|
[Sponsors] |
[snappyHexMesh] problems using snappyHexMesh 2.1.0 on a supercomputer |
|
LinkBack | Thread Tools | Search this Thread | Display Modes |
September 9, 2014, 02:28 |
problems using snappyHexMesh 2.1.0 on a supercomputer
|
#1 |
Member
sqing
Join Date: Sep 2012
Location: Dalian
Posts: 77
Rep Power: 14 |
Hi foamers,
I'm using snappyHexMesh on a supercomputer, but there is something wrong that I can't solve. Can anyone give me some hints? (OpenFoam-2.1.0 and red-hat 5.3) here is the log file for snappyHexMesh: Code:
srun.sz: job 5712297 queued and waiting for resources srun.sz: job 5712297 has been allocated resources /*---------------------------------------------------------------------------*\ | ========= | | | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox | | \\ / O peration | Version: 2.1.0 | | \\ / A nd | Web: www.OpenFOAM.org | | \\/ M anipulation | | \*---------------------------------------------------------------------------*/ Build : 2.1.0-bd7367f93311 Exec : /home/export/base/envisiongrp/envision_lijun/OpenFOAM/OpenFOAM-2.1.0/platforms/linux64IccDPOpt/bin/snappyHexMesh Date : Sep 09 2014 Time : 09:11:57 Host : "cn40404" PID : 26954 Case : /home/export/base/envisiongrp/envision_lijun/CFDcalc/calc/panan/pananSnappyTest0/project/sector_0 nProcs : 1 sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE). fileModificationChecking : Monitoring run-time modified files using timeStampMaster allowSystemOperations : Disallowing user-supplied system call operations // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // Create time Create mesh for time = 0 Read mesh in = 5.8 s Overall mesh bounding box : (562162.0001 3202162 0) (566161.9999 3206162 5000) Relative tolerance : 1e-06 Absolute matching distance : 0.00754983432931 Reading refinement surfaces. Read refinement surfaces in = 3.42 s Reading refinement shells. Read refinement shells in = 0 s Setting refinement level of surface to be consistent with shells. Checked shell refinement in = 0 s Reading features. Read features in = 0 s Determining initial surface intersections ----------------------------------------- Edge intersection testing: Number of edges : 3030000 Number of edges to retest : 3030000 #0 Foam::error::printStack(Foam::Ostream&) in "/home/export/base/envisiongrp/envision_lijun/OpenFOAM/OpenFOAM-2.1.0/platforms/linux64IccDPOpt/lib/libOpenFOAM.so" #1 Foam::sigFpe::sigHandler(int) in "/home/export/base/envisiongrp/envision_lijun/OpenFOAM/OpenFOAM-2.1.0/platforms/linux64IccDPOpt/lib/libOpenFOAM.so" #2 __restore_rt at sigaction.c:0 #3 Foam::triangleFuncs::intersectAxesBundle(Foam::Vector<double> const&, Foam::Vector<double> const&, Foam::Vector<double> const&, int, Foam::Field<Foam::Vector<double> > const&, double, Foam::Vector<double>&) in "/home/export/base/envisiongrp/envision_lijun/OpenFOAM/OpenFOAM-2.1.0/platforms/linux64IccDPOpt/lib/libmeshTools.so" #4 Foam::triangleFuncs::intersectBb(Foam::Vector<double> const&, Foam::Vector<double> const&, Foam::Vector<double> const&, Foam::treeBoundBox const&) in "/home/export/base/envisiongrp/envision_lijun/OpenFOAM/OpenFOAM-2.1.0/platforms/linux64IccDPOpt/lib/libmeshTools.so" #5 Foam::treeDataTriSurface::overlaps(int, Foam::treeBoundBox const&) const in "/home/export/base/envisiongrp/envision_lijun/OpenFOAM/OpenFOAM-2.1.0/platforms/linux64IccDPOpt/lib/libmeshTools.so" #6 Foam::indexedOctree<Foam::treeDataTriSurface>::divide(Foam::List<int> const&, Foam::treeBoundBox const&, Foam::List<Foam::List<int> >&) const