./Allwmake fails to find the location for including phaseSystem.H etc

[djinnome]

Hi folks,

I am using Ubuntu 18.04 and
After installing openfoam2406 through apt-get and starting it up, I created a python virtual environment for bird called openfoam.

$ git clone https://github.com/NREL/BioReactorDesign
$ cd BioReactorDesign
$ pyenv virtualenv 3.10.16 openfoam
$ pyenv local openfoam
$ pip install uv
$ uv pip install -e .
Using Python 3.10.16 environment at: /home/zuck016/.pyenv/versions/3.10.16/envs/openfoam
Resolved 28 packages in 1.71s
      Built nrel-bird @ file:///home/zuck016/Projects/BioReactorDesign
Prepared 1 package in 1.42s
Uninstalled 1 package in 0.94ms
Installed 1 package in 1ms
 ~ nrel-bird==0.0.18 (from file:///home/zuck016/Projects/BioReactorDesign)

Then I tried to make birdmultiphaseEulerFoam but it fails to link the local files correctly and fails. Is this because I have a super old version of Ubuntu? Or is it something else?

$ cd ./OFsolvers/birdmultiphaseEulerFoam
$ openfoam2406 --help

Usage: openfoam [OPTION] [[--] application ...]

options:
  -c                Shell commands read from the first non-option argument
  -Dkey[=value]     Define key/value to pass as a preference
  -sp               Single precision
  -dp               Double precision
  -spdp             Mixed single/double precision
  -int32            Label-size 32
  -int64            Label-size 64
  -etc=DIR          Additional project etc/ directory
  -prefix=DIR       Alternative OpenFOAM project directory
  -show-api         Print META-INFO api value and exit
  -show-patch       Print META-INFO patch value and exit
  -show-prefix      Print project directory and exit
  -test-tutorial    Forward arguments to bin/foamTestTutorial
  -init=FILE        Alternative initialization file (expert option)
  -version          Same as -show-api
  -verbose          Set FOAM_VERBOSE=true (interactive only)
  --                The end of option processing.
                    An argument of - or / is equivalent to --.
  -help             Print the usage

Open an interactive bash session with an OpenFOAM environment,
or run an OpenFOAM application (with arguments) after first sourcing
the OpenFOAM etc/bashrc file from the project directory:
(/usr/lib/openfoam/openfoam2406)

For a persistent OpenFOAM environment, the following can be added to your
~/.bashrc file:

    source /usr/lib/openfoam/openfoam2406/etc/bashrc

For more information: www.openfoam.com

$ openfoam2406 
openfoam = /usr/lib/openfoam/openfoam2406

 * Using:     OpenFOAM-v2406 (2406) - visit www.openfoam.com
 * Build:     _9bfe8264-20241212 (patch=241212)
 * Arch:      label=32;scalar=64
 * Platform:  linux64GccDPInt32Opt (mpi=sys-openmpi)

