CFD Online Discussion Forums - [PyFoam] stuck: Text file busy

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stuck: Text file busy

Hello Foamers,

I have successfully used pyFoam in the past to plot residuals during runs, but now that I have upgraded to OF2.4.x there seems to be a compatibility issue. PyFoam just hangs at the first timestep. Running the case without pyFoam does not produce the error, so I don't think it has to do with my /system/ files, but I have attached them nonetheless. The command I am running is:

Code:

decomposePar -force -cellDist

mpiexec -np 4 renumberMesh -overwrite -parallel

pyFoamPlotRunner.py mpiexec -np 4 simpleFoam -parallel

And the resulting error message is:

Code:

/*---------------------------------------------------------------------------*\

| =========                 |                                                 |

| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |

|  \\    /   O peration     | Version:  2.4.x                                 |

|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |

|    \\/     M anipulation  |                                                 |

\*---------------------------------------------------------------------------*/

Build  : 2.4.x-664271ec09a7

Exec   : simpleFoam -parallel

Date   : Jun 30 2015

Time   : 20:42:07

Host   : "linux-8o2d.site"

PID    : 8243

Case   : /home/chris/Dropbox/REDstack/spacerCFD/spacerCFD_2D/spacer2d-mapped

nProcs : 4

Slaves :

3

(

"linux-8o2d.site.8244"

"linux-8o2d.site.8245"

"linux-8o2d.site.8246"

)



Pstream initialized with:

floatTransfer      : 0

nProcsSimpleSum    : 0

commsType          : nonBlocking

polling iterations : 0

sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).

fileModificationChecking : Monitoring run-time modified files using timeStampMaster

allowSystemOperations : Allowing user-supplied system call operations



// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

Create time



Create mesh for time = 0



Reading field p



Reading field U



Reading/calculating face flux field phi



Selecting incompressible transport model Newtonian

Selecting RAS turbulence model laminar

No finite volume options present





SIMPLE: convergence criteria

field p         tolerance 1e-05

field U         tolerance 1e-05





Starting time loop



Time = 1

Traceback (most recent call last):

  File "/usr/bin/pyFoamPlotRunner.py", line 4, in <module>

    __import__('pkg_resources').run_script('PyFoam==0.6.4', 'pyFoamPlotRunner.py')

  File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 534, in run_script

    self.require(requires)[0].run_script(script_name, ns)

  File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 1438, in run_script

    execfile(script_filename, namespace, namespace)

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.4-py2.7.egg/EGG-INFO/scripts/pyFoamPlotRunner.py", line 5, in <module>

    PlotRunner()

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.4-py2.7.egg/PyFoam/Applications/PlotRunner.py", line 59, in __init__

    **kwargs)

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.4-py2.7.egg/PyFoam/Applications/PyFoamApplication.py", line 356, in __init__

    result=self.run()

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.4-py2.7.egg/PyFoam/Applications/PlotRunner.py", line 142, in run

    run.start()

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.4-py2.7.egg/PyFoam/Execution/BasicRunner.py", line 363, in start

    self.lineHandle(line)

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.4-py2.7.egg/PyFoam/Execution/GnuplotRunner.py", line 179, in lineHandle

    GnuplotCommon.lineHandle(self,line)

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.4-py2.7.egg/PyFoam/Execution/AnalyzedCommon.py", line 84, in lineHandle

    self.analyzer.analyzeLine(line)

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.4-py2.7.egg/PyFoam/LogAnalysis/FoamLogAnalyzer.py", line 138, in analyzeLine

    self.analyzers[nm].doAnalysis(line)

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.4-py2.7.egg/PyFoam/LogAnalysis/TimeLineAnalyzer.py", line 43, in doAnalysis

    self.notifyNewTime(m)

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.4-py2.7.egg/PyFoam/LogAnalysis/TimeLineAnalyzer.py", line 32, in notifyNewTime

    self.notify(float(m.group(2)))

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.4-py2.7.egg/PyFoam/LogAnalysis/LogLineAnalyzer.py", line 65, in notify

    f(*data)

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.4-py2.7.egg/PyFoam/LogAnalysis/FoamLogAnalyzer.py", line 84, in setTime

    listener.timeChanged()

