Modeller and Fedora 14 / python 2.7
I wonder if anyone could help, please.
After upgrading our systems from Fedora 12 to Fedora 14 we are unable to run modeller. It installs but fails to run, reporting the following errors:
Traceback (most recent call last):
File "modeller_gi60681617.py", line 2, in<module>
from modeller import * # Load standard Modeller classes
File "/usr/lib64/python2.7/site-packages/modeller/__init__.py", line 72, in<module>
import _modeller
ImportError: No module named _modeller
Do you know of any problems with Modeller and recent versions of Fedora? Can you confirm that Modeller will work with Python 2.7 - the version that runs on Fedora 14 systems. The package is essential for one of our research groups and I would be very grateful for any help or advice you can give me.
Many thanks,
Susan Hutchinson
On 3/17/11 6:18 AM, Susan Hutchinson wrote: > Do you know of any problems with Modeller and recent versions of Fedora? > Can you confirm that Modeller will work with Python 2.7 - the version > that runs on Fedora 14 systems. The package is essential for one of our > research groups and I would be very grateful for any help or advice you > can give me.
Python 2.7 is not supported "out of the box": see http://salilab.org/modeller/release.html#rpm where we state the versions of Python that are supported (2.3 through 2.6). Since Python 2.7 was released after Modeller 9v8, we could not include Python 2.7 support.
The good news, however, is that the binary interface did not change between Python 2.5 and Python 2.7, so you can simply make a couple of links to add 2.7 support to Modeller. Try the following command (should be run all on one line):
cd /usr/lib64/python2.7/site-packages/ && sudo ln -sf ../../python2.5/site-packages/_modeller.so _modeller.so && sudo ln -sf /usr/lib/modeller9v8/modlib/modeller modeller
(If you don't have sudo set up on your system simply remove the two 'sudo's from this command and run the whole thing as the root user.)
This is assuming you installed the Modeller RPM package on a 64-bit Fedora machine. If you have a 32-bit machine, replace 'lib64' with 'lib'.
Ben Webb, Modeller Caretaker
Hi Ben, >> Do you know of any problems with Modeller and recent versions of Fedora? >> Can you confirm that Modeller will work with Python 2.7 - the version >> that runs on Fedora 14 systems. The package is essential for one of our >> research groups and I would be very grateful for any help or advice you >> can give me. > > Python 2.7 is not supported "out of the box": see > http://salilab.org/modeller/release.html#rpm > where we state the versions of Python that are supported (2.3 through > 2.6). Since Python 2.7 was released after Modeller 9v8, we could not > include Python 2.7 support. > > The good news, however, is that the binary interface did not change > between Python 2.5 and Python 2.7, so you can simply make a couple of > links to add 2.7 support to Modeller. Try the following command > (should be run all on one line): > > cd /usr/lib64/python2.7/site-packages/ && sudo ln -sf > ../../python2.5/site-packages/_modeller.so _modeller.so && sudo ln -sf > /usr/lib/modeller9v8/modlib/modeller modeller > > (If you don't have sudo set up on your system simply remove the two > 'sudo's from this command and run the whole thing as the root user.) > > This is assuming you installed the Modeller RPM package on a 64-bit > Fedora machine. If you have a 32-bit machine, replace 'lib64' with 'lib'. > > Thanks so much for this - it works perfectly.
Susan Hutchinson
Hi I am running modeller in Fedora 14. Rhis is waht I did to make Modller work in Fedora.
ln -s /usr/lib/modeller9v8/lib/x86_64-intel8/_modeller.so /usr/lib64/python2.7/site-packages/_modeller.so and ln -s /usr/lib/modeller9v8/modlib/modeller/ /usr/lib64/python2.7/site-packages/modeller/
It means that you will have to make a new link from modeller to youe new python 2.7 installation.
Knut J
On 03/17/2011 02:18 PM, Susan Hutchinson wrote: > I wonder if anyone could help, please. > > After upgrading our systems from Fedora 12 to Fedora 14 we are unable to > run modeller. It installs but fails to run, reporting the following errors: > > Traceback (most recent call last): > > File "modeller_gi60681617.py", line 2, in<module> > > from modeller import * # Load standard Modeller classes > > File "/usr/lib64/python2.7/site-packages/modeller/__init__.py", line > 72, in<module> > > import _modeller > > ImportError: No module named _modeller > > Do you know of any problems with Modeller and recent versions of Fedora? > Can you confirm that Modeller will work with Python 2.7 - the version > that runs on Fedora 14 systems. The package is essential for one of our > research groups and I would be very grateful for any help or advice you > can give me. > > Many thanks, > > Susan Hutchinson >
On 3/18/11 2:16 PM, Knut J Bjuland wrote: > Hi I am running modeller in Fedora 14. Rhis is waht I did to make > Modller work in Fedora. > > ln -s /usr/lib/modeller9v8/lib/x86_64-intel8/_modeller.so > /usr/lib64/python2.7/site-packages/_modeller.so > and > ln -s /usr/lib/modeller9v8/modlib/modeller/ > /usr/lib64/python2.7/site-packages/modeller/
This is essentially the same as what I already suggested, with one difference: it will use the Python 2.3 interface rather than the 2.5 one. I don't recommend that, since the 2.3 interface is not compatible with 2.7. At best you'll get a warning every time you import the modeller package.
Ben Webb, Modeller Caretaker
participants (3)
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Knut J Bjuland -
Modeller Caretaker -
Susan Hutchinson