in "/home/export/base/envisiongrp/envision_lijun/OpenFOAM/OpenFOAM-2.1.0/platforms/linux64IccDPOpt/lib/libmeshTools.so" #7 Foam::indexedOctree<Foam::treeDataTriSurface>::divide(Foam::treeBoundBox const&, Foam::DynamicList<Foam::List<int>, 0u, 2u, 1u>&, int) const in "/home/export/base/envisiongrp/envision_lijun/OpenFOAM/OpenFOAM-2.1.0/platforms/linux64IccDPOpt/lib/libmeshTools.so" #8 Foam::indexedOctree<Foam::treeDataTriSurface>::indexedOctree(Foam::treeDataTriSurface const&, Foam::treeBoundBox const&, int, double, double) in "/home/export/base/envisiongrp/envision_lijun/OpenFOAM/OpenFOAM-2.1.0/platforms/linux64IccDPOpt/lib/libmeshTools.so" #9 Foam::triSurfaceMesh::tree() const in "/home/export/base/envisiongrp/envision_lijun/OpenFOAM/OpenFOAM-2.1.0/platforms/linux64IccDPOpt/lib/libmeshTools.so" #10 Foam::triSurfaceMesh::findLineAny(Foam::Field<Foam::Vector<double> > const&, Foam::Field<Foam::Vector<double> > const&, Foam::List<Foam::PointIndexHit<Foam::Vector<double> > >&) const in "/home/export/base/envisiongrp/envision_lijun/OpenFOAM/OpenFOAM-2.1.0/platforms/linux64IccDPOpt/lib/libmeshTools.so" #11 Foam::refinementSurfaces::findHigherIntersection(Foam::Field<Foam::Vector<double> > const&, Foam::Field<Foam::Vector<double> > const&, Foam::List<int> const&, Foam::List<int>&, Foam::List<int>&) const in "/home/export/base/envisiongrp/envision_lijun/OpenFOAM/OpenFOAM-2.1.0/platforms/linux64IccDPOpt/lib/libautoMesh.so" #12 Foam::meshRefinement::updateIntersections(Foam::List<int> const&) in "/home/export/base/envisiongrp/envision_lijun/OpenFOAM/OpenFOAM-2.1.0/platforms/linux64IccDPOpt/lib/libautoMesh.so" #13 Foam::meshRefinement::meshRefinement(Foam::fvMesh&, double, bool, Foam::refinementSurfaces const&, Foam::refinementFeatures const&, Foam::shellSurfaces const&) in "/home/export/base/envisiongrp/envision_lijun/OpenFOAM/OpenFOAM-2.1.0/platforms/linux64IccDPOpt/lib/libautoMesh.so" #14 main in "/home/export/base/envisiongrp/envision_lijun/OpenFOAM/OpenFOAM-2.1.0/platforms/linux64IccDPOpt/bin/snappyHexMesh" #15 __libc_start_main in "/lib64/libc.so.6" #16 Foam::regIOobject::writeObject(Foam::IOstream::streamFormat, Foam::IOstream::versionNumber, Foam::IOstream::compressionType) const in "/home/export/base/envisiongrp/envision_lijun/OpenFOAM/OpenFOAM-2.1.0/platforms/linux64IccDPOpt/bin/snappyHexMesh" srun.sz: error: cn40404: task 0: Floating point exception Last edited by wyldckat; September 13, 2014 at 05:46. |
|
September 13, 2014, 05:52 |
|
#2 |
Retired Super Moderator
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
Posts: 10,980
Blog Entries: 45
Rep Power: 128 |
Greetings Sunxing,
This is a possible source of major problems: Code:
Overall mesh bounding box : (562162.0001 3202162 0) (566161.9999 3206162 5000) In addition, if possible, upgrading to OpenFOAM 2.1.1 or 2.1.x might fix some problems that existed in snappyHexMesh back in 2.1.0. Best regards, Bruno
__________________
|
|
September 13, 2014, 09:17 |
|
#3 | |
Member
sqing
Join Date: Sep 2012
Location: Dalian
Posts: 77
Rep Power: 14 |
Quote:
Thanks for your reply. I forgot to metion that this error just happen when it was parallel processing. If i do it without parallel there is nothing wrong, while it is very time consuming. regards, sunxing |
||
September 13, 2014, 09:50 |
|
#4 | |
Retired Super Moderator
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
Posts: 10,980
Blog Entries: 45
Rep Power: 128 |
Hi Sunxing,
