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HPC system startup manual (version 1.80)
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Notes

download
Added the chapter of Torque/Maui

P2

batch job system
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SACLA DatabaseChanged the section 5 for Data

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handling in SACLA HPC system
Replacement SACLA HPC system
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specified in the ssh command.
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Obverview.
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P3, P4software List and how to use.

Overview
The high performance computing (HPC) system in the SACLA facility consists of 60 computenodes, with two 24-core processors per node, for a total of 2880cores. The theoretical peak computeperformance is 138.2 TFLOPS. The system supports a 2PB shared storage system, managed by theLustre file system. Nodes are interconnected with Infiniband with a 100 Gbps bandwidth. This manual
introduces the startup from account creation to the launch of software installed in the SACLA HPCsystem.

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Account creation
After your experiment proposal accepted, a responsible researcher of the SACLA is assigned toyour proposal. Contact him by e-mail and request the use of the SACLA HPC system. He will create
your account and give the username and password. Note that “/home” directory is limited by quota to100 GB per user. When you are going to use more storage area for a large amount of experimental
data and the result data of the analysis, “work” directory can be used. Please talk with your contact
researcher for the use of “/work” directory.

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How to login SACLA HPC system
The access of the SACLA HPC system is limited to be within SPring-8 local network. First of all,you have to connect your computer to the SPring-8 local network by using VPN service. After that,you can login the HPC server through SSH protocol.
[ step 1. Connect the SPring-8 network with VPN service. ]Access the web page: https://hpc.spring8.or.jp with a web browser.

Login the web page of VPN installation service. (Enter your username and password given inSec. 2)

Download and install VPN connection software into your computer. Supported OS for VPN
service is as follows.
[Windows]
Windows 11
Microsoft-supported versions of Windows 11 and 10 for ARM64-based PCs
Windows 10 x64(64-bit)
Windows 8.1 x86(32-bit) and x64(64-bit)[Mac]macOS 12, 11.x (64-bit), 10.15(64-bit), and 10.14(64-bit)[Linux]Red Hat 8.3 and 7.9 (64-bit)
Ubuntu 20.04 (LTS) and 18.04 (LTS)(both 64-bit)SUSE (SLES) 15.3 and 12.5

[ step 2. Login SACLA HPC system. ]Type “ssh -X [username]@xhpcfep.hpc.spring8.or.jp”. The username is given in Sec.2.

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RIKENEnter your password given in Sec.2.

4Batch job system

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The queuing system on SACLA HPC system is PBS . You need three main commands to use thissystem: qstat, qsub, and qdel.
[qstat]“qstat” display status of PBS batch jobs, queues, or servers.
[qsub]“qsub” submits a job. In its simple form you would run “qsub myscript”, where myscript is a shell
script that runs your job. For those who don't want to write scripts, you can do an interactive qsub withthe -I option. You can also use -X option for enabling X11 forwarding (e.g. “qsub –I –X”).
[qdel]“qdel job_number” deletes your job.

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Data handling in SACLA HPC system
Access the web page: http://xhpcfep.hpc.spring8.or.jp/#SaclaSoftware via VPN service.

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Installed software List and how to use
The available software is listed below.

[ FireFox ]Login the SACLA HPC system as stated in Sec. 3.

Type “qsub -I -X” in the terminal window.

Type “firefox” in the terminal window.

[ Evince ]Login the SACLA HPC system as stated in Sec. 3.

Type “qsub -I -X” in the terminal window.

Type “evince” in the terminal window.

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[ Hdfview ]Login the SACLA HPC system as stated in Sec. 3.

Type “qsub -I -X” in the terminal window.

Type “module load hdfview”Type “HDFView” in the terminal window.

[ ImageJ ]

Login the SACLA HPC system as stated in Sec. 3.

Type “qsub -I -X” in the terminal window.

Type “module load ImageJ”

Type “ImageJ” in the terminal window.

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