CentOS-5 x86_64 python 2.6.6 (self compiled –enable-unicode=ucs4 –enable-shared –enable-threads) issue with 1.1/2.0

This topic has 6 replies, 2 voices, and was last updated 13 years, 8 months ago by Anonymous.

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- April 6, 2011 at 6:34 pm #853
  Anonymous
  I installed both:
  PyRosetta-Release1.1-r34968.linux.64Bit.tar.bz2
  PyRosetta.ScientificLinux-r40608.linux.64Bit.tar.bz2
  
  PyRosetta-Release1.1-r34968:
  [tru@mestizo ~]$ iPyRosetta /c5/shared/pyrosetta/PyRosetta-Release1.1-r34968.linux.64Bit/IPython/Magic.py:38: DeprecationWarning: the sets module is deprecated from sets import Set Python 2.6.6 (r266:84292, Apr 6 2011, 19:50:10) Type "copyright", "credits" or "license" for more information.
  IPython 0.9.1 -- An enhanced Interactive Python. ? -> Introduction and overview of IPython's features. %quickref -> Quick reference. help -> Python's own help system. object? -> Details about 'object'. ?object also works, ?? prints more. In [1]: Do you really want to exit ([y]/n)? y but: [tru@mestizo ~]$ python -c 'import rosetta' Traceback (most recent call last): File "", line 1, in File "/c5/shared/pyrosetta/PyRosetta-Release1.1-r34968.linux.64Bit/rosetta/__init__.py", line 14, in import utility, core File "/c5/shared/pyrosetta/PyRosetta-Release1.1-r34968.linux.64Bit/rosetta/utility/__init__.py", line 1, in from _rosetta_utility_000 import * ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /c5/shared/pyrosetta/PyRosetta-Release1.1-r34968.linux.64Bit/rosetta/libmini.so)
  too new glibc for us [tru@mestizo PyRosetta-r40608.linux.64Bit]$ ldd /c5/shared/pyrosetta/PyRosetta-Release1.1-r34968.linux.64Bit/rosetta/libmini.so /c5/shared/pyrosetta/PyRosetta-Release1.1-r34968.linux.64Bit/rosetta/libmini.so: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /c5/shared/pyrosetta/PyRosetta-Rel ease1.1-r34968.linux.64Bit/rosetta/libmini.so) libz.so.1 => /usr/lib64/libz.so.1 (0x00002b43eeef0000) libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00002b43ef104000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002b43ef404000) libc.so.6 => /lib64/libc.so.6 (0x00002b43ef613000) libm.so.6 => /lib64/libm.so.6 (0x00002b43ef96a000) /lib64/ld-linux-x86-64.so.2 (0x0000003c47400000)
  PyRosetta.ScientificLinux-r40608.linux.64Bit:
  [tru@mestizo ~]$ iPyRosetta Traceback (most recent call last): File "/c5/shared/pyrosetta/PyRosetta-r40608.linux.64Bit/ipython.py", line 10, in import IPython.Shell ImportError: No module named IPython.Shell [tru@mestizo ~]$ type iPyRosetta iPyRosetta is hashed (/c5/shared/pyrosetta/PyRosetta-r40608.linux.64Bit/iPyRosetta) [tru@mestizo ~]$ /c5/shared/pyrosetta/PyRosetta-r40608.linux.64Bit/iPyRosetta Traceback (most recent call last): File "/c5/shared/pyrosetta/PyRosetta-r40608.linux.64Bit/ipython.py", line 10, in import IPython.Shell ImportError: No module named IPython.Shell
  [tru@mestizo ~]$ python -c 'import rosetta' [tru@mestizo ~]$ echo $? 0
- April 6, 2011 at 6:41 pm #5290
  Anonymous
  http://www.rosettacommons.org/node/1815 suggest recompiling python with a newer compiler…
  
  wouldn’t it be possible to have a rosetta/libmini.so recompiled on an older distribution or have access to the sources code to compile it on CentOS-5?
- April 6, 2011 at 8:33 pm #5294
  Anonymous
  Hi Tru,
  
  From the logs that posted it looks like there is no iPython installed on your system. You can get iPython here: http://ipython.scipy.org/moin/
  
  Also, it “python -c ‘import rosetta'” seems to executed without errors. So its look like it worked on your system. Have you tried using it? Try something like:
  
