Problem Installing PyRx

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[PyRx is no longer developed at MGL]

Problem Installing PyRx

Postby smolnar » Sat Aug 08, 2009 2:48 pm

I have just downloaded and run PyRx-0.2-Linux-x86-Install on my OpenSUSE AMD 64 bit computer. Unfortunately, when I ran the installer I got the following messages:

computation@linux-qcnb:/sdb6/Applications> PyRx-0.2-Linux-x86-Install
XIO: fatal IO error 11 (Resource temporarily unavailable) on X server ":0.0"
after 11297 requests (11296 known processed) with 0 events remaining.
computation@linux-qcnb:/sdb6/Applications> PyRx-0.2-Linux-x86-Install
Traceback (most recent call last):
File "/sdb6/Applications/PyRx/runPyRx.py", line 6, in <module>
import sys, os, pdb
File "/sdb6/Applications/MGLTools-1.5.4/lib/python2.5/pdb.py", line 11, in <module>
from repr import Repr
File "/sdb6/Applications/MGLTools-1.5.4/lib/python2.5/repr.py", line 6, in <module>
from itertools import islice
ImportError: /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/lib-dynload/itertools.so: wrong ELF class: ELFCLASS64

Please advise.

Thanks in advance.
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Re: Problem Installing PyRx

Postby sargis » Tue Aug 11, 2009 5:04 pm

Thank you for the message.
smolnar wrote:I have just downloaded and run PyRx-0.2-Linux-x86-Install on my OpenSUSE AMD 64 bit computer. Unfortunately, when I ran the installer I got the following messages:
computation@linux-qcnb:/sdb6/Applications> PyRx-0.2-Linux-x86-Install
XIO: fatal IO error 11 (Resource temporarily unavailable) on X server ":0.0"
after 11297 requests (11296 known processed) with 0 events remaining.

GUI installer fails to start when there are missing 32-bit X11 libraries. Please use TarArchive instead. See also:
libX11.so.6 not found on 64-bit Gentoo Linux

Please let me know if you have questions or need more information.

Thanks,
Sargis
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Re: Problem Installing PyRx

Postby smolnar » Tue Aug 11, 2009 6:01 pm

Thanks for your reply.

I have tried several things.

First of all, I downloaded the tar archieve. When I attempted to open it, tar -xzvf . . ., I got the message "tar: Error exit delayed from previous errors". So, I downloaded it again, and got the same the same error.

Next I installed the missing 32 bit library and ran the installer. This time I got a different error when I tried to run pyrx:

"computation@linux-qcnb:/sdb6/Applications/pyrx> runPyRx.py
'import site' failed; use -v for traceback
Traceback (most recent call last):
File "./runPyRx.py", line 6, in <module>
import sys, os, pdb
ImportError: No module named os
computation@linux-qcnb:/sdb6/Applications/pyrx> run.sh
Traceback (most recent call last):
File "/sdb6/Applications/pyrx/runPyRx.py", line 6, in <module>
import sys, os, pdb
File "/sdb6/Applications/MGLTools-1.5.4/lib/python2.5/pdb.py", line 11, in <module>
from repr import Repr
File "/sdb6/Applications/MGLTools-1.5.4/lib/python2.5/repr.py", line 6, in <module>
from itertools import islice
ImportError: /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/lib-dynload/itertools.so: wrong ELF class: ELFCLASS64"

Note that I tried both run.sh and runPyRx.py.
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Re: Problem Installing PyRx

Postby sargis » Tue Aug 11, 2009 8:50 pm

smolnar wrote:First of all, I downloaded the tar archieve. When I attempted to open it, tar -xzvf . . ., I got the message "tar: Error exit delayed from previous errors". So, I downloaded it again, and got the same the same error.

I'm not sure why tar gives this error message; I've got the same message but all the files seem to be unpacked fine.
smolnar wrote:Next I installed the missing 32 bit library and ran the installer. This time I got a different error when I tried to run pyrx:

"computation@linux-qcnb:/sdb6/Applications/pyrx> runPyRx.py
'import site' failed; use -v for traceback
Traceback (most recent call last):
File "./runPyRx.py", line 6, in <module>
import sys, os, pdb
ImportError: No module named os

./runPyRx.py is using systems default python and won't run unless all the dependencies are installed. Also, there is a problem with your default python, independent of PyRx. Run python -v to get more info.
smolnar wrote:computation@linux-qcnb:/sdb6/Applications/pyrx> run.sh
Traceback (most recent call last):
File "/sdb6/Applications/pyrx/runPyRx.py", line 6, in <module>
import sys, os, pdb
File "/sdb6/Applications/MGLTools-1.5.4/lib/python2.5/pdb.py", line 11, in <module>
from repr import Repr
File "/sdb6/Applications/MGLTools-1.5.4/lib/python2.5/repr.py", line 6, in <module>
from itertools import islice
ImportError: /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/lib-dynload/itertools.so: wrong ELF class: ELFCLASS64"

Note that I tried both run.sh and runPyRx.py.

