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Old   November 22, 2017, 08:20
Default OpenFOAM 5.x (mrklein patch) and macOS High Sierra
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Pierre-Olivier Dallaire
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Hi there,

I recently switched to macOS High Sierra and decided to compile OpenFOAM 5.x using mrklein's patch and I'm facing some challenges when compiling some of the apps. The problem seems to be related to the "postProcess.H". Here is one example for the coldEngineFoam solver:

wmake coldEngineFoam
xcrun c++ -arch x86_64 -std=c++14 -Ddarwin64 -DWM_ARCH_OPTION=64 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -Wextra -Wno-unused-parameter -Wno-overloaded-virtual -Wno-unused-variable -Wno-unused-local-typedef -Wno-invalid-offsetof -Wno-deprecated-register -Wno-undefined-var-template -O3 -DNoRepository -ftemplate-depth-100 -I. -I../engineFoam -I../XiFoam -I../../compressible/rhoPimpleFoam -I/Volumes/OpenFOAM/OpenFOAM-5.x/src/engine/lnInclude -I/Volumes/OpenFOAM/OpenFOAM-5.x/src/thermophysicalModels/specie/lnInclude -I/Volumes/OpenFOAM/OpenFOAM-5.x/src/transportModels/compressible/lnInclude -I/Volumes/OpenFOAM/OpenFOAM-5.x/src/thermophysicalModels/basic/lnInclude -I/Volumes/OpenFOAM/OpenFOAM-5.x/src/thermophysicalModels/reactionThermo/lnInclude -I/Volumes/OpenFOAM/OpenFOAM-5.x/src/TurbulenceModels/turbulenceModels/lnInclude -I/Volumes/OpenFOAM/OpenFOAM-5.x/src/TurbulenceModels/compressible/lnInclude -I/Volumes/OpenFOAM/OpenFOAM-5.x/src/finiteVolume/lnInclude -I/Volumes/OpenFOAM/OpenFOAM-5.x/src/sampling/lnInclude -I/Volumes/OpenFOAM/OpenFOAM-5.x/src/meshTools/lnInclude -IlnInclude -I. -I/Volumes/OpenFOAM/OpenFOAM-5.x/src/OpenFOAM/lnInclude -I/Volumes/OpenFOAM/OpenFOAM-5.x/src/OSspecific/POSIX/lnInclude -fPIC -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -c coldEngineFoam.C -o /Volumes/OpenFOAM/OpenFOAM-5.x/platforms/darwin64ClangDPInt32Opt/applications/solvers/combustion/coldEngineFoam/coldEngineFoam.o
In file included from coldEngineFoam.C:47:
In file included from /Volumes/OpenFOAM/OpenFOAM-5.x/src/OpenFOAM/lnInclude/postProcess.H:129:
../XiFoam/createFields.H:3:9: error: use of undeclared identifier 'psiuReactionThermo'
autoPtr<psiuReactionThermo> pThermo
^
../XiFoam/createFields.H:7:1: error: unknown type name 'psiuReactionThermo'
psiuReactionThermo& thermo = pThermo();
^
../XiFoam/createFields.H:7:30: error: use of undeclared identifier 'pThermo'
psiuReactionThermo& thermo = pThermo();
^
../XiFoam/createFields.H:10:1: error: unknown type name 'basicMultiComponentMixture'
basicMultiComponentMixture& composition = thermo.composition();
^
../XiFoam/createFields.H:93:9: error: use of undeclared identifier 'laminarFlameSpeed'
autoPtr<laminarFlameSpeed> unstrainedLaminarFlameSpeed


Another example for buoyantBoussinesqPimpleFoam:

wmake buoyantBoussinesqPimpleFoam
Making dependency list for source file buoyantBoussinesqPimpleFoam.C
xcrun c++ -arch x86_64 -std=c++14 -Ddarwin64 -DWM_ARCH_OPTION=64 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -Wextra -Wno-unused-parameter -Wno-overloaded-virtual -Wno-unused-variable -Wno-unused-local-typedef -Wno-invalid-offsetof -Wno-deprecated-register -Wno-undefined-var-template -O3 -DNoRepository -ftemplate-depth-100 -I. -I../buoyantBoussinesqSimpleFoam -I/Volumes/OpenFOAM/OpenFOAM-5.x/src/TurbulenceModels/turbulenceModels/lnInclude -I/Volumes/OpenFOAM/OpenFOAM-5.x/src/TurbulenceModels/incompressible/lnInclude -I/Volumes/OpenFOAM/OpenFOAM-5.x/src/transportModels -I/Volumes/OpenFOAM/OpenFOAM-5.x/src/transportModels/incompressible/singlePhaseTransportModel -I/Volumes/OpenFOAM/OpenFOAM-5.x/src/thermophysicalModels/radiation/lnInclude -I/Volumes/OpenFOAM/OpenFOAM-5.x/src/sampling/lnInclude -I/Volumes/OpenFOAM/OpenFOAM-5.x/src/meshTools/lnInclude -I/Volumes/OpenFOAM/OpenFOAM-5.x/src/finiteVolume/lnInclude -IlnInclude -I. -I/Volumes/OpenFOAM/OpenFOAM-5.x/src/OpenFOAM/lnInclude -I/Volumes/OpenFOAM/OpenFOAM-5.x/src/OSspecific/POSIX/lnInclude -fPIC -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -c buoyantBoussinesqPimpleFoam.C -o /Volumes/OpenFOAM/OpenFOAM-5.x/platforms/darwin64ClangDPInt32Opt/applications/solvers/heatTransfer/buoyantBoussinesqPimpleFoam/buoyantBoussinesqPimpleFoam.o
In file included from buoyantBoussinesqPimpleFoam.C:59:
In file included from /Volumes/OpenFOAM/OpenFOAM-5.x/src/OpenFOAM/lnInclude/postProcess.H:129:
../buoyantBoussinesqSimpleFoam/createFields.H:107:5: error: use of undeclared identifier 'simple'; did you mean 'pimple'?
simple.dict(),
^~~~~~
pimple
/Volumes/OpenFOAM/OpenFOAM-5.x/src/finiteVolume/lnInclude/createPimpleControl.H:1:15: note: 'pimple' declared here
pimpleControl pimple(mesh);
^
1 error generated.

