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49
_sources/tutorials.rst.txt
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@ -299,63 +299,34 @@ Docker has a lamentable use of space and by default does not clean up excess dat
Using Singularity
*****************
'Singularity <https://sylabs.io/>'_ 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

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49
cs/_sources/tutorials.rst.txt
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@ -299,63 +299,34 @@ Docker has a lamentable use of space and by default does not clean up excess dat
Using Singularity
*****************
'Singularity <https://sylabs.io/>'_ 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

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@ -24,7 +24,7 @@
<script src="https://unpkg.com/d3/dist/d3.min.js"></script>
<script>
window.addEventListener("load", function () {
var svgs = d3.selectAll(".mermaid#id-dc547208-7dbe-419c-ba88-117a7403453f svg");
var svgs = d3.selectAll(".mermaid#id-4f9d4b40-c51b-4635-bea3-66a3880d2bfa svg");
svgs.each(function() {
var svg = d3.select(this);
svg.html("<g>" + svg.html() + "</g>");
@ -442,7 +442,7 @@
<section id="flowchart-with-options">
<h1>Flowchart with options<a class="headerlink" href="#flowchart-with-options" title="Permalink to this heading"></a></h1>
<div id="id-dc547208-7dbe-419c-ba88-117a7403453f" class="mermaid">
<div id="id-4f9d4b40-c51b-4635-bea3-66a3880d2bfa" class="mermaid">
flowchart TB

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cs/searchindex.js
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@ -641,55 +641,23 @@
</section>
<section id="using-singularity">
<h2>Using Singularity<a class="headerlink" href="#using-singularity" title="Permalink to this heading"></a></h2>
<p>‚Singularity &lt;<a class="reference external" href="https://sylabs.io/">https://sylabs.io/</a>&gt;‘_ 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</p>
<p>[Singularity](<a class="reference external" href="https://sylabs.io/">https://sylabs.io/</a>) 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.</p>
<section id="downloading-image">
<h3>Downloading image<a class="headerlink" href="#downloading-image" title="Permalink to this heading"></a></h3>
<p>Singularity can use ODM Docker container after their download. It creates .sif images</p>
<p>For latest ODM Docker image</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>&gt;<span class="w"> </span>singularity<span class="w"> </span>pull<span class="w"> </span>--disable-cache<span class="w"> </span>docker://opendronemap/odm:latest
</pre></div>
</div>
<p>For latest ODM Docker image (Recommended)</p>
<p>For latest ODM GPU Docker image</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>&gt;<span class="w"> </span>singularity<span class="w"> </span>pull<span class="w"> </span>--disable-cache<span class="w"> </span>docker://opendronemap/odm:gpu
</pre></div>
</div>
</section>
<section id="using-singularity-sif-image">
<h3>Using Singularity SIF image<a class="headerlink" href="#using-singularity-sif-image" title="Permalink to this heading"></a></h3>
<p>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</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>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
</pre></div>
</div>
<p>Here is a linux example for the ODM with GPU</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>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
</pre></div>
</div>
<p>Once you have used one of the above commands to download and create the <cite>odm_latest.sif</cite> image, it can be ran using singularity.
Place your images in a directory named “images” (for example /my/project/images) , then simply run</p>
<p>..code:: bash</p>
<blockquote>
<div><p>singularity run –bind /my/project:datasets/code odm_latest.sif –project-path /datasets</p>
</div></blockquote>
<p>Like with docker, additional Options and Flags can be added to the command.</p>
</section>
</section>
<section id="using-odm-from-low-bandwidth-location">

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49
es/_sources/tutorials.rst.txt
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@ -299,63 +299,34 @@ Docker has a lamentable use of space and by default does not clean up excess dat
Using Singularity
*****************
'Singularity <https://sylabs.io/>'_ 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

