Cannot get qMDD revision

[Bruno Vitorge]

Hello everyone,
thank you for providing this software, I just started to try to process some NUS data. I encountered some error message:
when I start qMDD (the graphical interface), I got the following error:
Cannot get qMDD revision
The window with the message arrive two times, then qMDD is launched.

My installation:
I installed python 2.7 from Enthought (I installed the Canopy Express version).
Then I installed "qMDD Version 3.2" ( from "about" button in qMDD).
I'm behind a proy.
I used setenv http_proxy but with no effect.

To start easily the programme I created a file with these lines:

setenv MDD_NMR /sourcesoft/mddnmr2.2/mddnmr
setenv MDD_NMRbin ${MDD_NMR}/binLinux64
setenv http_proxy myproxy
set path=( $path . $MDD_NMRbin  ${MDD_NMR}/com)

and an executable script with these lines:

#!/bin/bash
# Bruno 17 Juil 2013
#to start qMDD need to enable python from Entought (Free Canopy Express)
# needed to use the "activate" file for setting the python environment
source ~/Enthought/Canopy_64bit/User/bin/activate
# Then in tcsh we set the environnement for qMDD
tcsh -c "source /soft/bin/qMDD_lab_env;qMDD"
echo "starting very slow, need to wait sorry"

I did that because our default shell is tcsh, (I think for nmrPipe tcsh is recommended) but to activate the python from Enthought (we have at least three others versions) it is not working in tcsh.

If you have any better way I would appreciate.
Regards, Bruno

[Maxim Mayzel]

Hi Bruno,

First of all, according to my experience Canopy works fine with tcsh, try to add following line to the end of your .cshrc file

set path=( ~/Enthought/Canopy_64bit/User/bin  $path)

Second, qMDD gets revision and updates from Bitbucket repository, it could be that there were some problems with Bitbucket , try one more time, I've just checked it works.

Best regards,

Maxim

четверг, 18 июля 2013 г., 15:09:42 UTC+2 пользователь Bruno Vitorge написал:

[Maxim Mayzel]

If these won't help the problem is because you are using proxy 
here's a solution http://stackoverflow.com/questions/1450132/proxy-with-urllib2
open $MDD_NMR/GUI/updater.py and insert following lines at line 28

proxy = urllib2.ProxyHandler({'http': 'YOUR_PROXY_IP'})
opener = urllib2.build_opener(proxy)
urllib2.install_opener(opener)

Let me know if these will help, I'll make an update

Maxim

четверг, 18 июля 2013 г., 22:14:23 UTC+2 пользователь Maxim Mayzel написал:

[Bruno Vitorge]

Thank you for your answers.
Does the insertion of the line:
"set path=( ~/Enthought/Canopy_64bit/User/bin  $path)"
in the .cshrc  will set python from Canopy the default python?

I added the three lines you suggested to the "updater.py" file,
but this doesn't change anything for the starting of qMDD, the error is still displayed.
The program  take more than one minutes to start (on 8CPU with 32Go of ram computer)

May I suggest to do the search for update and the updates manualy?
Usualy I install programs using root, and then use them with a "normal" user, so the update will not work.
Programs are installed for all the users in this way.

Thank you again for your help.

[Troels Emtekær Linnet]

Hi Bruno.

Maybe our setup can help you.

We have a shared path for software for our lab linux computers.

Each user has this in their .cshrc
source /ourlab2/software/cshrc

The global /ourlab2/software/cshrc contains many variable setup.
For example:

#-----------------------------------------------------------------
# Global shared bin
#-----------------------------------------------------------------
setenv PATH /ourlab2/software/bin:.:${PATH}

#-------------------------------------------------------
# Make users bin files available
#-------------------------------------------------------
setenv PATH {$HOME}/bin:${PATH}:/usr/sbin:/sbin

#-----------------------------------------------------------------
# nmrPipe
#-----------------------------------------------------------------
if (-e /ourlab2/software/nmrPipe/com/nmrInit.linux9.com) then
setenv NMR_CONT CORRECT_ALL
source /ourlab2/software/nmrPipe/com/nmrInit.linux9.com
endif

#--------------------------------------------------------------
# Enthought Python distribution
#--------------------------------------------------------------
setenv PATH ${PATH}:/ourlab2/software/python-enthought-dis/epd-7.3-2-rh5-x86_64/bin
alias ipython '/ourlab2/software/python-enthought-dis/epd-7.3-2-rh5-x86_64/bin/ipython'

----------------------

Anyway, we found that some of all these settings made a terrible mess.
And we want to only run qMDD on a machine with 24 cores, computer mr Haddock.
So, it get a little tricky.
The total setup is:

[tlinnet@tomat ~]$ which qMDD
/ourlab2/software/x64/bin/qMDD

cat /ourlab2/software/x64/bin/qMDD
#!/bin/tcsh
######### Check machine
if ( $HOST != "haddock") then
echo "You have to run on haddock. I do it for you"
ssh haddock -Y -t "cd $PWD; qMDD22; /bin/tcsh"
else
qMDD22
endif

We can then easily upgrade to new versions of qMDD, when we
have tested it. And we can call old versions.
Example. qMDD20, qMDD21, qMDD22

tlinnet@haddock ~]$ which qMDD22
/ourlab2/software/x64/bin/qMDD22

We need to unset PYTHONPATH and LD_LIBRARY_PATH,
since they can be messed up from earlier.
Then we set again for Nmrpipe.

