installation problem on 64 bit FC 11

[tevang]

Dear developers,

I tried to install the binary but I get the following error when launching:

File "/usr/local/PyRx/runPyRx.py", line 10, in <module>
import wx
File "/usr/local/PyRx/lib/python2.5/site-packages/wx-2.8-gtk2-unicode/wx/__init__.py", line 45, in <module>
from wx._core import *
File "/usr/local/PyRx/lib/python2.5/site-packages/wx-2.8-gtk2-unicode/wx/_core.py", line 4, in <module>
import _core_
ImportError: libSDL-1.2.so.0: cannot open shared object file: No such file or directory

I then created a symbolic link:
sudo ln -s /usr/lib64/libSDL-1.2.so.0 /usr/lib/libSDL-1.2.so.0

but the error message becomes:

Traceback (most recent call last):
File "/usr/local/PyRx/runPyRx.py", line 10, in <module>
import wx
File "/usr/local/PyRx/lib/python2.5/site-packages/wx-2.8-gtk2-unicode/wx/__init__.py", line 45, in <module>
from wx._core import *
File "/usr/local/PyRx/lib/python2.5/site-packages/wx-2.8-gtk2-unicode/wx/_core.py", line 4, in <module>
import _core_
ImportError: libSDL-1.2.so.0: wrong ELF class: ELFCLASS64

Finally I tried installing from source with admin privileges, and afterwards:

thomas@thomas:~/Documents/pyrx/PyRxDev$ sudo ./runPyRx.py
/usr/lib64/python2.6/site-packages/wx-2.8-gtk2-unicode/wx/_core.py:14450: UserWarning: wxPython/wxWidgets release number mismatch
warnings.warn("wxPython/wxWidgets release number mismatch")
No module named mglutil.util.packageFilePath
Traceback (most recent call last):
File "./runPyRx.py", line 16, in <module>
from PyRx.wxMainFrame import MainFrame
File "/home/thomas/Documents/pyrx/PyRxDev/PyRx/wxMainFrame.py", line 8, in <module>
from utils import rcFolder
File "/home/thomas/Documents/pyrx/PyRxDev/PyRx/utils.py", line 6, in <module>
from mglutil.util.packageFilePath import getResourceFolder
ImportError: No module named mglutil.util.packageFilePath

And without sudo:

thomas@thomas:~/Documents/pyrx/PyRxDev$ ./runPyRx.py
/usr/lib64/python2.6/site-packages/wx-2.8-gtk2-unicode/wx/_core.py:14450: UserWarning: wxPython/wxWidgets release number mismatch
warnings.warn("wxPython/wxWidgets release number mismatch")
No module named preferences.api
Traceback (most recent call last):
File "./runPyRx.py", line 16, in <module>
from PyRx.wxMainFrame import MainFrame
File "/home/thomas/Documents/pyrx/PyRxDev/PyRx/wxMainFrame.py", line 9, in <module>
from enthought.preferences.api import get_default_preferences
ImportError: No module named preferences.api



Any ideas what's wrong???

thanks in advance,
Thomas

[sargis]

Thank you for the message Thomas.

I tried to install the binary but I get the following error when launching:

File "/usr/local/PyRx/runPyRx.py", line 10, in <module>
import wx
File "/usr/local/PyRx/lib/python2.5/site-packages/wx-2.8-gtk2-unicode/wx/__init__.py", line 45, in <module>
from wx._core import *
File "/usr/local/PyRx/lib/python2.5/site-packages/wx-2.8-gtk2-unicode/wx/_core.py", line 4, in <module>
import _core_
ImportError: libSDL-1.2.so.0: cannot open shared object file: No such file or directory

I then created a symbolic link:
sudo ln -s /usr/lib64/libSDL-1.2.so.0 /usr/lib/libSDL-1.2.so.0

but the error message becomes:

Traceback (most recent call last):
File "/usr/local/PyRx/runPyRx.py", line 10, in <module>
import wx
File "/usr/local/PyRx/lib/python2.5/site-packages/wx-2.8-gtk2-unicode/wx/__init__.py", line 45, in <module>
from wx._core import *
File "/usr/local/PyRx/lib/python2.5/site-packages/wx-2.8-gtk2-unicode/wx/_core.py", line 4, in <module>
import _core_
ImportError: libSDL-1.2.so.0: wrong ELF class: ELFCLASS64

