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April 11, 2012, 21:57 

#21  
New Member
xiaoweii
Join Date: Mar 2012
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Hi Bruno,
Thanks for your reply. I run snappyHexMesh in OpenFOAM2.1.0 on Tianhe1A, a supercomputer. So the memory shouldn't be a problem. OMG! I will redownload a OpenFOAM2.1.0 and try again, hope that it will work. Thank you again! Best wishes! Xiaowg Quote:


May 21, 2012, 14:18 

#22 
Senior Member

Hi, as I'm experiencing the same error (http://www.cfdonline.com/Forums/ope...ssorx0a.html) is there any way to set up a case from scratch in such a way that this error here is avoided without the need to run changeDict?
Thank you! 

June 13, 2012, 10:44 
strange behaviour DecomposePar

#23 
Member
Lev
Join Date: Dec 2010
Posts: 31
Rep Power: 9 
Hello OF experts and users,
please assist me in struggling the following problem: during run of icoFoam i included my utility: Code:
.... runTime.write(); #include "utility.H"; Info<< "ExecutionTime = " << runTime.elapsedCpuTime() << " s" << " ClockTime = " << runTime.elapsedClockTime() << " s" << nl << endl; ...... Code:
scalar x,y,z; forAll(mesh.cellCentres(),ii) { x=y=z=0; x=mesh.cellCentres()[ii].x(); y=mesh.cellCentres()[ii].y(); z=mesh.cellCentres()[ii].z(); if(x<3.10&&x>3.03&&z<1.58&&z>1.55) { Info<<"ii="<<ii<<" y="<<y<<" u="<<U[ii]<<endl; } } Code:
ii=315457 y=0.996054 u=(0.00620626 6.79366e05 0.0108981) ii=315585 y=0.987859 u=(0.00614572 0.000243301 0.0243829) ii=315713 y=0.979032 u=(0.00606576 0.000949787 0.0380821) ii=315841 y=0.969524 u=(0.00595958 0.00210503 0.0521407) ii=315969 y=0.959283 u=(0.00582333 0.00378294 0.0664832) ii=316097 y=0.948252 u=(0.00565297 0.00606614 0.0810126) ii=316225 y=0.936371 u=(0.00544439 0.00904414 0.0956093) ii=316353 y=0.923574 u=(0.00519362 0.012812 0.110129) ii=316481 y=0.90979 u=(0.00489682 0.0174689 0.124403) ii=316609 y=0.894943 u=(0.00455088 0.0231161 0.13823) ii=316737 y=0.878951 u=(0.00415365 0.0298542 0.151383) ii=316865 y=0.861726 u=(0.00370377 0.0377802 0.163607) ii=316993 y=0.843174 u=(0.00320252 0.0469805 0.174613) ii=317121 y=0.82319 u=(0.002653 0.0575266 0.184092) ii=317249 y=0.801666 u=(0.00206075 0.0694652 0.191718) ii=317377 y=0.778482 u=(0.00143554 0.0828093 0.197153) ii=317505 y=0.753511 u=(0.000789686 0.0975293 0.200063) ii=317633 y=0.726614 u=(0.000139452 0.113541 0.200139) ii=317761 y=0.697644 u=(0.000496615 0.130699 0.197118) ii=317889 y=0.66644 u=(0.00109615 0.148783 0.190809) ii=318017 y=0.632829 u=(0.00163618 0.167488 0.181132) ii=318145 y=0.596627 u=(0.00209476 0.186432 0.168159) ii=318273 y=0.557634 u=(0.00245017 0.205152 0.152146) ii=318401 y=0.515634 u=(0.00268635 0.223128 0.133575) ii=318529 y=0.470396 u=(0.00279119 0.239814 0.113173) ii=318657 y=0.42167 u=(0.00276001 0.254686 0.0919138) ii=318785 y=0.369186 u=(0.002593 0.267305 0.0709739) ii=318913 y=0.312656 u=(0.00229841 0.277386 0.0516354) ii=319041 y=0.251767 u=(0.00188806 0.284874 0.0351015) ii=319169 y=0.186184 u=(0.00137428 0.289967 0.0222259) ii=319297 y=0.115543 u=(0.000771825 0.293112 0.0131436) ii=319425 y=0.0394559 u=(0.000105613 0.294848 0.0068923) ii=839745 y=0.0394559 u=(0.000582071 0.295449 0.00134095) ii=839873 y=0.115543 u=(0.00122611 0.294747 0.00626435) ii=840001 y=0.186184 u=(0.00177453 0.292263 0.0177436) ii=840129 y=0.251767 u=(0.00220134 0.287433 0.0335546) ii=840257 y=0.312656 u=(0.00249681 0.279854 0.053115) ii=840385 y=0.369186 u=(0.00265327 0.269405 0.075247) ii=840513 y=0.42167 u=(0.00266883 0.256237 0.0985297) ii=840641 y=0.470396 u=(0.00254961 0.240723 0.121556) ii=840769 y=0.515634 u=(0.00230948 0.223372 0.143094) ii=840897 y=0.557634 u=(0.00196405 0.204763 0.162169) ii=841025 y=0.596627 u=(0.00153323 0.185474 0.178093) ii=841153 y=0.632829 u=(0.00103735 0.166047 0.190452) ii=841281 y=0.66644 u=(0.000497004 0.146948 0.199071) ii=841409 y=0.697644 u=(7.11539e05 0.128564 0.203973) ii=841537 y=0.726614 u=(0.000650192 0.111193 0.205332) ii=841665 y=0.753511 u=(0.00122649 0.0950506 0.203423) ii=841793 y=0.778482 u=(0.00178946 0.0802759 0.198595) ii=841921 y=0.801666 u=(0.00233001 0.0669428 0.191226) ii=842049 y=0.82319 u=(0.0028412 0.0550705 0.181708) ii=842177 y=0.843174 u=(0.00331821 0.0446353 0.170421) ii=842305 y=0.861726 u=(0.00375808 0.0355805 0.15773) ii=842433 y=0.878951 u=(0.00415926 0.027827 0.143969) ii=842561 y=0.894943 u=(0.00452063 0.0212799 0.129439) ii=842689 y=0.90979 u=(0.00484285 0.0158363 0.114408) ii=842817 y=0.923574 u=(0.00512709 0.0113894 0.099104) ii=842945 y=0.936371 u=(0.00537485 0.00783297 0.0837236) ii=843073 y=0.948252 u=(0.00558836 0.00506389 0.0684298) ii=843201 y=0.959283 u=(0.00576992 0.00298402 0.0533565) ii=843329 y=0.969524 u=(0.00592204 0.00150175 0.0386111) ii=843457 y=0.979032 u=(0.00604735 0.00053254 0.0242779) ii=843585 y=0.987859 u=(0.00614837 5.53222e07 0.0104258) ii=843713 y=0.996054 u=(0.00622505 0.000147164 0.00250257) Code:
ii=103398 y=0.996054 u=(0.00619963 6.84788e05 0.0108932) ii=103526 y=0.987859 u=(0.00613874 0.000242565 0.0243827) ii=103654 y=0.979032 u=(0.00605887 0.000950786 0.0380804) ii=103782 y=0.969524 u=(0.00595275 0.00210967 0.0521367) ii=103910 y=0.959283 u=(0.00581652 0.00379168 0.0664762) ii=104038 y=0.948252 u=(0.00564615 0.00607851 0.0810015) ii=104166 y=0.936371 u=(0.00543755 0.00905979 0.0955933) ii=104294 y=0.923574 u=(0.00518676 0.0128303 0.110108) ii=104422 y=0.90979 u=(0.00488997 0.0174897 0.124375) ii=104550 y=0.894943 u=(0.00454407 0.0231361 0.138196) ii=104678 y=0.878951 u=(0.00414708 0.0298703 0.151337) DecomposePar Dict the following: Code:
numberOfSubdomains 6; method simple; simpleCoeffs { n ( 1 6 1 ); delta 0.00001; } hierarchicalCoeffs { n ( 1 2 2 ); delta 0.001; order xyz; } manualCoeffs { dataFile "cellDecomposition"; } scotchCoeffs { } 

