diff --git a/_sources/tutorials.rst.txt b/_sources/tutorials.rst.txt index 84bb69243..3ff1ff360 100644 --- a/_sources/tutorials.rst.txt +++ b/_sources/tutorials.rst.txt @@ -299,63 +299,34 @@ Docker has a lamentable use of space and by default does not clean up excess dat Using Singularity ***************** -'Singularity '_ is another container platform able to run Docker images. Singularity could be used from laptop to large HPC clusters, local university or company clusters, a single server, in the cloud... -A container is a single file without anything else to install +[Singularity](https://sylabs.io/) is another container platform able to run Docker images. Singularity can be run both on local machins and in instances where the user does not have root access. Instances where a user may not have root privlidges include HPC clusters and cloud cluster resources. +A container is a single file without anything else to install. Downloading image ================= Singularity can use ODM Docker container after their download. It creates .sif images -For latest ODM Docker image +For latest ODM Docker image (Recommended) .. code:: bash - - > singularity pull --disable-cache docker://opendronemap/odm:latest + singularity pull --disable-cache docker://opendronemap/odm:latest For latest ODM GPU Docker image .. code:: bash - - > singularity pull --disable-cache docker://opendronemap/odm:gpu + singularity pull --disable-cache docker://opendronemap/odm:gpu Using Singularity SIF image =========================== -As Singularity has a different way to map directories than Docker, a bash script file is a good solution to map ODM directories. -Here is a linux example for ODM :: +Once you have used one of the above commands to download and create the `odm_latest.sif` image, it can be ran using singularity. +Place your images in a directory named “images” (for example /my/project/images) , then simply run - images_dir=/path_to_image_dir/ - name=`basename $images_dir` - output_dir=/path_to_output_directories/$name - mkdir -p $output_dir - - singularity run - --bind $images_dir:/$output_dir/code/images,\ - --writable-tmpfs odm_latest.sif \ - --orthophoto-png --mesh-octree-depth 12 --ignore-gsd --dtm \ - --smrf-threshold 0.4 --smrf-window 24 --dsm --pc-csv --pc-las --orthophoto-kmz \ - --ignore-gsd --matcher-type flann --feature-quality ultra --max-concurrency 16 \ - --use-hybrid-bundle-adjustment --build-overviews --time --min-num-features 10000 \ - --project-path $output_dir - - -Here is a linux example for the ODM with GPU :: - - images_dir=/path_to_image_dir/ - name=`basename $images_dir` - output_dir=/path_to_output_directories/$name - mkdir -p $output_dir - - singularity run - --bind $images_dir:/$output_dir/code/images,\ - --writable-tmpfs odm_latest.sif \ - --orthophoto-png --mesh-octree-depth 12 --ignore-gsd --dtm \ - --smrf-threshold 0.4 --smrf-window 24 --dsm --pc-csv --pc-las --orthophoto-kmz \ - --ignore-gsd --matcher-type flann --feature-quality ultra --max-concurrency 16 \ - --use-hybrid-bundle-adjustment --build-overviews --time --min-num-features 10000 \ - --project-path $output_dir +..code:: bash + singularity run --bind /my/project:datasets/code odm_latest.sif --project-path /datasets +Like with docker, additional Options and Flags can be added to the command. ************************************* Using ODM from low-bandwidth location diff --git a/cs/.doctrees/environment.pickle b/cs/.doctrees/environment.pickle index da9d5e848..13ebef3ee 100644 Binary files a/cs/.doctrees/environment.pickle and b/cs/.doctrees/environment.pickle differ diff --git a/cs/.doctrees/flowchart.doctree b/cs/.doctrees/flowchart.doctree index 4ca54def9..65ea55054 100644 Binary files a/cs/.doctrees/flowchart.doctree and b/cs/.doctrees/flowchart.doctree differ diff --git a/cs/.doctrees/tutorials.doctree b/cs/.doctrees/tutorials.doctree index bc1e9eb73..36b9e830c 100644 Binary files a/cs/.doctrees/tutorials.doctree and b/cs/.doctrees/tutorials.doctree differ diff --git a/cs/_sources/tutorials.rst.txt b/cs/_sources/tutorials.rst.txt index 84bb69243..3ff1ff360 100644 --- a/cs/_sources/tutorials.rst.txt +++ b/cs/_sources/tutorials.rst.txt @@ -299,63 +299,34 @@ Docker has a lamentable use of space and by default does not clean up excess dat Using Singularity ***************** -'Singularity '_ is another container platform able to run Docker images. Singularity could be used from laptop to large HPC clusters, local university or company clusters, a single server, in the cloud... -A container is a single file without anything else to install +[Singularity](https://sylabs.io/) is another container platform able to run Docker images. Singularity can be run both on local machins and in instances where the user does not have root access. Instances where a user may not have root privlidges include HPC clusters and cloud cluster resources. +A container is a single file without anything else to install. Downloading image ================= Singularity can use ODM Docker container after their download. It creates .sif images -For latest ODM Docker image +For latest ODM Docker image (Recommended) .. code:: bash - - > singularity pull --disable-cache docker://opendronemap/odm:latest + singularity pull --disable-cache docker://opendronemap/odm:latest For latest ODM GPU Docker image .. code:: bash - - > singularity pull --disable-cache docker://opendronemap/odm:gpu + singularity pull --disable-cache docker://opendronemap/odm:gpu Using Singularity SIF image =========================== -As Singularity has a different way to map directories than Docker, a bash script file is a good solution to map ODM directories. -Here is a linux example for ODM :: +Once you have used one of the above commands to download and create the `odm_latest.sif` image, it can be ran using singularity. +Place your images in a directory named “images” (for example /my/project/images) , then simply run - images_dir=/path_to_image_dir/ - name=`basename $images_dir` - output_dir=/path_to_output_directories/$name - mkdir -p $output_dir - - singularity run - --bind $images_dir:/$output_dir/code/images,\ - --writable-tmpfs odm_latest.sif \ - --orthophoto-png --mesh-octree-depth 12 --ignore-gsd --dtm \ - --smrf-threshold 0.4 --smrf-window 24 --dsm --pc-csv --pc-las --orthophoto-kmz \ - --ignore-gsd --matcher-type flann --feature-quality ultra --max-concurrency 16 \ - --use-hybrid-bundle-adjustment --build-overviews --time --min-num-features 10000 \ - --project-path $output_dir - - -Here is a linux example for the ODM with GPU :: - - images_dir=/path_to_image_dir/ - name=`basename $images_dir` - output_dir=/path_to_output_directories/$name - mkdir -p $output_dir - - singularity run - --bind $images_dir:/$output_dir/code/images,\ - --writable-tmpfs odm_latest.sif \ - --orthophoto-png --mesh-octree-depth 12 --ignore-gsd --dtm \ - --smrf-threshold 0.4 --smrf-window 24 --dsm --pc-csv --pc-las --orthophoto-kmz \ - --ignore-gsd --matcher-type flann --feature-quality ultra --max-concurrency 16 \ - --use-hybrid-bundle-adjustment --build-overviews --time --min-num-features 10000 \ - --project-path $output_dir +..code:: bash + singularity run --bind /my/project:datasets/code odm_latest.sif --project-path /datasets +Like with docker, additional Options and Flags can be added to the command. ************************************* Using ODM from low-bandwidth location diff --git a/cs/flowchart/index.html b/cs/flowchart/index.html index dfeed7f71..e091634fb 100644 --- a/cs/flowchart/index.html +++ b/cs/flowchart/index.html @@ -24,7 +24,7 @@