OpenFOAM shell session - use 'exit' to quit

openfoam2406:~/Projects/BioReactorDesign/OFsolvers/birdmultiphaseEulerFoam/
zuck016$ ls
Allwclean  functionObjects  interfacialCompositionModels  multiphaseCompressibleMomentumTransportModels  multiphaseReactions  README.md
Allwmake   include          interfacialModels             multiphaseEulerFoam                            phaseSystems
openfoam2406:~/Projects/BioReactorDesign/OFsolvers/birdmultiphaseEulerFoam/
zuck016$ ./Allwclean 
wclean libso phaseSystems
wclean libso interfacialModels
wclean libso interfacialCompositionModels
wclean libso multiphaseCompressibleMomentumTransportModels
wclean libso multiphaseSystems
wclean libso functionObjects
openfoam2406:~/Projects/BioReactorDesign/OFsolvers/birdmultiphaseEulerFoam/
zuck016$ ./Allwmake 
TargetType: 
Compiling enabled on 4 cores
wmake functionObjects
    ln: ./lnInclude
Making dependencies: disengagement.C
Making dependencies: phaseMap.C
Making dependencies: sizeDistribution.C
Making dependencies: phaseForces.C
wmkdepend: could not open 'wmkdepend: could not open 'phaseSystem.H' for source file 'phaseForces/phaseForces.C': No such file or directory
populationBalanceModel.H' for source file 'sizeDistribution/sizeDistribution.C': No such file or directory
wmkdepend: could not open 'setWriter.H' for source file 'sizeDistribution/sizeDistribution.C': No such file or directory
wmkdepend: could not open 'phaseSystem.H' for source file 'phaseMap/phaseMap.C': No such file or directory
wmkdepend: could not open 'phaseSystem.H' for source file 'disengagement/disengagement.C': No such file or directory
wmkdepend: could not open 'BlendedInterfacialModel.H' for source file 'phaseForces/phaseForces.C': No such file or directory
wmkdepend: could not open 'dragModel.H' for source file 'phaseForces/phaseForces.C': No such file or directory
wmkdepend: could not open 'virtualMassModel.H' for source file 'phaseForces/phaseForces.C': No such file or directory
wmkdepend: could not open 'liftModel.H' for source file 'phaseForces/phaseForces.C': No such file or directory
wmkdepend: could not open 'wallLubricationModel.H' for source file 'phaseForces/phaseForces.C': No such file or directory
wmkdepend: could not open 'turbulentDispersionModel.H' for source file 'phaseForces/phaseForces.C': No such file or directory
g++ -std=c++14 -m64 -pthread -DOPENFOAM=2406 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -Wextra -Wold-style-cast -Wnon-virtual-dtor -Wno-unused-parameter -Wno-invalid-offsetof -Wno-attributes -Wno-unknown-pragmas -O3  -DNoRepository -ftemplate-depth-100  -I../phaseSystems/lnInclude -I../interfacialModels/lnInclude -I/usr/lib/openfoam/openfoam2406/src/transportModels/lnInclude -I/usr/lib/openfoam/openfoam2406/src/thermophysicalModels/basic/lnInclude -I/usr/lib/openfoam/openfoam2406/src/MomentumTransportModels/momentumTransportModels/lnInclude -I/usr/lib/openfoam/openfoam2406/src/MomentumTransportModels/compressible/lnInclude -I/usr/lib/openfoam/openfoam2406/src/MomentumTransportModels/phaseCompressible/lnInclude -I/usr/lib/openfoam/openfoam2406/src/finiteVolume/lnInclude -I/usr/lib/openfoam/openfoam2406/src/meshTools/lnInclude -I/usr/lib/openfoam/openfoam2406/src/fileFormats/lnInclude -I/usr/lib/openfoam/openfoam2406/src/functionObjects/field/lnInclude -I/usr/lib/openfoam/openfoam2406/src/sampling/lnInclude -iquote. -IlnInclude -I/usr/lib/openfoam/openfoam2406/src/OpenFOAM/lnInclude -I/usr/lib/openfoam/openfoam2406/src/OSspecific/POSIX/lnInclude   -fPIC -c sizeDistribution/sizeDistribution.C -o Make/linux64GccDPInt32Opt/sizeDistribution/sizeDistribution.o
g++ -std=c++14 -m64 -pthread -DOPENFOAM=2406 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -Wextra -Wold-style-cast -Wnon-virtual-dtor -Wno-unused-parameter -Wno-invalid-offsetof -Wno-attributes -Wno-unknown-pragmas -O3  -DNoRepository -ftemplate-depth-100  -I../phaseSystems/lnInclude -I../interfacialModels/lnInclude -I/usr/lib/openfoam/openfoam2406/src/transportModels/lnInclude -I/usr/lib/openfoam/openfoam2406/src/thermophysicalModels/basic/lnInclude -I/usr/lib/openfoam/openfoam2406/src/MomentumTransportModels/momentumTransportModels/lnInclude -I/usr/lib/openfoam/openfoam2406/src/MomentumTransportModels/compressible/lnInclude -I/usr/lib/openfoam/openfoam2406/src/MomentumTransportModels/phaseCompressible/lnInclude -I/usr/lib/openfoam/openfoam2406/src/finiteVolume/lnInclude -I/usr/lib/openfoam/openfoam2406/src/meshTools/lnInclude -I/usr/lib/openfoam/openfoam2406/src/fileFormats/lnInclude -I/usr/lib/openfoam/openfoam2406/src/functionObjects/field/lnInclude -I/usr/lib/openfoam/openfoam2406/src/sampling/lnInclude -iquote. -IlnInclude -I/usr/lib/openfoam/openfoam2406/src/OpenFOAM/lnInclude -I/usr/lib/openfoam/openfoam2406/src/OSspecific/POSIX/lnInclude   -fPIC -c phaseForces/phaseForces.C -o Make/linux64GccDPInt32Opt/phaseForces/phaseForces.o
g++ -std=c++14 -m64 -pthread -DOPENFOAM=2406 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -Wextra -Wold-style-cast -Wnon-virtual-dtor -Wno-unused-parameter -Wno-invalid-offsetof -Wno-attributes -Wno-unknown-pragmas -O3  -DNoRepository -ftemplate-depth-100  -I../phaseSystems/lnInclude -I../interfacialModels/lnInclude -I/usr/lib/openfoam/openfoam2406/src/transportModels/lnInclude -I/usr/lib/openfoam/openfoam2406/src/thermophysicalModels/basic/lnInclude -I/usr/lib/openfoam/openfoam2406/src/MomentumTransportModels/momentumTransportModels/lnInclude -I/usr/lib/openfoam/openfoam2406/src/MomentumTransportModels/compressible/lnInclude -I/usr/lib/openfoam/openfoam2406/src/MomentumTransportModels/phaseCompressible/lnInclude -I/usr/lib/openfoam/openfoam2406/src/finiteVolume/lnInclude -I/usr/lib/openfoam/openfoam2406/src/meshTools/lnInclude -I/usr/lib/openfoam/openfoam2406/src/fileFormats/lnInclude -I/usr/lib/openfoam/openfoam2406/src/functionObjects/field/lnInclude -I/usr/lib/openfoam/openfoam2406/src/sampling/lnInclude -iquote. -IlnInclude -I/usr/lib/openfoam/openfoam2406/src/OpenFOAM/lnInclude -I/usr/lib/openfoam/openfoam2406/src/OSspecific/POSIX/lnInclude   -fPIC -c phaseMap/phaseMap.C -o Make/linux64GccDPInt32Opt/phaseMap/phaseMap.o