Any idea?

Regards,

PO
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Old   November 22, 2017, 08:39
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Hi,

It is easier for me to answer this type of questions on GitHub (just create an issue).

It would be easier to diagnose your problem if you post whole log.Allwmake file. It looks like postProcess.H error, yet in both errors, you have posted, reason for the error in createFields.H.

So let's try to resolve the bug here (i.e. no need for separate issue in GitHub). Could you post:

1. log.Allwmake (guess, it is rather large, so use something Dropbox-like and post like here).
2. Output of
Code:
sw_vers
3. Output of
Code:
clang --version
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Old   November 22, 2017, 08:59
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Quote:
Originally Posted by alexeym View Post
Hi,

It is easier for me to answer this type of questions on GitHub (just create an issue).

It would be easier to diagnose your problem if you post whole log.Allwmake file. It looks like postProcess.H error, yet in both errors, you have posted, reason for the error in createFields.H.

So let's try to resolve the bug here (i.e. no need for separate issue in GitHub). Could you post:

1. log.Allwmake (guess, it is rather large, so use something Dropbox-like and post like here).
2. Output of
Code:
ProductName:	Mac OS X
ProductVersion:	10.13.1
BuildVersion:	17B48
3. Output of
Code:
Apple LLVM version 9.0.0 (clang-900.0.38)
Target: x86_64-apple-darwin17.2.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
I have attached the log file, thanks for your help !
Attached Files
File Type: txt log.Allwmake.txt (5.6 KB, 3 views)
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Old   November 22, 2017, 17:05
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Hi,

Unfortunately I was not able to reproduce your error neither with commit 718111a3b, nor with commit 61d4e1a8e (latest). Could you post EXACT steps you have taken to get the error?
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Old   November 22, 2017, 19:03
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Quote:
Originally Posted by alexeym View Post
Hi,

Unfortunately I was not able to reproduce your error neither with commit 718111a3b, nor with commit 61d4e1a8e (latest). Could you post EXACT steps you have taken to get the error?
Hi Alexey,

Summary of my steps are:

1) Installed a fresh copy of macOS High Sierra over the week-end and installed Xcode
2) Compiled couple things with Clang from source: coreutils, bison-2.7, gawk, flex, gettext, cgal, gmp, mpfr, etc ... and openmpi, scotch, metis and parmetis.
3) git clone OpenFOAM-5.x and git clone openfoam-os-x
4) Applied patch OpenFOAM-5.x-718111a3b.patch
5) Customized OpenFOAM-5.x/etc/bashrc and OpenFOAM-5.x/etc/config.sh/*
6) And compiled OpenFOAM

I have uploaded a copy of the OpenFOAM-5.x volume here:

https://www.dropbox.com/s/u3b7u4wrur...undle.zip?dl=0

Let me know if you need more info,

Thanks !

PO
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Old   November 23, 2017, 03:21
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Hi,

You have missed "git checkout" step but it is not so important, patch works on the latest source tree.

Though there are few strange things:

- I have downloaded your sparsebundle, mounted it into $HOME/OpenFOAM, corrected Scotch and METIS paths, and everything builds quite fine.

- Your sparsebundle mounts with quarantine flag, not sure if the same happens on your machine and if it interferes with build (theoretically it should).

- In the log-file you have attached, error happened in coldEngineFoam solver. In the sparsebundle this solver is built.
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Old   November 23, 2017, 09:14
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Hi,

I tried again but this time I applied git checkout - same issues.

Are you using the same macOS version, same clang version? I never had this issue before, I might try to compile OpenFAM with gcc-5.5.0 instead.

I don't get the quarantine warning since I'm the owner of the disk image.

Thanks

PO
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Old   November 23, 2017, 09:32
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Hi,

As I said, git checkout is not crucial for the build, yesterday I have built version 5.x with and without checkout step.