Parallel? But the output text you provided clearly states that only one processor was being used: Quote:
In addition, on the line "Exec:" it does not show the "-parallel" option, therefore it's very unlikely this was executed in parallel. Best regards, Bruno |
||
September 13, 2014, 10:17 |
|
#5 |
Member
sqing
Join Date: Sep 2012
Location: Dalian
Posts: 77
Rep Power: 14 |
Hi Bruno,
Sorry that i offered the wrong log file. It should be: Code:
/*---------------------------------------------------------------------------*\ | ========= | | | \\ / F ield | OpenFOAM: The Open Source CFD Toolbox | | \\ / O peration | Version: 2.1.0 | | \\ / A nd | Web: www.OpenFOAM.org | | \\/ M anipulation | | \*---------------------------------------------------------------------------*/ Build : 2.1.0-bd7367f93311 Exec : /home/export/base/envisiongrp/envision_lijun/OpenFOAM/OpenFOAM-2.1.0/platforms/linux64IccDPOpt/bin/snappyHexMesh -parallel Date : Sep 11 2014 Time : 19:35:41 Host : "cn40553" PID : 6592 Case : /home/export/base/envisiongrp/envision_lijun/CFDcalc/calc/dongxinghe/DXH10_snappy/project/sector_00 nProcs : 50 Slaves : 49 ( "cn40553.6593" "cn40553.6594" "cn40553.6595" "cn40553.6596" "cn40553.6597" "cn40553.6598" "cn40553.6599" "cn40553.6600" "cn40553.6601" "cn40554.2019" "cn40554.2020" "cn40554.2021" "cn40554.2022" "cn40554.2023" "cn40554.2024" "cn40554.2025" "cn40554.2026" "cn40554.2027" "cn40554.2028" "cn40555.11904" "cn40555.11905" "cn40555.11906" "cn40555.11907" "cn40555.11908" "cn40555.11909" "cn40555.11910" "cn40555.11911" "cn40555.11912" "cn40555.11913" "cn40556.25572" "cn40556.25573" "cn40556.25574" "cn40556.25575" "cn40556.25576" "cn40556.25577" "cn40556.25578" "cn40556.25579" "cn40556.25580" "cn40556.25581" "cn40557.25994" "cn40557.25995" "cn40557.25996" "cn40557.25997" "cn40557.25998" "cn40557.25999" "cn40557.26000" "cn40557.26001" "cn40557.26002" "cn40557.26003" ) Pstream initialized with: floatTransfer : 0 nProcsSimpleSum : 0 commsType : nonBlocking sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE). fileModificationChecking : Monitoring run-time modified files using timeStampMaster allowSystemOperations : Disallowing user-supplied system call operations // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * // Create time Create mesh for time = 0 Read mesh in = 2.46 s Overall mesh bounding box : (317267.9718 4392949.972 0) (318768.0282 4394450.028 6000) Relative tolerance : 1e-06 Absolute matching distance : 0.00636398752405 Reading refinement surfaces. Read refinement surfaces in = 9.66 s Reading refinement shells. Read refinement shells in = 0 s Setting refinement level of surface to be consistent with shells. Checked shell refinement in = 0 s Reading features. Read features in = 0 s Determining initial surface intersections ----------------------------------------- Edge intersection testing: Number of edges : 37800000 Number of edges to retest : 37800000 Number of intersected edges : 252077 Calculated surface intersections in = 13.92 s Initial mesh : cells:12500000 faces:37800000 points:12801051 Cells per refinement level: 0 12500000 Adding patches for surface regions ---------------------------------- Patch Type Region ----- ---- ------ terrain: 6 wall terrain Added patches in = 0.08 s Selecting decompositionMethod hierarchical Refinement phase ---------------- [37] Found point (318018 4393700 4000) in cell 204850 on processor 37 Surface refinement iteration 0 ------------------------------ Marked for refinement due to surface intersection : 500000 