AlphaFold-Sapelo2 - Revision history

Shtsai at 19:07, 27 March 2026

2026-03-27T19:07:15Z

← Older revision		Revision as of 15:07, 27 March 2026
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	[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]

	=== Category ===		== Category ==
	Bioinformatics		Bioinformatics

	=== Program On ===		== Program On ==
	Sapelo2		Sapelo2

	=== Version ===		== Version ==
	2.3.2		2.3.2

	=== Author / Distributor ===		== Author / Distributor ==
	Please see https://github.com/deepmind/alphafold		Please see https://github.com/deepmind/alphafold

	=== Description ===		== Description ==
	From https://github.com/deepmind/alphafold: "This package provides an implementation of the inference pipeline of AlphaFold v2.0. This is a completely new model that was entered in CASP14 and published in Nature. "		From https://github.com/deepmind/alphafold: "This package provides an implementation of the inference pipeline of AlphaFold v2.0. This is a completely new model that was entered in CASP14 and published in Nature. "

	=== Running Program ===		== Running Program ==
	Also refer to [[Running Jobs on Sapelo2]]		Also refer to [[Running Jobs on Sapelo2]]

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	Please note that we use '''--use_precomputed_msas=true''' option in the above alphafold command line.		Please note that we use '''--use_precomputed_msas=true''' option in the above alphafold command line.

	=== Documentation ===		== Documentation ==

	Details and references are at https://github.com/deepmind/alphafold.		Details and references are at https://github.com/deepmind/alphafold.
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	[[#top\|Back to Top]]		[[#top\|Back to Top]]

	=== Installation ===		== Installation ==

	*Version 2.3.2: Installed using EasyBuild.		*Version 2.3.2: Installed using EasyBuild.
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	*The database files are installed in /db/AlphaFold/2.3.2/		*The database files are installed in /db/AlphaFold/2.3.2/

	=== System ===		== System ==
	64-bit Linux		64-bit Linux

Jordan: /* Documentation */

2025-08-13T20:56:02Z

Documentation

← Older revision		Revision as of 16:56, 13 August 2025
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	Details and references are at https://github.com/deepmind/alphafold.		Details and references are at https://github.com/deepmind/alphafold.

	'''Version 2.3.2:''' ~~Dull~~ help options		'''Version 2.3.2:''' Full help options
	<pre class="gcommand">		<pre class="gcommand">
	ml AlphaFold/2.3.2-foss-2023a-CUDA-12.1.1		ml AlphaFold/2.3.2-foss-2023a-CUDA-12.1.1

Jordan: /* Running Program */

2025-08-13T20:53:20Z

Running Program

← Older revision		Revision as of 16:53, 13 August 2025
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	export ALPHAFOLD_DATA_DIR=/db/AlphaFold/2.3.2		export ALPHAFOLD_DATA_DIR=/db/AlphaFold/2.3.2
	</pre>		</pre>
	~~However, when you load the <code>AlphaFold/2.3.1-foss-2022a-CUDA-11.7.0</code> module, this environment variable will be automatically set.~~

	'''Note:''' ~~If you run this program on the gpu_p partition, please~~ request a P100, A100, or H100 GPU device. This version requires a GPU device and it should work on the P100, A100, and H100 devices.		'''Note:''' Remember to request a P100, A100, or H100 GPU device. This version requires a GPU device and it should work on the P100, A100, and H100 devices.


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	An example of the options to use for the alphafold script:		An example of the options to use for the alphafold script:
	<pre class="gscript">		<pre class="gscript">
	alphafold --data_dir ~~/apps~~/db/AlphaFold/2.3.1 --output_dir ./output --model_names model_1 --fasta_paths ./query.fasta --max_template_date 2021-11-17		alphafold --data_dir /db/AlphaFold/2.3.1 --output_dir ./output --model_names model_1 --fasta_paths ./query.fasta --max_template_date 2021-11-17
	</pre>		</pre>

Jordan: /* Documentation */

2025-08-13T20:45:37Z

Documentation

← Older revision		Revision as of 16:45, 13 August 2025
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	Details and references are at https://github.com/deepmind/alphafold.		Details and references are at https://github.com/deepmind/alphafold.

	'''Version 2.3.2:''' ~~Short~~ help options		'''Version 2.3.2:''' Dull help options
	<pre class="gcommand">		<pre class="gcommand">
	ml AlphaFold/2.3.2-foss-2023a-CUDA-12.1.1		ml AlphaFold/2.3.2-foss-2023a-CUDA-12.1.1

Jordan: Overhauled the documentation after the July 2025 maintenance to reflect the fact that we have v2.3.2 installed centrally and nothing else for AF2.

2025-08-13T20:45:01Z

Overhauled the documentation after the July 2025 maintenance to reflect the fact that we have v2.3.2 installed centrally and nothing else for AF2.

Show changes

Jordan at 17:12, 26 November 2024

2024-11-26T17:12:59Z

← Older revision		Revision as of 13:12, 26 November 2024
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	</pre>		</pre>

	Please note~~. We~~ use '''--use_precomputed_msas=true''' option in the above alphafold command line.		Please note that we use '''--use_precomputed_msas=true''' option in the above alphafold command line.