June 13, 2012, 16:59 

#24 
Super Moderator
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
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Greetings Lev,
It's quite simple:
Bruno
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Last edited by wyldckat; June 14, 2012 at 16:35. Reason: see "edit:" 

June 14, 2012, 01:29 

#25 
Member
Lev
Join Date: Dec 2010
Posts: 31
Rep Power: 9 
Hello, Bruno
unfortunately command "PInfo" give a compilation error as "PInfo was not declared in this scope ". But the problem is not only at the screen output, but also i do not know how to order the code to analyze whole mesh that is spread to many processors (as is working with single run). And i need the results to be collected and to be written in the log file. Like this command in single run Code:
OFstream k(runTime.path()/"k.dat"); .... k<<"velocity "<<U[ii]<<endl; Regards Lev 

June 14, 2012, 16:41 

#26 
Super Moderator
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
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Hi Lev,
Sorry about that. Apparently PInfo doesn't exist. But I vaguely remember reading about it... weird OK, by the description of what you're trying to do, it looks like to me that the probe or sampling utilities and/or function objects would be more suitable for what you want to do. And then there is also "swak4Foam": http://openfoamwiki.net/index.php/Contrib/swak4Foam Other than this... try searching this forum for more answers... I know they're in here somewhere... Best regards, Bruno
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August 31, 2012, 18:25 

#27  
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Bruno Santos
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Greetings!
I saw just now the solution and remembered about this thread. Quote:
Quote:
Best regards, Bruno
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February 22, 2013, 11:47 

