http://localhost The NIG Supercomputer en Fri, 03 Apr 2026 08:57:08 Z http://localhost/en/advanced_guides/AlphaFold/Alphafold_2_1/ http://localhost/en/advanced_guides/AlphaFold/Alphafold_2_1/ Fri, 03 Apr 2026 08:57:08 Z Introduction The NIG supercomputer provides the singularity image with alphafold 2.1 installed ( pat... http://localhost/en/advanced_guides/AlphaFold/Alphafold_2_2/ http://localhost/en/advanced_guides/AlphaFold/Alphafold_2_2/ Fri, 03 Apr 2026 08:57:08 Z Introduction The NIG supercomputer provides the singularity image with alphafold 2.2.2 installed and... http://localhost/en/advanced_guides/AlphaFold/Alphafold_2_3/ http://localhost/en/advanced_guides/AlphaFold/Alphafold_2_3/ Fri, 03 Apr 2026 08:57:08 Z Introduction The NIG supercomputer provides the apptainer singularity image with alphafold 2.3.2 ins... http://localhost/en/advanced_guides/AlphaFold/Alphafold_3_0_1/ http://localhost/en/advanced_guides/AlphaFold/Alphafold_3_0_1/ Fri, 03 Apr 2026 08:57:08 Z Overview AlphaFold3 is a protein structure prediction program developed by DeepMind. On the NIG supe... http://localhost/en/advanced_guides/Rhelixa_RNAseq/ http://localhost/en/advanced_guides/Rhelixa_RNAseq/ Fri, 03 Apr 2026 08:57:08 Z The RNA-seq*1 analysis pipeline has been provided by Rhelixa Corporation (CTO: Ryu Nakaki), which ha... http://localhost/en/advanced_guides/Rhelixa_RNAseq/Rhelixa_RNAseq_manual/ http://localhost/en/advanced_guides/Rhelixa_RNAseq/Rhelixa_RNAseq_manual/ Fri, 03 Apr 2026 08:57:08 Z Rhelixa Co., Ltd. 13 Aug 2020 First edition. 1. Configuration and Use 1. 1 Execution Specify the fol... http://localhost/en/advanced_guides/TogoImputation/imputation_server/ http://localhost/en/advanced_guides/TogoImputation/imputation_server/ Fri, 03 Apr 2026 08:57:08 Z The Imputation Server is a service to support imputation analysis of SNP array data. Michigan Imputa... http://localhost/en/advanced_guides/TogoImputation/imputation_server_hail/ http://localhost/en/advanced_guides/TogoImputation/imputation_server_hail/ Fri, 03 Apr 2026 08:57:08 Z This Tutorial 3 describes how to set up an environment for analysing the results of an imputation se... http://localhost/en/advanced_guides/TogoImputation/imputation_server_hibag/ http://localhost/en/advanced_guides/TogoImputation/imputation_server_hibag/ Fri, 03 Apr 2026 08:57:08 Z Connecting to NIG Guacamole desktop environment You need to sign in to NIG Guacamole desktop environ... http://localhost/en/advanced_guides/TogoImputation/imputation_server_install/ http://localhost/en/advanced_guides/TogoImputation/imputation_server_install/ Fri, 03 Apr 2026 08:57:08 Z Configuration and usage Installing jq The command is essential, so if you don't have it, install it.... http://localhost/en/advanced_guides/TogoImputation/imputation_server_tutorial/ http://localhost/en/advanced_guides/TogoImputation/imputation_server_tutorial/ Fri, 03 Apr 2026 08:57:08 Z Procedures for using this system This system executes workflows in the following steps. 1. Prepare t... http://localhost/en/advanced_guides/TogoImputation/imputation_server_tutorial2/ http://localhost/en/advanced_guides/TogoImputation/imputation_server_tutorial2/ Fri, 03 Apr 2026 08:57:08 Z Procedures for using this system This system executes workflows in the following steps. 