[phenixbb] Rosetta installation problems
Georg Mlynek
georg.mlynek at univie.ac.at
Mon Oct 8 12:26:55 PDT 2018
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
> <mailto: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 <mailto: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 <mailto: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 <mailto: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 <mailto: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
> <http://CCI.LBL.gov>
>
>
> On Sat, Oct 6, 2018 at 4:15 AM Simone Pellegrino
> <simonpelle81 at gmail.com
> <mailto: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
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>
>
> --
> 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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>
>
> --
> Dr. Simone Pellegrino
> I.G.B.M.C.
> 1, Rue Laurent Fries
> 67404 Illkirch Cedex
> France
>
>
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