  $ python
  >>> import rosetta
  >>> roosetta.init()
- April 8, 2011 at 12:23 pm #5320
  Anonymous
  ipython should be provided by pyrosetta (as stated on their page), python import just works fine
  Python 2.6.6 (r266:84292, Apr 6 2011, 19:50:10) [GCC 4.1.2 20080704 (Red Hat 4.1.2-48)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import rosetta >>> rosetta.init() PYROSETTA_DATABASE environment variable was set to: /c5/shared/pyrosetta/PyRosetta-r40608.linux.64Bit/minirosetta_database... using it... PyRosetta-40608 retrieved from: https://svn.rosettacommons.org/source/trunk/mini (C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.
  core.init: Mini-Rosetta version 40608 from https://svn.rosettacommons.org/source/trunk/mini core.init: command: app -database /c5/shared/pyrosetta/PyRosetta-r40608.linux.64Bit/minirosetta_database -ex1 -ex2aro core.init: 'RNG device' seed mode, using '/dev/urandom', seed=1664975131 seed_offset=0 real_seed=1664975131 core.init.random: RandomGenerator:init: Normal mode, seed=1664975131 RG_type=mt19937
- April 8, 2011 at 8:22 pm #5321
  Anonymous
  I have added ipython module to my python 2.6.6, now that works as expected for pyrosetta-2.0:
  
  [tru@liberte ~]$ iPyRosetta Python 2.6.6 (r266:84292, Apr 6 2011, 19:50:10) Type "copyright", "credits" or "license" for more information.
  IPython 0.10.1 -- An enhanced Interactive Python. ? -> Introduction and overview of IPython's features. %quickref -> Quick reference. help -> Python's own help system. object? -> Details about 'object'. ?object also works, ?? prints more. In [1]: import rosetta In [2]: rosetta.init() PYROSETTA_DATABASE environment variable was set to: /c5/shared/pyrosetta/PyRosetta-r40608.linux.64Bit/minirosetta_database... using it... PyRosetta-40608 retrieved from: https://svn.rosettacommons.org/source/trunk/mini (C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team. core.init: Mini-Rosetta version 40608 from https://svn.rosettacommons.org/source/trunk/mini core.init: command: app -database /c5/shared/pyrosetta/PyRosetta-r40608.linux.64Bit/minirosetta_database -ex1 -ex2aro core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-314165490 seed_offset=0 real_seed=-314165490 core.init.random: RandomGenerator:init: Normal mode, seed=-314165490 RG_type=mt19937 In [3]:
- April 8, 2011 at 8:23 pm #5322
  Anonymous
  still not good for pyrosetta-1.1:
  [tru@liberte ~]$ iPyRosetta /c5/shared/pyrosetta/PyRosetta-Release1.1-r34968.linux.64Bit/IPython/Magic.py:38: DeprecationWarning: the sets module is deprecated from sets import Set Python 2.6.6 (r266:84292, Apr 6 2011, 19:50:10) Type "copyright", "credits" or "license" for more information.
  IPython 0.9.1 -- An enhanced Interactive Python. ? -> Introduction and overview of IPython's features. %quickref -> Quick reference. help -> Python's own help system. object? -> Details about 'object'. ?object also works, ?? prints more. In [1]: import rosetta ImportError Traceback (most recent call last) /Bis/home/tru/ in () /c5/shared/pyrosetta/PyRosetta-Release1.1-r34968.linux.64Bit/rosetta/__init__.py in () 12 warnings.filterwarnings("ignore", "to-Python converter for .+ already registered; second conversion method ignored.", RuntimeWarning, "^rosetta\.") 13 ---> 14 import utility, core 15 16 import rosetta.utility /c5/shared/pyrosetta/PyRosetta-Release1.1-r34968.linux.64Bit/rosetta/utility/__init__.py in () ----> 1 from _rosetta_utility_000 import * 2 from _rosetta_utility_001 import * ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found (required by /c5/shared/pyrosetta/PyRosetta-Release1.1-r34968.linux.64Bit/rosetta/libmini.so)
- April 11, 2011 at 3:34 pm #5340
  Anonymous
  PyRosetta-1.1 is an old release (more then two year old now) and it should be consider as deprecated now. If you want to make it work you will need to find a way to install older version of GLIBC (3.4.9 as your error message suggested).
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