At least output of "sw_vers" and "clang++ --version" is the same as yours. Though it is not fresh install of High Sierra.
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Old   May 24, 2018, 11:18
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Hello,

I am trying to recompile OpenFOAM on macOS High Sierra (10.13.4) with the latest Xcode but I am unable to apply the patch. I've followed the thread and cloned the repos:

Code:
% git clone https://github.com/OpenFOAM/OpenFOAM-5.x.git OpenFOAM
Cloning into 'OpenFOAM'...
remote: Counting objects: 103058, done.
remote: Compressing objects: 100% (61/61), done.
remote: Total 103058 (delta 19), reused 26 (delta 11), pack-reused 102986
Receiving objects: 100% (103058/103058), 62.92 MiB | 7.05 MiB/s, done.
Resolving deltas: 100% (72925/72925), done.

% git clone https://github.com/mrklein/openfoam-os-x.git         
Cloning into 'openfoam-os-x'...
remote: Counting objects: 1003, done.
remote: Compressing objects: 100% (12/12), done.
remote: Total 1003 (delta 5), reused 10 (delta 2), pack-reused 989
Receiving objects: 100% (1003/1003), 1.63 MiB | 1.80 MiB/s, done.
Resolving deltas: 100% (611/611), done.
However, I cannot apply the patch, as it says it is already applied:

Code:
% cd OpenFOAM 

% ls ../openfoam-os-x/OpenFOAM-5.x-0183d1d9e.patch 
../openfoam-os-x/OpenFOAM-5.x-0183d1d9e.patch

% git checkout 0183d1d9e                          
M	applications/solvers/multiphase/reactingEulerFoam/interfacialCompositionModels/interfaceCompositionModels/InterfaceCompositionModel/InterfaceCompositionModel.C
M	applications/solvers/multiphase/reactingEulerFoam/interfacialCompositionModels/interfaceCompositionModels/InterfaceCompositionModel/InterfaceCompositionModel.H
M	applications/test/Dictionary/Make/files
M	applications/test/Dictionary/Make/options
M	applications/test/Dictionary/Test-Dictionary.C
M	src/OpenFOAM/interpolations/patchToPatchInterpolation/PatchToPatchInterpolation.H
M	src/OpenFOAM/interpolations/primitivePatchInterpolation/PrimitivePatchInterpolation.H
M	src/OpenFOAM/matrices/LduMatrix/LduMatrix/LduMatrix.C
M	src/OpenFOAM/matrices/LduMatrix/LduMatrix/LduMatrix.H
M	src/OpenFOAM/matrices/LduMatrix/LduMatrix/LduMatrixATmul.C
M	src/OpenFOAM/matrices/LduMatrix/LduMatrix/LduMatrixOperations.C
M	src/OpenFOAM/matrices/LduMatrix/LduMatrix/LduMatrixPreconditioner.C
M	src/OpenFOAM/matrices/LduMatrix/LduMatrix/LduMatrixSmoother.C
M	src/OpenFOAM/matrices/LduMatrix/LduMatrix/LduMatrixSolver.C
M	src/OpenFOAM/matrices/LduMatrix/LduMatrix/LduMatrixUpdateMatrixInterfaces.C
M	src/OpenFOAM/matrices/LduMatrix/LduMatrix/SolverPerformance.C
M	src/OpenFOAM/matrices/LduMatrix/LduMatrix/SolverPerformance.H
M	src/OpenFOAM/matrices/LduMatrix/Preconditioners/DiagonalPreconditioner/DiagonalPreconditioner.C
M	src/OpenFOAM/matrices/LduMatrix/Preconditioners/DiagonalPreconditioner/DiagonalPreconditioner.H
M	src/OpenFOAM/matrices/LduMatrix/Preconditioners/NoPreconditioner/NoPreconditioner.C
M	src/OpenFOAM/matrices/LduMatrix/Preconditioners/NoPreconditioner/NoPreconditioner.H
M	src/OpenFOAM/matrices/LduMatrix/Solvers/DiagonalSolver/DiagonalSolver.C
M	src/OpenFOAM/matrices/LduMatrix/Solvers/DiagonalSolver/DiagonalSolver.H
M	src/OpenFOAM/matrices/LduMatrix/Solvers/SmoothSolver/SmoothSolver.C
M	src/OpenFOAM/matrices/LduMatrix/Solvers/SmoothSolver/SmoothSolver.H
M	src/OpenFOAM/meshes/MeshObject/MeshObject.C
M	src/OpenFOAM/meshes/primitiveMesh/PrimitivePatch/PrimitivePatch.H
M	src/OpenFOAM/meshes/primitiveShapes/objectHit/PointHit.H
M	src/OpenFOAM/meshes/primitiveShapes/objectHit/PointIndexHit.H
M	src/finiteVolume/finiteVolume/fvc/fvcDDt.C
M	src/finiteVolume/finiteVolume/fvc/fvcDDt.H
M	src/finiteVolume/finiteVolume/gradSchemes/LeastSquaresGrad/LeastSquaresGrad.C
M	src/finiteVolume/finiteVolume/gradSchemes/LeastSquaresGrad/LeastSquaresGrad.H
M	src/finiteVolume/finiteVolume/gradSchemes/LeastSquaresGrad/LeastSquaresGrads.C
M	src/finiteVolume/finiteVolume/gradSchemes/LeastSquaresGrad/LeastSquaresVectors.C
M	src/finiteVolume/finiteVolume/gradSchemes/LeastSquaresGrad/LeastSquaresVectors.H
M	src/fvOptions/sources/general/codedSource/CodedSource.C
M	src/fvOptions/sources/general/semiImplicitSource/SemiImplicitSource.C
M	tutorials/combustion/PDRFoam/flamePropagationWithObstacles/0.orig/B
Note: checking out '0183d1d9e'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b <new-branch-name>