	=== Documentation ===		=== Documentation ===

Moses: /* A method to accelerate your calculations */

2024-05-08T16:59:01Z

A method to accelerate your calculations

← Older revision		Revision as of 12:59, 8 May 2024
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	3. It will check your running elements with an interval of 5 minutes. If the "stop string" is found in a .err file of a running element, the script will automatically cancel the element for you, such that you can start step 2 as early as possible.		3. It will check your running elements with an interval of 5 minutes. If the "stop string" is found in a .err file of a running element, the script will automatically cancel the element for you, such that you can start step 2 as early as possible.

	4. You can stop running of the script (i.e. stop monitoring elements in step 1) by typing Ctrl + c keys on your keyboard.		4. You can stop running the script (i.e. stop monitoring elements in step 1) by typing Ctrl + c keys on your keyboard.

Moses: /* A method to accelerate your calculations */

2024-05-08T16:50:51Z

A method to accelerate your calculations

← Older revision		Revision as of 12:50, 8 May 2024
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	and those FASTA files are stored in a folder called inputs in your current job working folder (--fasta_paths=./inputs/$file).		and those FASTA files are stored in a folder called inputs in your current job working folder (--fasta_paths=./inputs/$file).


	Below is the shell script check_and_stop_elements.sh. You are welcome to copy it for your use:		Below is the shell script check_and_stop_elements.sh. You are welcome to copy it for your use:
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	./check_and_stop_elements.sh 28026197		./check_and_stop_elements.sh 28026197
	</pre>		</pre>


	Below is example outputs from running the above command line:		Below is example outputs from running the above command line:
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	Checking alphaMSAs.28026199.err ... the stop string is NOT found!		Checking alphaMSAs.28026199.err ... the stop string is NOT found!
	</pre>		</pre>


	Once all elements in step 1 have completed the MSA generation, you can go to step 2. As mentioned above, if the computation in step 2 takes less than 4 hours, you can run the job using the V100 scavenge GPU nodes via batch partition. Below is an example job submission script (sub_step2.sh) for running step 2 on the V100 scavenge GPU nodes:		Once all elements in step 1 have completed the MSA generation, you can go to step 2. As mentioned above, if the computation in step 2 takes less than 4 hours, you can run the job using the V100 scavenge GPU nodes via batch partition. Below is an example job submission script (sub_step2.sh) for running step 2 on the V100 scavenge GPU nodes:

Moses: /* A method to accelerate your calculations */

2024-05-08T16:50:13Z

A method to accelerate your calculations

← Older revision		Revision as of 12:50, 8 May 2024
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	In order to achieve this, you need to find a way to stop all running element jobs (or elements) in step 1 after all element jobs in step 1 have completed the MSA generation.		In order to achieve this, you need to find a way to stop all running element jobs (or elements) in step 1 after all element jobs in step 1 have completed the MSA generation.


	With the help from a GACRC user, we have prepared a shell script called '''check_and_stop_elements.sh''':		With the help from a GACRC user, we have prepared a shell script called '''check_and_stop_elements.sh''':
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	4. You can stop running of the script (i.e. stop monitoring elements in step 1) by typing Ctrl + c keys on your keyboard.		4. You can stop running of the script (i.e. stop monitoring elements in step 1) by typing Ctrl + c keys on your keyboard.


	As a quick demo, below is an example job submission script (sub_step1.sh) for running step 1 on batch:		As a quick demo, below is an example job submission script (sub_step1.sh) for running step 1 on batch:

Moses: /* A method to accelerate your calculations */

2024-05-08T16:49:45Z

A method to accelerate your calculations

← Older revision		Revision as of 12:49, 8 May 2024
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	With the help from a GACRC user, we have prepared a shell script called '''check_and_stop_elements.sh''':		With the help from a GACRC user, we have prepared a shell script called '''check_and_stop_elements.sh''':

	1. This script will check for the presence of the "stop string", i.e., '''Running model model_1_multimer_v3_pred_0''', in the .err file of each running element you started in step 1.		1. This script will check for the presence of the "stop string", i.e., '''Running model model_1_multimer_v3_pred_0''', in the .err file of each running element you started in step 1.

	2. You will run this script in an interactive session (see [[Running_Jobs_on_Sapelo2#How_to_open_an_interactive_session\|here]]) or in an OOD X Desktop session (see [[OnDemand#X_Desktop_Session_.28A.K.A._The_Interactive_X_login_app.29\|here]]) to monitor your elements during the time of elements running.		2. You will run this script in an interactive session (see [[Running_Jobs_on_Sapelo2#How_to_open_an_interactive_session\|here]]) or in an OOD X Desktop session (see [[OnDemand#X_Desktop_Session_.28A.K.A._The_Interactive_X_login_app.29\|here]]) to monitor your elements during the time of elements running.

	3. It will check your running elements with an interval of 5 minutes. If the "stop string" is found in a .err file of a running element, the script will automatically cancel the element for you, such that you can start step 2 as early as possible.		3. It will check your running elements with an interval of 5 minutes. If the "stop string" is found in a .err file of a running element, the script will automatically cancel the element for you, such that you can start step 2 as early as possible.

	4. You can stop running of the script (i.e. stop monitoring elements in step 1) by typing Ctrl + c keys on your keyboard.		4. You can stop running of the script (i.e. stop monitoring elements in step 1) by typing Ctrl + c keys on your keyboard.