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Use of Fugaku

Fugaku is a supercomputer that provides computational resources, storage, and visualization tools for users. Users are given a home directory, data directory, and share directory with specific storage limits. Jobs can be submitted interactively or in batch mode to different resource groups. Visualization applications like ParaView, VisIt, and domain-specific tools are available via Open OnDemand or Spack.

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Iqbal Tawakal
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44 views18 pages

Use of Fugaku

Fugaku is a supercomputer that provides computational resources, storage, and visualization tools for users. Users are given a home directory, data directory, and share directory with specific storage limits. Jobs can be submitted interactively or in batch mode to different resource groups. Visualization applications like ParaView, VisIt, and domain-specific tools are available via Open OnDemand or Spack.

Uploaded by

Iqbal Tawakal
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
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Use of Fugaku

Jorji Nonaka
RIKEN R-CCS

December 2023
General Information
 Startup Guide
 https://www.hpci-office.jp/fugaku/user-info/index.html

 Users’ Guide
 Fugaku Website -> Resource -> Users’ Guide
 Use and Job Execution
 Programming Guide
 Spack, Open OnDemand, Pre/post Environment, Visualization, etc.
HPC School 2023 Group ID (ra022304)
 Home Directory
 /home/ra022304/User_ID
 Limit of 20GB (Individual)

 Data Directory (Main working directory)


 /vol0300/data/ra022304/User_ID
 5TB (Shared)

 Share Directory (To share files with the students)


 /vol0300/share/ra022304
 5TB (Shared)
Job submission
 Computational resource (until March 31, 2024)
 Limit of 53,000 Node Hours
 Resource Groups
 int (Interactive Jobs)
 1 to 12 Nodes
 small (Small Batch Jobs)
 1 to 384 Nodes
 excl_HPCS_2312-2 (Exclusive use for HPC School 2023)
 96 Nodes (From Dec. 11 0:00 to Dec. 16 24:00)
Interactive Job Submission (pjsub)
Example
$ pjsub --interact -L “rscgrp=int” -L “node=1” --mpi “max-proc-per-node
=4” -L “elapse=1:00:00” --sparam “wait-time=600”

 Interactive Mode
 --interact –L “rscgrp=int”
 Number of nodes (with max. MPI processes per node [Ex. 4])
 -L "node=1" --mpi "max-proc-per-node=4”
 Elapse Time (with waiting time [Ex.: 10 minutes])
 -L "elapse=1:00:00" --sparam “wait-time=600”
Interactive Job Submission (pjsub)
With some options
$ pjsub -x PJM_LLIO_GFSCACHE=/vol0004 --interact -L "rscgrp=int"
-L "eco_state=2" -L "node=1" --mpi "max-proc-per-node=4" -L "elapse
=1:00:00" --sparam "wait-time=600"

 To mount other volumes (Ex.: /vol0004 for Spack and other OSS)
 -x PJM_LLIO_GFSCACHE=/vol0004
 Setting execution mode
 Eco Mode: -L "eco_state=2“
 Boost Eco Mode: -L "freq=2200, eco_state=2"
Some Compilers
Compile and Run
Fugaku Website -> Resource -> Users’ Guide -> programming Guide
Programming Native compilers Cross compilers Clang mode
Language (A64FX Compute Nodes) (x86 Login Nodes)
FORTRAN mpifrt mpifrtpx -Nclang
C mpifcc mpifccpx -Nclang
C++ mpiFCC mpiFCCpx -Nclang

Output after mpirun (as files) https://www.fugaku.r-ccs.riken.jp/en/restriction/20221017_01

stdout
./output.{Job ID}/{rank number in 1000 *}/{mpiexec count}/stdout. {mpiexec count}. {rank}
stderr
./output.{Job ID}/{rank number in 1000 *}/{mpiexec count}/stderr. {mpiexec count}. {rank}
Batch Job Submission (pjsub)
From login node Example of job_script.sh
$ pjsub job_script.sh #!/bin/sh
#PJM -g ra022304
#PJM -L "rscgrp=small"
#PJM -L "node=1"
To check the job status #PJM -L "elapse=00:15:00"
$ pjstat #PJM --mpi "max-proc-per-node=4"
#PJM -x PJM_LLIO_GFSCACHE=/vol0004
#PJM -s # Statistical information output
stdout
export OMP_NUM_THREADS=12
output.{Job_ID} directory
mpirun -n 4 ./a.out
Fugaku Website
Open
OnDemand
User Portal

Resource
Groups

Manuals
Users’ Guide
Fugaku User Portal (User Info)

• User ID
• Group ID
• Home Directory
Fugaku User Portal (Disk Info)

Disk
accounting Share Directory
/vol0300/share/ra022304
(5 TB Limit)

Home Directory
/vol0300/ra022304/…
(20 GB Limit)
Fugaku User Portal (Resources)

Job Computational Resources


accounting (Limit: 53,000 Node Hour)
(term) Until Mar. 31, 2024
Open OnDemand (CLI Terminal)
Open OnDemand (File Upload / Download)
Upload Download

Available
Directories
File Upload (Drag & Drop)
Resource Groups (for submitting jobs)

small
Batch Jobs
1 to 384 Nodes

int
Interactive Jobs
1 to 12 Nodes

excl_HPCS_2312-2
Exclusive Usage
(during HPC School 2023)
Visualization Applications (Open OnDemand)
 General-Purpose
 AVS/Express (Non-OSS)
 ParaView
 VisIt

 Domain Specific
 VMD
 OVITO
 PyMol
 …
Visualization Applications (Spack)
Via “Fugaku Shell Access”
Public Instance
 Pre/Post Environment
 GMT

 ImageMagick

 NCView

 GNUPlot

 ParaView (GUI)

 Compute Node
 ParaView (Server)

 POV-Ray

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