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Old   January 18, 2010, 09:08
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  #181
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Bernhard Gschaider
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Quote:
Originally Posted by braennstroem View Post
Hi Bernhard,
yes, you are right. Though, where do I set the option? Using:

pfile=BoundaryDict(case2,time="10")

I get: TypeError: __init__() got an unexpected keyword argument 'time'

Thanks for your help!
Fabian
OK. I see the problem.

BoundaryDict is a convenience-class around ParsedBoundaryDict (which takes the absolute path to the file) that uses a SolutionDirectory as a parameter and uses the boundaryDict-method of that class to get the actual filename. The problem is that obviously BoundaryDict does not accept a time-parameter and therefor can't pass that to SolutionDirectory. One solution would be to use the ParsedBoundaryDict-class directly, but that doesn't have the patches-method you're using. The other fix would be to add the time-parameter to the BoundaryDict-constructor and pass it. I will do this one of these days if I remember it (Bug-report might help)

Bernhard
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Old   January 21, 2010, 08:23
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Quote:
Originally Posted by gschaider View Post
The only thing that in my experience works with 0.98 is hardcopies with the hardcopy-option (you won't see any "live" windows)
Bernhard

Bernhard,

we updated to matplotlib 0.99. Using pyFoamPlotWatcher I get no error but also no rendering live window. I have not yet tried saving hardcopies.

Regards
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Old   January 21, 2010, 09:20
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  #183
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Quote:
Originally Posted by bastil View Post
we updated to matplotlib 0.99. Using pyFoamPlotWatcher I get no error but also no rendering live window. I have not yet tried saving hardcopies.
I'm sorry. My current experience with Matplotlib is that it generates nice graphs, but that it's behaviour changes widely between versions (not only matplotlib, but also the used backend is important). For live-plotting I'd recommend gnuplot as it is much faster (not as nice-looking, but that is where the speed comes from).
The only systems I have access to are
- MacOS X: live-plotting works, but I don't use it
- CentOS 5: in order to get live-plotting to work I'd have to rebuild essential parts of the system and I have no intention of doing that
(I don't have access to Ubuntu or Suse-systems)

If somebody comes up with a patch that makes live-plotting possible on a wider range of systems I will gladly include it, but I don't intend to work on it myself. Sorry.

Bernhard
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Old   January 30, 2010, 08:57
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  #184
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Hi Bernhard,

When I tried to use pyFoam and run pyFoamRunner.py --clear icoFoam -case cavity in OF-1.6.x, I got the error information:

Traceback (most recent call last):
File "/usr/local/bin/pyFoamPlotRunner.py", line 3, in <module>
from PyFoam.Applications.PlotRunner import PlotRunner
File "/usr/local/lib/python2.6/dist-packages/PyFoam/Applications/PlotRunner.py", line 8, in <module>
from PyFoam.Execution.GnuplotRunner import GnuplotRunner
File "/usr/local/lib/python2.6/dist-packages/PyFoam/Execution/GnuplotRunner.py", line 4, in <module>
from StepAnalyzedCommon import StepAnalyzedCommon
File "/usr/local/lib/python2.6/dist-packages/PyFoam/Execution/StepAnalyzedCommon.py", line 4, in <module>
from AnalyzedCommon import AnalyzedCommon
File "/usr/local/lib/python2.6/dist-packages/PyFoam/Execution/AnalyzedCommon.py", line 6, in <module>
from PyFoam.Basics.PlotTimelinesFactory import createPlotTimelines,createPlotTimelinesDirect
File "/usr/local/lib/python2.6/dist-packages/PyFoam/Basics/PlotTimelinesFactory.py", line 4, in <module>
from GnuplotTimelines import GnuplotTimelines
File "/usr/local/lib/python2.6/dist-packages/PyFoam/Basics/GnuplotTimelines.py", line 4, in <module>
from PyFoam.ThirdParty.Gnuplot import Gnuplot,Data
File "/usr/local/lib/python2.6/dist-packages/PyFoam/ThirdParty/Gnuplot/__init__.py", line 166, in <module>
from PlotItems import PlotItem, Func, File, Data, GridData
File "/usr/local/lib/python2.6/dist-packages/PyFoam/ThirdParty/Gnuplot/PlotItems.py", line 27, in <module>
import Numeric as numpy
ImportError: No module named Numeric