cells. Determined cells to refine in = 0.95 s Selected for refinement : 500000 cells (out of 12500000) Edge intersection testing: Number of edges : 49062222 Number of edges to retest : 14518296 Number of intersected edges : 1009563 Refined mesh in = 5.19 s After refinement surface refinement iteration 0 : cells:16000000 faces:49062222 points:17064279 Cells per refinement level: 0 12000000 1 4000000 Balanced mesh in = 7.98 s After balancing surface refinement iteration 0 : cells:16000000 faces:49062222 points:17064279 Cells per refinement level: 0 12000000 1 4000000 Surface refinement iteration 1 ------------------------------ Marked for refinement due to surface intersection : 2000000 cells. Determined cells to refine in = 0.5 s Selected for refinement : 2093173 cells (out of 16000000) Edge intersection testing: Number of edges : 96061644 Number of edges to retest : 59514734 Number of intersected edges : 4037188 Refined mesh in = 16.57 s After refinement surface refinement iteration 1 : cells:30652211 faces:96061644 points:34761292 Cells per refinement level: 0 11906827 1 2745384 2 16000000 Balanced mesh in = 43.47 s After balancing surface refinement iteration 1 : cells:30652211 faces:96061644 points:34761292 Cells per refinement level: 0 11906827 1 2745384 2 16000000 Surface refinement iteration 2 ------------------------------ No cells marked for refinement since reached limit 30000000. Determined cells to refine in = 1.79 s Selected for refinement : 0 cells (out of 30652211) Stopping refining since too few cells selected. Removing mesh beyond surface intersections ------------------------------------------ Found point (318018 4393700 4000) in cell -1 in global region 1 out of 2 regions. Keeping all cells in region 1 containing point (318018 4393700 4000) Selected for keeping : 17201334 cells. Edge intersection testing: Number of edges : 55670113 Number of edges to retest : 4037054 Number of intersected edges : 4037188 Shell refinement iteration 0 ---------------------------- Marked for refinement due to refinement shells : 0 cells. Determined cells to refine in = 29.13 s Selected for internal refinement : 0 cells (out of 17201334) Stopping refining since too few cells selected. Splitting mesh at surface intersections --------------------------------------- Introducing baffles for 4037188 faces that are intersected by the surface. Edge intersection testing: Number of edges : 59707272 Number of edges to retest : 32082314 Number of intersected edges : 8030964 Created baffles in = 14 s After introducing baffles : cells:17201334 faces:59707272 points:22730384 Cells per refinement level: 0 3605746 1 1373002 2 12222586 Introducing baffles to block off problem cells ---------------------------------------------- markFacesOnProblemCells : marked 8070117 additional internal faces to be converted into baffles. Analyzed problem cells in = 3.52 s Introducing baffles to delete problem cells. Edge intersection testing: Number of edges : 67777389 Number of edges to retest : 24222615 Number of intersected edges : 8030967 Created baffles in = 11.38 s After introducing baffles : cells:17201334 faces:67777389 points:22793116 Cells per refinement level: 0 3605746 1 1373002 2 12222586 Remove unreachable sections of mesh ----------------------------------- [14] [14] [14] --> FOAM FATAL IO ERROR: [14] error in IOstream "IOstream" for operation operator>>(Istream&, List<T>&) : reading first token [14] [14] file: IOstream at line 0. [14] [14] From