I don't understand why it picks up python from MGLTools-1.5.4. run.sh sets PYRX_HOME=`pwd`and runs $PYRX_HOME/bin/python2.5; if you cd PyRx and then run ./run.sh after tar -xzvf . . . it should be completely independent of MGLTools. Note that, unless you renamed it, the name of the folder is PyRx with capital P and R. Could you please ls and see if there is LICENSE.txt and README.txt for PyRx? Thanks!
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Re: Problem Installing PyRx

Postby smolnar » Wed Aug 12, 2009 1:23 am

It gets weirder and weirder, at least to me.

First of all, both License.txt and README.txt are installed.

Now as far as the version of python that's installed:

as root I get:

linux-qcnb:~ # python -v
# installing zipimport hook
import zipimport # builtin
# installed zipimport hook
# /usr/lib64/python2.5/site.pyc matches /usr/lib64/python2.5/site.py
import site # precompiled from /usr/lib64/python2.5/site.pyc
# /usr/lib64/python2.5/os.pyc matches /usr/lib64/python2.5/os.py
import os # precompiled from /usr/lib64/python2.5/os.pyc
import posix # builtin
# /usr/lib64/python2.5/posixpath.pyc matches /usr/lib64/python2.5/posixpath.py
import posixpath # precompiled from /usr/lib64/python2.5/posixpath.pyc
# /usr/lib64/python2.5/stat.pyc matches /usr/lib64/python2.5/stat.py
import stat # precompiled from /usr/lib64/python2.5/stat.pyc
# /usr/lib64/python2.5/UserDict.pyc matches /usr/lib64/python2.5/UserDict.py
import UserDict # precompiled from /usr/lib64/python2.5/UserDict.pyc
# /usr/lib64/python2.5/copy_reg.pyc matches /usr/lib64/python2.5/copy_reg.py
import copy_reg # precompiled from /usr/lib64/python2.5/copy_reg.pyc
# /usr/lib64/python2.5/types.pyc matches /usr/lib64/python2.5/types.py
import types # precompiled from /usr/lib64/python2.5/types.pyc
import _types # builtin
# /usr/lib64/python2.5/warnings.pyc matches /usr/lib64/python2.5/warnings.py
import warnings # precompiled from /usr/lib64/python2.5/warnings.pyc
# /usr/lib64/python2.5/linecache.pyc matches /usr/lib64/python2.5/linecache.py
import linecache # precompiled from /usr/lib64/python2.5/linecache.pyc
import encodings # directory /usr/lib64/python2.5/encodings
# /usr/lib64/python2.5/encodings/__init__.pyc matches /usr/lib64/python2.5/encodings/__init__.py
import encodings # precompiled from /usr/lib64/python2.5/encodings/__init__.pyc
# /usr/lib64/python2.5/codecs.pyc matches /usr/lib64/python2.5/codecs.py
import codecs # precompiled from /usr/lib64/python2.5/codecs.pyc
import _codecs # builtin
# /usr/lib64/python2.5/encodings/aliases.pyc matches /usr/lib64/python2.5/encodings/aliases.py
import encodings.aliases # precompiled from /usr/lib64/python2.5/encodings/aliases.pyc
# /usr/lib64/python2.5/encodings/utf_8.pyc matches /usr/lib64/python2.5/encodings/utf_8.py
import encodings.utf_8 # precompiled from /usr/lib64/python2.5/encodings/utf_8.pyc
Python 2.5.1 (r251:54863, Sep 21 2007, 22:46:31)
[GCC 4.2.1 (SUSE Linux)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
dlopen("/usr/lib64/python2.5/lib-dynload/readline.so", 2);
import readline # dynamically loaded from /usr/lib64/python2.5/lib-dynload/readline.so
# /usr/lib64/python2.5/atexit.pyc matches /usr/lib64/python2.5/atexit.py
import atexit # precompiled from /usr/lib64/python2.5/atexit.pyc
# /usr/lib64/python2.5/rlcompleter.pyc matches /usr/lib64/python2.5/rlcompleter.py
import rlcompleter # precompiled from /usr/lib64/python2.5/rlcompleter.pyc

but, if I do python -v as the user I get:

setting PYTHONHOME environment
computation@linux-qcnb:~> python -v
# installing zipimport hook
import zipimport # builtin
# installed zipimport hook
# /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/site.pyc matches /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/site.py
import site # precompiled from /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/site.pyc
# /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/os.pyc matches /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/os.py
import os # precompiled from /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/os.pyc
import posix # builtin
# /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/posixpath.pyc matches /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/posixpath.py
import posixpath # precompiled from /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/posixpath.pyc
# /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/stat.pyc matches /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/stat.py
import stat # precompiled from /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/stat.pyc
# /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/UserDict.pyc matches /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/UserDict.py
import UserDict # precompiled from /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/UserDict.pyc
# /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/copy_reg.pyc matches /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/copy_reg.py
import copy_reg # precompiled from /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/copy_reg.pyc
# /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/types.pyc matches /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/types.py
import types # precompiled from /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/types.pyc
import _types # builtin
# /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/sitecustomize.pyc matches /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/sitecustomize.py
import sitecustomize # precompiled from /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/sitecustomize.pyc
import Support # directory /sdb6/Applications/MGLTools-1.5.4/MGLToolsPckgs/Support
# /sdb6/Applications/MGLTools-1.5.4/MGLToolsPckgs/Support/__init__.pyc matches /sdb6/Applications/MGLTools-1.5.4/MGLToolsPckgs/Support/__init__.py
import Support # precompiled from /sdb6/Applications/MGLTools-1.5.4/MGLToolsPckgs/Support/__init__.pyc
# /sdb6/Applications/MGLTools-1.5.4/MGLToolsPckgs/Support/path.pyc matches /sdb6/Applications/MGLTools-1.5.4/MGLToolsPckgs/Support/path.py
import Support.path # precompiled from /sdb6/Applications/MGLTools-1.5.4/MGLToolsPckgs/Support/path.pyc
# /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/user.pyc matches /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/user.py
import user # precompiled from /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/user.pyc
# /sdb6/Applications/MGLTools-1.5.4/MGLToolsPckgs/Support/version.pyc matches /sdb6/Applications/MGLTools-1.5.4/MGLToolsPckgs/Support/version.py
import Support.version # precompiled from /sdb6/Applications/MGLTools-1.5.4/MGLToolsPckgs/Support/version.pyc
# /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/warnings.pyc matches /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/warnings.py
import warnings # precompiled from /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/warnings.pyc
# /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/linecache.pyc matches /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/linecache.py
import linecache # precompiled from /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/linecache.pyc
import encodings # directory /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/encodings
# /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/encodings/__init__.pyc matches /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/encodings/__init__.py
import encodings # precompiled from /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/encodings/__init__.pyc
# /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/codecs.pyc matches /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/codecs.py
import codecs # precompiled from /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/codecs.pyc
import _codecs # builtin
# /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/encodings/aliases.pyc matches /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/encodings/aliases.py
import encodings.aliases # precompiled from /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/encodings/aliases.pyc
# /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/encodings/utf_8.pyc matches /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/encodings/utf_8.py
import encodings.utf_8 # precompiled from /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/encodings/utf_8.pyc
Python 2.5.1 (r251:54863, Oct 4 2007, 11:36:18)
[GCC 4.1.1 20070105 (Red Hat 4.1.1-52)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
dlopen("/sdb6/Applications/MGLTools-1.5.4/lib/python2.5/lib-dynload/readline.so", 2);
import readline # dynamically loaded from /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/lib-dynload/readline.so
# /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/atexit.pyc matches /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/atexit.py
import atexit # precompiled from /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/atexit.pyc
# /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/rlcompleter.pyc matches /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/rlcompleter.py
import rlcompleter # precompiled from /sdb6/Applications/MGLTools-1.5.4/lib/python2.5/rlcompleter.pyc

run.sh has all of the correct paths:

#!/usr/bin/env sh

PYRX_HOME=/sdb5/Applications/PyRx
LD_LIBRARY_PATH="$PYRX_HOME/lib/vtk-5.2:$PYRX_HOME/lib/wx-2.8:$PYRX_HOME/lib:$PYRX_HOME/lib/openbabel:$LD_LIBRARY_PATH"
export LD_LIBRARY_PATH
BABEL_DATADIR=$PYRX_HOME/share/openbabel/
export BABEL_DATADIR
BABEL_LIBDIR=$PYRX_HOME/lib/openbabel/2.2.1
export BABEL_LIBDIR
$PYRX_HOME/bin/python2.5 $PYRX_HOME/runPyRx.py

runPyRx.py is looking for a module os which my system says isn't present.
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Re: Problem Installing PyRx

Postby sargis » Wed Aug 12, 2009 4:40 pm

You must have added /sdb6/Applications/MGLTools-1.5.4/bin in front of your path which explains why root sees system's default python. This still doesn't explain the problem with PyRx. Are you setting PYTHONHOME or PYTHONPATH env variables or sourcing a script, such as mglenv.sh, that sets these variables? If so, please unset these variables before starting PyRx. I'll modify run.sh to make sure that it unsets PYTHONHOME and PYTHONPATH to avoid this kind of problems in the future. Thank you.
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Re: Problem Installing PyRx

Postby smolnar » Wed Aug 12, 2009 5:21 pm

Thanks for the unset suggestion. I modified run.sh:

#!/bin/bash
unset PYTHONHOME
unset PYTHONPATH

PYRX_HOME=`pwd`
LD_LIBRARY_PATH="$PYRX_HOME/lib/vtk-5.2:$PYRX_HOME/lib/wx-2.8:$PYRX_HOME/lib:$PYRX_HOME/lib/openbabel:$LD_LIBRARY_PATH"
export LD_LIBRARY_PATH
BABEL_DATADIR=$PYRX_HOME/share/openbabel/
export BABEL_DATADIR
BABEL_LIBDIR=$PYRX_HOME/lib/openbabel/2.2.1
export BABEL_LIBDIR
$PYRX_HOME/bin/python2.5 $PYRX_HOME/runPyRx.py

Running the modified file resulted in:

#!/bin/bash
unset PYTHONHOME
unset PYTHONPATH

PYRX_HOME=`pwd`
LD_LIBRARY_PATH="$PYRX_HOME/lib/vtk-5.2:$PYRX_HOME/lib/wx-2.8:$PYRX_HOME/lib:$PYRX_HOME/lib/openbabel:$LD_LIBRARY_PATH"
export LD_LIBRARY_PATH
BABEL_DATADIR=$PYRX_HOME/share/openbabel/
export BABEL_DATADIR
BABEL_LIBDIR=$PYRX_HOME/lib/openbabel/2.2.1
export BABEL_LIBDIR
$PYRX_HOME/bin/python2.5 $PYRX_HOME/runPyRx.py

So now the system is no longer looking at the mgltools directories, but missing a library.

This is change, not necessarily progress.
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Re: Problem Installing PyRx

Postby smolnar » Wed Aug 12, 2009 5:33 pm

Sorry, my last note was a bit mangled at the end.

The modified fun.sh is:

#!/bin/bash
unset PYTHONHOME
unset PYTHONPATH

PYRX_HOME=`pwd`
LD_LIBRARY_PATH="$PYRX_HOME/lib/vtk-5.2:$PYRX_HOME/lib/wx-2.8:$PYRX_HOME/lib:$PYRX_HOME/lib/openbabel:$LD_LIBRARY_PATH"
export LD_LIBRARY_PATH
BABEL_DATADIR=$PYRX_HOME/share/openbabel/
export BABEL_DATADIR
BABEL_LIBDIR=$PYRX_HOME/lib/openbabel/2.2.1
export BABEL_LIBDIR
$PYRX_HOME/bin/python2.5 $PYRX_HOME/runPyRx.py

and the result of running the modified file is:

computation@linux-qcnb:/sdb5/Applications/PyRx> run_mod.sh
Traceback (most recent call last):
File "/sdb5/Applications/PyRx/runPyRx.py", line 9, in <module>
import wx
File "/sdb5/Applications/PyRx/lib/python2.5/site-packages/wx-2.8-gtk2-unicode/wx/__init__.py", line 45, in <module>
from wx._core import *
File "/sdb5/Applications/PyRx/lib/python2.5/site-packages/wx-2.8-gtk2-unicode/wx/_core.py", line 4, in <module>
import _core_
ImportError: libgio-2.0.so.0: cannot open shared object file: No such file or directory
computation@linux-qcnb:/sdb5/Applications/PyRx>
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Re: Problem Installing PyRx

Postby sargis » Wed Aug 12, 2009 6:02 pm

Thanks for the Traceback. Please install the missing library: libgio-2.0 . On my Fedora it comes with glib2, but on SUSE, it seems to be shipped as a separate package.
Google libgio-2.0 suse. See also http://www.playonlinux.com/en/topic-2415-2.html. Please let me know if PyRx fails to start with this lib installed. Thank you.
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Re: Problem Installing PyRx

Postby smolnar » Thu Aug 13, 2009 1:24 pm

I finally found a libgio my system likes: libgio-2_0-0-32bit-2.16.3-24.1.x86_64.rpm from /joha_ma/openSUSE_10.3/x86_64/.

So now I get a different set of errors:

computation@linux-qcnb:/sdb5/Applications/PyRx> run_mod.sh
Traceback (most recent call last):
File "/sdb5/Applications/PyRx/runPyRx.py", line 9, in <module>
import wx
File "/sdb5/Applications/PyRx/lib/python2.5/site-packages/wx-2.8-gtk2-unicode/wx/__init__.py", line 45, in <module>
from wx._core import *
File "/sdb5/Applications/PyRx/lib/python2.5/site-packages/wx-2.8-gtk2-unicode/wx/_core.py", line 4, in <module>
import _core_
ImportError: /usr/lib/libgio-2.0.so.0: undefined symbol: g_checksum_update

I have to say that I am rapidly becoming disenchanted with OpenSUSE, but I'm not quite ready to redo my production machine.
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