|
[Sponsors] |
[PyFoam] First discussion thread about PyFoam |
|
LinkBack | Thread Tools | Search this Thread | Display Modes |
March 5, 2009, 07:29 |
Hi Bernhard,
I tried updating
|
#101 |
Member
Jason Dale
Join Date: Mar 2009
Location: UK
Posts: 80
Rep Power: 17 |
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 |
|
March 5, 2009, 08:03 |
Hi Jason!
No idea. Try runn
|
#102 |
Assistant Moderator
Bernhard Gschaider
Join Date: Mar 2009
Posts: 4,225
Rep Power: 51 |
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 Bernhard
__________________
Note: I don't use "Friend"-feature on this forum out of principle. Ah. And by the way: I'm not on Facebook either. So don't be offended if I don't accept your invitation/friend request |
|
March 7, 2009, 14:22 |
Hi everyone,
first of all:
|
#103 |
Senior Member
Tomislav Maric
Join Date: Mar 2009
Location: Darmstadt, Germany
Posts: 284
Blog Entries: 5
Rep Power: 21 |
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
__________________
When asking a question, prepare a SSCCE. |
|
March 9, 2009, 07:49 |
Hi Tomislav!
As you're usin
|
#104 |
Assistant Moderator
Bernhard Gschaider
Join Date: Mar 2009
Posts: 4,225
Rep Power: 51 |
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
__________________
Note: I don't use "Friend"-feature on this forum out of principle. Ah. And by the way: I'm not on Facebook either. So don't be offended if I don't accept your invitation/friend request |
|
March 12, 2009, 08:46 |
Hi Bernhard,
The next time
|
#106 |
Member
Jason Dale
Join Date: Mar 2009
Location: UK
Posts: 80
Rep Power: 17 |
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 |
|
March 12, 2009, 10:38 |
Hi Bernhard,
Sorry I was be
|
#107 |
Member
Jason Dale
Join Date: Mar 2009
Location: UK
Posts: 80
Rep Power: 17 |
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 |
|
March 12, 2009, 11:59 |
Hi Jason!
"Don't see graphs
|
#108 |
Assistant Moderator
Bernhard Gschaider
Join Date: Mar 2009
Posts: 4,225
Rep Power: 51 |
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 Bernhard
__________________
Note: I don't use "Friend"-feature on this forum out of principle. Ah. And by the way: I'm not on Facebook either. So don't be offended if I don't accept your invitation/friend request |
|
March 12, 2009, 12:44 |
Hi,
I must need glasses, to
|
#109 |
Member
Jason Dale
Join Date: Mar 2009
Location: UK
Posts: 80
Rep Power: 17 |
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 |
|
March 13, 2009, 04:47 |
Hi Jason!
As described in t
|
#110 |
Assistant Moderator
Bernhard Gschaider
Join Date: Mar 2009
Posts: 4,225
Rep Power: 51 |
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
__________________
Note: I don't use "Friend"-feature on this forum out of principle. Ah. And by the way: I'm not on Facebook either. So don't be offended if I don't accept your invitation/friend request |
|
March 13, 2009, 05:45 |
Thanks Bernhard,
I got conf
|
#111 |
Member
Jason Dale
Join Date: Mar 2009
Location: UK
Posts: 80
Rep Power: 17 |
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 |
|
March 28, 2009, 10:00 |
|
#112 |
Senior Member
|
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!
__________________
Best regards, Dr. Alexander VAKHRUSHEV Christian Doppler Laboratory for "Metallurgical Applications of Magnetohydrodynamics" Simulation and Modelling of Metallurgical Processes Department of Metallurgy University of Leoben http://smmp.unileoben.ac.at |
|
March 31, 2009, 04:35 |
|
#113 | |
Senior Member
|
There is a line:
Quote:
__________________
Best regards, Dr. Alexander VAKHRUSHEV Christian Doppler Laboratory for "Metallurgical Applications of Magnetohydrodynamics" Simulation and Modelling of Metallurgical Processes Department of Metallurgy University of Leoben http://smmp.unileoben.ac.at |
||
March 31, 2009, 08:13 |
|
#114 | |
Assistant Moderator
Bernhard Gschaider
Join Date: Mar 2009
Posts: 4,225
Rep Power: 51 |
Quote:
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"} 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 |
||
April 12, 2009, 05:10 |
|
#115 | |
Senior Member
Daniel WEI (老魏)
Join Date: Mar 2009
Location: Beijing, China
Posts: 689
Blog Entries: 9
Rep Power: 21 |
Quote:
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
__________________
~ Daniel WEI ------------- Boeing Research & Technology - China Beijing, China |
||
April 18, 2009, 06:16 |
Installation
|
#116 |
Senior Member
Sebastian Gatzka
Join Date: Mar 2009
Location: Frankfurt, Germany
Posts: 729
Rep Power: 20 |
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']
__________________
Schrödingers wife: "What did you do to the cat? It's half dead!" |
|
April 18, 2009, 11:07 |
|
#117 | |
Assistant Moderator
Bernhard Gschaider
Join Date: Mar 2009
Posts: 4,225
Rep Power: 51 |
Quote:
it says FoamInformation NOT FoamInstallation. What I usually recommend is copy/pasting that kind of stuff from the Browser to the Terminal Bernhard |
||
April 18, 2009, 11:18 |
|
#118 |
Senior Member
Sebastian Gatzka
Join Date: Mar 2009
Location: Frankfurt, Germany
Posts: 729
Rep Power: 20 |
Well, this is embarrassing. My fault & Thank you!
__________________
Schrödingers wife: "What did you do to the cat? It's half dead!" |
|
April 25, 2009, 03:43 |
|
#119 |
Member
Sebastian
Join Date: Mar 2009
Location: Munich, Germany
Posts: 30
Rep Power: 17 |
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 fightingfalcon23 |
|
April 25, 2009, 04:23 |
|
#120 |
Member
Sebastian
Join Date: Mar 2009
Location: Munich, Germany
Posts: 30
Rep Power: 17 |
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')) |
|
Thread Tools | Search this Thread |
Display Modes | |
|
|
Similar Threads | ||||
Thread | Thread Starter | Forum | Replies | Last Post |
Divergence detected in AMG solver: k when udf loaded | google9002 | Fluent UDF and Scheme Programming | 3 | November 7, 2019 23:34 |
udf problem | jane | Fluent UDF and Scheme Programming | 37 | February 20, 2018 04:17 |
Guide: Getting Started with the CFD Online Discussion Forums | pete | Site Help, Feedback & Discussions | 8 | July 29, 2016 05:00 |
Error messages | atg | enGrid | 7 | August 30, 2013 11:16 |
Phase locked average in run time | panara | OpenFOAM | 2 | February 20, 2008 14:37 |