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Old   February 26, 2020, 20:06
Default swak4foam compiling issues on a cluster
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Sam
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Hi guys,

I am struggling to compile swak4foam for OpenFoam version 2.4.0 on a cluster. The log file of ./Allwmake is too big to attach so the first lines are described below. If you require the file, I could send it to you.

This is a clean install
Reading variables from 'swakConfiguration'
Checking swak4Foam-version and generating file
abort: no repository found in '/rdsgpfs/general/user/saj216/home/WORK/CFD-PC/swak4Foam' (.hg not found)!
Swak version is 0.4.1
Bison is version 2.7.12-4996
Flex is version 2.5.35 (Minor version: 35)
OpenFOAM-version: Major 2 Minor 4 Patch 0 (-1 == x / 0) Fork: openfoam
No swak4FoamParsers/foamVersion4swak.H. Generated
wmakeLnInclude: linking include files to simpleFunctionObjects/lnInclude
wmakeLnInclude: linking include files to ./lnInclude
Making dependency list for source file helpers/exprString.C
Making dependency list for source file helpers/printSwakVersion.C
Making dependency list for source file ../filesThatAreOnlyInSomeDistributions/OutputFilerDropin/outputFilterOutputControl.C
Making dependency list for source file helpers/switchableNotImplemented.C
could not open file foamString.H for source file helpers/exprString.C due to No such file or directory
Making dependency list for source file helpers/DebugOStream.C
Making dependency list for source file entryToExpression/entryToExpression.C
Making dependency list for source file entryToExpression/directEntryToExpression.C
Making dependency list for source file entryToExpression/stringEntryToExpression.C
Making dependency list for source file entryToExpression/boolEntryToExpression.C
Making dependency list for source file entryToExpression/vectorEntryToExpression.C
Making dependency list for source file entryToExpression/tensorEntryToExpression.C
Making dependency list for source file entryToExpression/symmTensorEntryToExpression.C
Making dependency list for source file entryToExpression/sphericalTensorEntryToExpression.C
Making dependency list for source file entryToExpression/dimensionedScalarEntryToExpression.C
Making dependency list for source file entryToExpression/dimensionedVectorEntryToExpression.C
Making dependency list for source file entryToExpression/dimensionedTensorEntryToExpression.C
Making dependency list for source file entryToExpression/dimensionedSymmTensorEntryToExpression.C
Making dependency list for source file entryToExpression/dimensionedSphericalTensorEntryToExpression.C
Making dependency list for source file repositories/RepositoryBase.C
Making dependency list for source file repositories/SurfacesRepository.C
could not open file foamTime.H for source file repositories/RepositoryBase.C due to No such file or directory
Making dependency list for source file repositories/MeshesRepository.C
Making dependency list for source file repositories/SetsRepository.C
could not open file foamTime.H for source file repositories/SetsRepository.C due to No such file or directory
Making dependency list for source file repositories/GlobalVariablesRepository.C
could not open file foamTime.H for source file repositories/GlobalVariablesRepository.C due to No such file or directory
Making dependency list for source file namedEnums/MeshInterpolationOrder.C
Making dependency list for source file namedEnums/LogicalAccumulationNamedEnum.C
Making dependency list for source file namedEnums/NumericAccumulationNamedEnum.C
Making dependency list for source file ExpressionDriverWriter.C
Making dependency list for source file ExpressionResult/ExpressionResult.C
Making dependency list for source file ExpressionResult/StoredExpressionResult.C
Making dependency list for source file ExpressionResult/DelayedExpressionResult.C
could not open file foamString.H for source file ExpressionResult/StoredExpressionResult.C due to No such file or directory
Making dependency list for source file ExpressionResult/StackExpressionResult.C
Making dependency list for source file ExpressionResult/StoredStackExpressionResult.C
could not open file foamString.H for source file ExpressionResult/DelayedExpressionResult.C due to No such file or directory
Making dependency list for source file setsAndSurfaces/swakRegistryProxySurface.C
could not open file foamString.H for source file ExpressionDriverWriter.C due to No such file or directory
Making dependency list for source file setsAndSurfaces/swakRegistryProxySet.C
Making dependency list for source file makeSwakDataEntry.C
Making dependency list for source file FieldValueExpressionParser.yy
could not open file foamString.H for source file FieldValueExpressionParser.yy due to No such file or directory
could not open file foamString.H for source file makeSwakDataEntry.C due to No such file or directory
could not open file Function1.H for source file makeSwakDataEntry.C due to No such file or directory
could not open file FieldValueExpressionParser.tab.hh for source file FieldValueExpressionParser.yy due to No such file or directory
Making dependency list for source file PatchValueExpressionParser.yy
Making dependency list for source file SubsetValueExpressionParser.yy
Making dependency list for source file CommonValueExpressionDriver.C
could not open file directMappedFvPatch.H for source file FieldValueExpressionParser.yy due to No such file or directory
could not open file directMappedWallFvPatch.H for source file FieldValueExpressionParser.yy due to No such file or directory