4
es/flowchart/index.html
Wyświetl plik

@ -24,7 +24,7 @@
<script src="https://unpkg.com/d3/dist/d3.min.js"></script>
<script>
window.addEventListener("load", function () {
var svgs = d3.selectAll(".mermaid#id-0ca248c5-781d-4a82-9e25-b7b1299a76c3 svg");
var svgs = d3.selectAll(".mermaid#id-147597ca-9f3d-49db-a833-53384613f7a8 svg");
svgs.each(function() {
var svg = d3.select(this);
svg.html("<g>" + svg.html() + "</g>");
@ -442,7 +442,7 @@
<section id="flowchart-with-options">
<h1>Flowchart with options<a class="headerlink" href="#flowchart-with-options" title="Enlace permanente a este encabezado"></a></h1>
<div id="id-0ca248c5-781d-4a82-9e25-b7b1299a76c3" class="mermaid">
<div id="id-147597ca-9f3d-49db-a833-53384613f7a8" class="mermaid">
flowchart TB

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es/searchindex.js
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52
es/tutorials/index.html
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@ -641,55 +641,23 @@
</section>
<section id="using-singularity">
<h2>Using Singularity<a class="headerlink" href="#using-singularity" title="Enlace permanente a este encabezado"></a></h2>
<p>“Singularity &lt;<a class="reference external" href="https://sylabs.io/">https://sylabs.io/</a>&gt;”_ 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</p>
<p>[Singularity](<a class="reference external" href="https://sylabs.io/">https://sylabs.io/</a>) 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.</p>
<section id="downloading-image">
<h3>Downloading image<a class="headerlink" href="#downloading-image" title="Enlace permanente a este encabezado"></a></h3>
<p>Singularity can use ODM Docker container after their download. It creates .sif images</p>
<p>For latest ODM Docker image</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>&gt;<span class="w"> </span>singularity<span class="w"> </span>pull<span class="w"> </span>--disable-cache<span class="w"> </span>docker://opendronemap/odm:latest
</pre></div>
</div>
<p>For latest ODM Docker image (Recommended)</p>
<p>For latest ODM GPU Docker image</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>&gt;<span class="w"> </span>singularity<span class="w"> </span>pull<span class="w"> </span>--disable-cache<span class="w"> </span>docker://opendronemap/odm:gpu
</pre></div>
</div>
</section>
<section id="using-singularity-sif-image">
<h3>Using Singularity SIF image<a class="headerlink" href="#using-singularity-sif-image" title="Enlace permanente a este encabezado"></a></h3>
<p>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</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>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
</pre></div>
</div>
<p>Here is a linux example for the ODM with GPU</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>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
</pre></div>
</div>
<p>Once you have used one of the above commands to download and create the <cite>odm_latest.sif</cite> image, it can be ran using singularity.
Place your images in a directory named “images” (for example /my/project/images) , then simply run</p>
<p>..code:: bash</p>
<blockquote>
<div><p>singularity run –bind /my/project:datasets/code odm_latest.sif –project-path /datasets</p>
</div></blockquote>
<p>Like with docker, additional Options and Flags can be added to the command.</p>
</section>
</section>
<section id="using-odm-from-low-bandwidth-location">

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fil/_sources/tutorials.rst.txt
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@ -299,63 +299,34 @@ Docker has a lamentable use of space and by default does not clean up excess dat
Using Singularity
*****************
'Singularity <https://sylabs.io/>'_ 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

4
fil/flowchart/index.html
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@ -23,7 +23,7 @@
<script src="https://unpkg.com/d3/dist/d3.min.js"></script>
<script>
window.addEventListener("load", function () {
var svgs = d3.selectAll(".mermaid#id-7370ddbb-5516-48ac-8d21-6e878e939fbf svg");
var svgs = d3.selectAll(".mermaid#id-7cc8dab0-e4e0-4d21-a897-3600c576f30c svg");
svgs.each(function() {
var svg = d3.select(this);
svg.html("<g>" + svg.html() + "</g>");
@ -441,7 +441,7 @@
<section id="flowchart-with-options">
<h1>Flowchart with options<a class="headerlink" href="#flowchart-with-options" title="Permalink to this heading"></a></h1>
<div id="id-7370ddbb-5516-48ac-8d21-6e878e939fbf" class="mermaid">
<div id="id-7cc8dab0-e4e0-4d21-a897-3600c576f30c" class="mermaid">
flowchart TB

