Colombia 2024 - Revision history

Yambowikiadmin at 15:32, 31 October 2024

2024-10-31T15:32:08Z

← Older revision		Revision as of 15:32, 31 October 2024
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			=== General info ===

	[[File:2024-10-16 08-37.png\|thumb\|smr 3966]]		[[File:2024-10-16 08-37.png\|thumb\|smr 3966]]

			[https://indico.ictp.it/event/10504/overview\| Workshop on High Performance Computing for Materials Characterization, Design and Discovery]
			12-26 October 2024, Barranquilla - Colombia

	=== General instructions to run tutorials ===		=== General instructions to run tutorials ===



	Computational resources are managed on Cineca HPC by the job scheduling system [https://slurm.schedmd.com/overview.html Slurm]. Most part of Yambo tutorials during this school can be run in serial, except some that need to be executed on multiple processors. Generally, Slurm batch jobs are submitted using a script, but the tutorials can be also run interactively. The two procedures are explained below.		Computational resources are managed on Cineca HPC by the job scheduling system [https://slurm.schedmd.com/overview.html Slurm]. Most part of Yambo tutorials during this school can be run in serial, except some that need to be executed on multiple processors. Generally, Slurm batch jobs are submitted using a script, but the tutorials can be also run interactively. The two procedures are explained below.

Yambowikiadmin: /* Open an interactive session */

2024-10-16T07:35:13Z

Open an interactive session

← Older revision		Revision as of 07:35, 16 October 2024
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	This procedure is suggested for most of the tutorials, since the majority of these is meant to be run in serial (relatively to MPI parallelization) from the command line. Use the command below to open an interactive session of 1:30 hour (complete documentation [https://slurm.schedmd.com/srun.html here]):		This procedure is suggested for most of the tutorials, since the majority of these is meant to be run in serial (relatively to MPI parallelization) from the command line. Use the command below to open an interactive session of 1:30 hour (complete documentation [https://slurm.schedmd.com/srun.html here]):
	$ srun --nodes=1 --ntasks-per-node=4 --cpus-per-task=8 --account=tra24_ictpcolo --partition=dcgp_usr_prod --time=1:30:00 --gres=tmpfs:10g --pty /bin/bash		$ srun --nodes=1 --ntasks-per-node=4 --cpus-per-task=4 --account=tra24_ictpcolo --partition=dcgp_usr_prod --time=1:30:00 --gres=tmpfs:10g --pty /bin/bash
	srun: job 8338413 queued and waiting for resources		srun: job 8338413 queued and waiting for resources
	srun: job 8338413 has been allocated resources		srun: job 8338413 has been allocated resources

Yambowikiadmin: /* Run a job using a batch script */

2024-10-16T07:34:34Z

Run a job using a batch script

← Older revision		Revision as of 07:34, 16 October 2024
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	One option is to submit the job using a batch script <code>job.sh</code>, whose generic structure is the following:		One option is to submit the job using a batch script <code>job.sh</code>, whose generic structure is the following:
	$ more job.sh		$ more job.sh
	~~#!/bin/bash~~		#SBATCH --account=tra24_ictpcolo # Charge resources used by this job to specified account
	#SBATCH --account=tra24_ictpcolo # Charge resources used by this job to specified account		#SBATCH --time=00:10:00 # Set a limit on the total run time of the job allocation in hh:mm:ss
	#SBATCH --time=00:10:00 # Set a limit on the total run time of the job allocation in hh:mm:ss		#SBATCH --job-name=<JOB> # Specify a name for the job allocation
	#SBATCH --job-name=JOB # Specify a name for the job allocation		#SBATCH --partition=dcgp_usr_prod # Request a specific partition for the resource allocation
	#SBATCH --partition= dcgp_usr_prod # Request a specific partition for the resource allocation		#SBATCH --nodes=1 # Number of nodes to be allocated for the job
	#SBATCH --nodes=~~<N>~~ # Number of nodes to be allocated for the job		#SBATCH --ntasks-per-node=4 # Number of MPI tasks invoked per node
	#SBATCH --ntasks-per-node=~~<nt>~~ # Number of MPI tasks invoked per node		#SBATCH --cpus-per-task=4 # Number of OMP threads per task
	#SBATCH --cpus-per-task=~~<nc>~~ # Number of OMP threads per task		#SBATCH --gres=tmpfs:10g
	export OMP_NUM_THREADS=~~<nc>~~		export OMP_NUM_THREADS=4
	module purge		module purge
	module load profile/chem-phys		module load profile/chem-phys