You'll need to add 32-bit Support into 64-bit Fedora to make it work. Use yum install SDL.i586, for instance. The following link provides complete list of packages: http://beginlinux.com/blog/2009/09/inst ... fedora-11/

Finally I tried installing from source with admin privileges, and afterwards:

thomas@thomas:~/Documents/pyrx/PyRxDev$ sudo ./runPyRx.py
/usr/lib64/python2.6/site-packages/wx-2.8-gtk2-unicode/wx/_core.py:14450: UserWarning: wxPython/wxWidgets release number mismatch
warnings.warn("wxPython/wxWidgets release number mismatch")
No module named mglutil.util.packageFilePath
Traceback (most recent call last):
File "./runPyRx.py", line 16, in <module>
from PyRx.wxMainFrame import MainFrame
File "/home/thomas/Documents/pyrx/PyRxDev/PyRx/wxMainFrame.py", line 8, in <module>
from utils import rcFolder
File "/home/thomas/Documents/pyrx/PyRxDev/PyRx/utils.py", line 6, in <module>
from mglutil.util.packageFilePath import getResourceFolder
ImportError: No module named mglutil.util.packageFilePath

And without sudo:

thomas@thomas:~/Documents/pyrx/PyRxDev$ ./runPyRx.py
/usr/lib64/python2.6/site-packages/wx-2.8-gtk2-unicode/wx/_core.py:14450: UserWarning: wxPython/wxWidgets release number mismatch
warnings.warn("wxPython/wxWidgets release number mismatch")
No module named preferences.api
Traceback (most recent call last):
File "./runPyRx.py", line 16, in <module>
from PyRx.wxMainFrame import MainFrame
File "/home/thomas/Documents/pyrx/PyRxDev/PyRx/wxMainFrame.py", line 9, in <module>
from enthought.preferences.api import get_default_preferences
ImportError: No module named preferences.api

Any ideas what's wrong???

./runPyRx.py won't work unless you installed PyRx from source. Please use run.sh that sets up all necessary env variables before starting runPyRx.py.

[tevang]

Hi Sargis,

I installed SDL.i586 and the rest of the libraries recommended in the link you send me, and then I ran the binary with sudo, but got 2 SELinux alerts (cannot attach them). After applying the recommended fixes and re-executed sudo /usr/local/PyRx/run.sh I could see the start up window but a few seconds later it broke with the following output message:

sudo /usr/local/PyRx/run.sh
[sudo] password for thomas:

(python2.5:12011): Gtk-WARNING **: Unable to locate theme engine in module_path: "nodoka",

(python2.5:12011): Gtk-WARNING **: Unable to locate theme engine in module_path: "nodoka",
Gtk-Message: Failed to load module "pk-gtk-module": libpk-gtk-module.so: cannot open shared object file: No such file or directory
Gtk-Message: Failed to load module "canberra-gtk-module": libcanberra-gtk-module.so: cannot open shared object file: No such file or directory
Gtk-Message: Failed to load module "gnomebreakpad": libgnomebreakpad.so: cannot open shared object file: No such file or directory
/usr/local/PyRx/run.sh: line 10: 12011 Segmentation fault $PYRX_HOME/bin/python2.5 $PYRX_HOME/runPyRx.py


Of these modules I could only find libcanberra.i586 which I installed. Finally I executed manually the command in run.sh and $PYRX_HOME/bin/python2.5 $PYRX_HOME/runPyRx.py. Due to a warning message that nodoka is missing I installed whatever package I could find with the word "nodoka". However I still get the following:

Gtk-Message: Failed to load module "pk-gtk-module": libpk-gtk-module.so: cannot open shared object file: No such file or directory
Gtk-Message: Failed to load module "canberra-gtk-module": libcanberra-gtk-module.so: cannot open shared object file: No such file or directory
Gtk-Message: Failed to load module "gnomebreakpad": libgnomebreakpad.so: cannot open shared object file: No such file or directory
/home/thomas/Documents/MGLTools-1.5.4/lib/python2.5/site-packages/numpy/core/multiarray.so: wrong ELF class: ELFCLASS64
Traceback (most recent call last):
File "/usr/local/PyRx/runPyRx.py", line 16, in <module>
from PyRx.wxMainFrame import MainFrame
File "/usr/local/PyRx/lib/python2.5/site-packages/PyRx/wxMainFrame.py", line 14, in <module>
from mayaviActions import AddMayaviMenus, ID_RUN
File "/usr/local/PyRx/lib/python2.5/site-packages/PyRx/mayaviActions.py", line 7, in <module>
from enthought.pyface.action.api import Action
File "/usr/local/PyRx/lib/python2.5/site-packages/TraitsGUI-3.0.4.dev_r22713-py2.5.egg/enthought/pyface/action/api.py", line 16, in <module>
from action import Action
File "/usr/local/PyRx/lib/python2.5/site-packages/TraitsGUI-3.0.4.dev_r22713-py2.5.egg/enthought/pyface/action/action.py", line 20, in <module>
from enthought.traits.ui.api import Image
File "/usr/local/PyRx/lib/python2.5/site-packages/Traits-3.0.4.dev_r22852-py2.5-linux-i686.egg/enthought/traits/ui/api.py", line 92, in <module>
from editors.api \
File "/usr/local/PyRx/lib/python2.5/site-packages/Traits-3.0.4.dev_r22852-py2.5-linux-i686.egg/enthought/traits/ui/editors/__init__.py", line 19, in <module>
from api import *
File "/usr/local/PyRx/lib/python2.5/site-packages/Traits-3.0.4.dev_r22852-py2.5-linux-i686.egg/enthought/traits/ui/editors/api.py", line 3, in <module>
from array_editor import ArrayEditor
File "/usr/local/PyRx/lib/python2.5/site-packages/Traits-3.0.4.dev_r22852-py2.5-linux-i686.egg/enthought/traits/ui/editors/array_editor.py", line 25, in <module>
import numpy
File "/home/thomas/Documents/MGLTools-1.5.4/lib/python2.5/site-packages/numpy/__init__.py", line 39, in <module>
import core
File "/home/thomas/Documents/MGLTools-1.5.4/lib/python2.5/site-packages/numpy/core/__init__.py", line 5, in <module>
import multiarray
ImportError: /home/thomas/Documents/MGLTools-1.5.4/lib/python2.5/site-packages/numpy/core/multiarray.so: wrong ELF class: ELFCLASS64

[sargis]

Hi Thomas,

ImportError: /home/thomas/Documents/MGLTools-1.5.4/lib/python2.5/site-packages/numpy/core/multiarray.so: wrong ELF class: ELFCLASS64

Please run the following commands before starting PyRx:

Code: Select all

unset PYTHONHOME
unset PYTHONPATH

I would recommend installing PyRx 0.3 on FC11, then updating to 0.4 as instructed in http://pyrx.scripps.edu/downloads. run.sh in 0.3 does that and has more resent version of third party packages. I've created 0.4 from older version of third party packages to be compatible with RHEL5/CentOS5 and forgot to replace run.sh to avoid these kind of problems. Thanks!

[tevang]

Sargis,

that's what I get when I upgrade from 0.3:

Gtk-Message: Failed to load module "pk-gtk-module": libpk-gtk-module.so: cannot open shared object file: No such file or directory
Gtk-Message: Failed to load module "canberra-gtk-module": libcanberra-gtk-module.so: cannot open shared object file: No such file or directory
Gtk-Message: Failed to load module "gnomebreakpad": libgnomebreakpad.so: cannot open shared object file: No such file or directory
Traceback (most recent call last):
File "/usr/local/PyRx/runPyRx.py", line 37, in <module>
frame = MainFrame(None, -1, size=(width, height-200))
File "/usr/local/PyRx/lib/python2.5/site-packages/PyRx/wxMainFrame.py", line 125, in __init__
import preferences
File "/usr/local/PyRx/lib/python2.5/site-packages/PyRx/preferences.py", line 31, in <module>
from traitedBabel import openbabelParameters, openbabelAutoDockParameters
File "/usr/local/PyRx/lib/python2.5/site-packages/PyRx/traitedBabel.py", line 576, in <module>
openbabelParameters = OpenBabelParameters()
File "/sargis/PyRx/lib/python2.5/site-packages/AppTools-3.3.0-py2.5.egg/enthought/preferences/preferences_helper.py", line 46, in __init__
File "/sargis/PyRx/lib/python2.5/site-packages/AppTools-3.3.0-py2.5.egg/enthought/preferences/preferences_helper.py", line 167, in _initialize
File "/sargis/PyRx/lib/python2.5/site-packages/AppTools-3.3.0-py2.5.egg/enthought/preferences/preferences_helper.py", line 151, in _get_value
File "/sargis/PyRx/lib/python2.5/site-packages/Traits-3.2.0-py2.5-linux-i686.egg/enthought/traits/trait_types.py", line 1929, in validate
File "/sargis/PyRx/lib/python2.5/site-packages/Traits-3.2.0-py2.5-linux-i686.egg/enthought/traits/trait_handlers.py", line 175, in error
TraitError: The 'force_field' trait of an OpenBabelParameters instance must be 'uff' or 'mmff94' or 'ghemical', but a value of 'UFF' <type 'str'> was specified.
None

