[daily]

I have OF running in a Docker container. I want to make a small change to reactingFoam.C. However, when I try to run wmake, it doesn't do anything. Is tyhis a Docekr problem and is there a solution.

[hyFoam]

Hi,

1) Have you created a copy of the solver directory into your user directory?
2) Have you edited Make/files to

reactingFoam.C

EXE = $(FOAM_USER_APPBIN)/myreactingFoam

and run

wclean
wmake

Cheers,
Vincent

[daily]

Vicent,

Thanks for the suggestion. I copied the solver directory into my user directory as you suggested. The files file is as you suggested. I then ran wclean and wmake (in my user directory). The result is listed below. Apparently there is a permissions issue when trying to write the binary.

Thanks for any suggestions.

John


[ofuser@480bb0f83044 reactingFoam]$ wmake
Making dependency list for source file reactingFoam.C
g++ -std=c++11 -m64 -DOPENFOAM=1806 -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 -Wno-unknown-pragmas -O3 -DNoRepository -ftemplate-depth-100 -I/opt/OpenFOAM/OpenFOAM-v1806/src/finiteVolume/lnInclude -I/opt/OpenFOAM/OpenFOAM-v1806/src/meshTools/lnInclude -I/opt/OpenFOAM/OpenFOAM-v1806/src/sampling/lnInclude -I/opt/OpenFOAM/OpenFOAM-v1806/src/TurbulenceModels/turbulenceModels/lnInclude -I/opt/OpenFOAM/OpenFOAM-v1806/src/TurbulenceModels/compressible/lnInclude -I/opt/OpenFOAM/OpenFOAM-v1806/src/thermophysicalModels/specie/lnInclude -I/opt/OpenFOAM/OpenFOAM-v1806/src/thermophysicalModels/reactionThermo/lnInclude -I/opt/OpenFOAM/OpenFOAM-v1806/src/transportModels/compressible/lnInclude -I/opt/OpenFOAM/OpenFOAM-v1806/src/thermophysicalModels/basic/lnInclude -I/opt/OpenFOAM/OpenFOAM-v1806/src/thermophysicalModels/chemistryModel/lnInclude -I/opt/OpenFOAM/OpenFOAM-v1806/src/ODE/lnInclude -I/opt/OpenFOAM/OpenFOAM-v1806/src/combustionModels/lnInclude -IlnInclude -I. -I/opt/OpenFOAM/OpenFOAM-v1806/src/OpenFOAM/lnInclude -I/opt/OpenFOAM/OpenFOAM-v1806/src/OSspecific/POSIX/lnInclude -fPIC -c reactingFoam.C -o Make/linux64GccDPInt32Opt/reactingFoam.o
g++ -std=c++11 -m64 -DOPENFOAM=1806 -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 -Wno-unknown-pragmas -O3 -DNoRepository -ftemplate-depth-100 -I/opt/OpenFOAM/OpenFOAM-v1806/src/finiteVolume/lnInclude -I/opt/OpenFOAM/OpenFOAM-v1806/src/meshTools/lnInclude -I/opt/OpenFOAM/OpenFOAM-v1806/src/sampling/lnInclude -I/opt/OpenFOAM/OpenFOAM-v1806/src/TurbulenceModels/turbulenceModels/lnInclude -I/opt/OpenFOAM/OpenFOAM-v1806/src/TurbulenceModels/compressible/lnInclude -I/opt/OpenFOAM/OpenFOAM-v1806/src/thermophysicalModels/specie/lnInclude -I/opt/OpenFOAM/OpenFOAM-v1806/src/thermophysicalModels/reactionThermo/lnInclude -I/opt/OpenFOAM/OpenFOAM-v1806/src/transportModels/compressible/lnInclude -I/opt/OpenFOAM/OpenFOAM-v1806/src/thermophysicalModels/basic/lnInclude -I/opt/OpenFOAM/OpenFOAM-v1806/src/thermophysicalModels/chemistryModel/lnInclude -I/opt/OpenFOAM/OpenFOAM-v1806/src/ODE/lnInclude -I/opt/OpenFOAM/OpenFOAM-v1806/src/combustionModels/lnInclude -IlnInclude -I. -I/opt/OpenFOAM/OpenFOAM-v1806/src/OpenFOAM/lnInclude -I/opt/OpenFOAM/OpenFOAM-v1806/src/OSspecific/POSIX/lnInclude -fPIC -Xlinker --add-needed -Xlinker --no-as-needed Make/linux64GccDPInt32Opt/reactingFoam.o -L/opt/OpenFOAM/OpenFOAM-v1806/platforms/linux64GccDPInt32Opt/lib \
-lfiniteVolume -lfvOptions -lmeshTools -lsampling -lturbulenceModels -lcompressibleTurbulenceModels -lreactionThermophysicalModels -lspecie -lcompressibleTransportModels -lfluidThermophysicalModels -lchemistryModel -lODE -lcombustionModels -lOpenFOAM -ldl \
-lm -o /opt/OpenFOAM/OpenFOAM-v1806/platforms/linux64GccDPInt32Opt/bin/reactingFoam
/usr/bin/ld: cannot open output file /opt/OpenFOAM/OpenFOAM-v1806/platforms/linux64GccDPInt32Opt/bin/reactingFoam: Permission denied
collect2: error: ld returned 1 exit status
make: *** [/opt/OpenFOAM/OpenFOAM-v1806/platforms/linux64GccDPInt32Opt/bin/reactingFoam] Error 1

