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

[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


[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?

[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()

[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

[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]:

[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)

[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).

[Author]

Posts