function IOstream::fatalCheck(const char*) const [14] in file db/IOstreams/IOstreams/IOstream.C at line 111. [14] srun.sz: Job step aborted: Waiting up to 2 seconds for job step to finish. FOAM parallel run exiting [14] In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 14) slurmd[cn40556]: *** STEP 5720419.0 KILLED AT 2014-09-11T19:38:30 WITH SIGNAL 9 *** slurmd[cn40555]: *** STEP 5720419.0 KILLED AT 2014-09-11T19:38:33 WITH SIGNAL 9 *** slurmd[cn40553]: *** STEP 5720419.0 KILLED AT 2014-09-11T19:38:25 WITH SIGNAL 9 *** slurmd[cn40557]: *** STEP 5720419.0 KILLED AT 2014-09-11T19:38:34 WITH SIGNAL 9 *** slurmd[cn40554]: *** STEP 5720419.0 KILLED AT 2014-09-11T19:38:26 WITH SIGNAL 9 *** slurmd[cn40556]: *** STEP 5720419.0 KILLED AT 2014-09-11T19:38:30 WITH SIGNAL 9 *** slurmd[cn40553]: *** STEP 5720419.0 KILLED AT 2014-09-11T19:38:25 WITH SIGNAL 9 *** slurmd[cn40554]: *** STEP 5720419.0 KILLED AT 2014-09-11T19:38:26 WITH SIGNAL 9 *** slurmd[cn40555]: *** STEP 5720419.0 KILLED AT 2014-09-11T19:38:33 WITH SIGNAL 9 *** slurmd[cn40557]: *** STEP 5720419.0 KILLED AT 2014-09-11T19:38:34 WITH SIGNAL 9 *** srun.sz: error: cn40556: tasks 30,32,34-36,38-39: Killed srun.sz: error: cn40554: tasks 10-19: Killed srun.sz: error: cn40557: tasks 40-49: Killed srun.sz: error: cn40553: tasks 0-9: Killed srun.sz: error: cn40555: tasks 20-29: Killed srun.sz: error: cn40556: tasks 31,33,37: Killed sunxing |
|
September 13, 2014, 13:27 |
|
#6 |
Retired Super Moderator
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
Posts: 10,980
Blog Entries: 45
Rep Power: 128 |
Hi Sunxing,
OK, I've done a bit of searching here in the forum and one recurring situation with this kind of error message is usually related to the MPI toolbox or how OpenFOAM is connecting to it:
Best regards, Bruno |
|
September 14, 2014, 21:05 |
|
#7 |
Member
sqing
Join Date: Sep 2012
Location: Dalian
Posts: 77
Rep Power: 14 |
Hi Bruno,
Thanks very much for your patience and the full answer. Following your advise, I have tested the same case with 8 processors and it failed again. But for another case of less girds it succeed with 128 processors. Here are the snappyHexMeshDict and log file: Best regards sunxng |
|
September 15, 2014, 15:24 |
|
#8 | |
Retired Super Moderator
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
Posts: 10,980
Blog Entries: 45
Rep Power: 128 |
Hi Sunxing,
You forgot to attach the file "include/snappyPara", which apparently has the settings for the few important variables I was looking for, which might be the source of the problem. By the way, do you know which MPI toolbox is being used? The following commands should give you some feedback: Code:
echo $FOAM_MPI mpirun --version I did some more searching for the latest error message you got, namely: Code:
In: PMI_Abort(1, Fatal error in MPI_Recv: Message truncated, error stack: MPIDI_CH3U_Receive_data_found(284): Message from rank 3 and tag 1 truncated; 105 bytes received but buffer size is 4 ) Perhaps the system administrators of the supercomputer you're using have updated the MPI toolbox and not rebuilt OpenFOAM 2.1.0 with that new version of the MPI? Best regards, Bruno --------------------- edit: I went looking for where the crash is likely to be occurring and according to the last output message given to you by snappyHexMesh, this seems to be the problem: https://github.com/OpenFOAM/OpenFOAM...nement.C#L1835 Quote:
__________________
Last edited by wyldckat; September 15, 2014 at 15:40. Reason: see "edit:" |
