CP2K - Revision history

Dmitri: /* Multi-process MPI job on one node */

2025-09-26T22:26:35Z

Multi-process MPI job on one node

← Older revision		Revision as of 22:26, 26 September 2025
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	#SBATCH --ntasks-per-node=40		#SBATCH --ntasks-per-node=40
	#SBATCH --cpus-per-task=1		#SBATCH --cpus-per-task=1
	#SBATCH --mem=~~100gb~~		#SBATCH --mem=20gb
	#SBATCH --time=0-01:00:00		#SBATCH --time=0-01:00:00

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	Note, that this script requests a compute node from the '''cpu2019-bf05''' partition.		Note, that this script requests a compute node from the '''cpu2019-bf05''' partition.
	The nodes in this partitions have '''40 cpu-cores each''', this is why the script also requests '''40 single-threaded MPI processes''' for the '''CP2K''' code.		The nodes in this partitions have '''40 cpu-cores each''', this is why the script also requests '''40 single-threaded MPI processes''' for the '''CP2K''' code.

			This job should run for about '''3 min 50 sec''' and use about '''16GB of memory'''.
			The CPU utilization should be about '''98%'''.

	= Links =		= Links =
	[[ARC Software]]		[[ARC Software]]

2025-09-26T22:23:45Z

Running CP2K jobs using containers

@@ Line 161: / Line 161: @@
 == Running CP2K jobs using containers ==
 === Multi-process MPI job on one node ===
@@ Line 207: / Line 173: @@
 #SBATCH --ntasks-per-node=40
 #SBATCH --cpus-per-task=1
-#SBATCH --mem=16gb
+#SBATCH --mem=100gb
 #SBATCH --time=0-01:00:00
@@ Line 215: / Line 181: @@
 echo "Start: `date`"
-INPUT=/global/software/cp2k/examples/2025.2/H2O-32_md.inp
+INPUT=/global/software/cp2k/examples/2025.2/H2O-128_md.inp
 export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
@@ Line 225: / Line 191: @@
 Note, that this script requests a compute node from the '''cpu2019-bf05''' partition.
 The nodes in this partitions have '''40 cpu-cores each''', this is why the script also requests '''40 single-threaded MPI processes''' for the '''CP2K''' code.
 = Links =
 [[ARC Software]]

2025-09-26T22:13:29Z

Running CP2K jobs using containers

2025-09-26T21:49:04Z

Mixed MPI/OpenMP job on one node

← Older revision		Revision as of 21:49, 26 September 2025
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	=== Mixed MPI/OpenMP job on one node ===		=== Mixed MPI/OpenMP job on one node ===

	It seems that '''CP2K''' runs best when '''each MPI process runs in two OpenMP threads'''~~, <code>mix.slurm</code>~~.		It seems that '''CP2K''' runs best when '''each MPI process runs in two OpenMP threads'''.
	Here is an example for such '''job topology''':		Here is an example for such '''job topology''', <code>mix.slurm</code>:
	<source lang=bash>		<source lang=bash>
	#! /bin/bash		#! /bin/bash

2025-09-26T21:48:46Z

Mixed MPI/OpenMP job on one node

← Older revision		Revision as of 21:48, 26 September 2025
Line 228:		Line 228:
	=== Mixed MPI/OpenMP job on one node ===		=== Mixed MPI/OpenMP job on one node ===

	It seems that '''CP2K''' runs best when '''each MPI process runs in two OpenMP threads'''.		It seems that '''CP2K''' runs best when '''each MPI process runs in two OpenMP threads''', <code>mix.slurm</code>.
	Here is an example for such '''job topology''':		Here is an example for such '''job topology''':
	<source lang=bash>		<source lang=bash>

2025-09-26T21:48:30Z

Multi-process MPI job on one node

← Older revision		Revision as of 21:48, 26 September 2025
Line 198:		Line 198:
	=== Multi-process MPI job on one node ===		=== Multi-process MPI job on one node ===

