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June 29, 2012, 07:38 |
Open MPI-fork() error
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#1 |
Senior Member
Jian Zhong
Join Date: Feb 2012
Location: Birmingham
Posts: 109
Rep Power: 14 |
Hi,
I run a parallel case from 0s to 20.8s. But there is an error in 20.8s as follow. Could anyone know how to solve it? Time = 20.8 Courant Number mean: 0.208474 max: 0.316474 DILUPBiCG: Solving for Ux, Initial residual = 0.000518377, Final residual = 1.4007e-06, No Iterations 1 DILUPBiCG: Solving for Uy, Initial residual = 0.0138311, Final residual = 4.40116e-06, No Iterations 2 DILUPBiCG: Solving for Uz, Initial residual = 0.0111841, Final residual = 3.21597e-06, No Iterations 2 DILUPBiCG: Solving for C, Initial residual = 0.000130826, Final residual = 5.54248e-08, No Iterations 1 [1] #0 Foam::error:rintStack(Foam::Ostream&)[5] #0 Foam::error:rintStack(Foam::Ostream&)[3] #0 Foam::error:rintStack(Foam::Ostream&)[7] #0 Foam::error:rintStack(Foam::Ostream&)-------------------------------------------------------------------------- An MPI process has executed an operation involving a call to the "fork()" system call to create a child process. Open MPI is currently operating in a condition that could result in memory corruption or other system errors; your MPI job may hang, crash, or produce silent data corruption. The use of fork() (or system() or other calls that create child processes) is strongly discouraged. The process that invoked fork was: Local host: u2n126 (PID 19527) MPI_COMM_WORLD rank: 1 If you are *absolutely sure* that your application will successfully and correctly survive a call to fork(), you may disable this warning by setting the mpi_warn_on_fork MCA parameter to 0. |
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June 30, 2012, 08:37 |
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#2 | |
Retired Super Moderator
Bruno Santos
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Greetings zxj160,
Not much information to go on with to diagnose the issue. According to the error message, it looks like you're trying to launch another application from within the solver during parallel execution. I've searched online for the last message line and picked up on this: Quote:
Bruno
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June 30, 2012, 13:42 |
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#3 | |
Senior Member
Jian Zhong
Join Date: Feb 2012
Location: Birmingham
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Quote:
By the way, I find that the cyclic inlet and outlet patch can not accept any other type of BC (eg. zeroGradient), only cyclic for all the variables. My velocity in the inlet and outlet is cyclic. But I want to set the passive scalar fixvalue (0) for the inlet and zeroGradient for the outlet. Do you have any idea of this problem? Many thanks. |
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June 30, 2012, 18:49 |
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#4 |
Retired Super Moderator
Bruno Santos
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Mmm... I vaguely remember that OpenFOAM calls an external application when it wants to do a printStack (i.e., when it tries to do a controlled crash and show how it got where it is when it crashes)... so that's why it wants to fork()...
Have you tried one of the "directMapped*" BCs instead of "cyclic"?
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July 1, 2012, 07:13 |
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#5 | |
Senior Member
Jian Zhong
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Location: Birmingham
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Quote:
I know a sub-derived cyclic BC, fan ,is used like: ad { type fan; patchType cyclic; f List<scalar> 2(10.0 -1.0); value uniform 0; } I want to set inlet { type fixedValue; patchType cyclic; value uniform 0; } But I remember someone said that cyclic BC can only accept cyclic and its sub-derived BC (e.g. fan BC). I do not know whether my inlet idea is correct or not. |
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July 1, 2012, 07:14 |
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#6 | |
Senior Member
Jian Zhong
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Location: Birmingham
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Quote:
outlet { type zeroGradient; patchType cyclic; } |
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July 1, 2012, 16:27 |
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#7 |
Retired Super Moderator
Bruno Santos
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Hi zxj160,
Unfortunately I don't know. All I know is that the cyclic boundary condition is conceptually similar to the symmetry boundary condition, in the sense that it does everything on its own. directMapped samples the result from one end and places it in the other, having to be defined in the "polyMesh/boundary" file the particular sampling location. And by the example you gave of the cyclic fan, it looks like you'll have to code your own BC derived from the cyclic one. This is in case the directMapped one or derived ones from then don't do what you want! Best regards, Bruno
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July 4, 2012, 11:39 |
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#8 | |
Senior Member
Jian Zhong
Join Date: Feb 2012
Location: Birmingham
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Quote:
I am trying to use directMapped. But I am new to it. I do not know how to use it. Could you explain the meaning of each keywords. The following comes from pisoFoam/pitzDailyDirectMapped in the tutorials. blockMeshDict inlet { type directMappedPatch; offset ( 0.0495 0 0 ); sampleRegion region0; sampleMode nearestCell; samplePatch none; } 0/U boundaryField { inlet { type directMapped; value uniform (10 0 0); interpolationScheme cell; setAverage true; average (10 0 0); } The distance between my inlet and outlet is 30m. Many thanks, Jian |
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July 4, 2012, 19:23 |
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#9 |
Retired Super Moderator
Bruno Santos
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Hi Jian,
Most of the parameters here are self-explanatory. When in doubt about other options for most of those parameters: Use bananas As for "offset", it's sort-of simple: it indicates the relative position of the other patch to look at for cell data.