Note, there is a soft link ln -s from:
/ourlab2/software/epd ->
/ourlab2/software/python-enthought-dis/epd-7.3-2-rh5-x86_64

Note: the call to the EPD python.
/usr/bin/env /ourlab2/software/epd/bin/python

cat /sbinlab2/software/x64/bin/qMDD22

#!/bin/tcsh
############# Check at set correct PATHS
unsetenv PYTHONPATH
unsetenv LD_LIBRARY_PATH
setenv MDD_NMR /ourlab2/software/mddnmr2.2

setenv MDD_NMRbin ${MDD_NMR}/binLinux64

set path=( $path $MDD_NMRbin ${MDD_NMR}/com )

#Nmrpipe
if (-e /ourlab2/software/nmrPipe/com/nmrInit.linux9.com) then
setenv NMR_CONT CORRECT_ALL
source /ourlab2/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 /ourlab2/software/epd/bin/python $prog $*:q -style $style &
else
set prog=$MDD_NMR/GUI/qMDD.py
/usr/bin/env /ourlab2/software/epd/bin/python $prog $*:q
endif


Troels Emtekær Linnet


2013/7/19 Bruno Vitorge <bruno....@gmail.com>:

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[Maxim Mayzel]

Hi Bruno,

On Friday, July 19, 2013 4:22:00 PM UTC+2, Bruno Vitorge wrote:

Thank you for your answers.
Does the insertion of the line:
"set path=( ~/Enthought/Canopy_64bit/User/bin  $path)"
in the .cshrc  will set python from Canopy the default python?

 

Yes, it will set Canopy python as default python for particular user 

 

I added the three lines you suggested to the "updater.py" file,
but this doesn't change anything for the starting of qMDD, the error is still displayed.
The program  take more than one minutes to start (on 8CPU with 32Go of ram computer)

Ok, I got it, the reason is probably the following. Updater is started in the same thread as the main program, and while it's trying to get an update execution of the main program is hanged. That's of course wrong and  I'll fix this. 

Another point, if program is installed under different account and user cannot update the program automatic update shouldn't start at all, that's easy to fix.

Anyway this won't solve connection or proxy problem and to be honest I don't know how to solve it by myself since I'm not using proxy and I don't have a problem. If you are familiar with python, could you test if you can connect to google.com for example using this post as a guideline 

http://stackoverflow.com/questions/1450132/proxy-with-urllib2

Best,

Maxim

[Bruno Vitorge]

Thank you Troels for  your help.
I don't really want to change the default python, I'm a bit afraid by the impact on the other program we are using.

Le samedi 20 juillet 2013 19:06:13 UTC+2, Maxim Mayzel a écrit :

Hi Bruno,

On Friday, July 19, 2013 4:22:00 PM UTC+2, Bruno Vitorge wrote:

Thank you for your answers.
Does the insertion of the line:
"set path=( ~/Enthought/Canopy_64bit/User/bin  $path)"
in the .cshrc  will set python from Canopy the default python?

 

Yes, it will set Canopy python as default python for particular user 

 

I added the three lines you suggested to the "updater.py" file,
but this doesn't change anything for the starting of qMDD, the error is still displayed.
The program  take more than one minutes to start (on 8CPU with 32Go of ram computer)

Ok, I got it, the reason is probably the following. Updater is started in the same thread as the main program, and while it's trying to get an update execution of the main program is hanged. That's of course wrong and  I'll fix this. 

Another point, if program is installed under different account and user cannot update the program automatic update shouldn't start at all, that's easy to fix.

Glad to have helped for finding this.
 

Anyway this won't solve connection or proxy problem and to be honest I don't know how to solve it by myself since I'm not using proxy and I don't have a problem. If you are familiar with python, could you test if you can connect to google.com for example using this post as a guideline 

http://stackoverflow.com/questions/1450132/proxy-with-urllib2

I do a bit of python programming, if I manage to do useful things I will tell you. 

Best,

Maxim

Best,
Bruno

[Troels Emtekær Linnet]

Hi bruno.

I understand this!

We setup to use enthought, because the need of wxPython.
And our RHEL satelite computers, in many cases did not have that package.
But if you setup qMDD on a powerfull computer, and just resolve python
packages there,
everything will go fine.

A nice script for quickly changing to the powerfull computer, could be:
> cat haddock
#!/bin/tcsh
ssh haddock -Y -t "cd $PWD; /bin/tcsh"

So when a user writes "haddock", it changes computer, and go into the
current working directory.
I always "hate", when you SSH into a computer, and the folder changes
to the HOME folder.

Cheers!


Troels Emtekær Linnet


2013/7/22 Bruno Vitorge <bruno....@gmail.com>:

[Bruno Vitorge]

Hi  Troels,
I finally found some time to try your files. They are working very well, the program is starting much much faster.
Thank you a lot. Now I just have to learn how to use it :-).

I did not find the way to fix the proxy problem yet.