	One node '''MPI muti-process''' based job script example:		One node '''MPI muti-process''' based job script example, <code>mpi.slurm</code>:
	<source lang=bash>		<source lang=bash>
	#! /bin/bash		#! /bin/bash

2025-09-26T21:48:14Z

Shared memory OpenMP job

← Older revision		Revision as of 21:48, 26 September 2025
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	=== Shared memory OpenMP job ===		=== Shared memory OpenMP job ===

	One node '''OpenMP shared memory''' based job script example:		One node '''OpenMP shared memory''' based job script example, <code>omp.slurm</code>:
	<source lang=bash>		<source lang=bash>
	#! /bin/bash		#! /bin/bash
Line 195:		Line 195:
	Note, that this script requests a compute node from the '''cpu2019-bf05''' partition.		Note, that this script requests a compute node from the '''cpu2019-bf05''' partition.
	The nodes in this partitions have '''40 cpu-cores each''', this is why the script also requests '''40 CPU-cores''' for the '''CP2K''' code.		The nodes in this partitions have '''40 cpu-cores each''', this is why the script also requests '''40 CPU-cores''' for the '''CP2K''' code.

	~~To run this job~~
	~~<source lang=bash>~~
	~~# Change to the directory with the job script, this is where the output files will be.~~
	~~$ cd cp2k-omp-test~~

	~~# Check the files in the directory.~~
	~~$ ls -l~~
	~~-rw-r--r-- 1 drozmano drozmano 674 Sep 26 15:37 omp.slurm~~

	~~# Submit the job to SLURM~~
	~~$ sbatch omp.slurm~~

	~~</source>~~

	=== Multi-process MPI job on one node ===		=== Multi-process MPI job on one node ===

2025-09-26T21:47:35Z

Shared memory OpenMP job

@@ Line 195: / Line 195: @@
 Note, that this script requests a compute node from the '''cpu2019-bf05''' partition.
 The nodes in this partitions have '''40 cpu-cores each''', this is why the script also requests '''40 CPU-cores''' for the '''CP2K''' code.
 === Multi-process MPI job on one node ===

2025-09-26T21:33:26Z

Mix MPI/OpenMP job on one node

← Older revision		Revision as of 21:33, 26 September 2025
Line 226:		Line 226:
	The nodes in this partitions have '''40 cpu-cores each''', this is why the script also requests '''40 single-threaded MPI processes''' for the '''CP2K''' code.		The nodes in this partitions have '''40 cpu-cores each''', this is why the script also requests '''40 single-threaded MPI processes''' for the '''CP2K''' code.

	=== ~~Mix~~ MPI/OpenMP job on one node ===		=== Mixed MPI/OpenMP job on one node ===

	It seems that '''CP2K''' runs best when '''each MPI process runs in two OpenMP threads'''.		It seems that '''CP2K''' runs best when '''each MPI process runs in two OpenMP threads'''.
Line 233:		Line 233:
	#! /bin/bash		#! /bin/bash
	# ------------------------------------------------------------		# ------------------------------------------------------------
	#SBATCH --job-name=cp2k-~~mpi~~-test		#SBATCH --job-name=cp2k-mix-test

	#SBATCH --nodes=1		#SBATCH --nodes=1

2025-09-26T21:32:00Z

Multi-process MPI job on one node

← Older revision		Revision as of 21:32, 26 September 2025
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	INPUT=/global/software/cp2k/examples/2025.2/H2O-32_md.inp		INPUT=/global/software/cp2k/examples/2025.2/H2O-32_md.inp

	export OMP_NUM_THREADS=1		export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
	apptainer run -B/work,/bulk,/global/software $CONT mpiexec -n $SLURM_TASKS_PER_NODE cp2k -i $INPUT		apptainer run -B/work,/bulk,/global/software $CONT mpiexec -n $SLURM_TASKS_PER_NODE cp2k -i $INPUT