could not open file directMappedPointPatch.H for source file FieldValueExpressionParser.yy due to No such file or directory
could not open file FixedValuePointPatchField.H for source file FieldValueExpressionParser.yy due to No such file or directory
could not open file ZeroGradientPointPatchField.H for source file FieldValueExpressionParser.yy due to No such file or directory
could not open file CalculatedPointPatchField.H for source file FieldValueExpressionParser.yy due to No such file or directory
could not open file foamString.H for source file SubsetValueExpressionParser.yy due to No such file or directory
could not open file foamString.H for source file PatchValueExpressionParser.yy due to No such file or directory
could not open file foamString.H for source file CommonValueExpressionDriver.C due to No such file or directory
could not open file SubsetValueExpressionParser.tab.hh for source file SubsetValueExpressionParser.yy due to No such file or directory
Making dependency list for source file FieldValueExpressionLexer.ll
could not open file PatchValueExpressionParser.tab.hh for source file PatchValueExpressionParser.yy due to No such file or directory
Making dependency list for source file FieldValueExpressionDriver.C
could not open file directMappedPatchBase.H for source file PatchValueExpressionParser.yy due to No such file or directory
could not open file foamString.H for source file FieldValueExpressionLexer.ll due to No such file or directory
Making dependency list for source file PatchValueExpressionLexer.ll
Making dependency list for source file PatchValueExpressionDriver.C
could not open file foamString.H for source file FieldValueExpressionDriver.C due to No such file or directory
could not open file FieldValueExpressionParser.tab.hh for source file FieldValueExpressionLexer.ll due to No such file or directory
could not open file directMappedFvPatch.H for source file FieldValueExpressionLexer.ll due to No such file or directory
could not open file directMappedWallFvPatch.H for source file FieldValueExpressionLexer.ll due to No such file or directory
could not open file directMappedPointPatch.H for source file FieldValueExpressionLexer.ll due to No such file or directory
could not open file FixedValuePointPatchField.H for source file FieldValueExpressionLexer.ll due to No such file or directory
could not open file ZeroGradientPointPatchField.H for source file FieldValueExpressionLexer.ll due to No such file or directory
could not open file CalculatedPointPatchField.H for source file FieldValueExpressionLexer.ll due to No such file or directory
could not open file FieldValueExpressionParser.tab.hh for source file FieldValueExpressionDriver.C due to No such file or directory
Making dependency list for source file SubsetValueExpressionLexer.ll
could not open file foamString.H for source file PatchValueExpressionLexer.ll due to No such file or directory
could not open file foamString.H for source file PatchValueExpressionDriver.C due to No such file or directory
could not open file directMappedFvPatch.H for source file FieldValueExpressionDriver.C due to No such file or directory
could not open file directMappedWallFvPatch.H for source file FieldValueExpressionDriver.C due to No such file or directory
could not open file directMappedPointPatch.H for source file FieldValueExpressionDriver.C due to No such file or directory
could not open file FixedValuePointPatchField.H for source file FieldValueExpressionDriver.C due to No such file or directory
could not open file ZeroGradientPointPatchField.H for source file FieldValueExpressionDriver.C due to No such file or directory
could not open file CalculatedPointPatchField.H for source file FieldValueExpressionDriver.C due to No such file or directory
could not open file PatchValueExpressionParser.tab.hh for source file PatchValueExpressionLexer.ll due to No such file or directory
could not open file directMappedPatchBase.H for source file PatchValueExpressionLexer.ll due to No such file or directory
could not open file PatchValueExpressionParser.tab.hh for source file PatchValueExpressionDriver.C due to No such file or directory
could not open file directMappedPatchBase.H for source file PatchValueExpressionDriver.C due to No such file or directory
could not open file FieldValueExpressionParser.tab.hh for source file PatchValueExpressionDriver.C due to No such file or directory
could not open file directMappedFvPatch.H for source file PatchValueExpressionDriver.C due to No such file or directory
could not open file directMappedWallFvPatch.H for source file PatchValueExpressionDriver.C due to No such file or directory
could not open file directMappedPointPatch.H for source file PatchValueExpressionDriver.C due to No such file or directory
could not open file FixedValuePointPatchField.H for source file PatchValueExpressionDriver.C due to No such file or directory
could not open file ZeroGradientPointPatchField.H for source file PatchValueExpressionDriver.C due to No such file or directory
could not open file CalculatedPointPatchField.H for source file PatchValueExpressionDriver.C due to No such file or directory
could not open file SubsetValueExpressionParser.tab.hh for source file PatchValueExpressionDriver.C due to No such file or directory
Making dependency list for source file SubsetValueExpressionDriver.C

I am aware of the issue stated in the URL regarding the module load issue. https://openfoamwiki.net/index.php/I...e_load_is_used

I have tried this and it was unsuccessful .

