RedHat6 compatability issues

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Mostafa

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Apr 14, 2014, 1:33:50 PM4/14/14
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Hi MDD users
In my quest !! of installing qMDD I get an error " wrong ELF class: ELFCLASS64"  Which I think refers to the redhat6  redhat5 issues since the latest version of qMDD is rh5. Does any one have any suggestions for what to do?

thanks
mostafa

Maxim Mayzel

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Apr 15, 2014, 4:26:48 AM4/15/14
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Dear Mostafa,

Could you be more explicit in your "bug reports" and your guess "qMDD is rh5" is wrong.
qMDD is a GUI for MDDNMR and it is written in python. To make it work you should have python 2.7,and numpy and pyside libraries.
Although you can install these libraries by yourself, I would recommend to use EPD/Canopy or Anaconda python, once it's installed you can try if it works or not (it should)
start python in the console and type  from PySide import *, you should see something similar 
$> python
Python 2.7.6 |Anaconda 1.9.1 (x86_64)| (default, Jan 10 2014, 11:23:15)
[GCC 4.0.1 (Apple Inc. build 5493)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from PySide import *
>>>

If it works, qMDD works as well.
Best,
Maxim

Mostafa

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Apr 15, 2014, 10:20:52 AM4/15/14
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Dear Maxim
I went through the protocol provided by you and i think there isnt any proble in the MDDNMR setup. The problem is python ( i've installed EPD) can not import pyside and after I open python and enter from PySide import * it gives me  this message "ImportError: /home/mj1612/epd-7.3-2-rh5-x86_64/lib/libpyside-python2.7.so.1.1: undefined symbol: _ZN9QMetaType15registerTypedefEPKci"

I cant figure out this problem and I guess its not related to MDDNMR

Thanks a lot

Mostafa

Troels Emtekær Linnet

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Apr 15, 2014, 3:27:43 PM4/15/14
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Hi Mostafa.

Here is a link how to make a good bug-report.
http://www.chiark.greenend.org.uk/~sgtatham/bugs.html

It is close to impossible to help you with the information you provide.

Could you maybe provide some of the following in the terminal
1) > uname -a
2) > cat /etc/redhat-release
3) > which python
4) > python -V
5) > echo $PYTHONPATH
6) > echo $LD_LIBRARY_PATH

I think your problem is already partly answered on the mailing list.
https://groups.google.com/forum/#!searchin/mddnmr/epd/mddnmr/gXHy3QeVjfM/wmw--i1xXKMJ

For example.
Let's say i want to run qMDD on our RHEL 5 server: biocfile1

We have just extracted the enthought EPD package to a separate folder
on our server, not
modifying any host files or system files.

See what happens:
**************************************************************************************************************************************
tlinnet@linmac:Desktop$ ssh -X biocfile1

Last login: Tue Apr 15 21:07:47 2014 from vpn-bio.science.ku.dk

[tlinnet@biocfile1 ~]$ which qMDD22
/sbinlab2/software/x64/bin/qMDD22

[tlinnet@biocfile1 ~]$ cat /sbinlab2/software/x64/bin/qMDD22
#!/bin/tcsh
#############Check at set correct PATHS
unsetenv PYTHONPATH
unsetenv LD_LIBRARY_PATH
setenv MDD_NMR /sbinlab2/software/mddnmr2.2
setenv MDD_NMRbin ${MDD_NMR}/binLinux64
set path=( $path $MDD_NMRbin ${MDD_NMR}/com )

#NmrMpipe
if (-e /sbinlab2/software/nmrPipe/com/nmrInit.linux9.com) then
setenv NMR_CONT CORRECT_ALL
source /sbinlab2/software/nmrPipe/com/nmrInit.linux9.com
endif
if( ! $?MDDTHREADS && $HOST == "haddock" ) set MDDTHREADS=23
###########################
set gui=1
set i=0
foreach a ($argv)
@ i+=1
if ( $a == 'nogui' ) then
set gui=0
set argv[$i]=''
endif
end

if ( `uname` == 'Linux' ) then
set style='cleanlooks'
else
set style=''
endif

if ( $gui == 1 ) then
set prog=$MDD_NMR/GUI/qMDDGUI.py
/usr/bin/env /sbinlab2/software/epd/bin/python $prog $*:q -style $style &
else
set prog=$MDD_NMR/GUI/qMDD.py
/usr/bin/env /sbinlab2/software/epd/bin/python $prog $*:q
endif

[tlinnet@biocfile1 ~]$ /sbinlab2/software/epd/bin/python
Enthought Python Distribution -- www.enthought.com
Version: 7.3-2 (64-bit)

Python 2.7.3 |EPD 7.3-2 (64-bit)| (default, Apr 11 2012, 17:52:16)
[GCC 4.1.2 20080704 (Red Hat 4.1.2-44)] on linux2
Type "credits", "demo" or "enthought" for more information.
>>> import PySide
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/sbinlab2/software/x64/lib64/python2.6/site-packages/PySide/__init__.py",
line 2, in <module>
import private
File "/sbinlab2/software/x64/lib64/python2.6/site-packages/PySide/private.py",
line 2, in <module>
from QtCore import __moduleShutdown
ImportError: /sbinlab2/software/x64/lib64/python2.6/site-packages/PySide/QtCore.so:
ELF file OS ABI invalid
>>>

[tlinnet@biocfile1 ~]$ echo $PYTHONPATH
/sbinlab2/software/CCP4-Linux_6.3.0/ccp4-6.3.0/share/python:.:/sbinlab2/software/x64/haddock2.1:/sbinlab2/software/x64/lib64/python2.6/site-packages:/sbinlab2/software/x64/ccpnmr/ccpnmr2.3/python

[tlinnet@biocfile1 ~]$ echo $LD_LIBRARY_PATH
/sbinlab2/software/CCP4-Linux_6.3.0/ccp4-6.3.0/lib:/usr/lib64:/sbinlab2/software/x64/gromacs/lib:/sbinlab2/software/nmrPipe/nmrbin.linux9/lib:/sbinlab2/software/x64/lib

[tlinnet@biocfile1 ~]$ unsetenv PYTHONPATH
[tlinnet@biocfile1 ~]$ unsetenv LD_LIBRARY_PATH

[tlinnet@biocfile1 ~]$ /sbinlab2/software/epd/bin/python
Enthought Python Distribution -- www.enthought.com
Version: 7.3-2 (64-bit)

Python 2.7.3 |EPD 7.3-2 (64-bit)| (default, Apr 11 2012, 17:52:16)
[GCC 4.1.2 20080704 (Red Hat 4.1.2-44)] on linux2
Type "credits", "demo" or "enthought" for more information.
>>> import PySide

**************************************************************************************************************************************


So, you have either one of the problems

1) You have 64 bit software installed on a 32 bit machine
2) Your PYTHONPATH and LD_LIBRARY_PATH has been modified somewhere.
unset them, and just execute the python from the EPD directory.

If you have further problems, try reading this link how to make a good
bug-report.
http://www.chiark.greenend.org.uk/~sgtatham/bugs.html

It is close to impossible to help you with the information you provide now. :-)

Best
Troels

Troels Emtekær Linnet
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Mostafa

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Apr 16, 2014, 11:52:20 AM4/16/14
to mdd...@googlegroups.com, Mostafa
Hi

problem solved it was case number 2 .. thanks a lot for the help
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