Best regards, Bruno
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January 17, 2013, 03:47 |
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#10 |
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Bernhard
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I am experiencing the same kind of error with OpenFOAM 2.1.1 while using the mapped boundary condition. Does any of you know if there are updates on this MPI-fork() issue?
Is it safe to run with mpi_warn_on_fork switched of? |
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January 17, 2013, 10:08 |
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#11 |
Retired Super Moderator
Bruno Santos
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Greetings Bernhard,
I suppose it's somewhat safe to turn off that warning, even if it's just for one test run. But the problem might be larger, since if it's triggering that warning, that's very likely because your case is crashing. As I wrote above, the printStack method launches an application that helps diagnose where the crash occurred. As for the direct mapped problem, it would be good to know if you're able to reproduce the same error with a simple case or a modified tutorial case! By the way, knowing which MPI version you're using could also help! And if you're using GridEngine, do not use Open-MPI 1.5.3 that comes with OpenFOAM. Either downgrade to Open-MPI 1.4.x or upgrade to 1.6.x. Best regards, Bruno
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January 17, 2013, 17:27 |
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#12 |
Senior Member
Bernhard
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I am quite convinced that it is not my case that is causing the error, and I will try to construct a minimal reconstructive case. If I replace mapped by fixedValue there are no issues by the way.
I am using PBS and OpenMPI 1.4.4. I don't know if there are known issues with this set-up? |
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January 18, 2013, 18:11 |
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#13 |
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Bernhard
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Ok, so I re-setup my case. I did not do anything special or different from the earlier situation, but for some reason I do not encounter this issue anymore. Wyldcat, I think I have to agree with you on the printStack, but I am still a bit puzzled...
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January 18, 2013, 18:50 |
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#14 |
Retired Super Moderator
Bruno Santos
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Hi Bernhard,
I can't remember about any problems with PBS and Open-MPI 1.4.4, so my guess is that the problem is related to a crash. As for things now working as intended, there are few possible scenarios:
Best regards, Bruno
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January 19, 2013, 15:39 |
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#15 |
Senior Member
Bernhard
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Hi Bruno.
1. I did not change the boundary file for the new setup. 2. I tried quite a few decompositions, so I can rule that out. 3. On the cluster I've used here, I have the nodes available for myself and the system is maintained by a bunch of professionals, and I did not have any hardware stability issues ever. Now I am rechecking things, I see that in the failed case, for some files I have both a .gz and an uncompressed file. I don't know which have been read, but probably not the intended one for some variables. Have been looking for the error in the wrong spot, as this have to be it. Although OpenFOAM should read the files according to the settings in the controlDict, but I think it does not do so. |
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January 19, 2013, 15:50 |
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#16 | |
Retired Super Moderator
Bruno Santos
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Hi Bernhard,
Quote:
But that's one interesting detail that I'll try to keep in mind: always check if there are duplicate files inside the "constant" and time folders!! Best regards, Bruno
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December 18, 2014, 16:58 |
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#17 |
New Member
Join Date: Dec 2012
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I've had the same problem. This is one of those problem drive me crazy! I could unreasonably solve the problem by modifying fvSolution dictionary (changing a smoother). The other time I could get rid of it by changing my decomposition scheme. I still don't know how and why it happens but apparently it comes from ghost cells that are not identifiable by MPI.
Goodluck Smran |
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February 16, 2016, 09:13 |
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#18 |
Senior Member
Illya Shevchuk
Join Date: Aug 2009
Location: Darmstadt, Germany
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Is there any update to this issue?
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February 21, 2016, 14:03 |
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#19 | |
Retired Super Moderator
Bruno Santos
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Quick answer: No one ever managed to give me more details on how to reproduce this error, therefore I didn't manage to find a solution for this .
If you can provide me with more details, then it'll be easier to diagnose and solve the problem. If not, then try the information provided here: Notes about running OpenFOAM in parallel - specially this information: Quote:
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February 22, 2016, 05:04 |
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#20 |
Senior Member
Illya Shevchuk
Join Date: Aug 2009
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Thanks a lot, Bruno.
I regularly received the error using OF2.1.x on our local computational cluster. But since it has moved to a new OS this weekend, I'll first have to test if the problem still persists. |
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