並列計算について

[matsui]

皆様はじめまして。こんにちは。

OpenFOAM初心者の学生のmatsuiです。

現在OpenFOAM2.2.xを利用してbuoyantPimpleFoamで解析をしています。

このソルバーで並列計算をしようと思ったのですが、うまくいきません。

どなたかご教授ください。

行った手順としましては、systemにdecomposeParDictを作成しblockMeshを実行後にdecomposeParを実行しました。

その後

$　bsub -o . -m 計算機名 -J ジョブ名 -n 3 mpirun -np 3 buoyantPimpleFoam -parallel

このコマンドでソルバーを実行したのですが、エラーが出てしまい解析を行うことが出来ませんでした。

なぜ並列計算が出来ないのかわからず困っています。

並列計算ではなく通常の計算であれば正常に解析が始まることは確認済みです。

どこの設定が間違っているか、皆様のご助言をいただければ幸いです。

エラーの文章を記載します。（ソルバーを実行した際のログにかかれていたものです。エラーの手前の文章から記載します。）

Calculating field g.h

Reading field p_rgh

Creating field dpdt

Creating field kinetic energy K

No finite volume options present

Selecting radiationModel viewFactor

Selecting absorptionEmissionModel constantAbsorptionEmission

Selecting scatterModel none

[1] #0  [2] #0  Foam::error::printStack(Foam::Ostream&)Foam::error::printStack(Foam::Ostream&)[0] #0  Foam::error::printStack(Foam::Ostream&) in "/home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"

[2] #1  Foam::sigSegv::sigHandler(int) in "/home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"

[1] #1  Foam::sigSegv::sigHandler(int) in "/home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"

[0] #1  Foam::sigSegv::sigHandler(int) in "/home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"

[2] #2   in "/hom in "/home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"

[0] #2  e/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libOpenFOAM.so"

[1] #2  __restore_rt__restore_rt__restore_rt at sigaction.c:0

[0] #3  Foam::singleCellFvMesh::agglomerateMesh(Foam::fvMesh const&, Foam::List<Foam::List<int> > const&) at sigaction.c:0

[2] #3   at sigaction.c:0

[1] #3  Foam::singleCellFvMesh::agglomerateMesh(Foam::fvMesh const&, Foam::List<Foam::List<int> > const&)Foam::singleCellFvMesh::agglomerateMesh(Foam::fvMesh const&, Foam::List<Foam::List<int> > const&) in "/home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libfiniteVolume.so"

[2] #4  Foam::singleCellFvMesh::singleCellFvMesh(Foam::IOobject const&, Foam::fvMesh const&, Foam::List<Foam::List<int> > const&) in "/home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libfiniteVolume.so"

[1] #4  Foam::singleCellFvMesh::singleCellFvMesh(Foam::IOobject const&, Foam::fvMesh const&, Foam::List<Foam::List<int> > const&) in "/home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libfiniteVolume.so"

[0] #4  Foam::singleCellFvMesh::singleCellFvMesh(Foam::IOobject const&, Foam::fvMesh const&, Foam::List<Foam::List<int> > const&) in "/home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x in "/home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libfiniteVolume.so"

[2] #5  Foam::radiation::viewFactor::viewFactor(Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh> const&)/platforms/l in "/home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/platforms/linux64Gcinux64GccDPcDPOpt/lib/libfiniteVolume.so"

[0] #5  Opt/lib/libfiniteVolume.so"

Foam::radiation::viewFactor::viewFactor(Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh> const&)[1] #5  Foam::radiation::viewFactor::viewFactor(Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh> const&) in "/home/imoan/centFOAM//OpenFO in "/home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/plaAM/OpenFOAM-2.2.x/platftforms/linux64GccDPOpt/lib/libradiationModorms/linux64GccDPOpt/lib/libradiatiels.so"

[0] #onModels.so"6  

[2] #6  Foam::radiation::radiationModel::addTConstructorToTable<Foam::radiation::viewFactor>::New(Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh> const&)Foam::radiation::radiationModel::addTConstructorToTable<Foam::radiation::viewFactor>::New(Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh> const&) in "/home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libradiationModels.so"

[1] #6  Foam::radiation::radiationModel::addTConstructorToTable<Foam::radiation::viewFactor>::New(Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh> const&) in "/home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libradiationModels.so"

[0] #7  Foam::radiation::radiationModel::New(Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh> const&) in "/home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libradiationModels.so"

[1] #7  Foam::radiation::radiationModel::New(Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh> const&) in "/home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libradiationModels.so"

[2] #7  Foam::radiation::radiationModel::New(Foam::GeometricField<double, Foam::fvPatchField, Foam::volMesh> const&) in "/home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libradiationModels.so"

[2] #8   in "/home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libradiationModels.so"

[1] #8   in "/home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libradiationModels.so"

