DMRIharmonization-Sapelo2 - Revision history

Shtsai at 00:31, 5 April 2026

2026-04-05T00:31:29Z

← Older revision		Revision as of 20:31, 4 April 2026
Line 1:		Line 1:
	[[Category:Sapelo2]][[Category:Software]][[Category:Engineering]]		[[Category:Sapelo2]][[Category:Software]][[Category:Engineering]]

	=== Category ===		== Category ==

	Engineering		Engineering

	=== Program On ===		== Program On ==

	Sapelo2		Sapelo2

	=== Version ===		== Version ==

	20240227		20240227

	=== Author / Distributor ===		== Author / Distributor ==

	See https://github.com/pnlbwh/dMRIharmonization		See https://github.com/pnlbwh/dMRIharmonization

	=== Description ===		== Description ==

	"dMRIharmonization repository is developed by Tashrif Billah, Sylvain Bouix, Suheyla Cetin Karayumak, and Yogesh Rathi, Brigham and Women's Hospital (Harvard Medical School)."		"dMRIharmonization repository is developed by Tashrif Billah, Sylvain Bouix, Suheyla Cetin Karayumak, and Yogesh Rathi, Brigham and Women's Hospital (Harvard Medical School)."
	More details are at https://github.com/pnlbwh/dMRIharmonization.		More details are at https://github.com/pnlbwh/dMRIharmonization.

	=== Running Program ===		== Running Program ==

	* Version 20240227 is installed as a Python virtual environment on Sapelo2 at /apps/gb/dMRIharmonization/20240227		* Version 20240227 is installed as a Python virtual environment on Sapelo2 at /apps/gb/dMRIharmonization/20240227
Line 78:		Line 78:
	</pre>		</pre>

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

	<pre class="gcommand">		<pre class="gcommand">
Line 131:		Line 131:
	[[#top\|Back to Top]]		[[#top\|Back to Top]]

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

	Source code is download from https://github.com/pnlbwh/dMRIharmonization		Source code is download from https://github.com/pnlbwh/dMRIharmonization

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

Moses at 14:01, 17 September 2024

2024-09-17T14:01:34Z

← Older revision		Revision as of 10:01, 17 September 2024
Line 62:		Line 62:

	harmonization.py --nproc 24 <your other options and arguments>		harmonization.py --nproc 24 <your other options and arguments>

			deactivate
	</syntaxhighlight>In your actual submission script, please ensure that you request the appropriate computing resources for your job. For example, you can request CPU cores for running parallel processes using the Slurm headers, such as <code>--ntasks=24</code> and <code>--cpus-per-task=1</code>.		</syntaxhighlight>In your actual submission script, please ensure that you request the appropriate computing resources for your job. For example, you can request CPU cores for running parallel processes using the Slurm headers, such as <code>--ntasks=24</code> and <code>--cpus-per-task=1</code>.

Moses: /* Running Program */

2024-09-17T13:58:21Z

Running Program

← Older revision		Revision as of 09:58, 17 September 2024
Line 38:		Line 38:
	</pre>		</pre>

	Below is an example of a job submission script (sub.sh) to run '''harmonization.py''' with 24 parallel processes on a single compute node on the batch ~~parttition~~:<syntaxhighlight lang="shell">		Below is an example of a job submission script (sub.sh) to run '''harmonization.py''' with 24 parallel processes on a single compute node on the batch partition:<syntaxhighlight lang="shell">
	#!/bin/bash		#!/bin/bash
	#SBATCH --job-name=test_dMRIharmonization		#SBATCH --job-name=test_dMRIharmonization

Moses at 13:54, 17 September 2024

2024-09-17T13:54:51Z

← Older revision		Revision as of 09:54, 17 September 2024
Line 69:		Line 69:
	* The value for the header <code>--ntasks</code>, e.g., <code>--ntasks=24</code>, should match the number specified for the <code>--nproc</code> option on your command line, i.e., <code>--nproc=24</code>.		* The value for the header <code>--ntasks</code>, e.g., <code>--ntasks=24</code>, should match the number specified for the <code>--nproc</code> option on your command line, i.e., <code>--nproc=24</code>.
	* We highly recommend setting <code>--cpus-per-task=1</code> and exporting <code>OMP_NUM_THREADS=1</code> by including <code>export OMP_NUM_THREADS=1</code>in your job submission script.		* We highly recommend setting <code>--cpus-per-task=1</code> and exporting <code>OMP_NUM_THREADS=1</code> by including <code>export OMP_NUM_THREADS=1</code>in your job submission script.


	Here is an example of job submission command:		Here is an example of job submission command:

Moses: /* Installation */

2024-09-17T13:53:16Z

Installation

← Older revision		Revision as of 09:53, 17 September 2024
Line 130:		Line 130:
	=== Installation ===		=== Installation ===

	Source code is download from https://~~support.10xgenomics~~.com/~~single-cell-gene-expression/software/downloads~~/~~latest~~		Source code is download from https://github.com/pnlbwh/dMRIharmonization

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

Moses at 13:52, 17 September 2024

2024-09-17T13:52:50Z

Show changes

Moses at 13:46, 17 September 2024

2024-09-17T13:46:38Z

← Older revision		Revision as of 09:46, 17 September 2024
Line 62:		Line 62:

	harmonization.py --nproc 24 <your other options and arguments>		harmonization.py --nproc 24 <your other options and arguments>
	</syntaxhighlight>In ~~the real~~ submission script, please request appropriate computing resources for your job~~, for~~ example, CPU cores ~~by above~~ Slurm headers ~~for '''~~--ntasks=24~~'''~~ and ~~'''~~--cpus-per-task=1.~~'''~~		</syntaxhighlight>In your actual submission script, please ensure that you request the appropriate computing resources for your job. For example, you can request CPU cores using the Slurm headers, such as <code>--ntasks=24</code> and <code>--cpus-per-task=1</code>.