[sargis]

Thomas,

File "/sargis/PyRx/lib/python2.5/site-packages/Traits-3.2.0-py2.5-linux-i686.egg/enthought/traits/trait_handlers.py", line 175, in error
TraitError: The 'force_field' trait of an OpenBabelParameters instance must be 'uff' or 'mmff94' or 'ghemical', but a value of 'UFF' <type 'str'> was specified.
None

Please remove ~/.mgltools/PyRx/preferences.ini and start run.sh again. You can also update /usr/local/PyRx/lib/python2.5/site-packages/PyRx with PyRx-0.4-Source.zip to avoid this problem.

Gtk-Message: Failed to load module "gnomebreakpad": libgnomebreakpad.so: cannot open shared object file: No such file or directory

I Googled this and it seems that you can safely ignore this message. Thanks.

[tevang]

Yes, it finally works!!!

I'm just wondering what's the maximum scale of docking one can do with PyRx? Speaking with numbers, is it possible to submit 1,5 million jobs to opal and get results within the same month?


thanks,
Thomas

[sargis]

Yes, it finally works!!!

Great! I hope you will enjoy it!

I'm just wondering what's the maximum scale of docking one can do with PyRx? Speaking with numbers, is it possible to submit 1,5 million jobs to opal and get results within the same month?

I've tested it with up to, around, 500 compounds. I'd recommend to start with just a few compounds to troubleshoot possible problems that might arise. While it might be possible to submit 1,5 million jobs to opal and get results within the same month, the GUI part becomes sluggish with around 3K compounds on my PC with 2GB of memory.

[tevang]

Sargis,

can you give me an idea of how fast opal service is as an alternative to stand-alone docking? This is my own pet project:

http://sites.google.com/site/offtargetpipeline/

Among other analyses can do small-scale Virtual Screening with autodock 4 and Vina. I'm wondering if it would be faster to modify the code to submit jobs to opal instead of running them locally. Moreover, there's no Windows version of pdb2pqr to prepare protein-ligand complexes, hence the Electrostatic Energy and Electrostatic Potential Distribution Comparison within the binding cavity are not available in my Windows version. One alternative for that is to use the opal service. Do you know about how many jobs can the server handle?

thanks,
Thomas

[sargis]

Thomas,

can you give me an idea of how fast opal service is as an alternative to stand-alone docking?

You pay a slight overhead with opal service to send and receive data, but if you have on the order of 100s docking to perform, then it's 100 times faster compared to stand-alone docking.

This is my own pet project:

http://personalpages.manchester.ac.uk/p ... tents.html

Nice! It seems to be a good project to test on http://www.worldcommunitygrid.org

Among other analyses can do small-scale Virtual Screening with autodock 4 and Vina. I'm wondering if it would be faster to modify the code to submit jobs to opal instead of running them locally. Moreover, there's no Windows version of pdb2pqr to prepare protein-ligand complexes, hence the Electrostatic Energy and Electrostatic Potential Distribution Comparison within the binding cavity are not available in my Windows version. One alternative for that is to use the opal service.

This depends if the code will be written for an end user or for internal use. Modifying the code to submit jobs to opal will be beneficial for an end user, but it adds an extra level of complexity that requires additional time to code, debug and maintain the code. If the code is written for internal use, then it's better to write scripts to support running it on a local cluster.

Do you know about how many jobs can the server handle?

I don't know this number. So far I haven't hit the limit. One limitation that I encounter is Java out of memory errors. I run the jobs that cause these kind of errors on a local cluster instead.