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Old   March 5, 2009, 08:29
Default Hi Bernhard, I tried updating
  #101
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Jason Dale
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Hi Bernhard,
I tried updating PyFoam to 0.5.1 so I can use it with OF v1.5.

Now I have the same problem as I had on the 8/11/07 above. The line you told me to change seems to already be changed in this new version. I added the line print mpirun and I get this error output:

user@linux:~/OpenFOAM/user-1.4.1/Trap> pyFoamPlotRunner.py --procnr=4 twoPhaseEulerFoam . cyclone1-newidea11
['mpirun', '--mca', 'pls_rsh_agent', 'rsh', '-np', '4', '-x', 'PATH', '-x', 'LD_LIBRARY_PATH', '-x', 'WM_PROJECT_DIR', '-x', 'FOAM_MPI_LIBBIN', '-x', 'MPI_BUFFER_SIZE', '/home/user/OpenFOAM/OpenFOAM-1.4.1/applications/bin/linuxGccDPOpt/twoPhaseEuler Foam', '.', 'cyclone1-newidea11', '-parallel']
[linux:11236] [0,0,0] ORTE_ERROR_LOG: Error in file runtime/orte_init_stage1.c at line 312
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):

orte_pls_base_select failed
--> Returned value -1 instead of ORTE_SUCCESS

--------------------------------------------------------------------------
[linux:11236] [0,0,0] ORTE_ERROR_LOG: Error in file runtime/orte_system_init.c at line 42
[linux:11236] [0,0,0] ORTE_ERROR_LOG: Error in file runtime/orte_init.c at line 52
--------------------------------------------------------------------------
Open RTE was unable to initialize properly. The error occured while
attempting to orte_init(). Returned value -1 instead of ORTE_SUCCESS.
--------------------------------------------------------------------------
Getting LinuxMem: [Errno 2] No such file or directory: '/proc/11236/status'


Would appreciate any help.

Thanks

Jason
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Old   March 5, 2009, 09:03
Default Hi Jason! No idea. Try runn
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Hi Jason!

No idea. Try running the command "by hand" (basically the above list with spaces instead of '.'). Adapt the command line until it runs. Then use the settings (http://openfoamwiki.net/index.php/Co...call_to_mpirun) to emulate the working command line for PyFoam

BTW: check with "which mpirun" which mpirun you're using

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Old   March 7, 2009, 15:22
Default Hi everyone, first of all:
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Hi everyone,

first of all: thank You Berhhard for pyFoam. I'm having some problems and haven't been able to make full use of it, but even pyFoamCloneCase and pyFoamClearCase, etc. make my life easier.

Ok, now to the problems:

my configuration:

HP Compaq 6820s Notebook PC - Business Notebook (Laptop) and Tablet PC
Chipset
Mobile Intel® GM965
Memory
3 GB 667 MHz DDR2 SDRAM
OS
Ubuntu 8.10 Intrepid
FOAM
latest 1.5-dev from the SVN

my problem:

I've installed pyFoam as non-root user, tried the test, and used scripts like the ones mentioned above. I want to use Runner utilities and control the runs with Networking utilities, but when I tried pyFoamRunner, here's what happened:

tomislav@icarus:run$ pyFoamRunner.py icoFoam ./ cavity
Error in /home/tomislav/OpenFOAM/PyFOAM/bin/pyFoamRunner.py : Case /home/tomislav/OpenFOAM/tomislav-1.5-dev/run does not have a 'system' directory

and within a directory,

tomislav@icarus:run$ cd cavity/
tomislav@icarus:cavity$ pyFoamRunner.py icoFoam . .
/*---------------------------------------------------------------------------*\
| ========= | |
| \ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \ / O peration | Version: 1.5-dev |
| \ / A nd | Web: http://www.OpenFOAM.org |
| \/ M anipulation | |
\*---------------------------------------------------------------------------*/

Usage: icoFoam [-case dir] [-parallel] [-help] [-doc] [-srcDoc]