g++ -std=c++14 -m64 -pthread -DOPENFOAM=2406 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -Wextra -Wold-style-cast -Wnon-virtual-dtor -Wno-unused-parameter -Wno-invalid-offsetof -Wno-attributes -Wno-unknown-pragmas -O3  -DNoRepository -ftemplate-depth-100  -I../phaseSystems/lnInclude -I../interfacialModels/lnInclude -I/usr/lib/openfoam/openfoam2406/src/transportModels/lnInclude -I/usr/lib/openfoam/openfoam2406/src/thermophysicalModels/basic/lnInclude -I/usr/lib/openfoam/openfoam2406/src/MomentumTransportModels/momentumTransportModels/lnInclude -I/usr/lib/openfoam/openfoam2406/src/MomentumTransportModels/compressible/lnInclude -I/usr/lib/openfoam/openfoam2406/src/MomentumTransportModels/phaseCompressible/lnInclude -I/usr/lib/openfoam/openfoam2406/src/finiteVolume/lnInclude -I/usr/lib/openfoam/openfoam2406/src/meshTools/lnInclude -I/usr/lib/openfoam/openfoam2406/src/fileFormats/lnInclude -I/usr/lib/openfoam/openfoam2406/src/functionObjects/field/lnInclude -I/usr/lib/openfoam/openfoam2406/src/sampling/lnInclude -iquote. -IlnInclude -I/usr/lib/openfoam/openfoam2406/src/OpenFOAM/lnInclude -I/usr/lib/openfoam/openfoam2406/src/OSspecific/POSIX/lnInclude   -fPIC -c disengagement/disengagement.C -o Make/linux64GccDPInt32Opt/disengagement/disengagement.o
In file included from phaseMap/phaseMap.C:26:0:
phaseMap/phaseMap.H:61:10: fatal error: phaseSystem.H: No such file or directory
 #include "phaseSystem.H"
          ^~~~~~~~~~~~~~~
compilation terminated.
In file included from phaseForces/phaseForces.C:26:0:
phaseForces/phaseForces.H:71:10: fatal error: phaseSystem.H: No such file or directory
 #include "phaseSystem.H"
          ^~~~~~~~~~~~~~~
compilation terminated.
/usr/lib/openfoam/openfoam2406/wmake/rules/General/transform:37: recipe for target 'Make/linux64GccDPInt32Opt/phaseMap/phaseMap.o' failed
make: *** [Make/linux64GccDPInt32Opt/phaseMap/phaseMap.o] Error 1
make: *** Waiting for unfinished jobs....
/usr/lib/openfoam/openfoam2406/wmake/rules/General/transform:37: recipe for target 'Make/linux64GccDPInt32Opt/phaseForces/phaseForces.o' failed
make: *** [Make/linux64GccDPInt32Opt/phaseForces/phaseForces.o] Error 1
In file included from disengagement/disengagement.C:26:0:
disengagement/disengagement.H:86:10: fatal error: phaseSystem.H: No such file or directory
 #include "phaseSystem.H"
          ^~~~~~~~~~~~~~~
compilation terminated.
/usr/lib/openfoam/openfoam2406/wmake/rules/General/transform:37: recipe for target 'Make/linux64GccDPInt32Opt/disengagement/disengagement.o' failed
make: *** [Make/linux64GccDPInt32Opt/disengagement/disengagement.o] Error 1
In file included from sizeDistribution/sizeDistribution.C:26:0:
sizeDistribution/sizeDistribution.H:77:10: fatal error: populationBalanceModel.H: No such file or directory
 #include "populationBalanceModel.H"
          ^~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
/usr/lib/openfoam/openfoam2406/wmake/rules/General/transform:37: recipe for target 'Make/linux64GccDPInt32Opt/sizeDistribution/sizeDistribution.o' failed
make: *** [Make/linux64GccDPInt32Opt/sizeDistribution/sizeDistribution.o] Error 1
openfoam2406:~/Projects/BioReactorDesign/OFsolvers/birdmultiphaseEulerFoam/
zuck016$ 