1. Prepare r... http://localhost/en/advanced_guides/benchmark/benchmark_dorado/ http://localhost/en/advanced_guides/benchmark/benchmark_dorado/ Fri, 03 Apr 2026 08:57:08 Z 1. Introduction This benchmark compares the computational time for basecalling of nanopore sequencin... http://localhost/en/advanced_guides/benchmark/benchmark_parabricks/ http://localhost/en/advanced_guides/benchmark/benchmark_parabricks/ Fri, 03 Apr 2026 08:57:08 Z 1. Overview This page presents the results of detailed performance testing of the genome analysis to... http://localhost/en/advanced_guides/bionemo/ http://localhost/en/advanced_guides/bionemo/ Fri, 03 Apr 2026 08:57:08 Z Overview BioNeMo is a drug discovery support platform developed by NVIDIA, which enables efficient m... http://localhost/en/advanced_guides/commentary/ http://localhost/en/advanced_guides/commentary/ Fri, 03 Apr 2026 08:57:08 Z @nigyta - How to use Jupyter Notebook with the NIG Supercomputer (Qiita 20 Apr 2020) - tips for usin... http://localhost/en/advanced_guides/experimental/ http://localhost/en/advanced_guides/experimental/ Fri, 03 Apr 2026 08:57:08 Z - biocontainers_image - Program to search Apptainer image files for biocontainers. http://localhost/en/advanced_guides/parabricks/ http://localhost/en/advanced_guides/parabricks/ Fri, 03 Apr 2026 08:57:08 Z System Overview NVIDIA Clara Parabricks is a genome analysis pipeline which is compatible with GATK.... http://localhost/en/advanced_guides/topics/advanced_guide_2020-2022/ http://localhost/en/advanced_guides/topics/advanced_guide_2020-2022/ Fri, 03 Apr 2026 08:57:08 Z --- NBDC-DDBJ Imputation Server (beta) 18 Oct 2022. The Imputation Server is a service to support im... http://localhost/en/advanced_guides/topics/advanced_guide_2023/ http://localhost/en/advanced_guides/topics/advanced_guide_2023/ Fri, 03 Apr 2026 08:57:08 Z --- The omics data graphing tool RIAS®️ Visualization is now available. :::danger This service ended... http://localhost/en/advanced_guides/topics/advanced_guide_2025/ http://localhost/en/advanced_guides/topics/advanced_guide_2025/ Fri, 03 Apr 2026 08:57:08 Z --- PortablePipeline 5 June 2025 The NGS analysis pipeline tool PortablePipeline has been updated to... http://localhost/en/application/agreement_signing/ http://localhost/en/application/agreement_signing/ Fri, 03 Apr 2026 08:57:08 Z アカウントの新規登録の際には、責任者の方からの誓約書の提出が必要です。 誓約書には署名欄があり、電子サイン(Adobe Acrobat Sign)をお願いしております。 参考 - 「電子サインの作成方... http://localhost/en/application/agreement_signing/signing_PDF_domestic_resident/ http://localhost/en/application/agreement_signing/signing_PDF_domestic_resident/ Fri, 03 Apr 2026 08:57:08 Z The helpdesk of the NIG Supercomputer() will send an email to the responsible person and the applica... http://localhost/en/application/agreement_signing/signing_PDF_non-resident/ http://localhost/en/application/agreement_signing/signing_PDF_non-resident/ Fri, 03 Apr 2026 08:57:08 Z The helpdesk of the NIG Supercomputer() will send an email to the responsible person and the applica... http://localhost/en/application/billing_service/ http://localhost/en/application/billing_service/ Fri, 03 Apr 2026 08:57:08 Z Overview The NIG supercomputer is operated as a business of the Inter-University Research Institute ... http://localhost/en/application/change_account_info/ http://localhost/en/application/change_account_info/ Fri, 03 Apr 2026 08:57:08 Z If your affiliation or other details change, immediately change of your account information by click... http://localhost/en/application/handling_of_pii/ http://localhost/en/application/handling_of_pii/ Fri, 03 Apr 2026 08:57:08 Z Personal information (user name, contact information, etc.) provided when using the NIG supercompute... http://localhost/en/application/invoice/ http://localhost/en/application/invoice/ Fri, 03 Apr 2026 08:57:08 Z Issuing invoices Invoices Invoices will be issued at the beginning of the following month at the end... http://localhost/en/application/password/ http://localhost/en/application/password/ Fri, 03 Apr 2026 08:57:08 Z Procedure 1. Click here to go to the login page. 2. The following login screen will de displayed, en... http://localhost/en/application/reference/ http://localhost/en/application/reference/ Fri, 03 Apr 2026 08:57:08 Z Contact for questions about NIG supercomputer applications and the system provided by NIG