Do you know the reason? Thanks.
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Old   January 30, 2010, 13:38
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Quote:
Originally Posted by sandy View Post
Hi Bernhard,

When I tried to use pyFoam and run pyFoamRunner.py --clear icoFoam -case cavity in OF-1.6.x, I got the error information:

Traceback (most recent call last):
File "/usr/local/bin/pyFoamPlotRunner.py", line 3, in <module>

<snip>

File "/usr/local/lib/python2.6/dist-packages/PyFoam/ThirdParty/Gnuplot/PlotItems.py", line 27, in <module>
import Numeric as numpy
ImportError: No module named Numeric


Do you know the reason? Thanks.
Yeah. Neither numpy or Numeric (libraries for matrices in Python) are installed on your machine. The Gnuplot-library needs at least one of those.

Use the pyFoamVersion.py-utility to check for prerequisites

Bernhard
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Old   January 30, 2010, 19:15
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Quote:
Originally Posted by gschaider View Post
Yeah. Neither numpy or Numeric (libraries for matrices in Python) are installed on your machine. The Gnuplot-library needs at least one of those.

Use the pyFoamVersion.py-utility to check for prerequisites

Bernhard
Hi Bernhard, according to your sugestion, I tried to type:

pyFoamVersion.py

It gave the error information as follows:

PYTHONPATH:
Traceback (most recent call last):
File "/usr/local/bin/pyFoamVersion.py", line 11, in <module>
print "PYTHONPATH:", os.environ["PYTHONPATH"]
File "/usr/lib/python2.6/UserDict.py", line 22, in __getitem__
raise KeyError(key)
KeyError: 'PYTHONPATH'

What's the matter, you think? Thanks.


In order to fix up above error, I follow up to type:

export PYTHONPATH=/usr/local/lib/python-2.6/site-packages:$PYTHONPATH
export PATH=/usr/local/bin:$PATH

and type again:

pyFoamVersion.py

It gave the informations as follows:

PYTHONPATH: /usr/local/lib/python-2.6/site-packages:
OpenFOAM (1, 6, 'x') of the installed versions ['1.6.x']
pyFoam-Version: 0.5.3

Installed libraries:
Gnuplot : No Not a problem. Version from ThirdParty is used
ply : No Not a problem. Version from ThirdParty is used
Numeric : No Not a problem if numpy is present
numpy : No Not a problem if Numeric is present
matplotlib : No Only Gnuplot-plotting possible
psyco : No Not a problem. Acceleration not possible
hotshot : Yes
profile : No Not a problem. Can't profile using this library
cProfile : Yes


What is it? I knew little about it. Please help me out. Thanks.

Last edited by sandy; January 30, 2010 at 19:31.
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Old   January 31, 2010, 07:48
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  #187
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Quote:
Originally Posted by sandy View Post
Hi Bernhard, according to your sugestion, I tried to type:

pyFoamVersion.py

It gave the error information as follows:

PYTHONPATH:
Traceback (most recent call last):
File "/usr/local/bin/pyFoamVersion.py", line 11, in <module>
print "PYTHONPATH:", os.environ["PYTHONPATH"]
File "/usr/lib/python2.6/UserDict.py", line 22, in __getitem__
raise KeyError(key)
KeyError: 'PYTHONPATH'

What's the matter, you think? Thanks.


In order to fix up above error, I follow up to type:

export PYTHONPATH=/usr/local/lib/python-2.6/site-packages:$PYTHONPATH
export PATH=/usr/local/bin:$PATH
Right. Bug in pyFoamVersion (it doesn't expect a PYTHONPATH-less installation). I fixed this and it will be in the next distribution
Quote:
Originally Posted by sandy View Post
and type again:

pyFoamVersion.py

It gave the informations as follows:

PYTHONPATH: /usr/local/lib/python-2.6/site-packages:
OpenFOAM (1, 6, 'x') of the installed versions ['1.6.x']
pyFoam-Version: 0.5.3