[0] #8  mainmainmain in  in "/home/imoan/centFOAM/OpenFOAM/OpenFOAM in -2.2.x/plat"/home/iforms/linumoan/centFOAM/OpenFOx64GccDPOpt/bin/buoyaAM/OntPimpleFoam"

penF[1] #9  OAM-2.2.x/plat__libc_start_mainforms/linux64GccDPOpt/bin/buoyantPim"pleFoam"

[2] #9  __libc_start_main/home/imoan/centFOAM/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/bin/buoyantPimpleFoam"

[0] #9  __libc_start_main in "/lib64/libc.so.6"

[2] #10   in "/lib64/libc.so in "/lib64/libc.so.6"

.6"

[1] #10  [0] #10  __gxx_personality_v0__gxx_personality_v0__gxx_personality_v0 in "/home/imoan/centFOAM/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/bin/buoyantPimpleFoam"

[joker06:17290] *** Process received signal ***

[joker06:17290] Signal: Segmentation fault (11)

[joker06:17290] Signal code:  (-6)

[joker06:17290] Failing at address: 0x2060000438a

[joker06:17290] [ 0] /lib64/libc.so.6 [0x3948e302d0]

[joker06:17290] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3948e30265]

[joker06:17290] [ 2] /lib64/libc.so.6 [0x3948e302d0]

[joker06:17290] [ 3] /home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libfiniteVolume.so(_ZN4Foam16singleCellFvMesh15agglomerateMeshERKNS_6fvMeshERKNS_4ListINS4_IiEEEE+0xc5) [0x2b529371c4f5]

[joker06:17290] [ 4] /home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libfiniteVolume.so(_ZN4Foam16singleCellFvMeshC1ERKNS_8IOobjectERKNS_6fvMeshERKNS_4ListINS7_IiEEEE+0x74e) [0x2b529371f5ae]

[joker06:17290] [ 5] /home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libradiationModels.so(_ZN4Foam9radiation10viewFactorC1ERKNS_14GeometricFieldIdNS_12fvPatchFieldENS_7volMeshEEE+0x12e) [0x2b529568e61e]

[joker06:17290] [ 6] /home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libradiationModels.so(_ZN4Foam9radiation14radiationModel22addTConstructorToTableINS0_10viewFactorEE3NewERKNS_14GeometricFieldIdNS_12fvPatchFieldENS_7volMeshEEE+0x31) [0x2b52956982d1]

[joker06:17290] [ 7] /home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libradiationModels.so(_ZN4Foam9radiation14radiationModel3NewERKNS_14GeometricFieldIdNS_12fvPatchFieldENS_7volMeshEEE+0x4fe) [0x2b529566687e]

[joker06:17290] [ 8] buoyantPimpleFoam [0x483a1b]

[joker06:17290] [ 9] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3948e1d994]

[joker06:17290] [10] buoyantPimpleFoam(__gxx_personality_v0+0x341) [0x432309]

[joker06:17290] *** End of error message ***

 in "/home/imoan/centFOAM/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/bin/buoyantPimpleFoam"

[joker06:17288] *** Process received signal ***

[joker06:17288] Signal: Segmentation fault (11)

[joker06:17288] Signal code:  (-6)

[joker06:17288] Failing at address: 0x20600004388

[joker06:17288] [ 0] /lib64/libc.so.6 [0x3948e302d0]

[joker06:17288] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3948e30265]

[joker06:17288] [ 2] /lib64/libc.so.6 [0x3948e302d0]

[joker06:17288] [ 3] /home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libfiniteVolume.so(_ZN4Foam16singleCellFvMesh15agglomerateMeshERKNS_6fvMeshERKNS_4ListINS4_IiEEEE+0xc5) [0x2acbfbdc64f5]

[joker06:17288] [ 4] /home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libfiniteVolume.so(_ZN4Foam16singleCellFvMeshC1ERKNS_8IOobjectERKNS_6fvMeshERKNS_4ListINS7_IiEEEE+0x74e) [0x2acbfbdc95ae]

[joker06:17288] [ 5] /home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libradiationModels.so(_ZN4Foam9radiation10viewFactorC1ERKNS_14GeometricFieldIdNS_12fvPatchFieldENS_7volMeshEEE+0x12e) [0x2acbfdd3861e]

[joker06:17288] [ 6] /home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libradiationModels.so(_ZN4Foam9radiation14radiationModel22addTConstructorToTableINS0_10viewFactorEE3NewERKNS_14GeometricFieldIdNS_12fvPatchFieldENS_7volMeshEEE+0x31) [0x2acbfdd422d1]

[joker06:17288] [ 7] /home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libradiationModels.so(_ZN4Foam9radiation14radiationModel3NewERKNS_14GeometricFieldIdNS_12fvPatchFieldENS_7volMeshEEE+0x4fe) [0x2acbfdd1087e]

[joker06:17288] [ 8] buoyantPimpleFoam [0x483a1b]