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.4-py2.7.egg/PyFoam/Execution/StepAnalyzedCommon.py", line 39, in timeChanged

    self.picklePlots()

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.4-py2.7.egg/PyFoam/Execution/AnalyzedCommon.py", line 334, in picklePlots

    move(pickleFile+".tmp",pickleFile)

  File "/usr/lib64/python2.7/shutil.py", line 303, in move

    os.unlink(src)

OSError: [Errno 26] Text file busy: './Gnuplotting.analyzed/pickledPlots.tmp'

Howdy Foamers,

I have not been able to solve my problem yet, but I did some further reading and came to two possible sources of error.

-- First off, it looks like I had not installed PyFoam since I switch from python 2 to python 3. Oops.
-- Second, I was not correctly operating PyFoam in parallel correctly. I should have actually used the command

Code:

pyFoamPlotRunner.py --procnr=4 simpleFoam

Changing these two options made it so the tutorial cases run correctly, but my case is still not able to start. Would anyone be able to help me with my persistent problem regarding PyFoam?

Hey foamers,

I just finished the installation of PyFoam and unfortunately have equivalent problems when running the PyFoamRunner.
I am doing a single core simulation of OF´s damBreak tutorial. OF writes the first two time directories and stucks shortly after this.

My PyFoamRunner.py output following:

Code:

Starting time loop



Courant Number mean: 0 max: 0

Interface Courant Number mean: 0 max: 0

deltaT = 0.00119048

Time = 0.00119048

Traceback (most recent call last):

  File "/usr/bin/pyFoamRunner.py", line 5, in <module>

    pkg_resources.run_script('PyFoam==0.6.6', 'pyFoamRunner.py')

  File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 492, in run_script

    self.require(requires)[0].run_script(script_name, ns)

  File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 1350, in run_script

    execfile(script_filename, namespace, namespace)

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/EGG-INFO/scripts/pyFoamRunner.py", line 5, in <module>

    Runner()

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/PyFoam/Applications/Runner.py", line 66, in __init__

    **kwargs)

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/PyFoam/Applications/PyFoamApplication.py", line 426, in __init__

    result=self.run()

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/PyFoam/Applications/Runner.py", line 154, in run

    run.start()

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/PyFoam/Execution/BasicRunner.py", line 363, in start

    self.lineHandle(line)

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/PyFoam/Execution/AnalyzedRunner.py", line 49, in lineHandle

    StepAnalyzedCommon.lineHandle(self,line)

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/PyFoam/Execution/AnalyzedCommon.py", line 156, in lineHandle

    self.analyzer.analyzeLine(line)

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/PyFoam/LogAnalysis/FoamLogAnalyzer.py", line 139, in analyzeLine

    self.analyzers[nm].doAnalysis(line)

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/PyFoam/LogAnalysis/TimeLineAnalyzer.py", line 43, in doAnalysis

    self.notifyNewTime(m)

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/PyFoam/LogAnalysis/TimeLineAnalyzer.py", line 32, in notifyNewTime

    self.notify(float(m.group(2)))

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/PyFoam/LogAnalysis/LogLineAnalyzer.py", line 65, in notify

    f(*data)

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/PyFoam/LogAnalysis/FoamLogAnalyzer.py", line 85, in setTime

    listener.timeChanged()

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/PyFoam/Execution/StepAnalyzedCommon.py", line 45, in timeChanged

    self.picklePlots()

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/PyFoam/Execution/AnalyzedCommon.py", line 468, in picklePlots

    move(pickleFile+".tmp",pickleFile)

  File "/usr/lib64/python2.7/shutil.py", line 302, in move

    os.unlink(src)

OSError: [Errno 26] Text file busy: './PyFoamRunner.interFoam.analyzed/pickledPlots.tmp'

For the sake of completeness the output of pyFoamVersion.py

Code:

Machine info: Linux | localhost.localdomain | 3.19.8-100.fc20.x86_64 | #1 SMP Tue May 12 17:08:50 UTC 2015 | x86_64 | x86_64



Python version: 2.7.5 (default, Apr 10 2015, 08:09:05) 

[GCC 4.8.3 20140911 (Red Hat 4.8.3-7)]