Wrong number of arguments, expected 0 found 2


FOAM exiting

Getting LinuxMem: [Errno 2] No such file or directory: '/proc/6074/status'
Exception in thread Thread-3 (most likely raised during interpreter shutdown):
Traceback (most recent call last):
File "/usr/lib/python2.5/threading.py", line 486, in __bootstrap_inner
File "/usr/lib/python2.5/threading.py", line 664, in run
File "/usr/lib/python2.5/threading.py", line 353, in set
File "/usr/lib/python2.5/threading.py", line 268, in notifyAll
<type>: 'NoneType' object is not callable

Here's the test:

tomislav@icarus:cavity$ python
Python 2.5.2 (r252:60911, Oct 5 2008, 19:24:49)
[GCC 4.3.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import PyFoam
>>> from PyFoam import FoamInformation
>>> FoamInformation.
FoamInformation.__class__ FoamInformation.__reduce_ex__ FoamInformation.foamVersion
FoamInformation.__delattr__ FoamInformation.__repr__ FoamInformation.foamVersionNumber
FoamInformation.__dict__ FoamInformation.__setattr__ FoamInformation.getPathFromEnviron
FoamInformation.__doc__ FoamInformation.__str__ FoamInformation.injectVariables
FoamInformation.__file__ FoamInformation.changeFoamVersion FoamInformation.listdir
FoamInformation.__getattribute__ FoamInformation.config FoamInformation.oldAppConvention
FoamInformation.__hash__ FoamInformation.environ FoamInformation.path
FoamInformation.__init__ FoamInformation.error FoamInformation.popen4
FoamInformation.__name__ FoamInformation.foamInstalledVersions FoamInformation.re
FoamInformation.__new__ FoamInformation.foamMPI FoamInformation.warning
FoamInformation.__reduce__ FoamInformation.foamTutorials
>>> print FoamInformation.foamVersion
<function>
>>> print FoamInformation.foamVersion()
(1, 5, 'dev')
>>>

What am I doing wrong?

Thank you,

Tomislav
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Old   March 9, 2009, 08:49
Default Hi Tomislav! As you're usin
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Hi Tomislav!

As you're using a 1.5-version (which has a new calling convention) you'll also have to use that convention for the pyFoamRunner-stuff. So

pyFoamRunner.py icoFoam -case cavity

or from within the directory

pyFoamRunner.py icoFoam

If you want to use the 1.4.1-version instead

pyFoamRunner.py --foam=1.4.1 icoFoam . cavity
or
pyFoamRunner.py --foam=1.4.1 icoFoam . .

lets you do this

Bernhard
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Old   March 9, 2009, 09:02
Default Thanks, Bernhard. It works gre
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Thanks, Bernhard. It works great now.
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Old   March 12, 2009, 09:46
Default Hi Bernhard, The next time
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Hi Bernhard,

The next time I come to use it it works fine with no errors? It works in both 1.4.1 and 1.5. Spooky.

for your info when running 1.4.1 'which mpirun' produced
/OpenFOAM/OpenFOAM-1.4.1/src/openmpi-1.2.3/platforms/linuxGccDPOpt/bin/mpirun
when running 1.5
/OpenFOAM/ThirdParty/openmpi-1.2.6/platforms/linuxGccDPOpt/bin/mpirun

Thanks Anyway

Jason
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Old   March 12, 2009, 11:38
Default Hi Bernhard, Sorry I was be
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Hi Bernhard,

Sorry I was being stupid. It still doesn't work.

However if I manually type the following
mpirun --mca pls_rsh_agent rsh -np 4 -x PATH -x LD_LIBRARY_PATH -x WM_PROJECT_DIR /home/user/OpenFOAM/OpenFOAM-1.5/applications/bin/linuxGccDPOpt/twoPhaseEulerFoa m -parallel

I get the error from 05/03/09

I dont really know what I am doing but if I type

mpirun --mca pls_ssh_agent ssh -np 4 -x PATH -x LD_LIBRARY_PATH -x WM_PROJECT_DIR /home/user/OpenFOAM/OpenFOAM-1.5/applications/bin/linuxGccDPOpt/twoPhaseEulerFoa m -parallel

ie change rsh to ssh then the calculations progress but I dont see any graphs.

Do i need to make this change somewhere? If so where?

Thanks

Jason
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Old   March 12, 2009, 12:59
Default Hi Jason! "Don't see graphs
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Hi Jason!