[fmuni]

Hi,
Our OpenFOAM solvers require OpenFOAM-9 to compile. They don’t compile with OpenFOAM-v2406 or other ESI versions. We might update that in the future though.

[fmuni]

Actually, it might be useful to start making some progresses on this update.
If you like, you can start having a look into it. If you get the solver to compile with OF2406, we could merge your work in the repo.

[djinnome]

Hi folks, thanks for responding so quickly. I got the birdmultiphaseEulerFoam working under OpenFOAM9, but when I tried to make bdoFoam I got the following error. Please advise.

$ cd ~/Projects/BioReactorDesign/OFsolvers/bdoFoam
$ .  /opt/openfoam9/etc/bashrc
zuck016@agilebiocyc:~/Projects/BioReactorDesign/OFsolvers/bdoFoam$ ./Allwclean 
wclean libso twoPhaseSystem
wclean libso twoPhaseCompressibleTurbulenceModels
zuck016@agilebiocyc:~/Projects/BioReactorDesign/OFsolvers/bdoFoam$ ./Allwmake
Allwmake /home/zuck016/Projects/BioReactorDesign/OFsolvers/bdoFoam
wmake twoPhaseSystem
wmakeLnIncludeAll: running wmakeLnInclude on dependent libraries:
    wmakeLnInclude error: base directory ../../interfacialModels/ does not exist
    wmakeLnInclude error: base directory ../../interfacialCompositionModels/ does not exist
    wmakeLnInclude error: base directory ../../phaseSystems/ does not exist
    wmakeLnInclude: linking include files to ../twoPhaseCompressibleTurbulenceModels//lnInclude
    wmakeLnInclude error: base directory ../../derivedFvPatchFields/ does not exist
    wmakeLnInclude error: base directory /opt/openfoam9/src/transportModels/compressible/ does not exist
    wmakeLnInclude error: base directory /opt/openfoam9/src/TurbulenceModels/turbulenceModels/ does not exist
    wmakeLnInclude error: base directory /opt/openfoam9/src/TurbulenceModels/compressible/ does not exist
    wmakeLnInclude error: base directory /opt/openfoam9/src/TurbulenceModels/phaseCompressible/ does not exist
wmakeLnInclude: linking include files to ./lnInclude
Making dependency list for source file twoPhaseSystems.C
could not open file phaseSystem.H for source file twoPhaseSystems.C due to No such file or directory
could not open file MomentumTransferPhaseSystem.H for source file twoPhaseSystems.C due to No such file or directory
could not open file OneResistanceHeatTransferPhaseSystem.H for source file twoPhaseSystems.C due to No such file or directory
could not open file TwoResistanceHeatTransferPhaseSystem.H for source file twoPhaseSystems.C due to No such file or directory
could not open file PhaseTransferPhaseSystem.H for source file twoPhaseSystems.C due to No such file or directory
could not open file PopulationBalancePhaseSystem.H for source file twoPhaseSystems.C due to No such file or directory
could not open file InterfaceCompositionPhaseChangePhaseSystem.H for source file twoPhaseSystems.C due to No such file or directory
could not open file ThermalPhaseChangePhaseSystem.H for source file twoPhaseSystems.C due to No such file or directory
Making dependency list for source file newTwoPhaseSystem.C
could not open file phaseSystem.H for source file newTwoPhaseSystem.C due to No such file or directory
Making dependency list for source file twoPhaseSystem.C
could not open file dragModel.H for source file twoPhaseSystem.C due to No such file or directory
could not open file virtualMassModel.H for source file twoPhaseSystem.C due to No such file or directory
could not open file phaseSystem.H for source file twoPhaseSystem.C due to No such file or directory
Making dependency list for source file wallBoiling.C
could not open file phaseCompressibleTurbulenceModel.H for source file diameterModels/IATE/IATEsources/wallBoiling/wallBoiling.C due to No such file or directory
could not open file alphatWallBoilingWallFunctionFvPatchScalarField.H for source file diameterModels/IATE/IATEsources/wallBoiling/wallBoiling.C due to No such file or directory
could not open file diameterModel.H for source file diameterModels/IATE/IATEsources/wallBoiling/wallBoiling.C due to No such file or directory
could not open file phaseSystem.H for source file diameterModels/IATE/IATEsources/wallBoiling/wallBoiling.C due to No such file or directory
Making dependency list for source file phaseChange.C
