status 139
>>>>> stderr output:
>>>>> Segmentation fault (core dumped)
>>>>> Traceback (most recent call last):
>>>>>   File
>>>>> "/home/Downloads/phenix-installer-1.14-3260-intel-linux-2.6-x86_64-centos6/build/../modules/phenix/phenix/command_line/rosetta_refine.py",
>>>>> line 307, in <module>
>>>>>     run(sys.argv[1:], create_dir=True)
>>>>>   File
>>>>> "/home/Downloads/phenix-installer-1.14-3260-intel-linux-2.6-x86_64-centos6/build/../modules/phenix/phenix/command_line/rosetta_refine.py",
>>>>> line 191, in run
>>>>>     debug=params.output.debug)
>>>>>   File
>>>>> "/home/Downloads/phenix-installer-1.14-3260-intel-linux-2.6-x86_64-centos6/modules/phenix/phenix/rosetta/refine.py",
>>>>> line 313, in __init__
>>>>>     self.run_jobs()
>>>>>   File
>>>>> "/home/Downloads/phenix-installer-1.14-3260-intel-linux-2.6-x86_64-centos6/modules/phenix/phenix/rosetta/refine.py",
>>>>> line 387, in run_jobs
>>>>>     check_result(result)
>>>>>   File
>>>>> "/home/Downloads/phenix-installer-1.14-3260-intel-linux-2.6-x86_64-centos6/modules/phenix/phenix/rosetta/refine.py",
>>>>> line 378, in check_result
>>>>>     raise RuntimeError("Aborted due to error in job %d." %
>>>>> result.job_id)
>>>>> RuntimeError: Aborted due to error in job 1.
>>>>>
>>>>> Could you please help me in solving this issue?
>>>>> Many thanks in advance
>>>>> Best regards
>>>>> Simone
>>>>>
>>>>> --
>>>>> Dr. Simone Pellegrino
>>>>> I.G.B.M.C.
>>>>> 1, Rue Laurent Fries
>>>>> 67404 Illkirch Cedex
>>>>> France
>>>>> _______________________________________________
>>>>> phenixbb mailing list
>>>>> phenixbb at phenix-online.org
>>>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>>> Unsubscribe: phenixbb-leave at phenix-online.org
>>>>
>>>>
>>>
>>> --
>>> Dr. Simone Pellegrino
>>> I.G.B.M.C.
>>> 1, Rue Laurent Fries
>>> 67404 Illkirch Cedex
>>> France
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>> Unsubscribe: phenixbb-leave at phenix-online.org
>>
>>
>
> --
> Dr. Simone Pellegrino
> I.G.B.M.C.
> 1, Rue Laurent Fries
> 67404 Illkirch Cedex
> France
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org
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