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Hi i'm trying to get the generic unix build of modeller to run on a amd64 bix running fedora core 3. I've had a look at the python paths, and played with a few variables. It would seem the python interpreter cannot find the site packages, but imports the modeller addons fine. Does anyone have a tip on how to get the embedded python to find the site packages?
export PYTHONPATH=/usr/lib64/python2.3/ #export PYTHONHOME=/usr/local/modeller8v0/bin/lib/python2.3 export PYTHONHOME=/usr/lib64/python2.3/
[kbranson@culpeper ~]$ mod8v0 -
MODELLER 8v0, Apr 15, 2005 03:15pm
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2005 Andrej Sali All Rights Reserved
Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux culpeper.parkville.hsn.csiro.au 2.6.10-1.766_FC3smp x86_64 Date and time of compilation : 04/15/2005 15:36:51 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2005/05/14 11:21:41.002
'import site' failed; use -v for traceback >>> dir() ['ModellerError', '__builtins__', '__doc__', '__name__', 'alignment', 'density', 'energy_data', 'environ', 'group_restraints', 'info', 'io_data', 'libraries', 'log', 'model', 'modfile', 'profile', 'sequence_db', 'topology', 'util']
Dr Kim Branson Peter Doherty Fellow Protein Structure and Function St Vincents Institute for Medical Research 41 Victoria Parade, Fitzroy Victoria 3065, Australia. Phone: +613 9288 2480 Fax: +613 94162 676 Ph +613 9662 7136 kbranson@svi.edu.au kim.branson@gmail.com www.svi.edu.au
Sperom@verizon.net died in april. Please remove his e-mail from all lists.
-----Original Message----- From: modeller_usage-bounces@salilab.org [mailto:modeller_usage-bounces@salilab.org] On Behalf Of Kim Branson Sent: Friday, May 13, 2005 9:25 PM To: modeller_usage@salilab.org Subject: [modeller_usage] modv8.0 on amd64
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Hi i'm trying to get the generic unix build of modeller to run on a amd64 bix running fedora core 3. I've had a look at the python paths, and played with a few variables. It would seem the python interpreter cannot find the site packages, but imports the modeller addons fine. Does anyone have a tip on how to get the embedded python to find the site packages?
export PYTHONPATH=/usr/lib64/python2.3/ #export PYTHONHOME=/usr/local/modeller8v0/bin/lib/python2.3 export PYTHONHOME=/usr/lib64/python2.3/
[kbranson@culpeper ~]$ mod8v0 -
MODELLER 8v0, Apr 15, 2005 03:15pm
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2005 Andrej Sali All Rights Reserved
Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux culpeper.parkville.hsn.csiro.au 2.6.10-1.766_FC3smp x86_64 Date and time of compilation : 04/15/2005 15:36:51 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2005/05/14 11:21:41.002
'import site' failed; use -v for traceback >>> dir() ['ModellerError', '__builtins__', '__doc__', '__name__', 'alignment', 'density', 'energy_data', 'environ', 'group_restraints', 'info', 'io_data', 'libraries', 'log', 'model', 'modfile', 'profile', 'sequence_db', 'topology', 'util']
Dr Kim Branson Peter Doherty Fellow Protein Structure and Function St Vincents Institute for Medical Research 41 Victoria Parade, Fitzroy Victoria 3065, Australia. Phone: +613 9288 2480 Fax: +613 94162 676 Ph +613 9662 7136 kbranson@svi.edu.au kim.branson@gmail.com www.svi.edu.au
_______________________________________________ modeller_usage mailing list modeller_usage@salilab.org http://salilab.org/mailman/listinfo/modeller_usage
Kim Branson wrote: > Hi i'm trying to get the generic unix build of modeller to run on a > amd64 bix running fedora core 3. I've had a look at the python paths, > and played with a few variables. It would seem the python interpreter > cannot find the site packages, but imports the modeller addons fine. > Does anyone have a tip on how to get the embedded python to find the > site packages?
You should debug problems like this by doing import sys print sys.path
to see where Python is looking for its modules. Generally, setting PYTHONHOME should put it on the right track.
The Modeller addons work because they are linked into the Modeller 32-bit executable along with the 32-bit Python interpreter. However, while this 32-bit build will work on an AMD64 box, I'm not sure whether you'll be able to load 'standard' Python modules, as they are (I believe) compiled for 64-bit (at least, those which have some non-Python code incorporated in .so files are).
But some good news: we have x86_64 builds of Modeller in house. Not only will they load the 'proper' 64-bit Python (at least, they do under RH Enterprise 4, which I think is pretty similar to FC3) but they run faster than the 32-bit binaries (significantly faster for some parts of the code, such as profile building). I'll test them with the 8v0 codebase and get an RPM out, probably within a week or so.
Ben Webb, Modeller Caretaker
Modeller Caretaker wrote: > But some good news: we have x86_64 builds of Modeller in house. Not only > will they load the 'proper' 64-bit Python (at least, they do under RH > Enterprise 4, which I think is pretty similar to FC3) but they run > faster than the 32-bit binaries (significantly faster for some parts of > the code, such as profile building).
There is an experimental x86_64 build now available for those that want it, at http://salilab.org/modeller/download_installation.html
Ben Webb, Modeller Caretaker
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the link to the new binary appears to be broken.
http://salilab.org/modeller/8v0/mod8v0_x86-64-intel8 gives me a 404....
cheers
Kim
On 19/05/2005, at 1:37 PM, Modeller Caretaker wrote:
> Modeller Caretaker wrote: >> But some good news: we have x86_64 builds of Modeller in house. Not >> only will they load the 'proper' 64-bit Python (at least, they do >> under RH Enterprise 4, which I think is pretty similar to FC3) but >> they run faster than the 32-bit binaries (significantly faster for >> some parts of the code, such as profile building). > > There is an experimental x86_64 build now available for those that > want it, at > http://salilab.org/modeller/download_installation.html > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage > > Dr Kim Branson Peter Doherty Fellow Protein Structure and Function St Vincents Institute for Medical Research 41 Victoria Parade, Fitzroy Victoria 3065, Australia. Phone: +613 9288 2480 Fax: +613 94162 676 Ph +613 9662 7136 kbranson@svi.edu.au kim.branson@gmail.com www.svi.edu.au
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Kim Branson -
Modeller Caretaker -
Spero Manolatos