Error runining PyRosetta “undefined symbol: __sinh_finite”

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  • This topic has 4 replies, 2 voices, and was last updated 10 years ago by Anonymous.
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    • June 18, 2014 at 3:09 pm #1920
      Anonymous

        Hi all!
        *OS*: Mint Linux 17,
        64bit Linux (3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:11:08 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
        *Python*: Python 2.7.7 |Continuum Analytics, Inc.| (default, Jun 2 2014, 12:34:02) [GCC 4.1.2 20080704 (Red Hat 4.1.2-54)] on linux2
        *PyRosseta*: PyRosetta.Ubuntu-12.04LTS.64Bit.devel-r56795

        While trying to import PyRosseta I get the following error:
        “ImportError: rosetta/libmini.so: undefined symbol: __sinh_finite”

        Here are the full steps: Inside of a bash shell I do:
        . SetPyRosettaEnvironment.sh
        python
        import rosetta

        Here is the stack trace:
        Traceback (most recent call last): File ““, line 1, in File “rosetta/__init__.py”,
        line 30, in         import utility File “rosetta/utility/__init__.py”,
        line 1, in         from _utility_ import *
        ImportError: rosetta/libmini.so: undefined symbol: __sinh_finite

        Any help is very welcome.
        Thank you,
        Ajasja Ljubetič

      • June 18, 2014 at 4:00 pm #10105
        Anonymous

          This seems to be connected to Anaconda python.
          If I use the system python (
          Python 2.7.6 (default, Mar 22 2014, 22:59:56)
          [GCC 4.8.2] on linux2)
          Then I get a different error:
          File “rosetta/__init__.py”, line 45, in
          import numeric
          ImportError: No module named numeric

          And indeed the whole numeric subdirectory is missing under the rosetta module. Will try to re-download the tar.bz2 file.

        • June 18, 2014 at 4:36 pm #10107
          Anonymous

            Happy to report the PyRosetta.Ubuntu-12.04LTS.64Bit.namespace.mode=release.branch=release-r21 works correctly with the system python version!

            I did notice that the database directory is no longer named “rosetta_database”, but just “database”.
            In “SetPyRosettaEnvironment.sh” the line for the database is:
            export PYROSETTA_DATABASE=$PYROSETTA/rosetta_database
            (so the wrong name, but somehow the correct database directory is found nevertheless).

          • June 26, 2014 at 6:54 pm #10129
            Anonymous

              ajasja,

              I am having this missing numeric module when I tried to install on Ubuntu. What fixed this problem for you?

              Did you use a different file than the regular tar.bz2 file?

              Thanks for your help

            • June 30, 2014 at 8:33 pm #10133
              Anonymous

                Hi,

                Yes, I downloaded a different release. (What each release means is described here).

                Best regards,

                Ajasja

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