HEAD is now at 0183d1d9e... compressibleInterFoam: Generalized the handling of phase temperature BCs

% patch < ../openfoam-os-x/OpenFOAM-5.x-0183d1d9e.patch 
patching file Allwmake
patching file Allwmake
Reversed (or previously applied) patch detected!  Assume -R? [n] 
Apply anyway? [n] 
Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file Allwmake.rej
can't find file to patch at input line 139
Perhaps you should have used the -p or --strip option?
The text leading up to this was:
--------------------------
|diff --git a/applications/utilities/mesh/generation/foamyMesh/conformalVoronoiMesh/Make/options b/applications/utilities/mesh/generation/foamyMesh/conformalVoronoiMesh/Make/options
|index 627614817..fc45a114e 100644
|--- a/applications/utilities/mesh/generation/foamyMesh/conformalVoronoiMesh/Make/options
|+++ b/applications/utilities/mesh/generation/foamyMesh/conformalVoronoiMesh/Make/options
--------------------------
File to patch:
I have also tried to force the source to the tag "version-5.0" but the same problems remain:

Code:
% git checkout tags/version-5.0
M	Allwmake
M	applications/solvers/multiphase/reactingEulerFoam/interfacialCompositionModels/interfaceCompositionModels/InterfaceCompositionModel/InterfaceCompositionModel.C
M	applications/solvers/multiphase/reactingEulerFoam/interfacialCompositionModels/interfaceCompositionModels/InterfaceCompositionModel/InterfaceCompositionModel.H
M	applications/test/Dictionary/Make/files
M	applications/test/Dictionary/Make/options
M	applications/test/Dictionary/Test-Dictionary.C
M	src/OpenFOAM/interpolations/patchToPatchInterpolation/PatchToPatchInterpolation.H
M	src/OpenFOAM/interpolations/primitivePatchInterpolation/PrimitivePatchInterpolation.H
M	src/OpenFOAM/matrices/LduMatrix/LduMatrix/LduMatrix.C
M	src/OpenFOAM/matrices/LduMatrix/LduMatrix/LduMatrix.H
M	src/OpenFOAM/matrices/LduMatrix/LduMatrix/LduMatrixATmul.C
M	src/OpenFOAM/matrices/LduMatrix/LduMatrix/LduMatrixOperations.C
M	src/OpenFOAM/matrices/LduMatrix/LduMatrix/LduMatrixPreconditioner.C
M	src/OpenFOAM/matrices/LduMatrix/LduMatrix/LduMatrixSmoother.C
M	src/OpenFOAM/matrices/LduMatrix/LduMatrix/LduMatrixSolver.C
M	src/OpenFOAM/matrices/LduMatrix/LduMatrix/LduMatrixUpdateMatrixInterfaces.C
M	src/OpenFOAM/matrices/LduMatrix/LduMatrix/SolverPerformance.C
M	src/OpenFOAM/matrices/LduMatrix/LduMatrix/SolverPerformance.H
M	src/OpenFOAM/matrices/LduMatrix/Preconditioners/DiagonalPreconditioner/DiagonalPreconditioner.C
M	src/OpenFOAM/matrices/LduMatrix/Preconditioners/DiagonalPreconditioner/DiagonalPreconditioner.H
M	src/OpenFOAM/matrices/LduMatrix/Preconditioners/NoPreconditioner/NoPreconditioner.C
M	src/OpenFOAM/matrices/LduMatrix/Preconditioners/NoPreconditioner/NoPreconditioner.H
M	src/OpenFOAM/matrices/LduMatrix/Solvers/DiagonalSolver/DiagonalSolver.C
M	src/OpenFOAM/matrices/LduMatrix/Solvers/DiagonalSolver/DiagonalSolver.H
M	src/OpenFOAM/matrices/LduMatrix/Solvers/SmoothSolver/SmoothSolver.C
M	src/OpenFOAM/matrices/LduMatrix/Solvers/SmoothSolver/SmoothSolver.H
M	src/OpenFOAM/meshes/MeshObject/MeshObject.C
M	src/OpenFOAM/meshes/primitiveMesh/PrimitivePatch/PrimitivePatch.H
M	src/OpenFOAM/meshes/primitiveShapes/objectHit/PointHit.H
M	src/OpenFOAM/meshes/primitiveShapes/objectHit/PointIndexHit.H
M	src/finiteVolume/finiteVolume/fvc/fvcDDt.C
M	src/finiteVolume/finiteVolume/fvc/fvcDDt.H
M	src/finiteVolume/finiteVolume/gradSchemes/LeastSquaresGrad/LeastSquaresGrad.C
M	src/finiteVolume/finiteVolume/gradSchemes/LeastSquaresGrad/LeastSquaresGrad.H
M	src/finiteVolume/finiteVolume/gradSchemes/LeastSquaresGrad/LeastSquaresGrads.C
M	src/finiteVolume/finiteVolume/gradSchemes/LeastSquaresGrad/LeastSquaresVectors.C
M	src/finiteVolume/finiteVolume/gradSchemes/LeastSquaresGrad/LeastSquaresVectors.H
M	src/fvOptions/sources/general/codedSource/CodedSource.C
M	src/fvOptions/sources/general/semiImplicitSource/SemiImplicitSource.C
M	tutorials/combustion/PDRFoam/flamePropagationWithObstacles/0.orig/B
Previous HEAD position was 0183d1d9e... compressibleInterFoam: Generalized the handling of phase temperature BCs
HEAD is now at bed722318... Set version to 5.0