2
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@ -646,55 +646,23 @@ The resulting accuracy is comparable to the commercially available photogrammetr
</section>
<section id="using-singularity">
<h2>Using Singularity<a class="headerlink" href="#using-singularity" title="Permalink to this heading"></a></h2>
<p>'Singularity &lt;<a class="reference external" href="https://sylabs.io/">https://sylabs.io/</a>&gt;'_ 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</p>
<p>[Singularity](<a class="reference external" href="https://sylabs.io/">https://sylabs.io/</a>) 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.</p>
<section id="downloading-image">
<h3>Downloading image<a class="headerlink" href="#downloading-image" title="Permalink to this heading"></a></h3>
<p>Singularity can use ODM Docker container after their download. It creates .sif images</p>
<p>For latest ODM Docker image</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>&gt;<span class="w"> </span>singularity<span class="w"> </span>pull<span class="w"> </span>--disable-cache<span class="w"> </span>docker://opendronemap/odm:latest
</pre></div>
</div>
<p>For latest ODM Docker image (Recommended)</p>
<p>For latest ODM GPU Docker image</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>&gt;<span class="w"> </span>singularity<span class="w"> </span>pull<span class="w"> </span>--disable-cache<span class="w"> </span>docker://opendronemap/odm:gpu
</pre></div>
</div>
</section>
<section id="using-singularity-sif-image">
<h3>Using Singularity SIF image<a class="headerlink" href="#using-singularity-sif-image" title="Permalink to this heading"></a></h3>
<p>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</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>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
</pre></div>
</div>
<p>Here is a linux example for the ODM with GPU</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>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
</pre></div>
</div>
<p>Once you have used one of the above commands to download and create the <cite>odm_latest.sif</cite> image, it can be ran using singularity.
Place your images in a directory named “images” (for example /my/project/images) , then simply run</p>
<p>..code:: bash</p>
<blockquote>
<div><p>singularity run --bind /my/project:datasets/code odm_latest.sif --project-path /datasets</p>
</div></blockquote>
<p>Like with docker, additional Options and Flags can be added to the command.</p>
</section>
</section>
<section id="using-odm-from-low-bandwidth-location">

4
flowchart/index.html
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@ -23,7 +23,7 @@
<script src="https://unpkg.com/d3/dist/d3.min.js"></script>
<script>
window.addEventListener("load", function () {
var svgs = d3.selectAll(".mermaid#id-745209d0-5dc9-4c48-87a5-41c4b10e733d svg");
var svgs = d3.selectAll(".mermaid#id-ab48f41e-940b-443e-9907-a5d6221d86b7 svg");
svgs.each(function() {
var svg = d3.select(this);
svg.html("<g>" + svg.html() + "</g>");
@ -441,7 +441,7 @@
<section id="flowchart-with-options">
<h1>Flowchart with options<a class="headerlink" href="#flowchart-with-options" title="Permalink to this heading"></a></h1>
<div id="id-745209d0-5dc9-4c48-87a5-41c4b10e733d" class="mermaid">
<div id="id-ab48f41e-940b-443e-9907-a5d6221d86b7" class="mermaid">
flowchart TB

BIN
fr/.doctrees/environment.pickle
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fr/.doctrees/flowchart.doctree
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49
fr/_sources/tutorials.rst.txt
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@ -299,63 +299,34 @@ Docker has a lamentable use of space and by default does not clean up excess dat
Using Singularity
*****************
'Singularity <https://sylabs.io/>'_ 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