[hyFoam]

Hi John,


It shouldn't be creating the binary in

/opt/OpenFOAM/OpenFOAM-v1806/platforms/linux64GccDPInt32Opt/bin/
with $FOAM_USER_APPBIN


Could you please print the result of:
echo $FOAM_USER_APPBIN
echo $WM_PROJECT_DIR



Cheers,
Vincent

[daily]

[ofuser@480bb0f83044 bin]$ echo $FOAM_USER_APPBIN
/home/ofuser/OpenFOAM/ofuser-v1806/platforms/linux64GccDPInt32Opt/bin
[ofuser@480bb0f83044 bin]$ echo $WM_PROJECT_DIR
/opt/OpenFOAM/OpenFOAM-v1806

[daily]

So after beating my head against the wall trying to run wmake I am completely confused. When I run it, I get the output below. What is interesting is that I cannot find any directory with "linux64GccDPInt32Opt" in the path, nor can I create any directories or files, or edit files. The binary files are located at "/opt/OpenFOAM/OpenFOAM-v1806/bin" which is inconsistent with $FOAM_USER_APPBIN or $FOAM_APPBIN.

I have read that I can't carry out certain things within the Docker container. So I tried copying my solvers directory to the working directory. However, wmake doesn't run there at all.

HELP!

wmake: 'Make' directory does not exist in /opt/OpenFOAM/OpenFOAM-v1806/applications/solvers/combustion/reactingFoam/Make
Searching up directories tree for Make directory
mkdir: cannot create directory '/opt/OpenFOAM/OpenFOAM-v1806/build': Permission denied
/bin/sh: /opt/OpenFOAM/OpenFOAM-v1806/build/linux64GccDPInt32Opt/applications/solvers/combustion/reactingFoam/options: No such file or directory
make: *** No rule to make target `/opt/OpenFOAM/OpenFOAM-v1806/build/linux64GccDPInt32Opt/applications/solvers/combustion/reactingFoam/options'. Stop.
/bin/sh: /opt/OpenFOAM/OpenFOAM-v1806/build/linux64GccDPInt32Opt/applications/solvers/combustion/reactingFoam/options: No such file or directory
make: *** No rule to make target `/opt/OpenFOAM/OpenFOAM-v1806/build/linux64GccDPInt32Opt/applications/solvers/combustion/reactingFoam/options', needed by `all'. Stop.
wmake error: file '/opt/OpenFOAM/OpenFOAM-v1806/build/linux64GccDPInt32Opt/applications/solvers/combustion/reactingFoam/sourceFiles' could not be created in /opt/OpenFOAM/OpenFOAM-v1806/applications/solvers/combustion/reactingFoam

[wyldckat]

Originally Posted by daily

[ofuser@480bb0f83044 bin]$ echo $FOAM_USER_APPBIN
/home/ofuser/OpenFOAM/ofuser-v1806/platforms/linux64GccDPInt32Opt/bin

Quick answer: The second line indicates the complete path to the folder that is defined by OpenFOAM for building the user's own applications, hence the suggestion to use "FOAM_USER_APPBIN".

Please post the content of the file "Make/files" that you have in your own copy of the source code.

The following wiki page points to a more complete example of what is being suggested by hyFoam, namely how to create a modified solver: https://wiki.openfoam.com/Programming4

[daily]

Thanks, finally got it to run!

[esishad]

hi daily
I have the same problem, can you explain how did you compile the code in docker?

[olesen]

Originally Posted by esishad

hi daily
I have the same problem, can you explain how did you compile the code in docker?

Assuming that you are using the docker 'dev' version (ie, the one with source headers, wmake tools etc), there should not be any problem. However, you do need to be fully aware about what/where you are trying to compile. If you are trying to rebuild parts of the OpenFOAM source tree itself and/or trying to build into the OpenFOAM installation directory, you will not be able to do so. If you build into a mounted filesystem, typically the FOAM_USER_APPBIN and FOAM_USER_LIBBIN targets, it should be fine.


You have two aspects to remember:

1. when working with any system-installed libraries, be it OpenFOAM or any other installed library, they are located under /usr/bin, /usr/lib etc which are not writable by regular users and which should normally not be changed outside of using a packaging system (eg, deb or rpm installs)
2. when working with containers, consider everything in the container to be essentially immutable. Sure you can use 'sudo' within the container to install new packages etc, but they are discarded when the container exits.