Installed libraries:
Gnuplot : No Not a problem. Version from ThirdParty is used
ply : No Not a problem. Version from ThirdParty is used
Numeric : No Not a problem if numpy is present
numpy : No Not a problem if Numeric is present
matplotlib : No Only Gnuplot-plotting possible
psyco : No Not a problem. Acceleration not possible
hotshot : Yes
profile : No Not a problem. Can't profile using this library
cProfile : Yes


What is it? I knew little about it. Please help me out. Thanks.
As I thought. None of the two numeric-libraries is installed (Gnuplot needs them for performance reasons). Install one of them with the package-manager of your distro (preferably numpy, but Numeric is OK too)

Bernhard
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Old   January 31, 2010, 09:26
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  #188
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Hi Bernhard,

I installed those package by the code line:

sudo apt-get install python-gnuplot
sudo apt-get install python-ply

.....

except profile package. Do you know how to install it?

Further, I tried to type pyFoamPlotWather.py in the case,

pyFoamPlotWather.py cavity.log

It gave some new error informations:

gnuplot: /home/jinweiwei/OpenFOAM/ThirdParty-1.6.x/gcc-4.3.3/platforms/linux/lib/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib/libwx_baseu-2.8.so.0)
gnuplot: /home/jinweiwei/OpenFOAM/ThirdParty-1.6.x/gcc-4.3.3/platforms/linux/lib/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib/libwx_baseu-2.8.so.0)
gnuplot: /home/jinweiwei/OpenFOAM/ThirdParty-1.6.x/gcc-4.3.3/platforms/linux/lib/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib/libwx_baseu-2.8.so.0)
Traceback (most recent call last):
File "/usr/local/bin/pyFoamPlotWatcher.py", line 5, in <module>
PlotWatcher()
File "/usr/local/lib/python2.6/dist-packages/PyFoam/Applications/PlotWatcher.py", line 35, in __init__
nr=1)
File "/usr/local/lib/python2.6/dist-packages/PyFoam/Applications/PyFoamApplication.py", line 138, in __init__
self.run()
File "/usr/local/lib/python2.6/dist-packages/PyFoam/Applications/PlotWatcher.py", line 117, in run
run.start()
File "/usr/local/lib/python2.6/dist-packages/PyFoam/Execution/BasicWatcher.py", line 67, in start
self.lineHandle(line)
File "/usr/local/lib/python2.6/dist-packages/PyFoam/Execution/AnalyzedCommon.py", line 55, in lineHandle
self.analyzer.analyzeLine(line)
File "/usr/local/lib/python2.6/dist-packages/PyFoam/LogAnalysis/FoamLogAnalyzer.py", line 84, in analyzeLine
self.analyzers[nm].doAnalysis(line)
File "/usr/local/lib/python2.6/dist-packages/PyFoam/LogAnalysis/TimeLineAnalyzer.py", line 31, in doAnalysis
self.notify(float(m.group(2)))
File "/usr/local/lib/python2.6/dist-packages/PyFoam/LogAnalysis/LogLineAnalyzer.py", line 60, in notify
f(*data)
File "/usr/local/lib/python2.6/dist-packages/PyFoam/LogAnalysis/FoamLogAnalyzer.py", line 44, in setTime
listener.timeChanged()
File "/usr/local/lib/python2.6/dist-packages/PyFoam/Execution/StepAnalyzedCommon.py", line 24, in timeChanged
self.timeHandle()
File "/usr/local/lib/python2.6/dist-packages/PyFoam/Execution/GnuplotRunner.py", line 258, in timeHandle
self.plots[p].redo()
File "/usr/local/lib/python2.6/dist-packages/PyFoam/Basics/GeneralPlotTimelines.py", line 112, in redo
self.doReplot()
File "/usr/local/lib/python2.6/dist-packages/PyFoam/Basics/GnuplotTimelines.py", line 109, in doReplot
self.replot()
File "/usr/local/lib/python2.6/dist-packages/PyFoam/ThirdParty/Gnuplot/_Gnuplot.py", line 333, in replot
self.refresh()
File "/usr/local/lib/python2.6/dist-packages/PyFoam/ThirdParty/Gnuplot/_Gnuplot.py", line 226, in refresh
self(self.plotcmd + ' ' + string.join(plotcmds, ', '))
File "/usr/local/lib/python2.6/dist-packages/PyFoam/ThirdParty/Gnuplot/_Gnuplot.py", line 210, in __call__
self.gnuplot(s)
File "/usr/local/lib/python2.6/dist-packages/PyFoam/ThirdParty/Gnuplot/gp_unix.py", line 210, in __call__
self.flush()
IOError: [Errno 32] Broken pipe

