Runing Windninja on a singularity container

Version of Apptainer

What version of Apptainer (or Singularity) are you using? Run

apptainer --version (or singularity --version).

Expected behavior

running "momentum" simulation for dem "dem0" vegType "grass" windDir "0.0 deg" Run 0: Reading elevation file... Run 0: Run number 0 started with 1 threads. Run 0: Writing OpenFOAM files... Run 0: Converting DEM to STL format... Run 0: Transforming surface points to output wind height... Run 0: Generating mesh... Run 0: Running blockMesh... Run 0: (moveDynamicMesh) 6% complete... Run 0: (moveDynamicMesh) 14% complete... Run 0: (moveDynamicMesh) 20% complete... Run 0: (moveDynamicMesh) 28% complete... Run 0: (moveDynamicMesh) 36% complete... Run 0: (moveDynamicMesh) 42% complete... Run 0: (moveDynamicMesh) 50% complete... Run 0: (moveDynamicMesh) 58% complete... Run 0: (moveDynamicMesh) 64% complete... Run 0: (moveDynamicMesh) 72% complete... Run 0: (moveDynamicMesh) 78% complete... Run 0: (moveDynamicMesh) 86% complete... Run 0: (moveDynamicMesh) 94% complete... Run 0: (moveDynamicMesh) 100% complete... Run 0: Refining surface cells in mesh... Run 0: (refineMesh) 10% complete... Run 0: (refineMesh) 99% complete... Run 0: Renumbering mesh... Run 0: Applying initial conditions... Run 0: Solving for the flow field... Run 0: (solver) 16% complete... Run 0: (solver) 17% complete... Run 0: (solver) 18% complete... Run 0: (solver) 20% complete... Run 0: (solver) 21% complete... Run 0: (solver) 22% complete... Run 0: (solver) 24% complete... Run 0: (solver) 25% complete... Run 0: (solver) 26% complete... Run 0: (solver) 28% complete... Run 0: (solver) 29% complete... Run 0: (solver) 31% complete... Run 0: (solver) 32% complete... Run 0: (solver) 33% complete... Run 0: (solver) 35% complete... Run 0: (solver) 36% complete... Run 0: (solver) 37% complete...

Actual behavior

running "momentum" simulation for dem "dem0" vegType "grass" windDir "0.0 deg" Run 0: Reading elevation file... Run 0: Run number 0 started with 4 threads. Run 0: Writing OpenFOAM files... Run 0: Converting DEM to STL format... Run 0: Transforming surface points to output wind height... Run 0: Generating mesh... Run 0: Running blockMesh... Run 0: Decomposing domain for parallel mesh calculations... Run 0: Running moveDynamicMesh... Run 0: Reconstructing domain... Exception caught: Error during reconstructPar(). Exception caught: Error during reconstructPar(). python os.system() timer: 9.193330103997141 seconds What actually happened? Why was it incorrect? When I started debugging I found that the issue was with the root acces to the openMPI. I have tried the same with installing everything on a virtual machine with the same step and I was getting the results now the issue come when we are using multiple cores for openMPI when I change the number of threads to 1 the behaves as expects but this cost the run to increase its runtime from 10 mins to ~ 35mins when running a large simulation this sways alot in terms of weeks I was trying to figure out a work around and found a similar issue with docker. This Docekr crisis was averted by the solution in this issue. I have tried this solution too but no use. I have tried using --fakeroot but I have no success there.

Steps to reproduce this behavior

Build a docker image from Windninja repository then migrate it to singularity sif using the solution in this issue. then run a windninja run using multiple cores after downloading the dem using fetch_dem --point <some long> <some lat> 30.0 30.0 --buf_units kilometers --src srtm /output/demtest.tif

then run the simulation using WindNinja_cli to get an output

What OS/distro are you running

rocky linux Open HPC

$ cat /etc/os-release

VERSION="9.4 (Blue Onyx)" ID="rocky" ID_LIKE="rhel centos fedora" VERSION_ID="9.4" PLATFORM_ID="platform:el9" PRETTY_NAME="Rocky Linux 9.4 (Blue Onyx)" ANSI_COLOR="0;32" LOGO="fedora-logo-icon" CPE_NAME="cpe:/o:rocky:rocky:9::baseos" HOME_URL="https://rockylinux.org/" BUG_REPORT_URL="https://bugs.rockylinux.org/" SUPPORT_END="2032-05-31" ROCKY_SUPPORT_PRODUCT="Rocky-Linux-9" ROCKY_SUPPORT_PRODUCT_VERSION="9.4" REDHAT_SUPPORT_PRODUCT="Rocky Linux" REDHAT_SUPPORT_PRODUCT_VERSION="9.4"

How did you install Apptainer

using the documentaiton mentioned in the website the rockylinux+slurm+warewulf Write here how you installed Apptainer (or Singularity). Eg. RPM, source.

apptainer / apptainer