View Issue Details
| ID | Project | Category | View Status | Date Submitted | Last Update |
|---|---|---|---|---|---|
| 0000814 | OpenFOAM | Bug | public | 2013-04-09 20:43 | 2013-04-10 19:23 |
| Reporter | dkokron | Assigned To | henry | ||
| Priority | normal | Severity | major | Reproducibility | always |
| Status | resolved | Resolution | fixed | ||
| Platform | Fedora 18 64-bit | OS | Linux | OS Version | 3.8.5-201.fc18.x |
| Summary | 0000814: memory leak when using 'fourth' for gradSchemes | ||||
| Description | Using the 'fourth' option to compute gradients results in a memory leak that consumes all system memory (64GB) in ~25 times steps using my original case (9.5M cells). System: Linux xxxxxx 3.8.5-201.fc18.x86_64 #1 SMP Thu Mar 28 21:01:19 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Compiler: Intel(R) C++ Intel(R) 64 Compiler XE for applications running on Intel(R) 64, Version 13.1.1.163 Build 20130313 mpirun --version mpirun (Open MPI) 1.6.3 OpenFOAM: 2.2.x-2c25eeea8de3 valgrind --version valgrind-3.8.1 | ||||
| Steps To Reproduce | cd ~tutorials/incompressible/pisoFoam/les/motorBike/motorBike Edit system/fvSchemes, change grad(U) to fourth Edit system/controlDict, change endTime to 5 ./Allrun Rerun simpleFoam under valgrind mpirun --bysocket --bind-to-core --mca mpi_paffinity_alone 1 -np 8 valgrind --alignment=32 --leak-check=full --track-origins=yes --log-file=simpleFoam5dt.vg simpleFoam -parallel | ||||
| Additional Information | output from valgrind ==22154== 35,464,381 (240 direct, 35,464,141 indirect) bytes in 1 blocks are definitely lost in loss record 1,366 of 1,367 ==22154== at 0x4A09361: operator new(unsigned long) (vg_replace_malloc.c:298) ==22154== by 0x686C39B: Foam::fv::fourthGrad<Foam::Vector<double> >::calcGrad(Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&, Foam::word const&) const (fourthGrad.C:74) ==22154== by 0x4C6C5BE: Foam::fv::gradScheme<Foam::Vector<double> >::grad(Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&, Foam::word const&) const (gradScheme.C:154) ==22154== by 0x4C6BB30: Foam::tmp<Foam::GeometricField<Foam::outerProduct<Foam::Vector<double>, Foam::Vector<double> >::type, Foam::fvPatchField, Foam::volMesh> > Foam::fvc::grad<Foam::Vector<double> >(Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&) (fvcGrad.C:101) ==22154== by 0x50420D3: Foam::incompressible::RASModels::SpalartAllmaras::correct() (SpalartAllmaras.C:433) ==22154== by 0x41A2FD: main (simpleFoam.C:73) ==22154== ==22154== 88,252,416 bytes in 3 blocks are possibly lost in loss record 1,367 of 1,367 ==22154== at 0x4A08CE4: operator new[](unsigned long) (vg_replace_malloc.c:363) ==22154== by 0x4C49A45: Foam::GeometricField<Foam::Tensor<double>, Foam::fvPatchField, Foam::volMesh>::GeometricField(Foam::IOobject const&, Foam::GeometricField<Foam::Tensor<double>, Foam::fvPatchField, Foam::volMesh> const&) (List.C:94) ==22154== by 0x686C3FE: Foam::fv::fourthGrad<Foam::Vector<double> >::calcGrad(Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&, Foam::word const&) const (fourthGrad.C:82) ==22154== by 0x4C6C5BE: Foam::fv::gradScheme<Foam::Vector<double> >::grad(Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&, Foam::word const&) const (gradScheme.C:154) ==22154== by 0x4C6BB30: Foam::tmp<Foam::GeometricField<Foam::outerProduct<Foam::Vector<double>, Foam::Vector<double> >::type, Foam::fvPatchField, Foam::volMesh> > Foam::fvc::grad<Foam::Vector<double> >(Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&) (fvcGrad.C:101) ==22154== by 0x50420D3: Foam::incompressible::RASModels::SpalartAllmaras::correct() (SpalartAllmaras.C:433) ==22154== by 0x41A2FD: main (simpleFoam.C:73) Output