could not open file phaseSystem.H for source file diameterModels/IATE/IATEsources/phaseChange/phaseChange.C due to No such file or directory
could not open file ThermalPhaseChangePhaseSystem.H for source file diameterModels/IATE/IATEsources/phaseChange/phaseChange.C due to No such file or directory
could not open file MomentumTransferPhaseSystem.H for source file diameterModels/IATE/IATEsources/phaseChange/phaseChange.C due to No such file or directory
could not open file diameterModel.H for source file diameterModels/IATE/IATEsources/phaseChange/phaseChange.C due to No such file or directory
Making dependency list for source file randomCoalescence.C
could not open file diameterModel.H for source file diameterModels/IATE/IATEsources/randomCoalescence/randomCoalescence.C due to No such file or directory
could not open file phaseSystem.H for source file diameterModels/IATE/IATEsources/randomCoalescence/randomCoalescence.C due to No such file or directory
Making dependency list for source file turbulentBreakUp.C
could not open file diameterModel.H for source file diameterModels/IATE/IATEsources/turbulentBreakUp/turbulentBreakUp.C due to No such file or directory
could not open file phaseSystem.H for source file diameterModels/IATE/IATEsources/turbulentBreakUp/turbulentBreakUp.C due to No such file or directory
Making dependency list for source file wakeEntrainmentCoalescence.C
could not open file diameterModel.H for source file diameterModels/IATE/IATEsources/wakeEntrainmentCoalescence/wakeEntrainmentCoalescence.C due to No such file or directory
could not open file phaseSystem.H for source file diameterModels/IATE/IATEsources/wakeEntrainmentCoalescence/wakeEntrainmentCoalescence.C due to No such file or directory
Making dependency list for source file IATEsource.C
could not open file phaseCompressibleTurbulenceModel.H for source file diameterModels/IATE/IATEsources/IATEsource/IATEsource.C due to No such file or directory
could not open file diameterModel.H for source file diameterModels/IATE/IATEsources/IATEsource/IATEsource.C due to No such file or directory
could not open file phaseSystem.H for source file diameterModels/IATE/IATEsources/IATEsource/IATEsource.C due to No such file or directory
Making dependency list for source file IATE.C
could not open file fvOptions.H for source file diameterModels/IATE/IATE.C due to No such file or directory
could not open file diameterModel.H for source file diameterModels/IATE/IATE.C due to No such file or directory
could not open file phaseSystem.H for source file diameterModels/IATE/IATE.C due to No such file or directory
g++ -std=c++14 -m64 -Dlinux64 -DWM_ARCH_OPTION=64 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -Wextra -Wold-style-cast -Wnon-virtual-dtor -Wno-unused-parameter -Wno-invalid-offsetof -Wno-attributes -O3  -DNoRepository -ftemplate-depth-100 -I../../interfacialModels/lnInclude -I../../interfacialCompositionModels/lnInclude -I../../phaseSystems/lnInclude -I../twoPhaseCompressibleTurbulenceModels/lnInclude -I../../derivedFvPatchFields/lnInclude -I/opt/openfoam9/src/thermophysicalModels/basic/lnInclude -I/opt/openfoam9/src/thermophysicalModels/specie/lnInclude -I/opt/openfoam9/src/thermophysicalModels/reactionThermo/lnInclude -I/opt/openfoam9/src/transportModels/compressible/lnInclude -I/opt/openfoam9/src/TurbulenceModels/turbulenceModels/lnInclude -I/opt/openfoam9/src/TurbulenceModels/compressible/lnInclude -I/opt/openfoam9/src/TurbulenceModels/phaseCompressible/lnInclude -I/opt/openfoam9/src/combustionModels/lnInclude -I/opt/openfoam9/src/finiteVolume/lnInclude -I/opt/openfoam9/src/meshTools/lnInclude -I/opt/openfoam9/src/sampling/lnInclude -IlnInclude -I. -I/opt/openfoam9/src/OpenFOAM/lnInclude -I/opt/openfoam9/src/OSspecific/POSIX/lnInclude   -fPIC -c diameterModels/IATE/IATE.C -o Make/linux64GccDPInt32Opt/diameterModels/IATE/IATE.o
In file included from diameterModels/IATE/IATE.C:26:0:
diameterModels/IATE/IATE.H:50:10: fatal error: diameterModel.H: No such file or directory
 #include "diameterModel.H"
          ^~~~~~~~~~~~~~~~~
compilation terminated.
/opt/openfoam9/wmake/rules/General/transform:25: recipe for target 'Make/linux64GccDPInt32Opt/diameterModels/IATE/IATE.o' failed
make: *** [Make/linux64GccDPInt32Opt/diameterModels/IATE/IATE.o] Error 1
zuck016@agilebiocyc:~/Projects/BioReactorDesign/OFsolvers/bdoFoam$ 