4
fr/flowchart/index.html
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@ -24,7 +24,7 @@
<script src="https://unpkg.com/d3/dist/d3.min.js"></script>
<script>
window.addEventListener("load", function () {
var svgs = d3.selectAll(".mermaid#id-d1f45549-3e8c-41e7-99b4-7b731d2096f1 svg");
var svgs = d3.selectAll(".mermaid#id-ddb00518-0bcb-4d45-94f8-97bee6ec1196 svg");
svgs.each(function() {
var svg = d3.select(this);
svg.html("<g>" + svg.html() + "</g>");
@ -442,7 +442,7 @@
<section id="flowchart-with-options">
<h1>Flowchart with options<a class="headerlink" href="#flowchart-with-options" title="Lien permanent vers cette rubrique"></a></h1>
<div id="id-d1f45549-3e8c-41e7-99b4-7b731d2096f1" class="mermaid">
<div id="id-ddb00518-0bcb-4d45-94f8-97bee6ec1196" class="mermaid">
flowchart TB

2
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fr/tutorials/index.html
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@ -647,55 +647,23 @@ The resulting accuracy is comparable to the commercially available photogrammetr
</section>
<section id="using-singularity">
<h2>Using Singularity<a class="headerlink" href="#using-singularity" title="Lien permanent vers cette rubrique"></a></h2>
<p>“Singularity &lt;<a class="reference external" href="https://sylabs.io/">https://sylabs.io/</a>&gt;”_ 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</p>
<p>[Singularity](<a class="reference external" href="https://sylabs.io/">https://sylabs.io/</a>) 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.</p>
<section id="downloading-image">
<h3>Downloading image<a class="headerlink" href="#downloading-image" title="Lien permanent vers cette rubrique"></a></h3>
<p>Singularity can use ODM Docker container after their download. It creates .sif images</p>
<p>For latest ODM Docker image</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>&gt;<span class="w"> </span>singularity<span class="w"> </span>pull<span class="w"> </span>--disable-cache<span class="w"> </span>docker://opendronemap/odm:latest
</pre></div>
</div>
<p>For latest ODM Docker image (Recommended)</p>
<p>For latest ODM GPU Docker image</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>&gt;<span class="w"> </span>singularity<span class="w"> </span>pull<span class="w"> </span>--disable-cache<span class="w"> </span>docker://opendronemap/odm:gpu
</pre></div>
</div>
</section>
<section id="using-singularity-sif-image">
<h3>Using Singularity SIF image<a class="headerlink" href="#using-singularity-sif-image" title="Lien permanent vers cette rubrique"></a></h3>
<p>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</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>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
</pre></div>
</div>
<p>Here is a linux example for the ODM with GPU</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>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
</pre></div>
</div>
<p>Once you have used one of the above commands to download and create the <cite>odm_latest.sif</cite> image, it can be ran using singularity.
Place your images in a directory named “images” (for example /my/project/images) , then simply run</p>
<p>..code:: bash</p>
<blockquote>
<div><p>singularity run –bind /my/project:datasets/code odm_latest.sif –project-path /datasets</p>
</div></blockquote>
<p>Like with docker, additional Options and Flags can be added to the command.</p>
</section>
</section>
<section id="using-odm-from-low-bandwidth-location">

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id/_sources/tutorials.rst.txt
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@ -299,63 +299,34 @@ Docker has a lamentable use of space and by default does not clean up excess dat
Using Singularity
*****************
'Singularity <https://sylabs.io/>'_ 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