"Don't see graphs": You mean "Because it is not run in the PlotRunner"

To make this permanent change the "_pre" variable as described in:
http://openfoamwiki.net/index.php/Co...call_to_mpirun

BTW: Just as your message arrived I finalized a new release of pyFoam. It doesn't directly address your problem but it has an additional switch in pyfoamrc

[Debug]
parallelExectuion = True

that outputs which call to mpirun PyFoam uses.
Other features of the new release (among this better suppor for paraview) are listed in http://openfoamwiki.net/index.php/Co...PyFoam#History

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Old   March 12, 2009, 13:44
Default Hi, I must need glasses, to
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Hi,

I must need glasses, to me its not clear on the wiki which file to change so I changed this one in my source code.

~/PyFoam/PyFoam-0.5.1/PyFoam/Infrastructure/Configuration.py

and then reinstalled and now everything works.

Thanks

Jason
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Old   March 13, 2009, 05:47
Default Hi Jason! As described in t
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Hi Jason!

As described in the section above: either /etc/pyfoamrc (for system-wide changes) or ~/.pyFoam/pyfoamrc (just for you). You'll propably have to create these files

Changing the source-code is an alternative but will break your setup with the next update

Bernhard
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Old   March 13, 2009, 06:45
Default Thanks Bernhard, I got conf
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Thanks Bernhard,

I got confused because I couldn't find the files and didn't think of creating them myself.

Everything is working fine now.

Regards

Jason
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Old   March 28, 2009, 11:00
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Hi all!

Would you please help, how to tell pyFoamPlotWatcher to plot data for each ITERATION rather than for each TIMESTEP? I use customRegexp to plot data I need, but still graphics output is produced for each time step depended on deltaT, ignoring all other lines which meet regex.

Thank you!
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Old   March 31, 2009, 04:35
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There is a line:

Quote:
LogAnalysis/TimeLineAnalyzer.py: timeRegExp="^Time = (.+)$"
which controls watcher objects time triggers. So there 2 possible solutions for my task (excepting modification of timeRegExp variable):
  1. Print "Time = iteration_number" after each iteration to use logfile from standard out to plot residual with pyFoamPlotWatcher. But then time-step information is messed with iterations output.
  2. So I preffer to print iteration residuals to other output stream/log file inside solver to display internal loop convergence separately with pyFoam switching off all other plots.
Perhaps there ara some better solutions, but this one do not require much modification to python scripts or solver source code.
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Old   March 31, 2009, 08:13
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Quote:
Originally Posted by makaveli_lcf View Post
There is a line:



which controls watcher objects time triggers. So there 2 possible solutions for my task (excepting modification of timeRegExp variable):
  1. Print "Time = iteration_number" after each iteration to use logfile from standard out to plot residual with pyFoamPlotWatcher. But then time-step information is messed with iterations output.
  2. So I preffer to print iteration residuals to other output stream/log file inside solver to display internal loop convergence separately with pyFoam switching off all other plots.
Perhaps there ara some better solutions, but this one do not require much modification to python scripts or solver source code.
Hi Alexander!

One of the reasons that only the accumulated value for the iterations is plotted is that to me it seemed to be the most general measure BUT the value for single iterations is already there. In the *.analyzed directory (use --write with the watcher, the Runner should create this files automatically) you will find for instance files linear_p (with the values of the first iteration in each timestep), linear_p_2 (with the values of the second iteration) and so on. So if you want to plot the number of iterations for each solution of p use these and Gnuplot (or the plotting program of your choice). This is more or less what you

If you want to do it online these lines in customRegexp might for instance plot the number of iterations the first and the last solution of p in a timestep need. And how often p is solved (if this is variable in you algorithm)

Code:
{"expr":".+  Solving for p, Initial residual .+ No Iterations (%f%)","name":"Last iteration","accumulation":"last"}
{"expr":".+  Solving for p, Initial residual .+ No Iterations (%f%)","name":"First iteration","accumulation":"first"}
{"expr":".+  Solving for p, Initial residual .+ No Iterations (%f%)","name":"Nr of iterations","accumulation":"count"}
This is only possible using the customRegexp-file not from the command line

I don't want to introduce the notion of internal-loops to the time-counting mechanism, because as you noted in point 1 there is not good way to plot both (unless you want to crowd the linear graphs with p, p_1 to p_42)

Bernhard
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Old   April 12, 2009, 05:10
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Quote:
Originally Posted by braennstroem View Post
Hi Bernhard,

I have one more question ... what do you think is the best way to run different solvers, e.g. potentialFoam / simpleFoam / turbFoam / oodles, one after another. Do you think one of your 'utilities' can do that?

