Bwhall61 at 00:45, 18 November 2025

2025-11-18T00:45:31Z

← Older revision		Revision as of 00:45, 18 November 2025
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	---		---

			== A note on open source ==

			Beginning ~Dec 12, 2025 we are beginning to transition away from ChemAxon and OpenEye commercial licenses to use open source tools for our building pipeline. The following instructions will work for both commercial and open source versions. If you have access to the commercial tools, build the docker container with <code>--target full</code> (you can still run the open source software with this image, it will just default to commercial software). If you do not have the commercial tools, build the docker container with <code>--target oss</code>.

	== On epyc ==		== On epyc ==
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	cd zinc22-3d		cd zinc22-3d
	docker build -t [image_name] \		docker build -t [image_name] \
			--target [oss/full] \
	--build-context base=[base_dir] \		--build-context base=[base_dir] \
	--build-arg OPENBABEL_VERSION_NUMBER=[version_number] \		--build-arg OPENBABEL_VERSION_NUMBER=[version_number] \
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	=== Arguments ===		=== Arguments ===
			* '''[oss/full]'''
			** oss for open source version
			** full for commercial version

	* '''image_name'''		* '''image_name'''
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	* '''jchem_license_folder'''		* '''jchem_license_folder'''
	The folder that contains the JChem license file (''license.cxl'').		The folder that contains the JChem license file (''license.cxl''). (Only required for commercial building)

	* '''openeye_folder'''		* '''openeye_folder'''
	The folder that contains the OpenEye license file (''oe_license.txt'').		The folder that contains the OpenEye license file (''oe_license.txt''). (Only required for commercial building)

	---		---
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	<syntaxhighlight lang="bash">		<syntaxhighlight lang="bash">
	docker build -t building_pipeline \		docker build -t building_pipeline \
			--target full \
	--build-context base=/mnt/nfs/soft/dock/versions/dock385/pipeline_3D_ligands \		--build-context base=/mnt/nfs/soft/dock/versions/dock385/pipeline_3D_ligands \
	--build-arg OPENBABEL_VERSION_NUMBER=2.3.1 \		--build-arg OPENBABEL_VERSION_NUMBER=2.3.1 \

Bwhall61: Created page with "= Building Pipeline Docker & Apptainer Images = Brendan created a Dockerfile for the building pipeline to simplify the flow of submission and reduce the number of intermediate files created, to speed up building when carried out on Beegfs. This page describes how to create the building pipeline Docker image (on gimel/epyc/etc) and the Apptainer image (on Wynton). --- == On epyc == # Clone the version of the [https://github.com/docking-org/zinc22-3d zinc22-3d] buil..."

2025-09-05T22:01:34Z

Created page with "= Building Pipeline Docker & Apptainer Images = Brendan created a Dockerfile for the building pipeline to simplify the flow of submission and reduce the number of intermediate files created, to speed up building when carried out on Beegfs. This page describes how to create the building pipeline Docker image (on gimel/epyc/etc) and the Apptainer image (on Wynton). --- == On epyc == # Clone the version of the [https://github.com/docking-org/zinc22-3d zinc22-3d] buil..."

New page

= Building Pipeline Docker & Apptainer Images =

Brendan created a Dockerfile for the building pipeline to simplify the flow of submission and reduce the number of intermediate files created, to speed up building when carried out on Beegfs.

This page describes how to create the building pipeline Docker image (on gimel/epyc/etc) and the Apptainer image (on Wynton).

---

== On epyc ==

# Clone the version of the [https://github.com/docking-org/zinc22-3d zinc22-3d] building pipeline you want. For the official version corresponding with the current dock3-release, follow the zinc22-3d link from the [https://github.com/docking-org/dock3-release dock3-release GitHub].
# Run:

<syntaxhighlight lang="bash">
cd zinc22-3d
docker build -t [image_name] \
--build-context base=[base_dir] \
--build-arg OPENBABEL_VERSION_NUMBER=[version_number] \
--build-context jchem_license_folder=[jchem_license_folder] \
--build-context openeye_license_folder=[openeye_folder] .
</syntaxhighlight>

=== Arguments ===

* '''image_name'''
** The name of the docker image to make.
** If you are creating the image for everyone in the lab to use, name this ''building_pipeline''.
** For testing, use a different name.

* '''base_dir'''
This is the folder that contains:
<pre>
/soft/jchem-latest
/soft/dock-latest
/soft/corina-latest
/soft/openbabel-latest
/soft/extralibs-latest
/soft/pyenv-latest
</pre>

* '''version_number'''
The version of OpenBabel referenced in:
<pre>
/soft/openbabel-latest/lib/openbabel/[version_number]
/soft/openbabel-latest/share/openbabel/[version_number]
</pre>

* '''jchem_license_folder'''
The folder that contains the JChem license file (''license.cxl'').

* '''openeye_folder'''
The folder that contains the OpenEye license file (''oe_license.txt'').

---

=== Example (for lab-wide use only) ===

<syntaxhighlight lang="bash">
docker build -t building_pipeline \
--build-context base=/mnt/nfs/soft/dock/versions/dock385/pipeline_3D_ligands \
--build-arg OPENBABEL_VERSION_NUMBER=2.3.1 \
--build-context jchem_license_folder=/nfs/soft/jchem \
--build-context openeye_license_folder=/nfs/soft/openeye .
</syntaxhighlight>

'''Note:''' Only use the name ''building_pipeline'' if you are creating the image for everyone. For testing, please use a different name.

---

== Deploying the Docker Image ==

This will create the building pipeline image on the node you built it on. You now need to load it onto all compute nodes. Run this from an NFS directory (to make sure the logs are saved correctly):

<syntaxhighlight lang="bash">
/mnt/nfs/exk/work/bwhall61/deploy_building_pipeline_docker/deploy_image.sh [image_name]
</syntaxhighlight>

This will queue jobs to load the docker image on all of the compute nodes.

---

== Transferring to Wynton ==

# Save it as a ''.tar'' file:
<syntaxhighlight lang="bash">
docker save -o [image_name].tar [image_name]
</syntaxhighlight>

# Transfer the ''.tar'' file to Wynton.

# Build an Apptainer ''.sif'' image from it:
<syntaxhighlight lang="bash">
apptainer build [image_name].sif docker-archive://[image_name].tar
</syntaxhighlight>

This will give you an Apptainer ''.sif'' file which can then be used for the building pipeline.

Creating the building docker image - Revision history

Bwhall61 at 00:45, 18 November 2025