[phenixbb] Rosetta installation problems

Simone Pellegrino simonpelle81 at gmail.com
Mon Oct 8 11:24:12 PDT 2018


Hi Billy,

I have done this. Should I simply replace the previous text or add to the
existing site.settings file please? I did comment all the previous now.
Best
Simone


Il giorno lun 8 ott 2018 alle ore 17:38 Billy Poon <BKPoon at lbl.gov> ha
scritto:

> 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
>
>

-- 
Dr. Simone Pellegrino
I.G.B.M.C.
1, Rue Laurent Fries
67404 Illkirch Cedex
France
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20181008/5bf4f81b/attachment.htm>


More information about the phenixbb mailing list