Yambowikiadmin: /* Run a job using a batch script */

2024-10-16T07:28:04Z

Run a job using a batch script

← Older revision		Revision as of 07:28, 16 October 2024
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	#!/bin/bash		#!/bin/bash
	#SBATCH --account=tra24_ictpcolo # Charge resources used by this job to specified account		#SBATCH --account=tra24_ictpcolo # Charge resources used by this job to specified account
	~~#SBATCH --error=err.job-%j~~
	~~#SBATCH --output=out.job-%j~~
	#SBATCH --time=00:10:00 # Set a limit on the total run time of the job allocation in hh:mm:ss		#SBATCH --time=00:10:00 # Set a limit on the total run time of the job allocation in hh:mm:ss
	#SBATCH --job-name=JOB # Specify a name for the job allocation		#SBATCH --job-name=JOB # Specify a name for the job allocation

Yambowikiadmin: /* Run a job using a batch script */

2024-10-16T07:17:58Z

Run a job using a batch script

← Older revision		Revision as of 07:17, 16 October 2024
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	#!/bin/bash		#!/bin/bash
	#SBATCH --account=tra24_ictpcolo # Charge resources used by this job to specified account		#SBATCH --account=tra24_ictpcolo # Charge resources used by this job to specified account
			#SBATCH --error=err.job-%j
			#SBATCH --output=out.job-%j
	#SBATCH --time=00:10:00 # Set a limit on the total run time of the job allocation in hh:mm:ss		#SBATCH --time=00:10:00 # Set a limit on the total run time of the job allocation in hh:mm:ss
	#SBATCH --job-name=JOB # Specify a name for the job allocation		#SBATCH --job-name=JOB # Specify a name for the job allocation
	#SBATCH --partition= dcgp_usr_prod # Request a specific partition for the resource allocation		#SBATCH --partition= dcgp_usr_prod # Request a specific partition for the resource allocation
	#
	#SBATCH --nodes=<N> # Number of nodes to be allocated for the job		#SBATCH --nodes=<N> # Number of nodes to be allocated for the job
	#SBATCH --ntasks-per-node=<nt> # Number of MPI tasks invoked per node		#SBATCH --ntasks-per-node=<nt> # Number of MPI tasks invoked per node
	~~#SBATCH --ntasks-per-socket=<nt/2> # Tasks invoked on each socket~~
	#SBATCH --cpus-per-task=<nc> # Number of OMP threads per task		#SBATCH --cpus-per-task=<nc> # Number of OMP threads per task
			export OMP_NUM_THREADS=<nc>
	module purge		module purge
	module load profile/chem-phys		module load profile/chem-phys
	module load yambo/5.2.2--intel-oneapi-mpi--2021.10.0--oneapi--2023.2.0		module load yambo/5.2.2--intel-oneapi-mpi--2021.10.0--oneapi--2023.2.0
			mpirun --rank-by core -np ${SLURM_NTASKS} yambo -F <input> -J <output>
	~~export OMP_NUM_THREADS=<nc>~~
	~~mpirun~~ --rank-by core -np ${SLURM_NTASKS} yambo -F <input> -J <output>

	To submit the job, use the <code>sbatch</code> command:		To submit the job, use the <code>sbatch</code> command:

Yambowikiadmin at 06:39, 16 October 2024

2024-10-16T06:39:26Z

← Older revision		Revision as of 06:39, 16 October 2024
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	=== General instructions to run tutorials ===		=== General instructions to run tutorials ===

	Computational resources are managed on Cineca HPC by the job scheduling system [https://slurm.schedmd.com/overview.html Slurm]. Most part of Yambo tutorials during this school can be run in serial, except some that need to be executed on multiple processors. Generally, Slurm batch jobs are submitted using a script, but the tutorials ~~here are better understood if~~ run interactively. The two procedures ~~that we will use to submit interactive and non interactive jobs~~ are explained below.		Computational resources are managed on Cineca HPC by the job scheduling system [https://slurm.schedmd.com/overview.html Slurm]. Most part of Yambo tutorials during this school can be run in serial, except some that need to be executed on multiple processors. Generally, Slurm batch jobs are submitted using a script, but the tutorials can be also run interactively. The two procedures are explained below.

