diff --git a/IntroPhotogrammetry/OpenDroneMap/02-ODM-modules.md b/IntroPhotogrammetry/OpenDroneMap/02-ODM-modules.md index d919585..48d20a9 100644 --- a/IntroPhotogrammetry/OpenDroneMap/02-ODM-modules.md +++ b/IntroPhotogrammetry/OpenDroneMap/02-ODM-modules.md @@ -263,9 +263,10 @@ nano run_odm_latest.sh # nano, vim, mcedit are good text file editors # job standard output will go to the file slurm-%j.out (where %j is the job ID) # DEFINE SLURM VARIABLES #SBATCH --job-name="geo-odm" # custom SLURM job name visible in the queue -#SBATCH --partition=atlas # partition: atlas, gpu, bigmem, service +##SBATCH --partition=atlas # partition on Atlas: atlas, gpu, bigmem, service +#SBATCH --partition=short # partition on Ceres: short, medium, long, mem, longmem #SBATCH --nodes=1 # number of nodes -#SBATCH --ntasks=48 # 24 processor core(s) per node X 2 threads per core +#SBATCH --ntasks=48 # logical cores: 48 on atlas, 72 on short (Ceres) #SBATCH --time=04:00:00 # walltime limit (HH:MM:SS) #SBATCH --account= # EDIT ACCOUNT, provide your SCINet project account #SBATCH --mail-user=user.name@usda.gov # EDIT EMAIL, provide your email address @@ -275,12 +276,13 @@ nano run_odm_latest.sh # nano, vim, mcedit are good text file editors # LOAD MODULES, INSERT CODE, AND RUN YOUR PROGRAMS HERE -module load singularity # load container dependency -module load python/3.9.2 # load phython 3.9 (default) +module load apptainer # load container dependency # DEFINE CODE VARIABLES workdir=/project//.../ODM # EDIT PATH, path to your ODM directory; use `pwd` if the script is in ODM workdir project=PROJECT-1 # EDIT PROJECT NAME, name of the directory with input JPG imagery +ODM=3.3.0 + tag=$SLURM_JOB_ID # EDIT CUSTOM TAG, by default it is a SLURM job ID #tag=`date +%Y%b%d-%T | tr ':' '.'` # alternative TAG, use date in format 2022Aug16-16.57.59 to make the name unique images_dir=$workdir/IMAGES/$project # automatically generated path to input images when stored in ~/ODM/IMAGES; otherwise provide absolute path @@ -288,7 +290,7 @@ output_dir=$workdir/RESULTS/$project-$tag # automatically generated path to mkdir -p $output_dir/code/images # automatically generated images directory ln -s $images_dir/* $output_dir/code/images/ # automatically linked input imagery cp $BASH_SOURCE $output_dir/submit_odm.sh # automatically copied the SLURM script into the outputs directory (e.g., for future reuse or reference of used options) -odm=/reference/containers/opendronemap/2.8.3/opendronemap-2.8.3.sif # pre-configured odm image on Atlas +odm=/reference/containers/opendronemap/2.8.3/opendronemap-$ODM.sif # pre-configured odm image on Atlas # DEFINE ODM COMMAND singularity run --writable-tmpfs $odm \ @@ -298,9 +300,8 @@ singularity run --writable-tmpfs $odm \ --gcp $output_dir/code/images/gcp_list.txt \ --dsm --dtm --dem-resolution 1 --smrf-threshold 0.4 --smrf-window 24 \ --build-overviews \ ---use-hybrid-bundle-adjustment --max-concurrency 16 \ ---project-path $output_dir --ignore-gsd \ ---time +--use-hybrid-bundle-adjustment --max-concurrency 72 \ +--project-path $output_dir --ignore-gsd ```