% patch < ../openfoam-os-x/OpenFOAM-5.0.patch          
patching file Allwmake
Reversed (or previously applied) patch detected!  Assume -R? [n] 
Apply anyway? [n] y
Hunk #1 FAILED at 12.
Hunk #2 FAILED at 28.
2 out of 2 hunks FAILED -- saving rejects to file Allwmake.rej
patching file Allwmake
Reversed (or previously applied) patch detected!  Assume -R? [n] 
Apply anyway? [n] y
Hunk #1 FAILED at 12.
1 out of 1 hunk FAILED -- saving rejects to file Allwmake.rej
can't find file to patch at input line 121
Perhaps you should have used the -p or --strip option?
The text leading up to this was:
--------------------------
|diff --git a/applications/utilities/mesh/generation/foamyMesh/conformalVoronoiMesh/Make/options b/applications/utilities/mesh/generation/foamyMesh/conformalVoronoiMesh/Make/options
|index 6276148..fc45a11 100644
|--- a/applications/utilities/mesh/generation/foamyMesh/conformalVoronoiMesh/Make/options
|+++ b/applications/utilities/mesh/generation/foamyMesh/conformalVoronoiMesh/Make/options
--------------------------
File to patch: 
Skip this patch? [y]
I am surely missing something...

Thanks for any hints!
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Old   May 24, 2018, 12:31
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Alexey Matveichev
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@fmilicchio

Hi,

Surely it is too much for your adventurous soul, but did you try to follow guide (https://github.com/mrklein/openfoam-...n-&-Homebrew)? But if we try to avoid rhetorical questions and sarcasm:

- Where did you checked out sources?
- Why do you need whole patch-set repository instead of just single patch file?
- Do you know how to use patch command?

These four lines worked for me, for example, yesterday, when I was testing new patch for 5.x:

Code:
$ cd OpenFOAM-5.x
$ curl -L https://raw.githubusercontent.com/mrklein/openfoam-os-x/master/OpenFOAM-5.x-0183d1d9e.patch > OpenFOAM-5.x-0183d1d9e.patch
$ git checkout -b local-install 0183d1d9e
$ git apply OpenFOAM-5.x-0183d1d9e.patch
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Old   May 25, 2018, 08:33
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Quote:
Originally Posted by alexeym View Post
Hi,

Surely it is too much for your adventurous soul, but did you try to follow guide (https://github.com/mrklein/openfoam-...n-&-Homebrew)?
Obviously not.

Quote:
But if we try to avoid rhetorical questions and sarcasm
Sometimes people deserve it, in this case I feel like "how the hell did I ever miss that?".

However, might I suggest this? The README should contain a clear list of links to the wiki and a description, since a ChangeLog isn't welcoming to the restless soul: we're all tired and distracted, the wiki button isn't really that visible, we usually go down to the README. The main information point is there, in the README, which of course can contain a link to a ChangeLog.

Just my 2 cents for a more human-centered layout.

Quote:
- Where did you checked out sources?
- Why do you need whole patch-set repository instead of just single patch file?
- Do you know how to use patch command?
Because the last question gives the answer: I've always applied patches the way you see, never dug into the command, to be honest, and the disastrous results prove it.

Code:
$ cd OpenFOAM-5.x
$ curl -L https://raw.githubusercontent.com/mrklein/openfoam-os-x/master/OpenFOAM-5.x-0183d1d9e.patch > OpenFOAM-5.x-0183d1d9e.patch
$ git checkout -b local-install 0183d1d9e
$ git apply OpenFOAM-5.x-0183d1d9e.patch
I can see now, the patch works:

Code:
% git clone https://github.com/OpenFOAM/OpenFOAM-5.x.git
Cloning into 'OpenFOAM-5.x'...
remote: Counting objects: 103058, done.
remote: Compressing objects: 100% (61/61), done.
remote: Total 103058 (delta 19), reused 26 (delta 11), pack-reused 102986
Receiving objects: 100% (103058/103058), 62.92 MiB | 7.31 MiB/s, done.
Resolving deltas: 100% (72925/72925), done.