||
September 16, 2014, 22:06 |
|
#9 |
Member
sqing
Join Date: Sep 2012
Location: Dalian
Posts: 77
Rep Power: 14 |
Hi Bruno,
I don't know much about the MPI thing. I tried the commands you offered. If I source the OF-2.1.0, then the feedback is Code:
[envision_lijun@sn02 sector_0]$ echo $FOAM_MPI mpi [envision_lijun@sn02 sector_0]$ mpirun --version Missing: program name Program --version either does not exist, is not executable, or is an erroneous argument to mpirun. Code:
[envision_lijun@sn02 sector_0]$ echo $FOAM_MPI openmpi-1.6.5 [envision_lijun@sn02 sector_0]$ mpirun --version mpirun (Open MPI) 1.6.5 Maybe there are some errors in the MPI, but i don't know how to fix them and either has the permission to change something about MPI. So maybe i should seek for other method to generate grids. However, I want to know do the MPI errors have bad effects on my calculation progress? Best regards, sunxing |
|
September 20, 2014, 09:30 |
|
#10 | |||||
Retired Super Moderator
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
Posts: 10,980
Blog Entries: 45
Rep Power: 128 |
Hi Sunxing,
OK, you're limiting the maximum local cells to 10 million cells and the global to 30 million. This can lead to unexpected mesh refinements, which could imply why this error is occurring. In addition, I took another look at the output in one of your posts and there is this: Quote:
Try increasing the maximum limit to 60-90 million cells. The final mesh seems to only end up with roughly half of that. As to answer your recent post: Quote:
Code:
mpiexec --version Problem is that when "FOAM_MPI=mpi", this means that the MPI located at "/opt/mpi" is the one meant to be used. More specifically, you can try running: Code:
echo $MPI_ARCH_PATH ls -l $MPI_ARCH_PATH Quote:
Quote:
Quote:
Long answer: It depends. MPI related errors can be due to a variety of reasons, including incorrect use or a situation that was not contemplated in a specific MPI version. For example, what comes to my mind is that some MPI libraries might not take into account what should be done if an array of 0 size is sent through the MPI channels; it doesn't make much sense trying to send an array of 0 dimension via MPI, but this could work in some MPI toolboxes but not on others. Therefore, without more details, I can only suppose that perhaps you'll only have problems with this MPI toolbox in OpenFOAM 2.1.0 if and only if there is an identical situation in the solver, to the one you're triggering with snappyHexMesh. In other words, the solver can only work well in parallel if the mesh is good enough to use it in parallel. Best regards, Bruno
__________________
|
||||||
Thread Tools | Search this Thread |
Display Modes | |
|
|
Similar Threads | ||||
Thread | Thread Starter | Forum | Replies | Last Post |
[snappyHexMesh] SnappyHexMesh problems | sjtuwjh | OpenFOAM Meshing & Mesh Conversion | 5 | November 25, 2020 18:49 |
[snappyHexMesh] Problems with scaling meshes when meshing with SnappyHexmesh | Bnitter | OpenFOAM Meshing & Mesh Conversion | 1 | November 15, 2018 08:26 |
[snappyHexMesh] Problems meshing an impeller with snappyHexMesh | kandelabr | OpenFOAM Meshing & Mesh Conversion | 13 | June 9, 2017 06:18 |
[snappyHexMesh] Problems with coarse/unsnapped cells in snappyHexMesh | scareneb | OpenFOAM Meshing & Mesh Conversion | 2 | August 13, 2014 07:13 |
[snappyHexMesh] SnappyhexMesh and Symmetryplane | bastil | OpenFOAM Meshing & Mesh Conversion | 10 | October 7, 2008 17:07 |