As a simple test:

$ openfoam-docker -dev 



 --------------------------------------------------------------------------- 
  =========                 | 
  \\      /  F ield         | OpenFOAM in a container [from OpenCFD Ltd.] 
   \\    /   O peration     | 
    \\  /    A nd           | www.openfoam.com 
     \\/     M anipulation  | 
--------------------------------------------------------------------------- 
 Release notes:  https://www.openfoam.com/news/main-news/openfoam-v2112 
 Documentation:  https://www.openfoam.com/documentation/ 
 Issue Tracker:  https://develop.openfoam.com/Development/openfoam/issues/ 
 Local Help:     more /openfoam/README 
--------------------------------------------------------------------------- 
System   :  Ubuntu 20.04.3 LTS  (admin user: sudofoam) 
OpenFOAM :  /usr/lib/openfoam/openfoam2112 
Build    :  _d44c8318-20220111 OPENFOAM=2112 patch=0 

Note 
    Different OpenFOAM components and modules may be present (or missing) 
    on any particular container installation. 
    Eg, source code, tutorials, in-situ visualization, paraview plugins, 
        external linear-solver interfaces etc. 

--------------------------------------------------------------------------- 
openfoam2112:~/ 
openfoam$ pwd 
 /home/openfoam

 
 openfoam2112:~/ 
openfoam$ dir 
Make  Test-wordRe.C  testRegexps 


openfoam2112:~/ 
 openfoam$ wmake 
Making dependency list for source file Test-wordRe.C 
g++ -std=c++14 -m64 -pthread -DOPENFOAM=2112 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -Wextra -Wold-style-cast -Wnon-virtual-dtor -Wno-unused-parameter -Wno-invalid-of
fsetof -Wno-attributes -Wno-unknown-pragmas  -O3  -DNoRepository -ftemplate-depth-100  -iquote. -IlnInclude -I/usr/lib/openfoam/openfoam2112/src/OpenFOAM/lnInc
lude -I/usr/lib/openfoam/openfoam2112/src/OSspecific/POSIX/lnInclude   -fPIC -c Test-wordRe.C -o Make/linux64GccDPInt32Opt/Test-wordRe.o 
g++ -std=c++14 -m64 -pthread -DOPENFOAM=2112 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -Wextra -Wold-style-cast -Wnon-virtual-dtor -Wno-unused-parameter -Wno-invalid-of
fsetof -Wno-attributes -Wno-unknown-pragmas  -O3  -DNoRepository -ftemplate-depth-100  -iquote. -IlnInclude -I/usr/lib/openfoam/openfoam2112/src/OpenFOAM/lnInc
lude -I/usr/lib/openfoam/openfoam2112/src/OSspecific/POSIX/lnInclude   -fPIC -Xlinker --add-needed -Xlinker --no-as-needed  Make/linux64GccDPInt32Opt/Test-word
Re.o -L/usr/lib/openfoam/openfoam2112/platforms/linux64GccDPInt32Opt/lib \ 
     -lOpenFOAM -ldl  \ 
     -lm -o /home/openfoam/OpenFOAM/openfoam-v2112/platforms/linux64GccDPInt32Opt/bin/Test-wordRe 

After this the 'Test-wordRes' application is available for use within the container, but it is actually stored on the mounted directory outside of the container.

[esishad]

Thank you olesen for your complete answer, apparently my issue is because the code I'm trying to compile was for OpenFOAM v.2 and I'm using v.5 and it seems that some changes were made in file directories and some constant names that the code reads form OpenFOAM sources.

[digitaluser504]

I have a problem in which I cannot reach my company's Container registry via Azure Container Instances and Azure Container Apps, which has to do with VNET's and a private link to the company's registry, and the fact that dynamically launched containers can't be linked. Eventually I want to go to Kubernetes as a platform for my batch job workloads, but right now I have to find a quick solution that makes it able to have at least one container running, and maybe manually scale these when necessary (one is probably enough most of the times).

Right now, the way I am aiming to achieve this is by simply launching a VM (and maybe a couple more when necessary) and running a docker container on this VM with the (Python) application code.

Now I'm wondering if, and if yes how, the Docker container can use a (either system/user assigned) managed identity assigned to the VM. When assigned to an ACI container with a user managed identity assigned to it on startup, I could easily just have code like:

default_credential = DefaultAzureCredential()
q_client = QueueClient(
credential=default_credential,
queue_name='Queuename',
accounrt_url='someurl'
)
and be able to access - for instance - this queue. No need to request any kind of token, no need to specify any kind of environment variable.

Now I doubt this will work in a docker container running in a VM with a user identity assigned to it, since the user identity is not really assigned directly to the docker container. Is there any way to still achieve this or is this a fools errand and should I just work with environment variables for now? I don't really like the idea of the latter, but I haven't found a way to use managed identities this particular way.