Maybe you know how to fix it now? Please help me out.. Thanks.
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Old   February 1, 2010, 17:08
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Quote:
Originally Posted by sandy View Post
Hi Bernhard,

I installed those package by the code line:

sudo apt-get install python-gnuplot
sudo apt-get install python-ply

.....

except profile package. Do you know how to install it?

Further, I tried to type pyFoamPlotWather.py in the case,

pyFoamPlotWather.py cavity.log

It gave some new error informations:

gnuplot: /home/jinweiwei/OpenFOAM/ThirdParty-1.6.x/gcc-4.3.3/platforms/linux/lib/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/lib/libwx_baseu-2.8.so.0)
<snipY
IOError: [Errno 32] Broken pipe

Maybe you know how to fix it now? Please help me out.. Thanks.
I'm afraid this is the Linux-version of DLL-hell. One of the libraries gnuplot links against (WX-windows I guess) requires a different version of the C++-libraries than the compiler installed with OpenFOAM provides (don't know if it is too old or too young).
To verify this try running the command gnuplot from the command line. If it fails in the same way, then PyFoam is not to blame (and I don't know how to fix that kind of situation in a Debian/Ubuntu-system, sorry)

Bernhard
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Old   February 1, 2010, 21:14
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Hi Bernhard,

Thanks for your reply. However, if that, do you know how can I use gnuplot in Ubunto? Could you help me to fix up it?

If I can not use PyFoam and gnuplot all, how can I do in OpenFOAM, you think.

Sandy
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Old   February 2, 2010, 04:55
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Hi Sandy

Quote:
Originally Posted by sandy View Post
Thanks for your reply. However, if that, do you know how can I use gnuplot in Ubunto? Could you help me to fix up it?
First of all: open a terminal, type in
Code:
gnuplot -V
and report the exact output of this command here.

You do the same with
Code:
sudo apt-cache show gnuplot
And please tell me, which exact (!) version of Ubuntu you are using.

Cheers
Wolle
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Old   June 4, 2010, 09:54
Default pyFoamPlotWatcher.py with non-interactive opinion
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Hello pyFoamer,

i've got a question if there is a suitable method to interrupt the pyFoamPlotWatcher.py automatically if the parsed logfile doesn't change anymore?
According to the explanation in the wiki: "Watches the file until interrupted.", i'm looking for an non-interactive opinion!
The batch-system i use outputs only logfiles and i'm able to watch them with the pyFoamPlotWatcher.py. But after case solving i have to interrupt the watcher to go on with the queueing jobs. That's not useful when running a lot of cases in batch mode. But it is nice to watch the residuals from time to time.

Has anybody an idea to manage non-interactive plot watching with pyFoam?

~Stefan
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Old   June 4, 2010, 11:53
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Quote:
Originally Posted by SD@TUB View Post
Hello pyFoamer,

i've got a question if there is a suitable method to interrupt the pyFoamPlotWatcher.py automatically if the parsed logfile doesn't change anymore?
According to the explanation in the wiki: "Watches the file until interrupted.", i'm looking for an non-interactive opinion!
The batch-system i use outputs only logfiles and i'm able to watch them with the pyFoamPlotWatcher.py. But after case solving i have to interrupt the watcher to go on with the queueing jobs. That's not useful when running a lot of cases in batch mode. But it is nice to watch the residuals from time to time.

Has anybody an idea to manage non-interactive plot watching with pyFoam?

~Stefan
The reason why that wasn't implemented is that there is no sure-fire way to tell whether a file is closed for good (and a timeout approach brings problems with ... batch systems, as they tend to buffer large chunks and consequently there are long times between writes). So the only way would be an option --not-a-living-file. And such an option is not yet implemented.