% cd OpenFOAM-5.x 

% curl -L https://raw.githubusercontent.com/mrklein/openfoam-os-x/master/OpenFOAM-5.x-0183d1d9e.patch > OpenFOAM-5.x-0183d1d9e.patch
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100  112k  100  112k    0     0   110k      0  0:00:01  0:00:01 --:--:--  110k

% git checkout -b local-install 0183d1d9e
M	applications/solvers/multiphase/reactingEulerFoam/interfacialCompositionModels/interfaceCompositionModels/InterfaceCompositionModel/InterfaceCompositionModel.C
M	applications/solvers/multiphase/reactingEulerFoam/interfacialCompositionModels/interfaceCompositionModels/InterfaceCompositionModel/InterfaceCompositionModel.H
M	applications/test/Dictionary/Make/files
M	applications/test/Dictionary/Make/options
M	applications/test/Dictionary/Test-Dictionary.C
M	src/OpenFOAM/interpolations/patchToPatchInterpolation/PatchToPatchInterpolation.H
M	src/OpenFOAM/interpolations/primitivePatchInterpolation/PrimitivePatchInterpolation.H
M	src/OpenFOAM/matrices/LduMatrix/LduMatrix/LduMatrix.C
M	src/OpenFOAM/matrices/LduMatrix/LduMatrix/LduMatrix.H
M	src/OpenFOAM/matrices/LduMatrix/LduMatrix/LduMatrixATmul.C
M	src/OpenFOAM/matrices/LduMatrix/LduMatrix/LduMatrixOperations.C
M	src/OpenFOAM/matrices/LduMatrix/LduMatrix/LduMatrixPreconditioner.C
M	src/OpenFOAM/matrices/LduMatrix/LduMatrix/LduMatrixSmoother.C
M	src/OpenFOAM/matrices/LduMatrix/LduMatrix/LduMatrixSolver.C
M	src/OpenFOAM/matrices/LduMatrix/LduMatrix/LduMatrixUpdateMatrixInterfaces.C
M	src/OpenFOAM/matrices/LduMatrix/LduMatrix/SolverPerformance.C
M	src/OpenFOAM/matrices/LduMatrix/LduMatrix/SolverPerformance.H
M	src/OpenFOAM/matrices/LduMatrix/Preconditioners/DiagonalPreconditioner/DiagonalPreconditioner.C
M	src/OpenFOAM/matrices/LduMatrix/Preconditioners/DiagonalPreconditioner/DiagonalPreconditioner.H
M	src/OpenFOAM/matrices/LduMatrix/Preconditioners/NoPreconditioner/NoPreconditioner.C
M	src/OpenFOAM/matrices/LduMatrix/Preconditioners/NoPreconditioner/NoPreconditioner.H
M	src/OpenFOAM/matrices/LduMatrix/Solvers/DiagonalSolver/DiagonalSolver.C
M	src/OpenFOAM/matrices/LduMatrix/Solvers/DiagonalSolver/DiagonalSolver.H
M	src/OpenFOAM/matrices/LduMatrix/Solvers/SmoothSolver/SmoothSolver.C
M	src/OpenFOAM/matrices/LduMatrix/Solvers/SmoothSolver/SmoothSolver.H
M	src/OpenFOAM/meshes/MeshObject/MeshObject.C
M	src/OpenFOAM/meshes/primitiveMesh/PrimitivePatch/PrimitivePatch.H
M	src/OpenFOAM/meshes/primitiveShapes/objectHit/PointHit.H
M	src/OpenFOAM/meshes/primitiveShapes/objectHit/PointIndexHit.H
M	src/finiteVolume/finiteVolume/fvc/fvcDDt.C
M	src/finiteVolume/finiteVolume/fvc/fvcDDt.H
M	src/finiteVolume/finiteVolume/gradSchemes/LeastSquaresGrad/LeastSquaresGrad.C
M	src/finiteVolume/finiteVolume/gradSchemes/LeastSquaresGrad/LeastSquaresGrad.H
M	src/finiteVolume/finiteVolume/gradSchemes/LeastSquaresGrad/LeastSquaresGrads.C
M	src/finiteVolume/finiteVolume/gradSchemes/LeastSquaresGrad/LeastSquaresVectors.C
M	src/finiteVolume/finiteVolume/gradSchemes/LeastSquaresGrad/LeastSquaresVectors.H
M	src/fvOptions/sources/general/codedSource/CodedSource.C
M	src/fvOptions/sources/general/semiImplicitSource/SemiImplicitSource.C
M	tutorials/combustion/PDRFoam/flamePropagationWithObstacles/0.orig/B
Switched to a new branch 'local-install'

% git apply OpenFOAM-5.x-0183d1d9e.patch

% mkdir -p $HOME/.OpenFOAM

% echo 'WM_COMPILER=Clang' > $HOME/.OpenFOAM/prefs.sh

% echo 'WM_COMPILE_OPTION=Opt' >> $HOME/.OpenFOAM/prefs.sh

% echo 'WM_MPLIB=SYSTEMOPENMPI' >> $HOME/.OpenFOAM/prefs.sh

% echo 'export WM_NCOMPPROCS=$(sysctl -n hw.ncpu)' >> $HOME/.OpenFOAM/prefs.sh

% echo 'WM_LABEL_SIZE=32' >> $HOME/.OpenFOAM/prefs.sh

% echo 'WM_QUIET_RULES=Y' >> $HOME/.OpenFOAM/prefs.sh

% source etc/bashrc
paraview () {
	local _paraviews=(/Applications/[Pp][Aa][Rr][Aa][Vv][Ii][Ee][Ww]*.app) 
	$_paraviews/Contents/MacOS/paraview "$@"
}