4
id/flowchart/index.html
Wyświetl plik

@ -24,7 +24,7 @@
<script src="https://unpkg.com/d3/dist/d3.min.js"></script>
<script>
window.addEventListener("load", function () {
var svgs = d3.selectAll(".mermaid#id-84fe7431-0c90-463f-a366-e38b7b650f78 svg");
var svgs = d3.selectAll(".mermaid#id-998f26e8-8068-4203-be85-22a7ba1b1124 svg");
svgs.each(function() {
var svg = d3.select(this);
svg.html("<g>" + svg.html() + "</g>");
@ -442,7 +442,7 @@
<section id="flowchart-with-options">
<h1>Flowchart with options<a class="headerlink" href="#flowchart-with-options" title="Permalink to this heading"></a></h1>
<div id="id-84fe7431-0c90-463f-a366-e38b7b650f78" class="mermaid">
<div id="id-998f26e8-8068-4203-be85-22a7ba1b1124" class="mermaid">
flowchart TB

2
id/searchindex.js
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id/tutorials/index.html
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@ -647,55 +647,23 @@ The resulting accuracy is comparable to the commercially available photogrammetr
</section>
<section id="using-singularity">
<h2>Using Singularity<a class="headerlink" href="#using-singularity" title="Permalink to this heading"></a></h2>
<p>'Singularity &lt;<a class="reference external" href="https://sylabs.io/">https://sylabs.io/</a>&gt;'_ 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</p>
<p>[Singularity](<a class="reference external" href="https://sylabs.io/">https://sylabs.io/</a>) 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.</p>
<section id="downloading-image">
<h3>Downloading image<a class="headerlink" href="#downloading-image" title="Permalink to this heading"></a></h3>
<p>Singularity can use ODM Docker container after their download. It creates .sif images</p>
<p>For latest ODM Docker image</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>&gt;<span class="w"> </span>singularity<span class="w"> </span>pull<span class="w"> </span>--disable-cache<span class="w"> </span>docker://opendronemap/odm:latest
</pre></div>
</div>
<p>For latest ODM Docker image (Recommended)</p>
<p>For latest ODM GPU Docker image</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>&gt;<span class="w"> </span>singularity<span class="w"> </span>pull<span class="w"> </span>--disable-cache<span class="w"> </span>docker://opendronemap/odm:gpu
</pre></div>
</div>
</section>
<section id="using-singularity-sif-image">
<h3>Using Singularity SIF image<a class="headerlink" href="#using-singularity-sif-image" title="Permalink to this heading"></a></h3>
<p>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</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>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
</pre></div>
</div>
<p>Here is a linux example for the ODM with GPU</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>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
</pre></div>
</div>
<p>Once you have used one of the above commands to download and create the <cite>odm_latest.sif</cite> image, it can be ran using singularity.
Place your images in a directory named “images” (for example /my/project/images) , then simply run</p>
<p>..code:: bash</p>
<blockquote>
<div><p>singularity run --bind /my/project:datasets/code odm_latest.sif --project-path /datasets</p>
</div></blockquote>
<p>Like with docker, additional Options and Flags can be added to the command.</p>
</section>
</section>
<section id="using-odm-from-low-bandwidth-location">

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@ -299,63 +299,34 @@ Docker has a lamentable use of space and by default does not clean up excess dat
Using Singularity
*****************
'Singularity <https://sylabs.io/>'_ 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

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@ -23,7 +23,7 @@
<script src="https://unpkg.com/d3/dist/d3.min.js"></script>
<script>
window.addEventListener("load", function () {
var svgs = d3.selectAll(".mermaid#id-cec4b63a-0fd3-4018-ac02-cd7e7e467287 svg");
var svgs = d3.selectAll(".mermaid#id-f29a205b-40c3-416e-a9d2-7426fef2cd33 svg");
svgs.each(function() {
var svg = d3.select(this);
svg.html("<g>" + svg.html() + "</g>");
@ -441,7 +441,7 @@
<section id="flowchart-with-options">
<h1>Flowchart with options<a class="headerlink" href="#flowchart-with-options" title="Permalink to this heading"></a></h1>
<div id="id-cec4b63a-0fd3-4018-ac02-cd7e7e467287" class="mermaid">
<div id="id-f29a205b-40c3-416e-a9d2-7426fef2cd33" class="mermaid">
flowchart TB