Python executable: /bin/python



Python 2.7 is one development platform for PyFoam (along with Python 3)

PYTHONPATH: /usr/lib/python2.7/site-packages:/usr/lib64/python2.7/site-packages/openmpi:/usr/lib/python2.7/site-packages:



Location of this utility: /usr/bin/pyFoamVersion.py



 PyFoam WARNING on line 201 of file /usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/PyFoam/FoamInformation.py : Basedir /home/foamy/foam for fork extend does not exist or is not a directory 

 PyFoam WARNING on line 201 of file /usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/PyFoam/FoamInformation.py : Basedir /home/foamy/OpenFOAM for fork openfoamplus does not exist or is not a directory 

Version 3.0.x (reported as number 3.0 )Fork openfoam of the installed 1 versions:

openfoam-3.0.x : /opt/OpenFOAM/OpenFOAM-3.0.x



pyFoam-Version: 0.6.6



Path where PyFoam was found (PyFoam.__path__) is ['/usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/PyFoam']



Configuration search path: [('file', '/etc/pyFoam/pyfoamrc'), ('directory', '/etc/pyFoam/pyfoamrc.d'), ('file', '/home/foamy/.pyFoam/pyfoamrc'), ('directory', '/home/foamy/.pyFoam/pyfoamrc.d')]

Configuration files (used): []



Installed libraries:

cython               :  No       Not used. Maybe will by used later to spped up parts of PyFoam 

cProfile             :  Yes 

docutils             :  No       Not necessary. Needed for RestructuredText to HTML conversion 

Gnuplot              :  No       Not a problem. Version from ThirdParty is used 

hotshot              :  Yes 

line_profiler        :  No       Not a problem. Can't profile using this library 

ipdb                 :  No       Not necessary. Only makes debugging more comfortable 

IPython              :  No       Not necessary. But the interactive shell may be more comfortable 

matplotlib           :  No       Only Gnuplot-plotting possible 

mercurial            :  No       Not a problem. Used for experimental case handling 

pytest               :  No       Only needed for running the unit-tests (developers only) 

numpy                :  Yes      version: 1.11.2 

openpyxl             :  No       Not a problem. Only used for exporting pandas-data to Excel-files (advanced). If xlsxwriter is installed it will handle this (xlsxwriter is recommended anyway) 

xlsxwriter           :  No       Not a problem. Only used for exporting pandas-data to XLSX-files (advanced). If openpyxl is installed then this module can handle that 

pandas               :  No       Not a problem. Only used for handling of advanced data-handling 

ply                  :  No       Not a problem. Version from ThirdParty is used 

profile              :  Yes 

psyco                :  No       Not a problem. Acceleration not possible 

PyQt4                :  Yes      version: 4.8.5 

PyQt4.Qwt5           :  No       Only an alternate plotting back-end 

scipy                :  No       Not yet used. Possibly use signal-fitting etc 

Tkinter              :  No       Not a problem. Used for the old version of DisplayBlockmesh and some matplotlib-implementations 

twisted              :  No       Not yet used. Possibly reimplement MetaServer with it 

vtk                  :  No       Not a problem. Only used for some utilities 

xlwt                 :  No       Not a problem. Only used for exporting pandas-data to Excel-files 

xlrd                 :  No       Not a problem. Only used for importing Excel-files to pandas-data 

requests             :  No       Not a problem. Currently only needed for the blink(1)-support 



Library locations

cProfile             : /usr/lib64/python2.7/cProfile.pyc

hotshot              : /usr/lib64/python2.7/hotshot/__init__.pyc

numpy                : /usr/lib64/python2.7/site-packages/numpy/__init__.pyc

profile              : /usr/lib64/python2.7/profile.pyc

PyQt4                : /usr/lib64/python2.7/site-packages/PyQt4/__init__.pyc



Checking additional envirnoment variables



Checking for PYFOAM_DIR : Location of the PyFoam-installation. Not strictly necessary

PYFOAM_DIR missing from environment



Checking for PYFOAM_SITE_DIR : Location of non-PyFoam-disctributions script. Set and used by some Foam-distributions

PYFOAM_SITE_DIR missing from environment

Has anyone experienced anything similar or an idea on how to get the PyFoamRunner running successful ?