% ulimit -n 8912
But the compilation process does not:

Code:
% ./Allwmake 
Allwmake /Users/sensei/Downloads/from-git/OpenFOAM-5.x
xcrun cc -arch x86_64 -Ddarwin64 -DWM_ARCH_OPTION=64 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -O3   -fPIC -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -Wno-unused-function dirToString.c -o /Users/sensei/Downloads/from-git/OpenFOAM-5.x/wmake/platforms/darwin64Clang/dirToString
flex wmkdep.l; \
	xcrun cc -arch x86_64 -Ddarwin64 -DWM_ARCH_OPTION=64 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -O3   -fPIC -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -Wno-unused-function lex.yy.c -o /Users/sensei/Downloads/from-git/OpenFOAM-5.x/wmake/platforms/darwin64Clang/wmkdep
Allwmake src
version changed from previous build
removing .o files corresponding to OpenFOAM/global/global.o ...
wmakeLnInclude: linking include files to OpenFOAM/lnInclude
ln: ./DiagTensor.H: File exists
ln: ./Vector2D.H: File exists
ln: ./SphericalTensor2D.H: File exists
ln: ./barycentric.H: File exists
ln: ./barycentricTensor.H: File exists
ln: ./Tensor2D.H: File exists
ln: ./CompactSpatialTensor.H: File exists
ln: ./SpatialVector.H: File exists
ln: ./SpatialTensor.H: File exists
ln: ./symmTensor.H: File exists
ln: ./Tensor.H: File exists
ln: ./SphericalTensor.H: File exists
ln: ./barycentric2D.H: File exists
ln: ./scalar.H: File exists
ln: ./Scalar.C: File exists
ln: ./vector.H: File exists
ln: ./symmTensor2D.H: File exists
ln: ./processorTopology.H: File exists
ln: ./Dictionary.C: File exists
ln: ./Dictionary.H: File exists
ln: ./LduInterfaceField.H: File exists
ln: ./LduInterfaceField.C: File exists
ln: ./LduInterfaceFieldPtrsList.H: File exists
wmakeLnInclude: linking include files to OSspecific/POSIX/lnInclude
Allwmake src/Pstream
wmake dummy
wmakeLnInclude: linking include files to ./lnInclude
Making dependency list for source file UOPwrite.C
Making dependency list for source file UIPread.C
Making dependency list for source file UPstream.C
xcrun c++ -arch x86_64 -std=c++11 -Ddarwin64 -DWM_ARCH_OPTION=64 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -Wextra -Wno-unused-parameter -Wno-overloaded-virtual -Wno-unused-variable -Wno-unused-local-typedef -Wno-invalid-offsetof -Wno-deprecated-register -Wno-undefined-var-template -O3  -DNoRepository -ftemplate-depth-100  -IlnInclude -I. -I/Users/sensei/Downloads/from-git/OpenFOAM-5.x/src/OpenFOAM/lnInclude -I/Users/sensei/Downloads/from-git/OpenFOAM-5.x/src/OSspecific/POSIX/lnInclude   -fPIC -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -c UPstream.C -o /Users/sensei/Downloads/from-git/OpenFOAM-5.x/platforms/darwin64ClangDPInt32Opt/src/Pstream/dummy/UPstream.o
In file included from UPstream.C:26:
In file included from /Users/sensei/Downloads/from-git/OpenFOAM-5.x/src/OpenFOAM/lnInclude/UPstream.H:42:
In file included from /Users/sensei/Downloads/from-git/OpenFOAM-5.x/src/OpenFOAM/lnInclude/labelList.H:47:
In file included from /Users/sensei/Downloads/from-git/OpenFOAM-5.x/src/OpenFOAM/lnInclude/label.H:39:
In file included from /Users/sensei/Downloads/from-git/OpenFOAM-5.x/src/OpenFOAM/lnInclude/int.H:38:
In file included from /Users/sensei/Downloads/from-git/OpenFOAM-5.x/src/OpenFOAM/lnInclude/int32.H:43:
In file included from /Users/sensei/Downloads/from-git/OpenFOAM-5.x/src/OpenFOAM/lnInclude/word.H:42:
In file included from /Users/sensei/Downloads/from-git/OpenFOAM-5.x/src/OpenFOAM/lnInclude/string.h:51:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/string:470:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/string_view:169:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__string:56:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/algorithm:641:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstring:70:9: error: no member named 'memcpy' in the global namespace
using ::memcpy;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstring:71:9: error: no member named 'memmove' in the global namespace
using ::memmove;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstring:72:9: error: no member named 'strcpy' in the global namespace
using ::strcpy;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstring:73:9: error: no member named 'strncpy' in the global namespace
using ::strncpy;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstring:74:9: error: no member named 'strcat' in the global namespace
using ::strcat;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstring:75:9: error: no member named 'strncat' in the global namespace
using ::strncat;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstring:76:9: error: no member named 'memcmp' in the global namespace
using ::memcmp;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstring:77:9: error: no member named 'strcmp' in the global namespace
using ::strcmp;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstring:78:9: error: no member named 'strncmp' in the global namespace
using ::strncmp;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstring:79:9: error: no member named 'strcoll' in the global namespace; did you
      mean 'strtoll'?
using ::strcoll;
      ~~^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/usr/include/stdlib.h:177:3: note: 'strtoll' declared here
         strtoll(const char *__str, char **__endptr, int __base);
         ^
In file included from UPstream.C:26:
In file included from /Users/sensei/Downloads/from-git/OpenFOAM-5.x/src/OpenFOAM/lnInclude/UPstream.H:42:
In file included from /Users/sensei/Downloads/from-git/OpenFOAM-5.x/src/OpenFOAM/lnInclude/labelList.H:47:
In file included from /Users/sensei/Downloads/from-git/OpenFOAM-5.x/src/OpenFOAM/lnInclude/label.H:39:
In file included from /Users/sensei/Downloads/from-git/OpenFOAM-5.x/src/OpenFOAM/lnInclude/int.H:38:
In file included from /Users/sensei/Downloads/from-git/OpenFOAM-5.x/src/OpenFOAM/lnInclude/int32.H:43:
In file included from /Users/sensei/Downloads/from-git/OpenFOAM-5.x/src/OpenFOAM/lnInclude/word.H:42:
In file included from /Users/sensei/Downloads/from-git/OpenFOAM-5.x/src/OpenFOAM/lnInclude/string.h:51:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/string:470:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/string_view:169:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__string:56:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/algorithm:641:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstring:80:9: error: no member named 'strxfrm' in the global namespace
using ::strxfrm;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstring:81:9: error: no member named 'memchr' in the global namespace
using ::memchr;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstring:82:9: error: no member named 'strchr' in the global namespace
using ::strchr;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstring:83:9: error: no member named 'strcspn' in the global namespace
using ::strcspn;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstring:84:9: error: no member named 'strpbrk' in the global namespace
using ::strpbrk;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstring:85:9: error: no member named 'strrchr' in the global namespace
using ::strrchr;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstring:86:9: error: no member named 'strspn' in the global namespace
using ::strspn;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstring:87:9: error: no member named 'strstr' in the global namespace
using ::strstr;
      ~~^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstring:89:9: error: no member named 'strtok' in the global namespace
using ::strtok;
      ~~^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make: *** [/Users/sensei/Downloads/from-git/OpenFOAM-5.x/platforms/darwin64ClangDPInt32Opt/src/Pstream/dummy/UPstream.o] Error 1
I suspect I might have missed another step here...
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Old   June 6, 2018, 06:08
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Quote:
Originally Posted by fmilicchio View Post
I suspect I might have missed another step here...
The OS was completely messed up, now it works on a clean install.