	=== Tutorials databases ===		=== Tutorials databases ===

Yambowikiadmin at 06:38, 16 October 2024

2024-10-16T06:38:48Z

← Older revision		Revision as of 06:38, 16 October 2024
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			[[File:2024-10-16 08-37.png\|thumb\|smr 3966]]

	=== General instructions to run tutorials ===		=== General instructions to run tutorials ===

	Computational resources are managed by the job scheduling system [https://slurm.schedmd.com/overview.html Slurm]. Most part of Yambo tutorials during this school can be run in serial, except some that need to be executed on multiple processors. Generally, Slurm batch jobs are submitted using a script, but the tutorials here are better understood if run interactively. The two procedures that we will use to submit interactive and non interactive jobs are explained below.		Computational resources are managed on Cineca HPC by the job scheduling system [https://slurm.schedmd.com/overview.html Slurm]. Most part of Yambo tutorials during this school can be run in serial, except some that need to be executed on multiple processors. Generally, Slurm batch jobs are submitted using a script, but the tutorials here are better understood if run interactively. The two procedures that we will use to submit interactive and non interactive jobs are explained below.

	=== Tutorials databases ===		=== Tutorials databases ===

Yambowikiadmin: /* DAY 2 - Tuesday, October 19th */

2024-10-15T12:43:04Z

DAY 2 - Tuesday, October 19th

← Older revision		Revision as of 12:43, 15 October 2024
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	== DAY 2 - Tuesday, October 19<sup>th</sup> ==		== DAY 2 - Tuesday, October 19<sup>th</sup> ==

	'''16:00 - 17:30 ~~A tour through GW simulation in a complex material'''~~		'''16:00 - 17:30 [[GW on h-BN (standalone)\| GW in practice: how to obtain the quasi-particle band structure of a bulk material ]]

	~~To get all the tutorial files needed for the following tutorials, follow these steps:~~

	~~wget https://media.yambo-code.eu/educational/tutorials/files/hBN.tar.gz~~
	~~wget https://media.yambo-code.eu/educational/tutorials/files/MoS2_2Dquasiparticle_tutorial.tar.gz~~
	~~tar -xvf hBN.tar.gz~~
	~~tar -xvf MoS2_2Dquasiparticle_tutorial.tar.gz~~
	~~cd hBN~~

	~~Now you can start the tutorial~~ [[GW on h-BN (standalone)\| GW in practice: how to obtain the quasi-particle band structure of a bulk material ]]

Yambowikiadmin: /* DAY 1 - Monday, October 18th */

2024-10-15T12:42:53Z

DAY 1 - Monday, October 18th

@@ Line 81: / Line 81: @@
 '''14:45 - 15:00 Yambo [http://media.yambo-code.eu/educational/lectures/Yambo_Technical_Introduction.pdf Technical Introduction] and [http://media.yambo-code.eu/educational/lectures/Yambo_Philosophy.pdf Philosophy]'''
-'''15:00 - 17:30 From the DFT ground state to the complete setup of a Many Body calculation using Yambo'''
+'''15:00 - 17:30 [[First steps: a walk through from DFT to optical properties]]
 == DAY 2 - Tuesday, October 19<sup>th</sup> ==

Yambowikiadmin: /* Tutorials databases */

2024-10-15T12:42:37Z

Tutorials databases

← Older revision		Revision as of 12:42, 15 October 2024
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	/leonardo_scratch/large/usertrain/a08tra01		/leonardo_scratch/large/usertrain/a08tra01
	$ cd $SCRATCH		$ cd $SCRATCH
	$ cp -R $WORK/YAMBO_TUTORIALS/		$ cp -R $WORK/YAMBO_TUTORIALS/ .

	=== Run a job using a batch script ===		=== Run a job using a batch script ===