The problem appears when I run a simulation and it shows that funkysetfields has not been read correctly. As shown below.

/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 2.4.0 |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Build : 2.4.0-dcea1e13ff76
Exec : funkySetFields -time 0 -allowFunctionObjects
Date : Feb 27 2020
Time : 00:09:39
Host : "login-5"
PID : 9765
Case : /rdsgpfs/general/user/saj216/home/WORK/CFD-PC/interThermalPhaseFoam/tutorials/NusseltSmooth
nProcs : 1
sigFpe : Floating point exception trapping - not supported on this platform
fileModificationChecking : Monitoring run-time modified files using timeStampMaster
allowSystemOperations : Allowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
swakVersion: 0.4.1 (Release date: 2017-05-31)
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Create mesh for time = 0


Time = 0
swak4Foam: Allocating new repository for sampledGlobalVariables
Using dynamicCode for functionObject GlobalHeatTransfer at line 107 in ".GlobalHeatTransfer"
Creating new library in "dynamicCode/GlobalHeatTransfer/platforms/linux64IccDPOpt/lib/libGlobalHeatTransfer_c7a46865e42e8e66543e45f6e422 e87a5855ddfb.so"
Invoking "wmake -s libso /rdsgpfs/general/user/saj216/home/WORK/CFD-PC/interThermalPhaseFoam/tutorials/NusseltSmooth/dynamicCode/GlobalHeatTransfer"
wmakeLnInclude: linking include files to ./lnInclude
Making dependency list for source file FilterFunctionObjectTemplate.C
Making dependency list for source file functionObjectTemplate.C
'/rdsgpfs/general/user/saj216/home/WORK/CFD-PC/interThermalPhaseFoam/tutorials/NusseltSmooth/dynamicCode/GlobalHeatTransfer/../platforms/linux64IccDPOpt/lib/libGlobalHeatTransfer_c7a46865e42e8e66543e45f6e422 e87a5855ddfb.so' is up to date.
Using funkySetFieldsDict



Part: CreateFilmAlpha1
Modifying field alpha1 of type volScalarField

Putting "1" into field alpha1 at t = "0" if condition "pos().x<=d_f" is true
Keeping patches unaltered

swak4Foam: Allocating new repository for sampledMeshes
#0 Foam::error:rintStack(Foam::Ostream&) at ??:?
#1 Foam::sigSegv::sigHandler(int) at ??:?
#2 ? in "/lib64/libc.so.6"
#3 ? at ??:?
#4 ? at ??:?
#5 ? at ??:?
#6 __libc_start_main in "/lib64/libc.so.6"
#7 ? at ??:?
./PreRun.sh: line 7: 9765 Segmentation fault (core dumped) funkySetFields -time 0 -allowFunctionObjects

This issue did not appear when running the simulation on the a virtual machine for example using funkysetfields on the same OpenFoam version.

If anyone has any possible solutions I will be grateful.

Kind regards,

Sam
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Old   February 27, 2020, 13:19
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If you are not constrained with 2.4, and are in need of swak4Foam, I suggest you to consider OFv1912 whereto some of the functionalities of swak4Foam were transferred. If so, have a look at the release notes.
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Old   February 27, 2020, 13:23
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Sam
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Thank you for the reply.

Unfortunately, I am stuck with openfoam version 2.4 . What confuses me, is that it works fine on a normal linux setup but does not on the cluster with the same configuration.
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Old   February 27, 2020, 15:07
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Might be due to the difference in Linux distro? Clusters usually run by RedHat or oSUSE (possibly old yet stable versions). Might be module loading for Python3 rather than Python 2x in the cluster? May be you were able to run the case with Ubuntu on ur machine?

Every HPC should have maintainers, any chance to ask them?

Sorry, I am not that very helpful.
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Old   February 27, 2020, 15:57
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Is python 2x required instead of python 3 because I know that the module load python3 is used in my cluster. How did you know that?

I probably can run it on my computer, it would save time if i could run it on the cluster.

Thank you for your help.
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