from valgrind using my original case. ==20255== 593,879,832 bytes in 7 blocks are possibly lost in loss record 1,360 of 1,360 ==20255== at 0x4A08CE4: operator new[](unsigned long) (vg_replace_malloc.c:363) ==20255== by 0x4C49A45: Foam::GeometricField<Foam::Tensor<double>, Foam::fvPatchField, Foam::volMesh>::GeometricField(Foam::IOobject const&, Foam::GeometricField<Foam::Tensor<double>, Foam::fvPatchField, Foam::volMesh> const&) (List.C:94) ==20255== by 0x686C3FE: Foam::fv::fourthGrad<Foam::Vector<double> >::calcGrad(Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&, Foam::word const&) const (fourthGrad.C:82) ==20255== by 0x4C6C5BE: Foam::fv::gradScheme<Foam::Vector<double> >::grad(Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&, Foam::word const&) const (gradScheme.C:154) ==20255== by 0x4C6BB30: Foam::tmp<Foam::GeometricField<Foam::outerProduct<Foam::Vector<double>, Foam::Vector<double> >::type, Foam::fvPatchField, Foam::volMesh> > Foam::fvc::grad<Foam::Vector<double> >(Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&) (fvcGrad.C:101) ==20255== by 0x501D5F8: Foam::incompressible::RASModels::kOmegaSST::correct() (kOmegaSST.C:434) ==20255== by 0x41A2FD: main (simpleFoam.C:73) | ||||
| Tags | No tags attached. | ||||
|
|
I cannot reproduce the problem here on a smaller case, will also try the motorbike case. Is your OpenFOAM-2.2.x build up-to-date? Have you tried with gcc? (I am using gcc and Clang) |
|
|
I did a pull last week, not sure of the exact date. The specific rev is 2.2.x-2c25eeea8de3. I'll do another pull today, rebuild and test again. I have not tried compiling with GNU compilers yet. I will give it a try. |
|
|
I did a pull yesterday and rebuilt the whole code under GCC using debug. valgrind reports the same issue. 2.2.x-cbf764f7ad01 g++ --version g++ (GCC) 4.7.2 20121109 (Red Hat 4.7.2-8) c++DBUG = -ggdb3 -DFULLDEBUG c++OPT = -O0 -fdefault-inline trace from motorbike ==2508== 117,670,176 bytes in 4 blocks are possibly lost in loss record 420 of 420 ==2508== at 0x4A07CE4: operator new[](unsigned long) (vg_replace_malloc.c:363) ==2508== by 0x4C87AD8: Foam::List<Foam::Tensor<double> >::List(Foam::List<Foam::Tensor<double> > const&) (List.C:94) ==2508== by 0x4C834C2: Foam::Field<Foam::Tensor<double> >::Field(Foam::Field<Foam::Tensor<double> > const&) (Field.C:144) ==2508== by 0x4C8D199: Foam::DimensionedField<Foam::Tensor<double>, Foam::volMesh>::DimensionedField(Foam::IOobject const&, Foam::DimensionedField<Foam::Tensor<double>, Foam::volMesh> const&) (DimensionedField.C:192) ==2508== by 0x4C8AD01: Foam::GeometricField<Foam::Tensor<double>, Foam::fvPatchField, Foam::volMesh>::GeometricField(Foam::IOobject const&, Foam::GeometricField<Foam::Tensor<double>, Foam::fvPatchField, Foam::volMesh> const&) (GeometricField.C:486) ==2508== by 0x65004C4: Foam::fv::fourthGrad<Foam::Vector<double> >::calcGrad(Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&, Foam::word const&) const (fourthGrad.C:83) ==2508== by 0x4C72451: Foam::fv::gradScheme<Foam::Vector<double> >::grad(Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&, Foam::word const&) const (gradScheme.C:154) ==2508== by 0x4C6D62D: Foam::tmp<Foam::GeometricField<Foam::outerProduct<Foam::Vector<double>, Foam::Vector<double> >::type, Foam::fvPatchField, Foam::volMesh> > Foam::fvc::grad<Foam::Vector<double> >(Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&, Foam::word const&) (fvcGrad.C:101) ==2508== by 0x4C6967A: Foam::tmp<Foam::GeometricField<Foam::outerProduct<Foam::Vector<double>, Foam::Vector<double> >::type, Foam::fvPatchField, Foam::volMesh> > Foam::fvc::grad<Foam::Vector<double> >(Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&) (fvcGrad.C:147) ==2508== by 0x5097E34: Foam::incompressible::RASModels::SpalartAllmaras::correct() (SpalartAllmaras.C:405) ==2508== by 0x446CE3: main (simpleFoam.C:65) |
