fidSP.com

[Tatiana Didenko]

Hello!
I process 3D spectra in qMDD gui, and when I edit fidSP.com (a phase, for example) I see no changes in the resulting spectrum.
There is a response to recFT modifications though. Maybe it is a path problem? I could not find the error so far.
The same problem with remote host option: the name of the host does not appear in my proc.sh file.

Will greatly appreciate any help..

Tanya

[Tatiana Didenko]

Actually, I've found out what was the problem with fidSP: after the first run of reconstruction the program does not rewrite the existing files in .proc directory. Therefore, if I want to modify something, I have to delete all the files there.
Is it supposed to be like that?

The problem with host option is still not solved.

Tanya

[Maxim Mayzel]

Dear Tanya,

Please check your $path variable (echo $path in a terminal window)

You should have "." before path to MDD_NMR 

so in .cshrc you should have

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

Best, 

Maxim

[Tatiana Didenko]

Dear Maxim,

Thank you for the answer!

I also thought that it could be the problem ( it was discussed before in some topic) but I can't solve it.
Here is my .cshrc:

           setenv MDD_NMR /home/didenkot/mddnmr
           setenv MDD_NMRbin ${MDD_NMR}/binLinux64
           set path=( $path $MDD_NMRbin  ${MDD_NMR}/com  )

When I type 'echo $path' there are no dots before the paths though i have a line "set path = ( '.' $path )"

How exactly it should look like?  set path=( $path .$MDD_NMRbin  ${MDD_NMR}/com  ) ?

I put dots in several positions, still have the same problems (i did 'source .cshrc'), sometimes the program crashed.

The program works OK in general, but once the fidSP.com is created, it is not "changeable" so I have to delete it each time I apply changes.
 Also I still can't connect to the remote host: it uses a default name (your.host) instead of the real one.

(just in case, my OS is Fedora 17)


Tanya

[Vladislav Orekhov]

Hi Tanya,
We never observed this problem, perhaps because we do not work with  Fedora.
Please try to remove files FTx*sh in the .proc directory instead of removing fidSP.com .
Files FTx.sh* must be generated automatically from fidSP.com every time you run mddnmr4pipeN.sh with argument 1.
This is done in proc.sh . It looks like your FTx.sh* are not updated, which is strange.
You may check if path setting is right. For this, in .proc directory  run command
  which FTx.sh.2D
the right output should be
./FTx.sh.2D
or
FTx.sh.2D

Note, as soon as qMDD produces all necessary files and directories, the script proc.sh can be edited in any text editor run from the Unix command line. This may help for troubleshooting and more advanced scripting.

Vladislav

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[Tatiana Didenko]

Hi Vladislav!

I think it may very well be that the problem is related to the incompatible OS. I tried qMDD on OS X and it worked fine.

I have just started working with qMDD, I may be wrong but I think that those problems on Fedora started after the last qMDD update. But maybe it is not the case.

Thank you for help!

Tanya

[Maxim Mayzel]

What I mean is  the line  "set path = ( '.' $path )" that you have and definitely nothing like this ".$MDD_NMRbin"

Please send the output of "echo $path" command and "ls -a fidSP.com"  (does fidSP.com have 'w' attribute?)

And as Vladislav pointed out, qMDD is used to make all necessary files and directories, try to edit fidSP.com/proc.sh with standard text editors and run proc.sh from terminal manually.

Maxim

[Tatiana Didenko]

Hi Maxim,

here are the attributes of fidSP.com:  -rwxr-xr-x
Yes, it might be a permission problem somewhere.

Here is the output of echo$path: . /home/didenkot/nmrpipe/nmrbin.linux9 /home/didenkot/nmrpipe/com /usr/local/bin /home/didenkot/bin /home/didenkot . /bin /usr/bin /sbin /usr/sbin /etc /usr/etc /usr/bsd /usr/ucb /home/didenkot/mddnmr/binLinux64 /home/didenkot/mddnmr/com

Manual editing works.


Tanya

[Maxim Mayzel]

HI Tanya,

If it works from terminal, then it's definitely python problem

What python/PySide version do you have?

python --version and

python

import PySide

PySide.__version__

I would recommend you to try EPD python

http://www.enthought.com/products/edudownload.php

It's a bundle of python2.7 with many libraries (no need to install numpy, scipy, PySide manually), and so far we had no problems with this python distribution.

Best,

Maxim

среда, 16 января 2013 г., 20:14:09 UTC+1 пользователь Tatiana Didenko написал:

[Tatiana Didenko]

Hi Maxim,
I have python 2.7.3 and PySide 1.1.0

Those are the latest versions available for Fedora, can it be that the PySide is outdated? (there is a 1.1.2 version now)

Tanya

[Tatiana Didenko]

Also, i have a kind of related question: is it crucial to have a latest python on a cluster?

[Maxim Mayzel]

The same versions of Python & PySide we have. It seems that I would need to install Fedora to find out the problem.

As for the python on a cluster,  you don't need to have it. When we send calculations to the cluster we do following:

1) Archive MDD dir ("ar czf mdd.tgz MDD)

2) Copy data to the cluster ( scp regions.runs mdd.tgz login@host)  - you should have password free ssh login!

3) Run calculations (tar xzf mdd.tgz; $RUNQUE regions.runs). Where $RUNQUE is a dispatcher program that distribute calculations; for our one needs we made rather simple script "queMM.sh" that distribute calculations to different nodes via ssh.

4) Copy results back

So in order to send calculations to the cluster one should have:

1) MDDNMR installed on  the cluster (python is not needed)

2) Dispatcher program that would be able to distribute calculations specified in regions.runs file.

Best,

Maxim

[ramachandra dongre]

Dear Maxim,

Is it not possible to run it on the cluster just by copying  whole XYZ.proc directory to server and run the script "proc.sh"..?(assuming MDD is installed there as well).

best regards,

Ramachandra.

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Ramachandra Dongre
PhD student (AIO)
NMR Spectroscopy Research Group
Bijvoet Center for Biomolecular Research
Utrecht University
Bloembergen gebouw
Padualaan 8, 3584 CH Utrecht
Telephone: +31.(0)30.2532875
 Fax: +31.(0)30.2537623
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The Netherlands

[ramachandra dongre]

Hi Maxim,

some clarifications..."XYZ.proc" is an example .proc directory I was referring to, I remember there is similar directory in MDD reconstruction, I was not referring to that.

I would like to know about this dispatcher programe for cluster.

I have tried it on the cluster and it worked. I did not install any Dispatcher program. I used only one node. I did not run it across the nodes. I setup the MDD in my computer and transferred both the directories (spectra and .proc) to cluster and run "proc.sh". Am I doing rt..?

best regards,

RAMA