#28 
New Member
Marco Müller
Join Date: Feb 2013
Posts: 7
Rep Power: 6 
Hi all,
I'm following up with the issue that decomposePar does not preserve some boundaries and later on the solver complains about missing boundary definitions. Furthermore potentialFoam complains about the processorboundaries. My question is: Apart from the workarounds that have been constructed in the meanwhile to solve this: is there a outofboxsolution for OpenFOAM 2.1.1 that I am using out of box on ubuntu??? my script looks like this (without reconstructing) Code:
#!/bin/sh # Source tutorial run functions . $WM_PROJECT_DIR/bin/tools/RunFunctions cp r 0.org 0 > /dev/null 2>&1 runApplication blockMesh cp system/decomposeParDict.simple system/decomposeParDict runApplication decomposePar runParallel snappyHexMesh 2 overwrite parallel find . type f iname "*level*" exec rm {} \; ls d processor*  xargs i cp r 0.org/* ./{}/0/ $1 runParallel potentialFoam 2 initialiseUBCs noFunctionObjects writep runParallel `getApplication` 2 Thanks very much!! Marco 

February 23, 2013, 08:58 

#29 
Super Moderator
Bruno Santos
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Greetings Marco,
Well... there are 2... 2.5 tricks that I know of:
Best regards, Bruno
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February 25, 2013, 07:09 

#30 
New Member
Marco Müller
Join Date: Feb 2013
Posts: 7
Rep Power: 6 
Hey Bruno,
great help, thanks! I took version 2, which works fine. Thanks marco 

January 26, 2016, 06:29 

#31 
New Member
marzieh goodarzi
Join Date: Feb 2014
Location: TehranIran
Posts: 11
Rep Power: 5 
Hi dear FOAMuser
I have 3 machin include 12 core. I used scotch method for 12 processor, its ok on 1 machine. but when I used 2 or 3 machine for more processor, it dosent work without any error or warning. 

January 31, 2016, 12:32 

#32  
Super Moderator
Bruno Santos
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Quote:
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February 1, 2016, 07:26 

#33 
New Member
marzieh goodarzi
Join Date: Feb 2014
Location: TehranIran
Posts: 11
Rep Power: 5 
Hi dear Bruno
Thank you for your reply actually i dont know how the OpenFOAM installed, This system with OpenFOAM has been gave me. I use OpenFOAM2.3.1. I reproduce the problem with motor bike and have a same problem with scotch method. when I using simple method ( for decompose) for cavity case, its work with 36 processor but didnt work with scotch method. I try to run simple method for my 3D asymmetric diffuser but similar to scotch method it didnt work. my command for run is: mpirun np 36 $HOME/OpenFOAM/OpenFOAM2.3.1/foamExec pimpleFoam parallel Thanks Marzieh 

February 8, 2016, 08:16 

#34  
New Member
marzieh goodarzi
Join Date: Feb 2014
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Quote:


February 14, 2016, 17:15 

#35 
Super Moderator
Bruno Santos
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Quick answer: Sorry Marzieh, I've been having long work weeks, along with other responsibilities and I haven't managed during weekends to answer as many questions as I wanted here on the forum .
Let me refer you to this blog post of mine, which I forgot the other day to mention about it: Notes about running OpenFOAM in parallel In addition, I forgot to ask the following questions:


February 15, 2016, 12:38 

#36  
New Member
marzieh goodarzi
Join Date: Feb 2014
Location: TehranIran
Posts: 11
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Quote:
Your welcome dear bruno. Thank you for taking the time to reply me. 1. mpirun version 1.8.2 2. Linux ubuntu00 3.13.035generic #62~precise1Ubuntu SMP Mon Aug 18 14:52:04 UTC 2014 x86_64 x86_64 GNU/Linux 

February 21, 2016, 17:07 

#37 
Super Moderator
Bruno Santos
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Quick answer: I've search through my memories and tried to deduce the problem... and something doesn't add up.
This could be a problem with OpenMPI 1.8.2 or it could be due to a problem with incompatible MPI versions on each one of the 3 machines... but it's hard to prove that the issue is only reproducible if you decompose the mesh with scotch and run with pimpleFoam. I need the following details:


October 1, 2016, 10:43 

#38 
Member
Bashar
Join Date: Jul 2015
Posts: 68
Rep Power: 4 
Hi,
I am using openFoam 3.0.1 , and I am trying to run my case using the following steps: $ decomposePar its running ok. $ mpirun –np 6 renumberMesh –overwrite parallel gives me the following error: Code:
 mpirun was unable to launch the specified application as it could not find an executable: Executable: –np Node: basharhpc while attempting to start process rank 0.  I was using "mpirun np" on the same machine with pimpleFoam with no problems but when I tried to use it with "renumberMesh" I get this error . This is the first time for me to use the "renumberMesh". Bashar 

October 19, 2016, 02:05 
n

#39 
New Member
Maryam
Join Date: Dec 2015
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Try n instead of np:
mpirun n 6 renumberMesh overwrite parallel 

October 26, 2016, 18:19 

#40  
Member
Bashar
Join Date: Jul 2015
Posts: 68
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Quote:
I just used Code:
mpirun n 6 renumberMesh overwrite parallel Reagrds, bashar 

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