Permissions issues with Docker image

[jg110]

I'm using the Docker image of OpenFOAM 1706 on Fedora 28. When I try to run the install script, I get an error: mkdir: cannot create directory '/opt/OpenFOAM/user-v1706': Permission denied. Is there a reason hyStrath has to be installed to $FOAM_INST_DIR instead of $FOAM_RUN or something similar?

ls -al /opt shows the following for the /opt/OpenFOAM directory:

drwxr-xr-x. 5 1027 1001 4096 Jul 1 2017 OpenFOAM

I previously edited the permissions of this directory to allow the script to write to it, but the installation failed to find most of the source files (even though I could verify that they did exist in the correct places). I deleted the Docker container and reinstalled it for a fresh start; I have completed every step at https://www.openfoam.com/download/install-binary-linux.php using the 1706 install and start scripts from sourceforge. I suspect this problem is related, but I want to be sure I'm going about the installation process correctly before putting in a bunch of effort to get it working and messing up the Docker container's permissions in the process.

[vincentcasseau]

hyStrath should be installed in $WM_PROJECT_USER_DIR. For some users, $WM_PROJECT_USER_DIR is identical to $FOAM_INST_DIR/$userName-$WM_PROJECT_VERSION so I was not aware of the problem you described. Thanks for reporting it.

Could you please edit line 9 in install-CFD.sh, from sendingDir="$FOAM_INST_DIR/$userName-$WM_PROJECT_VERSION" to sendingDir="$WM_PROJECT_USER_DIR" and let me know if this works for you? If it does, I will correct all the install scripts and push the commit asap. Thanks.

[jg110]

That did get me a lot farther. Replacing the line allowed hyStrath to compile, but compilation fails. It may be a separate issue, but here's the end of the compilation output:

+ wmake
Making dependency list for source file hy2Foam.C
g++ -std=c++11 -m64 -DOPENFOAM_PLUS=1706 -Dlinux64 -DWM_ARCH_OPTION=64 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -Wextra -Wols/lnInclude -I/opt/OpenFOAM/OpenFOAM-v1706/src/finiteVolume/lnInclude -I/opt/OpenFOAM/OpenFOAM-v1706/src/meshTools/lI/opt/OpenFOAM/OpenFOAM-v1706/src/ODE/lnInclude -I/opt/OpenFOAM/OpenFOAM-v1706/src/transportModels/compressible/lnInophysicalModels/strath/strathSpecie/lnInclude -I/home/user/OpenFOAM/user-v1706/src/thermophysicalModels/strath/strat -I/home/user/OpenFOAM/user-v1706/src/thermophysicalModels/strath/strathSpecie/transport/speciesDiffusion/diffusivitn/multiSpeciesTransportModels/lnInclude -I/home/user/OpenFOAM/user-v1706/src/thermophysicalModels/strath/strathSpecipecie/rarefied/rarefactionParameters/lnInclude -I/home/user/OpenFOAM/user-v1706/src/thermophysicalModels/strath/straI/home/user/OpenFOAM/user-v1706/src/TurbulenceModels/compressible/lnInclude -I/home/user/OpenFOAM/user-v1706/src/hTC/OSspecific/POSIX/lnInclude   -fPIC -c hy2Foam.C -o Make/linux64GccDPInt32Opt/hy2Foam.o
In file included from hy2Foam.C:55:0:
/opt/OpenFOAM/OpenFOAM-v1706/src/OpenFOAM/lnInclude/postProcess.H:129:49: fatal error: createFields.H: No such file 
         #include INCLUDE_FILE(CREATE_FIELDS)
                                             ^
compilation terminated.
make: *** [Make/linux64GccDPInt32Opt/hy2Foam.o] Error 1

There are quite a few files called createFields.H within the OpenFOAM directory, as well as one within the hyStrath source directory within my home directory. They're all within various subdirectories of /opt/OpenFOAM/OpenFOAM-v1706/applications, if that matters.

This compilation error happened both when running install-all.sh and install-CFD.sh. install-DSMC.sh compiles successfully, although I had to apply the same fix to that script as you suggested for install-CFD.

[vincentcasseau]

Thanks very much. The installation path is fixed in commit 5da6723.

After a rearrangement of the hy2Foam solver directory earlier this week, I didn't have a file called createFields.H anymore. The problem is that postProcess.H needs one and somehow my compiler was too permissive and didn't warn me...

May I ask what compiler you are using: gcc or Intel?

Anyway, I created a new createFields.H in that directory to initialise the thermophysical and transport quantities (createThermoFields.H, createReactingFields.H and createVibrationalFields.H). This is done in commit 82b4136. Could you please let me know again that works for you? Thanks.

[jg110]

Thanks, I just pulled and it compiled successfully. I'm using the gcc compiler.

I'm currently running the laminar flat plate example, but can't get gnuplot to work. Running on a single core in a Docker container in a VM is very slow. Is there a way to use multiple cores when using hy2Foam? I found the -parallel option, but when I try to use it it gives an error saying I'm trying to run it in parallel on 1 processor. $(nproc) (and the VM settings I specified) show I'm running on 4 cores. Ksysguard (a process monitor) confirms that either checkMesh or hy2Foam is only using 1 core without using -parallel (the last output I can see in Bash is from checkMesh).

[vincentcasseau]

Just like any other solvers, after decomposition: mpirun -np $(nproc) hy2Foam -parallel > log.hy2Foam