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sw/tutorials/index.html
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@ -646,55 +646,23 @@ The resulting accuracy is comparable to the commercially available photogrammetr
</section>
<section id="using-singularity">
<h2>Using Singularity<a class="headerlink" href="#using-singularity" title="Permalink to this heading"></a></h2>
<p>'Singularity &lt;<a class="reference external" href="https://sylabs.io/">https://sylabs.io/</a>&gt;'_ 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</p>
<p>[Singularity](<a class="reference external" href="https://sylabs.io/">https://sylabs.io/</a>) 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.</p>
<section id="downloading-image">
<h3>Downloading image<a class="headerlink" href="#downloading-image" title="Permalink to this heading"></a></h3>
<p>Singularity can use ODM Docker container after their download. It creates .sif images</p>
<p>For latest ODM Docker image</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>&gt;<span class="w"> </span>singularity<span class="w"> </span>pull<span class="w"> </span>--disable-cache<span class="w"> </span>docker://opendronemap/odm:latest
</pre></div>
</div>
<p>For latest ODM Docker image (Recommended)</p>
<p>For latest ODM GPU Docker image</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>&gt;<span class="w"> </span>singularity<span class="w"> </span>pull<span class="w"> </span>--disable-cache<span class="w"> </span>docker://opendronemap/odm:gpu
</pre></div>
</div>
</section>
<section id="using-singularity-sif-image">
<h3>Using Singularity SIF image<a class="headerlink" href="#using-singularity-sif-image" title="Permalink to this heading"></a></h3>
<p>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</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>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
</pre></div>
</div>
<p>Here is a linux example for the ODM with GPU</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>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
</pre></div>
</div>
<p>Once you have used one of the above commands to download and create the <cite>odm_latest.sif</cite> image, it can be ran using singularity.
Place your images in a directory named “images” (for example /my/project/images) , then simply run</p>
<p>..code:: bash</p>
<blockquote>
<div><p>singularity run --bind /my/project:datasets/code odm_latest.sif --project-path /datasets</p>
</div></blockquote>
<p>Like with docker, additional Options and Flags can be added to the command.</p>
</section>
</section>
<section id="using-odm-from-low-bandwidth-location">

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49
te/_sources/tutorials.rst.txt
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@ -299,63 +299,34 @@ Docker has a lamentable use of space and by default does not clean up excess dat
Using Singularity
*****************
'Singularity <https://sylabs.io/>'_ 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

4
te/flowchart/index.html
Wyświetl plik

@ -24,7 +24,7 @@
<script src="https://unpkg.com/d3/dist/d3.min.js"></script>
<script>
window.addEventListener("load", function () {
var svgs = d3.selectAll(".mermaid#id-59df3783-d4ad-49f0-b6d1-5d1cfae2852f svg");
var svgs = d3.selectAll(".mermaid#id-644c1aae-b864-400e-9635-bccae6870552 svg");
svgs.each(function() {
var svg = d3.select(this);
svg.html("<g>" + svg.html() + "</g>");
@ -442,7 +442,7 @@
<section id="flowchart-with-options">
<h1>Flowchart with options<a class="headerlink" href="#flowchart-with-options" title="Permalink to this heading"></a></h1>
<div id="id-59df3783-d4ad-49f0-b6d1-5d1cfae2852f" class="mermaid">
<div id="id-644c1aae-b864-400e-9635-bccae6870552" class="mermaid">
flowchart TB