[fmuni]

bdoFoam requires openfoam-6. We still need to update it.

[djinnome]

I successfully installed openfoam6, but bdoFoam still does not compile:

$ sudo apt-get install openfoam6
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following packages were automatically installed and are no longer required:
  libptscotch-6.0 libptscotch-dev libscotch-6.0 libscotch-dev openfoam-selector openfoam2406-tutorials
Use 'sudo apt autoremove' to remove them.
The following NEW packages will be installed:
  openfoam6
0 upgraded, 1 newly installed, 0 to remove and 2 not upgraded.
Need to get 83.6 MB of archives.
After this operation, 546 MB of additional disk space will be used.
Get:1 http://downloads.sourceforge.net/project/foam/foam/ubuntu bionic/main amd64 openfoam6 amd64 20190620 [83.6 MB]
Fetched 83.6 MB in 4s (20.6 MB/s)    
Selecting previously unselected package openfoam6.
(Reading database ... 374083 files and directories currently installed.)
Preparing to unpack .../openfoam6_20190620_amd64.deb ...
Unpacking openfoam6 (20190620) ...
Setting up openfoam6 (20190620) ...

** To use OpenFOAM please add
**
**    . /opt/openfoam6/etc/bashrc
**
** To your ~/.bashrc

I then activated OpenFoam-6 and tried to run Allwmake

$ . /opt/openfoam6/etc/bashrc
(bird) zuck016@agilebiocyc:~/Projects/BioReactorDesign/OFsolvers/bdoFoam$ ./Allwclean 
wclean libso twoPhaseSystem
wclean libso twoPhaseCompressibleTurbulenceModels
(bird) zuck016@agilebiocyc:~/Projects/BioReactorDesign/OFsolvers/bdoFoam$ ./Allwmake
Allwmake /home/zuck016/Projects/BioReactorDesign/OFsolvers/bdoFoam
wmake twoPhaseSystem
wmakeLnIncludeAll: running wmakeLnInclude on dependent libraries:
    wmakeLnInclude error: base directory ../../interfacialModels/ does not exist
    wmakeLnInclude error: base directory ../../interfacialCompositionModels/ does not exist
    wmakeLnInclude error: base directory ../../phaseSystems/ does not exist
    wmakeLnInclude: linking include files to ../twoPhaseCompressibleTurbulenceModels//lnInclude
    wmakeLnInclude error: base directory ../../derivedFvPatchFields/ does not exist
wmakeLnInclude: linking include files to ./lnInclude
Making dependency list for source file twoPhaseSystems.C
could not open file phaseSystem.H for source file twoPhaseSystems.C due to No such file or directory
could not open file MomentumTransferPhaseSystem.H for source file twoPhaseSystems.C due to No such file or directory
could not open file OneResistanceHeatTransferPhaseSystem.H for source file twoPhaseSystems.C due to No such file or directory
could not open file TwoResistanceHeatTransferPhaseSystem.H for source file twoPhaseSystems.C due to No such file or directory
could not open file PhaseTransferPhaseSystem.H for source file twoPhaseSystems.C due to No such file or directory
could not open file PopulationBalancePhaseSystem.H for source file twoPhaseSystems.C due to No such file or directory
could not open file InterfaceCompositionPhaseChangePhaseSystem.H for source file twoPhaseSystems.C due to No such file or directory
could not open file ThermalPhaseChangePhaseSystem.H for source file twoPhaseSystems.C due to No such file or directory
Making dependency list for source file newTwoPhaseSystem.C
could not open file phaseSystem.H for source file newTwoPhaseSystem.C due to No such file or directory
Making dependency list for source file twoPhaseSystem.C
could not open file dragModel.H for source file twoPhaseSystem.C due to No such file or directory
could not open file virtualMassModel.H for source file twoPhaseSystem.C due to No such file or directory
could not open file phaseSystem.H for source file twoPhaseSystem.C due to No such file or directory
Making dependency list for source file wallBoiling.C
could not open file phaseCompressibleTurbulenceModel.H for source file diameterModels/IATE/IATEsources/wallBoiling/wallBoiling.C due to No such file or directory
could not open file alphatWallBoilingWallFunctionFvPatchScalarField.H for source file diameterModels/IATE/IATEsources/wallBoiling/wallBoiling.C due to No such file or directory
could not open file diameterModel.H for source file diameterModels/IATE/IATEsources/wallBoiling/wallBoiling.C due to No such file or directory
could not open file phaseSystem.H for source file diameterModels/IATE/IATEsources/wallBoiling/wallBoiling.C due to No such file or directory
Making dependency list for source file phaseChange.C