Greetings!
Fabian
Hi Fabian,

I still feel that I am new to this field, what would you do after turbFoam? If you take the sequence of potentialFoam / simpleFoam / turbFoam / oodles.

you see in oodles you have to give the i.c. and b.c. in the beginning, but what's your custom to get these values from tubFoam, they are different after all. (eg. how could you get nuSgs nuTilda from nut k ...? )

Am I missing some secrets that you all know? Thanks

Daniel
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Old   April 18, 2009, 06:16
Default Installation
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Hello World.

I'm not sure what went wrong, I followed the instruction to install as root.
This is what I get, when trying to test the installation:

Code:
>>> import PyFoam
>>> import PyFoam.FoamInstallation
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: No module named FoamInstallation
>>> print PyFoam.FoamInstallation.foamTutorials()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
AttributeError: 'module' object has no attribute 'FoamInstallation'
>>> import sys
>>> print sys.path
['', '/home/sega/OpenFOAM/ThirdParty/ParaView3.3-cvs/platforms/linuxGcc/Utilitie                                                                                                 s/VTKPythonWrapping', '/usr/lib/python25.zip', '/usr/lib/python2.5', '/usr/lib/p                                                                                                 ython2.5/plat-linux2', '/usr/lib/python2.5/lib-tk', '/usr/lib/python2.5/lib-dynl                                                                                                 oad', '/usr/local/lib/python2.5/site-packages', '/usr/lib/python2.5/site-package                                                                                                 s', '/usr/lib/python2.5/site-packages/Numeric', '/var/lib/python-support/python2                                                                                                 .5', '/var/lib/python-support/python2.5/gtk-2.0']
Any ideas what went wrong?
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Old   April 18, 2009, 11:07
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Quote:
Originally Posted by sega View Post
Hello World.

I'm not sure what went wrong, I followed the instruction to install as root.
This is what I get, when trying to test the installation:

Code:
>>> import PyFoam
>>> import PyFoam.FoamInstallation
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: No module named FoamInstallation
Any ideas what went wrong?
Yeah. You mistyped. On http://openfoamwiki.net/index.php/Co...e_installation
it says FoamInformation NOT FoamInstallation. What I usually recommend is copy/pasting that kind of stuff from the Browser to the Terminal

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Old   April 18, 2009, 11:18
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Well, this is embarrassing. My fault & Thank you!
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Old   April 25, 2009, 03:43
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Hi all together,

I am using pyFoam and never had problems untill now. But after updating ubuntu to Version 9.04, everytime I want to start a calculation, I get the following message:

"
/usr/local/lib/python2.6/dist-packages/PyFoam/FoamInformation.py:5: DeprecationWarning: The popen2 module is deprecated. Use the subprocess module.
from popen2 import popen4
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 86
with="steps",
^
SyntaxError: invalid syntax
"

At the beginning of the thread, I wrote about about a mistake with the pythonpath, but I don't know, how to deal with it. I tried to install pyFoam completely new (as root using "sudo") but after installation, I see the same message again!

Thanks for reading
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Old   April 25, 2009, 04:23
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Some more information,
when I try to install PyFoam as root (using "sudo"), I get two errors. But the the installation runs further.

The errors:

running install_lib
byte-compiling /usr/local/lib/python2.6/dist-packages/PyFoam/Basics/GnuplotTimelines.py to GnuplotTimelines.pyc
SyntaxError: ('invalid syntax', ('/usr/local/lib/python2.6/dist-packages/PyFoam/Basics/GnuplotTimelines.py', 17, 21, ' with="lines",\n'))

byte-compiling /usr/local/lib/python2.6/dist-packages/PyFoam/Execution/GnuplotRunner.py to GnuplotRunner.pyc
SyntaxError: ('invalid syntax', ('/usr/local/lib/python2.6/dist-packages/PyFoam/Execution/GnuplotRunner.py', 86, 52, ' with="steps",\n'))
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