	'''Please note:'''		'''Please note:'''

Moses at 13:45, 17 September 2024

2024-09-17T13:45:24Z

← Older revision		Revision as of 09:45, 17 September 2024
Line 28:		Line 28:
	To use it, please load the module and activate its env with:		To use it, please load the module and activate its env with:
	<pre class="gscript">		<pre class="gscript">
	ml dMRIharmonization/20240227		ml dMRIharmonization/20240227
	source ${EBROOTDMRIHARMONIZATION}/harmonization/bin/activate		source ${EBROOTDMRIHARMONIZATION}/harmonization/bin/activate
	source ${EBROOTDMRIHARMONIZATION}/../env.sh		source ${EBROOTDMRIHARMONIZATION}/../env.sh
	</pre>		</pre>

	To deactivate its env, please do:		To deactivate its env, please do:
	<pre class="gscript">		<pre class="gscript">
	deactivate		deactivate
	</pre>		</pre>

	~~<nowiki>#</nowiki>~~		Below is an example of a job submission script (sub.sh) to run harmonization.py with 24 parallel processes on a single compute node on the batch parttition:<syntaxhighlight lang="shell">

	Below is an example of a job submission script (sub.sh) to run harmonization.py on the batch ~~queue~~:
	<~~div class~~="~~gscript2~~">
	#!/bin/bash		#!/bin/bash
	#SBATCH --job-name=~~dc_h~~		#SBATCH --job-name=test_dMRIharmonization
	#SBATCH --partition=batch		#SBATCH --partition=batch
	#SBATCH --mem=~~160G~~		#SBATCH --mem=100G
	#SBATCH --nodes=1		#SBATCH --nodes=1
	#SBATCH --ntasks=24		#SBATCH --ntasks=24
	#SBATCH --cpus-per-task=1		#SBATCH --cpus-per-task=1
	#SBATCH --time=7-00		#SBATCH --time=7-00:00:00
	#SBATCH --constraint="Genoa\|Milan"		#SBATCH --constraint="Genoa\|Milan"

	#SBATCH --mail-type=ALL		#SBATCH --mail-type=ALL
	#SBATCH --mail-user=~~jbrown95~~@uga.edu		#SBATCH --mail-user=<yourMyID>@uga.edu

	cd $SLURM_SUBMIT_DIR		cd $SLURM_SUBMIT_DIR
Line 64:		Line 61:
	export OMP_NUM_THREADS=1		export OMP_NUM_THREADS=1

	~~site=dallas~~		harmonization.py --nproc 24 <your other options and arguments>
			</syntaxhighlight>In the real submission script, please request appropriate computing resources for your job, for example, CPU cores by above Slurm headers for '''--ntasks=24''' and '''--cpus-per-task=1.'''
	harmonization.py \
	--~~tar_list full_inputs/${site}_all.csv \~~
	~~--tar_name ${site} \~~
	~~--template ${site}_to_chicago_template~~/ \
	--~~nshm 8 \~~
	--~~nzero 10 \~~
	--~~nproc 24 \~~
	~~--process~~
	~~</div>~~

	~~In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.~~		'''Please note:'''

	~~Please use '''~~--constraint="Genoa\|Milan"~~''' header~~ in your job submission script for ~~a quicker~~ job ~~start time~~ and ~~optimal~~ job ~~performance~~.		* Use the header <code>--constraint="Genoa\|Milan"</code> in your job submission script for optimal job performance.
			* The value for <code>--ntasks</code>, e.g., <code>--ntasks=24</code>, should match the number specified for <code>--nproc</code>, i.e., <code>--nproc=24</code>.
			* We recommend setting <code>--cpus-per-task=1</code> and exporting <code>OMP_NUM_THREADS=1</code> by including <code>export OMP_NUM_THREADS=1</code>in your job submission script.

	Here is an example of job submission command:		Here is an example of job submission command:

Moses at 13:31, 17 September 2024

2024-09-17T13:31:03Z

Show changes

Moses: Created page with "Category:Sapelo2Category:SoftwareCategory:Engineering === Category === Engineering === Program On === Sapelo2 === Version === 20240227 === Author / Distributor === See https://github.com/pnlbwh/dMRIharmonization === Description === "dMRIharmonization repository is developed by Tashrif Billah, Sylvain Bouix, Suheyla Cetin Karayumak, and Yogesh Rathi, Brigham and Women's Hospital (Harvard Medical School)." For more information, please see https://..."

2024-09-17T13:21:36Z

Created page with "Category:Sapelo2 Category:Software Category:Engineering === Category === Engineering === Program On === Sapelo2 === Version === 20240227 === Author / Distributor === See https://github.com/pnlbwh/dMRIharmonization === Description === "dMRIharmonization repository is developed by Tashrif Billah, Sylvain Bouix, Suheyla Cetin Karayumak, and Yogesh Rathi, Brigham and Women's Hospital (Harvard Medical School)." For more information, please see https://..."

New page

[[Category:Sapelo2]][[Category:Software]][[Category:Engineering]]

=== Category ===

Engineering

=== Program On ===

Sapelo2

=== Version ===

20240227

=== Author / Distributor ===

See https://github.com/pnlbwh/dMRIharmonization

=== Description ===

"dMRIharmonization repository is developed by Tashrif Billah, Sylvain Bouix, Suheyla Cetin Karayumak, and Yogesh Rathi, Brigham and Women's Hospital (Harvard Medical School)." For more information, please see https://github.com/pnlbwh/dMRIharmonization.