[joker06:17288] [ 9] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3948e1d994]

[joker06:17288] [10] buoyantPimpleFoam(__gxx_personality_v0+0x341) [0x432309]

[joker06:17288] *** End of error message ***

 in "/home/imoan/centFOAM/OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/bin/buoyantPimpleFoam"

[joker06:17289] *** Process received signal ***

[joker06:17289] Signal: Segmentation fault (11)

[joker06:17289] Signal code:  (-6)

[joker06:17289] Failing at address: 0x20600004389

[joker06:17289] [ 0] /lib64/libc.so.6 [0x3948e302d0]

[joker06:17289] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3948e30265]

[joker06:17289] [ 2] /lib64/libc.so.6 [0x3948e302d0]

[joker06:17289] [ 3] /home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libfiniteVolume.so(_ZN4Foam16singleCellFvMesh15agglomerateMeshERKNS_6fvMeshERKNS_4ListINS4_IiEEEE+0xc5) [0x2b2b47dc34f5]

[joker06:17289] [ 4] /home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libfiniteVolume.so(_ZN4Foam16singleCellFvMeshC1ERKNS_8IOobjectERKNS_6fvMeshERKNS_4ListINS7_IiEEEE+0x74e) [0x2b2b47dc65ae]

[joker06:17289] [ 5] /home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libradiationModels.so(_ZN4Foam9radiation10viewFactorC1ERKNS_14GeometricFieldIdNS_12fvPatchFieldENS_7volMeshEEE+0x12e) [0x2b2b49d3561e]

[joker06:17289] [ 6] /home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libradiationModels.so(_ZN4Foam9radiation14radiationModel22addTConstructorToTableINS0_10viewFactorEE3NewERKNS_14GeometricFieldIdNS_12fvPatchFieldENS_7volMeshEEE+0x31) [0x2b2b49d3f2d1]

[joker06:17289] [ 7] /home/imoan/centFOAM//OpenFOAM/OpenFOAM-2.2.x/platforms/linux64GccDPOpt/lib/libradiationModels.so(_ZN4Foam9radiation14radiationModel3NewERKNS_14GeometricFieldIdNS_12fvPatchFieldENS_7volMeshEEE+0x4fe) [0x2b2b49d0d87e]

[joker06:17289] [ 8] buoyantPimpleFoam [0x483a1b]

[joker06:17289] [ 9] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3948e1d994]

[joker06:17289] [10] buoyantPimpleFoam(__gxx_personality_v0+0x341) [0x432309]

[joker06:17289] *** End of error message ***

--------------------------------------------------------------------------

mpirun noticed that process rank 2 with PID 17290 on node joker06 exited on signal 11 (Segmentation fault).

--------------------------------------------------------------------------

以上になります。よろしくお願いいたします。

[ohbuchi]

こんにちは。

計算機システムおよびバッチキューシステムの設定に依存したエラー

の様に見えます。

お使いの計算機のシステム管理者に相談するのが一番だと思います。


2014年12月27日土曜日 14時50分21秒 UTC+9 matsui:

[matsui]

ohbuchi様

ご助言ありがとうございます。

matsuiです。

計算機のシステムについて把握している者に尋ねたところ、このようなエラーが出る場合は計算の設定がおかしい時がほとんどだということでした。

また奇数のコアでは並列計算ができないと指摘を受けました。

そこでまず4つのコアに変更したのですが、同じ内容のエラーが書きだされてしまいました。

計算の設定がおかしい可能性が高いため設定を見直したいと思うのですが、並列計算でない場合には正常に解析が出来るため、decomposeParDictの中身がおかしいと考えれば良いでしょうか？

再び質問になってしまいますが、よろしくお願いいたします。

2015年1月5日月曜日 21時33分15秒 UTC+9 ohbuchi:

[Masashi Imano]

今野です．

エラメッセージに radiation や viewFactor に関する行が散見されますので，
まずは radiationModel を無効( none )にしたり，FvDOM 等別な放射モデルにする等して，
並列計算が失敗する原因を切り分けていってください．

2015年1月8日 16:17 matsui <naomi.m...@gmail.com>:

> --
> このメールは Google グループのグループ「OpenFOAM」に登録しているユーザーに送られています。
> このグループから退会し、グループからのメールの配信を停止するには openfoam+u...@googlegroups.com
> にメールを送信してください。
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> http://groups.google.com/group/openfoam からこのグループにアクセスしてください。
> その他のオプションについては https://groups.google.com/d/optout にアクセスしてください。



--
IMANO Masashi, Ph.D.

[matsui]

今野先生

matsuiです。

ご返答ありがとうございます。

お礼が遅れてしまい大変申し訳ありません。

ご助言の様に、ひとつずつ原因を探っていこうと思います。

また何かお聞きするかもしれませんが、その時もまたご助言を頂けると幸いです。