|
|
Can you reproduce the problem on a smaller case e.g. icoFoam running the cavity case? |
|
|
I am unable to reproduce the problem on the tutorials/incompressible/pisoFoam/les/motorBike/motorBike. |
|
|
fvSolution (1,290 bytes)
/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 2.2.0 |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
{
version 2.0;
format ascii;
class dictionary;
location "system";
object fvSolution;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
solvers
{
p
{
solver PCG;
preconditioner DIC;
tolerance 1e-06;
relTol 0;
}
U
{
solver PBiCG;
preconditioner DILU;
tolerance 1e-05;
relTol 0;
}
}
PISO
{
nCorrectors 2;
nNonOrthogonalCorrectors 0;
pRefCell 0;
pRefValue 0;
}
cache
{
grad(U) ;
}
// ************************************************************************* //
|
|
|
fvSchemes (1,424 bytes)
/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 2.2.0 |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
{
version 2.0;
format ascii;
class dictionary;
location "system";
object fvSchemes;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
ddtSchemes
{
default Euler;
}
gradSchemes
{
default Gauss linear;
grad(U) fourth;
}
divSchemes
{
default none;
div(phi,U) bounded Gauss linearUpwindV grad(U);
}
laplacianSchemes
{
default none;
laplacian(nu,U) Gauss linear orthogonal;
laplacian((1|A(U)),p) Gauss linear orthogonal;
}
interpolationSchemes
{
default linear;
interpolate(HbyA) linear;
}
snGradSchemes
{
default orthogonal;
}
fluxRequired
{
default no;
p ;
}
// ************************************************************************* //
|
|
|
I am able to reproduce the leak using tutorials/incompressible/icoFoam/cavity with the attached fvSchemes and fvSolution. This is the minimum set of changes needed to reproduce the leak in my environment. ==7073== 735,364 (1,344 direct, 734,020 indirect) bytes in 21 blocks are definitely lost in loss record 20 of 22 ==7073== at 0x4A08361: operator new(unsigned long) (vg_replace_malloc.c:298) ==7073== by 0x54F6BBA: Foam::zeroGradientFvPatchField<Foam::Tensor<double> >::clone(Foam::DimensionedField<Foam::Tensor<double>, Foam::volMesh> const&) const (zeroGradientFvPatchField.H:133) ==7073== by 0x5562C96: Foam::GeometricField<Foam::Tensor<double>, Foam::fvPatchField, Foam::volMesh>::GeometricBoundaryField::GeometricBoundaryField(Foam::DimensionedField<Foam::Tensor<double>, Foam::volMesh> const&, Foam::GeometricField<Foam::Tensor<double>, Foam::fvPatchField, Foam::volMesh>::GeometricBoundaryField const&) (GeometricBoundaryField.C:359) ==7073== by 0x5561AFC: Foam::GeometricField<Foam::Tensor<double>, Foam::fvPatchField, Foam::volMesh>::GeometricField(Foam::IOobject const&, Foam::GeometricField<Foam::Tensor<double>, Foam::fvPatchField, Foam::volMesh> const&) (GeometricField.C:486) ==7073== by 0x59B04C4: Foam::fv::fourthGrad<Foam::Vector<double> >::calcGrad(Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&, Foam::word const&) const (fourthGrad.C:83) ==7073== by 0x57BF60F: Foam::fv::gradScheme<Foam::Vector<double> >::grad(Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&, Foam::word const&) const (gradScheme.C:154) ==7073== by 0x57C0C17: Foam::linearUpwindV<Foam::Vector<double> >::correction(Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&) const (linearUpwindV.C:84) ==7073== by 0x59D9CBC: Foam::fv::gaussConvectionScheme<Foam::Vector<double> >::fvmDiv(Foam::GeometricField<double, Foam::fvsPatchField, Foam::surfaceMesh> const&, Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&) const (gaussConvectionScheme.C:103) ==7073== by 0x59E70D3: Foam::fv::boundedConvectionScheme<Foam::Vector<double> >::fvmDiv(Foam::GeometricField<double, Foam::fvsPatchField, Foam::surfaceMesh> const&, Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&) const (boundedConvectionScheme.C:77) ==7073== by 0x453C50: Foam::tmp<Foam::fvMatrix<Foam::Vector<double> > > Foam::fvm::div<Foam::Vector<double> >(Foam::GeometricField<double, Foam::fvsPatchField, Foam::surfaceMesh> const&, Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&, Foam::word const&) (fvmDiv.C:57) ==7073== by 0x44A8AB: Foam::tmp<Foam::fvMatrix<Foam::Vector<double> > > Foam::fvm::div<Foam::Vector<double> >(Foam::GeometricField<double, Foam::fvsPatchField, Foam::surfaceMesh> const&, Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&) (fvmDiv.C:83) ==7073== by 0x44523D: main (icoFoam.C:61) ==7073== ==7073== 1,650,582 (11,520 direct, 1,639,062 indirect) bytes in 48 blocks are definitely lost in loss record 21 of 22 ==7073== at 0x4A08361: operator new(unsigned long) (vg_replace_malloc.c:298) ==7073== by 0x59B04AF: Foam::fv::fourthGrad<Foam::Vector<double> >::calcGrad(Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&, Foam::word const&) const (fourthGrad.C:83) ==7073== by 0x57BF60F: Foam::fv::gradScheme<Foam::Vector<double> >::grad(Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&, Foam::word const&) const (gradScheme.C:154) ==7073== by 0x57C0C17: Foam::linearUpwindV<Foam::Vector<double> >::correction(Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&) const (linearUpwindV.C:84) ==7073== by 0x59D9CBC: Foam::fv::gaussConvectionScheme<Foam::Vector<double> >::fvmDiv(Foam::GeometricField<double, Foam::fvsPatchField, Foam::surfaceMesh> const&, Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&) const (gaussConvectionScheme.C:103) ==7073== by 0x59E70D3: Foam::fv::boundedConvectionScheme<Foam::Vector<double> >::fvmDiv(Foam::GeometricField<double, Foam::fvsPatchField, Foam::surfaceMesh> const&, Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&) const (boundedConvectionScheme.C:77) ==7073== by 0x453C50: Foam::tmp<Foam::fvMatrix<Foam::Vector<double> > > Foam::fvm::div<Foam::Vector<double> >(Foam::GeometricField<double, Foam::fvsPatchField, Foam::surfaceMesh> const&, Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&, Foam::word const&) (fvmDiv.C:57) ==7073== by 0x44A8AB: Foam::tmp<Foam::fvMatrix<Foam::Vector<double> > > Foam::fvm::div<Foam::Vector<double> >(Foam::GeometricField<double, Foam::fvsPatchField, Foam::surfaceMesh> const&, Foam::GeometricField<Foam::Vector<double>, Foam::fvPatchField, Foam::volMesh> const&) (fvmDiv.C:83) ==7073== by 0x44523D: main (icoFoam.C:61) |
|
|
Thanks for the simpler test setup, this helped pin-point the problem. Resolved by commit e04af4b8e013fdcc5b11f6e8eca174971a1b22b8 |
| Date Modified | Username | Field | Change |
|---|---|---|---|
| 2013-04-09 20:43 | dkokron | New Issue | |
| 2013-04-09 22:04 | henry | Note Added: 0002107 | |
| 2013-04-09 22:22 | dkokron | Note Added: 0002108 | |
| 2013-04-10 14:38 | dkokron | Note Added: 0002109 | |
| 2013-04-10 14:43 | henry | Note Added: 0002110 | |
| 2013-04-10 16:05 | henry | Note Added: 0002111 | |
| 2013-04-10 17:37 | dkokron | File Added: fvSolution | |
| 2013-04-10 17:37 | dkokron | File Added: fvSchemes | |
| 2013-04-10 17:40 | dkokron | Note Added: 0002112 | |
| 2013-04-10 17:41 | dkokron | Note Edited: 0002112 | |
| 2013-04-10 19:23 | henry | Note Added: 0002113 | |
| 2013-04-10 19:23 | henry | Status | new => resolved |
| 2013-04-10 19:23 | henry | Resolution | open => fixed |
| 2013-04-10 19:23 | henry | Assigned To | => henry |