Quote:

Originally Posted by Traction (Post 622087)

Code:

Starting time loop



Courant Number mean: 0 max: 0

Interface Courant Number mean: 0 max: 0

deltaT = 0.00119048

Time = 0.00119048

Traceback (most recent call last):

  File "/usr/bin/pyFoamRunner.py", line 5, in <module>

    pkg_resources.run_script('PyFoam==0.6.6', 'pyFoamRunner.py')

  File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 492, in run_script

    self.require(requires)[0].run_script(script_name, ns)

  File "/usr/lib/python2.7/site-packages/pkg_resources.py", line 1350, in run_script

    execfile(script_filename, namespace, namespace)

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/EGG-INFO/scripts/pyFoamRunner.py", line 5, in <module>

    Runner()

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/PyFoam/Applications/Runner.py", line 66, in __init__

    **kwargs)

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/PyFoam/Applications/PyFoamApplication.py", line 426, in __init__

    result=self.run()

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/PyFoam/Applications/Runner.py", line 154, in run

    run.start()

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/PyFoam/Execution/BasicRunner.py", line 363, in start

    self.lineHandle(line)

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/PyFoam/Execution/AnalyzedRunner.py", line 49, in lineHandle

    StepAnalyzedCommon.lineHandle(self,line)

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/PyFoam/Execution/AnalyzedCommon.py", line 156, in lineHandle

    self.analyzer.analyzeLine(line)

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/PyFoam/LogAnalysis/FoamLogAnalyzer.py", line 139, in analyzeLine

    self.analyzers[nm].doAnalysis(line)

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/PyFoam/LogAnalysis/TimeLineAnalyzer.py", line 43, in doAnalysis

    self.notifyNewTime(m)

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/PyFoam/LogAnalysis/TimeLineAnalyzer.py", line 32, in notifyNewTime

    self.notify(float(m.group(2)))

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/PyFoam/LogAnalysis/LogLineAnalyzer.py", line 65, in notify

    f(*data)

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/PyFoam/LogAnalysis/FoamLogAnalyzer.py", line 85, in setTime

    listener.timeChanged()

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/PyFoam/Execution/StepAnalyzedCommon.py", line 45, in timeChanged

    self.picklePlots()

  File "/usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/PyFoam/Execution/AnalyzedCommon.py", line 468, in picklePlots

    move(pickleFile+".tmp",pickleFile)

  File "/usr/lib64/python2.7/shutil.py", line 302, in move

    os.unlink(src)

OSError: [Errno 26] Text file busy: './PyFoamRunner.interFoam.analyzed/pickledPlots.tmp'

For the sake of completeness the output of pyFoamVersion.py

Code:

Machine info: Linux | localhost.localdomain | 3.19.8-100.fc20.x86_64 | #1 SMP Tue May 12 17:08:50 UTC 2015 | x86_64 | x86_64



Python version: 2.7.5 (default, Apr 10 2015, 08:09:05) 

[GCC 4.8.3 20140911 (Red Hat 4.8.3-7)]



Python executable: /bin/python



Python 2.7 is one development platform for PyFoam (along with Python 3)

PYTHONPATH: /usr/lib/python2.7/site-packages:/usr/lib64/python2.7/site-packages/openmpi:/usr/lib/python2.7/site-packages:



Location of this utility: /usr/bin/pyFoamVersion.py



 PyFoam WARNING on line 201 of file /usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/PyFoam/FoamInformation.py : Basedir /home/foamy/foam for fork extend does not exist or is not a directory 

 PyFoam WARNING on line 201 of file /usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/PyFoam/FoamInformation.py : Basedir /home/foamy/OpenFOAM for fork openfoamplus does not exist or is not a directory 

Version 3.0.x (reported as number 3.0 )Fork openfoam of the installed 1 versions:

openfoam-3.0.x : /opt/OpenFOAM/OpenFOAM-3.0.x



pyFoam-Version: 0.6.6



Path where PyFoam was found (PyFoam.__path__) is ['/usr/lib/python2.7/site-packages/PyFoam-0.6.6-py2.7.egg/PyFoam']