So as I see it there are two options:

1. you can write your own analyzer scripts (using the stuff in the examples-directory and the original watcher-script as a template)
2. Write a bug report at http://sourceforge.net/apps/mantisbt...?page_number=1 and I will try to squeeze it into the next release (which I hope to have out before the Workshop).

Bernhard
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Old   June 4, 2010, 16:17
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Thanks Bernhard for the prompt statement!

I understand the problem of buffering file streams by the batch system, since i noticed time delays about a few minutes between calculation and log output. The only truncation criterium of stop parsing the logfile i see is the specified endTime within controlDict.
I have little experience with batch systems (i use Torque by the way) so i'm not sure what cummunication standards used if a job is finished. Maybe this could be another idea.

I did various attempts of using the pyFoamPlotRunner.py with the job script provided by Torque, but it seems that there is no chance of getting this done.


~Stefan
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Old   June 9, 2010, 01:46
Default customRegexp file
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Hi everybody,

I successfully installed and ran pyFoam on my mac machine. I see residual plots. However, I could not find a way to plot other parameters (like Ux or gamma or Courant number) using line command or by editing customRegexp file. In fact, there is not such a file in my case directory!

Does any body know how to solve this problem?

Thanks,
Ali
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Old   June 9, 2010, 04:37
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Quote:
Originally Posted by ali805509 View Post
Hi everybody,

I successfully installed and ran pyFoam on my mac machine. I see residual plots. However, I could not find a way to plot other parameters (like Ux or gamma or Courant number) using line command or by editing customRegexp file. In fact, there is not such a file in my case directory!

Does any body know how to solve this problem?
This is not a problem, this is a feature:
custom in customRegExp means that it is customized for your case.

The most complete documentation on that topic (to my knowledge) is:
http://openfoamwiki.net/index.php/Co...omRegexp-files
(jump immediately to the section on the new format)

Bernhard
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Old   June 9, 2010, 17:51
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Thanks Bernhard.
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Old   June 14, 2010, 05:46
Default forceCoeffs
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Hello everybody,
first of all, I want to thank Bernhard for the effort he put on PyFoam. Good job guy!
Now the point: I am trying to adapt doInletVariation.py example to obtain an airfoil polar plot. This pyFoam utility should be able to run the same case with different velocity direction, extract the forceCoeffs values at the last time step and collect all the value in a single file.
I succeeded to include modification to velocity component and liftDir and dragDir using parsedParameterFile. However, since forceCoeffs is not a postprocess utility, I cannot use UtilityRunner to get the forceCoeffs value as made in the same example for the massFlow.
How can I get it? Suggestions?
Thanks,

mad
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Old   June 14, 2010, 07:11
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Hi!

Quote:
Originally Posted by maddalena View Post
Hello everybody,
first of all, I want to thank Bernhard for the effort he put on PyFoam. Good job guy!
Now the point: I am trying to adapt doInletVariation.py example to obtain an airfoil polar plot. This pyFoam utility should be able to run the same case with different velocity direction, extract the forceCoeffs values at the last time step and collect all the value in a single file.
I succeeded to include modification to velocity component and liftDir and dragDir using parsedParameterFile. However, since forceCoeffs is not a postprocess utility, I cannot use UtilityRunner to get the forceCoeffs value as made in the same example for the massFlow.
How can I get it? Suggestions?
As I understand it the execFlowFunctionObjects executes the function objects after the actual calculations (never used it myself) so that might replace calcMassFlow in the example.
Second solution would be to run the solver with a UtilityRunner instead of the BasicRunner and look for the forces.
Third solution would be to write a subclass of the LogAnalyzer-class. I will demonstrate that during the PyFoam-training in Gothenburg and the slides should be available afterwards.

Bernhard
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Old   June 14, 2010, 07:42
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... so I will try the 2nd solution, it seems the easiest to implement.
Or...
  • is there any already implemented function to read only the last line of a file?
  • Or maybe I can search in the forceCoeffs.dat the line starting with the latestTime and extract the coefficient values.
The point is that frm me is difficult to understand what is implemented and how to use it. I am really a newbie in pyFoam!
Thanks,

mad
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