[phenixbb] Rosetta installation problems

[Nigel Moriarty]

Simone

Please use the instructions on the online manual for installing Rosetta.

https://www.phenix-online.org/documentation/reference/rosetta_install.html

I suggest using a fresh Phenix install and check track of the command and
log outputs so we can check them all.

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 10:00 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
>
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