2
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52
te/tutorials/index.html
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@ -647,55 +647,23 @@ The resulting accuracy is comparable to the commercially available photogrammetr
</section>
<section id="using-singularity">
<h2>Using Singularity<a class="headerlink" href="#using-singularity" title="Permalink to this heading"></a></h2>
<p>'Singularity &lt;<a class="reference external" href="https://sylabs.io/">https://sylabs.io/</a>&gt;'_ 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</p>
<p>[Singularity](<a class="reference external" href="https://sylabs.io/">https://sylabs.io/</a>) 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.</p>
<section id="downloading-image">
<h3>Downloading image<a class="headerlink" href="#downloading-image" title="Permalink to this heading"></a></h3>
<p>Singularity can use ODM Docker container after their download. It creates .sif images</p>
<p>For latest ODM Docker image</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>&gt;<span class="w"> </span>singularity<span class="w"> </span>pull<span class="w"> </span>--disable-cache<span class="w"> </span>docker://opendronemap/odm:latest
</pre></div>
</div>
<p>For latest ODM Docker image (Recommended)</p>
<p>For latest ODM GPU Docker image</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>&gt;<span class="w"> </span>singularity<span class="w"> </span>pull<span class="w"> </span>--disable-cache<span class="w"> </span>docker://opendronemap/odm:gpu
</pre></div>
</div>
</section>
<section id="using-singularity-sif-image">
<h3>Using Singularity SIF image<a class="headerlink" href="#using-singularity-sif-image" title="Permalink to this heading"></a></h3>
<p>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</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>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
</pre></div>
</div>
<p>Here is a linux example for the ODM with GPU</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>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
</pre></div>
</div>
<p>Once you have used one of the above commands to download and create the <cite>odm_latest.sif</cite> image, it can be ran using singularity.
Place your images in a directory named “images” (for example /my/project/images) , then simply run</p>
<p>..code:: bash</p>
<blockquote>
<div><p>singularity run --bind /my/project:datasets/code odm_latest.sif --project-path /datasets</p>
</div></blockquote>
<p>Like with docker, additional Options and Flags can be added to the command.</p>
</section>
</section>
<section id="using-odm-from-low-bandwidth-location">

52
tutorials/index.html
Wyświetl plik

@ -646,55 +646,23 @@ The resulting accuracy is comparable to the commercially available photogrammetr
</section>
<section id="using-singularity">
<h2>Using Singularity<a class="headerlink" href="#using-singularity" title="Permalink to this heading"></a></h2>
<p>‘Singularity &lt;<a class="reference external" href="https://sylabs.io/">https://sylabs.io/</a>&gt;’_ 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</p>
<p>[Singularity](<a class="reference external" href="https://sylabs.io/">https://sylabs.io/</a>) 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.</p>
<section id="downloading-image">
<h3>Downloading image<a class="headerlink" href="#downloading-image" title="Permalink to this heading"></a></h3>
<p>Singularity can use ODM Docker container after their download. It creates .sif images</p>
<p>For latest ODM Docker image</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>&gt;<span class="w"> </span>singularity<span class="w"> </span>pull<span class="w"> </span>--disable-cache<span class="w"> </span>docker://opendronemap/odm:latest
</pre></div>
</div>
<p>For latest ODM Docker image (Recommended)</p>
<p>For latest ODM GPU Docker image</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>&gt;<span class="w"> </span>singularity<span class="w"> </span>pull<span class="w"> </span>--disable-cache<span class="w"> </span>docker://opendronemap/odm:gpu
</pre></div>
</div>
</section>
<section id="using-singularity-sif-image">
<h3>Using Singularity SIF image<a class="headerlink" href="#using-singularity-sif-image" title="Permalink to this heading"></a></h3>
<p>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</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>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
</pre></div>
</div>
<p>Here is a linux example for the ODM with GPU</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>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
</pre></div>
</div>
<p>Once you have used one of the above commands to download and create the <cite>odm_latest.sif</cite> image, it can be ran using singularity.
Place your images in a directory named “images” (for example /my/project/images) , then simply run</p>
<p>..code:: bash</p>
<blockquote>
<div><p>singularity run –bind /my/project:datasets/code odm_latest.sif –project-path /datasets</p>
</div></blockquote>
<p>Like with docker, additional Options and Flags can be added to the command.</p>
</section>
</section>
<section id="using-odm-from-low-bandwidth-location">