[phenixbb] Rosetta installation problems

Simone Pellegrino simonpelle81 at gmail.com
Mon Oct 8 13:58:28 PDT 2018 

Dear Georg,

I did it correctly then for the site.settings file.
I did install under /home, since I have not root rights. Do you think this
might be an issue please?

Many thanks
Best
Simone


Il giorno lun 8 ott 2018 alle ore 20:28 Georg Mlynek <
georg.mlynek at univie.ac.at> ha scritto:

> Dear Simone,
>
>  for site.settings, you should
>                         overwrite the one in the Rosetta
>                         directory with the new version, not add our
>                         text to the original one.
> Just for curiosity, did you install phenix and rosetta under usr/local or
> /home. The first one probably requires running the installation as root.
>
> Br, Georg.
>
>
> On 2018-10-08 20:24, Simone Pellegrino wrote:
>
> 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
>
>
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-- 
Dr. Simone Pellegrino
I.G.B.M.C.
1, Rue Laurent Fries
67404 Illkirch Cedex
France
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