Configuration search path: [('file', '/etc/pyFoam/pyfoamrc'), ('directory', '/etc/pyFoam/pyfoamrc.d'), ('file', '/home/foamy/.pyFoam/pyfoamrc'), ('directory', '/home/foamy/.pyFoam/pyfoamrc.d')]

Configuration files (used): []



Installed libraries:

cython               :  No       Not used. Maybe will by used later to spped up parts of PyFoam 

cProfile             :  Yes 

docutils             :  No       Not necessary. Needed for RestructuredText to HTML conversion 

Gnuplot              :  No       Not a problem. Version from ThirdParty is used 

hotshot              :  Yes 

line_profiler        :  No       Not a problem. Can't profile using this library 

ipdb                 :  No       Not necessary. Only makes debugging more comfortable 

IPython              :  No       Not necessary. But the interactive shell may be more comfortable 

matplotlib           :  No       Only Gnuplot-plotting possible 

mercurial            :  No       Not a problem. Used for experimental case handling 

pytest               :  No       Only needed for running the unit-tests (developers only) 

numpy                :  Yes      version: 1.11.2 

openpyxl             :  No       Not a problem. Only used for exporting pandas-data to Excel-files (advanced). If xlsxwriter is installed it will handle this (xlsxwriter is recommended anyway) 

xlsxwriter           :  No       Not a problem. Only used for exporting pandas-data to XLSX-files (advanced). If openpyxl is installed then this module can handle that 

pandas               :  No       Not a problem. Only used for handling of advanced data-handling 

ply                  :  No       Not a problem. Version from ThirdParty is used 

profile              :  Yes 

psyco                :  No       Not a problem. Acceleration not possible 

PyQt4                :  Yes      version: 4.8.5 

PyQt4.Qwt5           :  No       Only an alternate plotting back-end 

scipy                :  No       Not yet used. Possibly use signal-fitting etc 

Tkinter              :  No       Not a problem. Used for the old version of DisplayBlockmesh and some matplotlib-implementations 

twisted              :  No       Not yet used. Possibly reimplement MetaServer with it 

vtk                  :  No       Not a problem. Only used for some utilities 

xlwt                 :  No       Not a problem. Only used for exporting pandas-data to Excel-files 

xlrd                 :  No       Not a problem. Only used for importing Excel-files to pandas-data 

requests             :  No       Not a problem. Currently only needed for the blink(1)-support 



Library locations

cProfile             : /usr/lib64/python2.7/cProfile.pyc

hotshot              : /usr/lib64/python2.7/hotshot/__init__.pyc

numpy                : /usr/lib64/python2.7/site-packages/numpy/__init__.pyc

profile              : /usr/lib64/python2.7/profile.pyc

PyQt4                : /usr/lib64/python2.7/site-packages/PyQt4/__init__.pyc



Checking additional envirnoment variables



Checking for PYFOAM_DIR : Location of the PyFoam-installation. Not strictly necessary

PYFOAM_DIR missing from environment



Checking for PYFOAM_SITE_DIR : Location of non-PyFoam-disctributions script. Set and used by some Foam-distributions

PYFOAM_SITE_DIR missing from environment

Has anyone experienced anything similar or an idea on how to get the PyFoamRunner running successful ?

Hm. That is a strange one. The problem seems to be that the file ./PyFoamRunner.interFoam.analyzed/pickledPlots.tmp can not be removed because some other process is accessing it. Is the file there? Could you try "lsof ./PyFoamRunner.interFoam.analyzed/pickledPlots.tmp" and see if it gives any output? (If it doesn't then this unfortunately no proof that there was no other process at the time of moving). The file is released immediately before moving it. It COULD be a race condition in the operating system and that is hard to fix

Hello Mr. Gschaider,

thank you for your hint. I executed the lsof command as you suggested. The output shows that the file is in use during runtime (by my own user to be precise).

I use OpenFOAM in a virtual machine which contains some shared folders to make the simulation and result files available on other machines during runtime. I assume that these shared folders are monitored the whole time to provide a rapid availability on all systems which seems to be the main problem.

When I move the case directory to a local folder (not shared) and start the simulation there are no more errors and the pyFoamRunner works properly !

I´am looking forward to explore your tools.