Thanks for the patches!
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Old   June 6, 2018, 08:12
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Hi,

Glad it works now. Could you elaborate on

Quote:
Originally Posted by fmilicchio View Post
However, might I suggest this? The README should contain a clear list of links to the wiki and a description, since a ChangeLog isn't welcoming to the restless soul: we're all tired and distracted, the wiki button isn't really that visible, we usually go down to the README. The main information point is there, in the README, which of course can contain a link to a ChangeLog.
The first line of README.md is

Quote:
Patches for OpenFOAM(R) compilation on macOS. Detailed installation instructions can be found in wiki.
with word wiki being a link. Make it bold? Increase font size?
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Old   June 7, 2018, 04:43
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Quote:
Originally Posted by alexeym View Post
Glad it works now. Could you elaborate on
Sure. I never actually clean-installed macOS on this laptop, and probably years of updates with 32-64 bits libraries mixed took a toll. I started dealing with weird libraries issues, for instance the Accelerate framework could link but the executable complained about versions of LAPACK and BLAS. I could not correct the bug, if it ever was mine, so I formatted the drive and re-installed macOS, solving the issue with OpenFOAM's links (but not with Accelerate, unfortunately).

Quote:
with word wiki being a link. Make it bold? Increase font size?
From a UX standpoint, font weights or styles are not enough usually: I would suggest a bulleted list of links with clear descriptions, for instance (note "macOS" also in the title):

OpenFOAM(R) on macOS

Patches for OpenFOAM(R) compilation on macOS.
Disclaimer

This offering is not approved or endorsed by OpenCFD Limited, producer and distributor of the OpenFOAM software via www.openfoam.com, and owner of the OPENFOAM(R) and OpenCFD(R) trade marks.

Acknowledgement

OPENFOAM(R) is a registered trade mark of OpenCFD Limited, producer and distributor of the OpenFOAM software via www.openfoam.com.

PS. I would also stress much more in the installation page that a case-sensitive file system is mandatory, that is why you say to create a case-sensitive DMG. Usually macOS users don't know that APFS or HFS+ are by default case-insensitive and case-preserving on macOS.
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Old   March 27, 2020, 14:45
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Hi fmilicchio,
when you say "clean install", what do you mean? I am asking because i have the same error
" /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/cstring:89:9: error: no member named 'strtok' in the global namespace "
as you did in your last response (that you missed a step). Do you mean that you followed the whole process from the beginning?
- Delete Openfoam folder
- download .tgz files,
- make the corrections that were mentioned in your posts
- source the environment
- ./Allwmake
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