could not open file phaseSystem.H for source file diameterModels/IATE/IATEsources/phaseChange/phaseChange.C due to No such file or directory
could not open file ThermalPhaseChangePhaseSystem.H for source file diameterModels/IATE/IATEsources/phaseChange/phaseChange.C due to No such file or directory
could not open file MomentumTransferPhaseSystem.H for source file diameterModels/IATE/IATEsources/phaseChange/phaseChange.C due to No such file or directory
could not open file diameterModel.H for source file diameterModels/IATE/IATEsources/phaseChange/phaseChange.C due to No such file or directory
Making dependency list for source file randomCoalescence.C
could not open file diameterModel.H for source file diameterModels/IATE/IATEsources/randomCoalescence/randomCoalescence.C due to No such file or directory
could not open file phaseSystem.H for source file diameterModels/IATE/IATEsources/randomCoalescence/randomCoalescence.C due to No such file or directory
Making dependency list for source file turbulentBreakUp.C
could not open file diameterModel.H for source file diameterModels/IATE/IATEsources/turbulentBreakUp/turbulentBreakUp.C due to No such file or directory
could not open file phaseSystem.H for source file diameterModels/IATE/IATEsources/turbulentBreakUp/turbulentBreakUp.C due to No such file or directory
Making dependency list for source file wakeEntrainmentCoalescence.C
could not open file diameterModel.H for source file diameterModels/IATE/IATEsources/wakeEntrainmentCoalescence/wakeEntrainmentCoalescence.C due to No such file or directory
could not open file phaseSystem.H for source file diameterModels/IATE/IATEsources/wakeEntrainmentCoalescence/wakeEntrainmentCoalescence.C due to No such file or directory
Making dependency list for source file IATEsource.C
could not open file phaseCompressibleTurbulenceModel.H for source file diameterModels/IATE/IATEsources/IATEsource/IATEsource.C due to No such file or directory
could not open file diameterModel.H for source file diameterModels/IATE/IATEsources/IATEsource/IATEsource.C due to No such file or directory
could not open file phaseSystem.H for source file diameterModels/IATE/IATEsources/IATEsource/IATEsource.C due to No such file or directory
Making dependency list for source file IATE.C
could not open file diameterModel.H for source file diameterModels/IATE/IATE.C due to No such file or directory
could not open file phaseSystem.H for source file diameterModels/IATE/IATE.C due to No such file or directory
g++ -std=c++11 -m64 -Dlinux64 -DWM_ARCH_OPTION=64 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -Wextra -Wold-style-cast -Wnon-virtual-dtor -Wno-unused-parameter -Wno-invalid-offsetof -Wno-attributes -O3  -DNoRepository -ftemplate-depth-100 -I../../interfacialModels/lnInclude -I../../interfacialCompositionModels/lnInclude -I../../phaseSystems/lnInclude -I../twoPhaseCompressibleTurbulenceModels/lnInclude -I../../derivedFvPatchFields/lnInclude -I/opt/openfoam6/src/thermophysicalModels/basic/lnInclude -I/opt/openfoam6/src/thermophysicalModels/specie/lnInclude -I/opt/openfoam6/src/thermophysicalModels/reactionThermo/lnInclude -I/opt/openfoam6/src/transportModels/compressible/lnInclude -I/opt/openfoam6/src/TurbulenceModels/turbulenceModels/lnInclude -I/opt/openfoam6/src/TurbulenceModels/compressible/lnInclude -I/opt/openfoam6/src/TurbulenceModels/phaseCompressible/lnInclude -I/opt/openfoam6/src/combustionModels/lnInclude -I/opt/openfoam6/src/finiteVolume/lnInclude -I/opt/openfoam6/src/meshTools/lnInclude -I/opt/openfoam6/src/sampling/lnInclude -IlnInclude -I. -I/opt/openfoam6/src/OpenFOAM/lnInclude -I/opt/openfoam6/src/OSspecific/POSIX/lnInclude   -fPIC -c diameterModels/IATE/IATE.C -o Make/linux64GccDPInt32Opt/diameterModels/IATE/IATE.o
In file included from diameterModels/IATE/IATE.C:26:0:
diameterModels/IATE/IATE.H:50:10: fatal error: diameterModel.H: No such file or directory
 #include "diameterModel.H"
          ^~~~~~~~~~~~~~~~~
compilation terminated.
/opt/openfoam6/wmake/rules/General/transform:25: recipe for target 'Make/linux64GccDPInt32Opt/diameterModels/IATE/IATE.o' failed
make: *** [Make/linux64GccDPInt32Opt/diameterModels/IATE/IATE.o] Error 1
(bird) zuck016@agilebiocyc:~/Projects/BioReactorDesign/OFsolvers/bdoFoam$ 

[hsitaram]

Can you check this issue from earlier. #32
The compilation instructions are more clear here. I will add this to the readme right away. Thank you for your interest