The follow... http://localhost/en/application/registration/ http://localhost/en/application/registration/ Fri, 03 Apr 2026 08:57:08 Z :::danger This is an old document. Currently, the account application system is being replaced to en... http://localhost/en/application/renewal/ http://localhost/en/application/renewal/ Fri, 03 Apr 2026 08:57:08 Z - From 4 January, applying for a renewal of your account of the end of the currnt fiscal year will b... http://localhost/en/application/resource_extension/ http://localhost/en/application/resource_extension/ Fri, 03 Apr 2026 08:57:08 Z Usage plan - When you expand your available high-speed storage, or when you use the billing service,... http://localhost/en/application/ssh_copy_id/ http://localhost/en/application/ssh_copy_id/ Fri, 03 Apr 2026 08:57:08 Z The NIG supercomputer uses SSH login with public key cryptography. Please upload your public key to ... http://localhost/en/application/ssh_keys/ http://localhost/en/application/ssh_keys/ Fri, 03 Apr 2026 08:57:08 Z The NIG supercomputer uses SSH login with public key cryptography. Currently, ED25519 is generally r... http://localhost/en/application/terms_and_policies/legislation/ http://localhost/en/application/terms_and_policies/legislation/ Fri, 03 Apr 2026 08:57:08 Z Foreign Exchange and Foreign Trade Act 1. Foreign Exchange and Foreign Trade Act Article 25 2. The s... http://localhost/en/application/terms_and_policies/terms_of_use_2025/ http://localhost/en/application/terms_and_policies/terms_of_use_2025/ Fri, 03 Apr 2026 08:57:08 Z Terms of Use - Research Organization of Information and Systems Usage Regulations of the NIG Superco... http://localhost/en/application/terms_and_policies/user_issurance_criteria/ http://localhost/en/application/terms_and_policies/user_issurance_criteria/ Fri, 03 Apr 2026 08:57:08 Z Target users of the NIG supercomputer As a member of the Inter-University Research Institute Corpora... http://localhost/en/guides/Database/ http://localhost/en/guides/Database/ Fri, 03 Apr 2026 08:57:08 Z Human Genome Research Dataset Archive Dataset Description Japanese Genotype-phenotype Archive (JGA) ... http://localhost/en/guides/FAQ/faq_application/faq_account_application_system/ http://localhost/en/guides/FAQ/faq_application/faq_account_application_system/ Fri, 03 Apr 2026 08:57:08 Z I want to logout from the application form for use, but I cannot find the logout button. The red fra... http://localhost/en/guides/FAQ/faq_application/faq_agreement_signing/ http://localhost/en/guides/FAQ/faq_application/faq_agreement_signing/ Fri, 03 Apr 2026 08:57:08 Z What should I do if I am unable to electrically sign the pledge because I am using a mailer that can... http://localhost/en/guides/FAQ/faq_application/faq_change_StorageCapacity/ http://localhost/en/guides/FAQ/faq_application/faq_change_StorageCapacity/ Fri, 03 Apr 2026 08:57:08 Z How can I change my allocated storage space? You need to apply for using large-scale storage. Refer ... http://localhost/en/guides/FAQ/faq_application/faq_renewal/ http://localhost/en/guides/FAQ/faq_application/faq_renewal/ Fri, 03 Apr 2026 08:57:08 Z Currently, no papers or other deliverables have been published. I have not yet published a paper, wh... http://localhost/en/guides/FAQ/faq_application/faq_usage_plan/ http://localhost/en/guides/FAQ/faq_application/faq_usage_plan/ Fri, 03 Apr 2026 08:57:08 Z When I try to download the usage plan table, the following screen will appear on the web browser. If... http://localhost/en/guides/FAQ/faq_general_analysis_division/faq_login_general/ http://localhost/en/guides/FAQ/faq_general_analysis_division/faq_login_general/ Fri, 03 Apr 2026 08:57:08 Z Public key authentication failed. Public key authentication fails if write permission is granted to ... http://localhost/en/guides/FAQ/faq_general_analysis_division/faq_sshkeys_mac/ http://localhost/en/guides/FAQ/faq_general_analysis_division/faq_sshkeys_mac/ Fri, 03 Apr 2026 08:57:08 Z When I typed and executed it, and the output is . OpenSSH client is not installed, so first execute ... http://localhost/en/guides/FAQ/faq_general_analysis_division/faq_sshkeys_windows/ http://localhost/en/guides/FAQ/faq_general_analysis_division/faq_sshkeys_windows/ Fri, 03 Apr 2026 08:57:08 Z How to install the latest version of PowerShell This division explains how to update the PowerShell ... http://localhost/en/guides/FAQ/faq_os_migration/ http://localhost/en/guides/FAQ/faq_os_migration/ Fri, 03 Apr 2026 08:57:08 Z On this page, questions related to the OS migration during scheduled maintenance in FY2023 are liste... http://localhost/en/guides/FAQ/faq_os_migration/faq_os_migration_env-var/ http://localhost/en/guides/FAQ/faq_os_migration/faq_os_migration_env-var/ Fri, 03 Apr 2026 08:57:08 Z I want to reinstall my analysis environment along with the OS migration. (Ubuntu Linux 22.04) It dep... http://localhost/en/guides/FAQ/faq_os_migration/faq_os_migration_login/ http://localhost/en/guides/FAQ/faq_os_migration/faq_os_migration_login/ Fri, 03 Apr 2026 08:57:08 Z After the scheduled maintenance in FY2023, when I tried to qlogin, I got an error . This error can b... http://localhost/en/guides/FAQ/faq_personal_genome/faq_forticlient/ http://localhost/en/guides/FAQ/faq_personal_genome/faq_forticlient/ Fri, 03 Apr 2026 08:57:08 Z I don't know how to download the SSL-VPN client software FortiClient. Click on the URL below to acce... http://localhost/en/guides/FAQ/faq_personal_genome/faq_linux_basic/faq_linux_knowledge/ http://localhost/en/guides/FAQ/faq_personal_genome/faq_linux_basic/faq_linux_knowledge/ Fri, 03 Apr 2026 08:57:08 Z The following materials describe the necessary knowledge. Please refer to the links below. 1. Materi... http://localhost/en/guides/FAQ/faq_personal_genome/faq_ssl-vpn_connection/pg_login_ssl-vpn_connection_linux/ http://localhost/en/guides/FAQ/faq_personal_genome/faq_ssl-vpn_connection/pg_login_ssl-vpn_connection_linux/ Fri, 03 Apr 2026 08:57:08 Z For Linux, connect using the openfortivpn CUI. 1. Specify the configuration file as an argument and ... http://localhost/en/guides/FAQ/faq_personal_genome/faq_ssl-vpn_connection/pg_login_ssl-vpn_connection_mac/ http://localhost/en/guides/FAQ/faq_personal_genome/faq_ssl-vpn_connection/pg_login_ssl-vpn_connection_mac/ Fri, 03 Apr 2026 08:57:08 Z For MacOS, connect using the FortiClient GUI. 1. Enter 'User name' and 'Password'. - 'User name': en... http://localhost/en/guides/FAQ/faq_personal_genome/faq_ssl-vpn_connection/pg_login_ssl-vpn_connection_win/ http://localhost/en/guides/FAQ/faq_personal_genome/faq_ssl-vpn_connection/pg_login_ssl-vpn_connection_win/ Fri, 03 Apr 2026 08:57:08 Z For Windows, connect using the FortiClient GUI. 1. Enter 'User name' and 'Password'. - 'User name': ... http://localhost/en/guides/FAQ/faq_personal_genome/faq_ssl-vpn_install/pg_login_ssl-vpn_install_linux/ http://localhost/en/guides/FAQ/faq_personal_genome/faq_ssl-vpn_install/pg_login_ssl-vpn_install_linux/ Fri, 03 Apr 2026 08:57:08 Z For Linux and Windows Subsystem for Linux 2 (WSL2), use the CUI openfortivpn. For the latest version... http://localhost/en/guides/FAQ/faq_personal_genome/faq_ssl-vpn_install/pg_login_ssl-vpn_install_mac/ http://localhost/en/guides/FAQ/faq_personal_genome/faq_ssl-vpn_install/pg_login_ssl-vpn_install_mac/ Fri, 03 Apr 2026 08:57:08 Z Download the SSL-VPN client software "FortiClient" Click on the following URL to access the official... http://localhost/en/guides/FAQ/faq_personal_genome/faq_ssl-vpn_install/pg_login_ssl-vpn_install_win/ http://localhost/en/guides/FAQ/faq_personal_genome/faq_ssl-vpn_install/pg_login_ssl-vpn_install_win/ Fri, 03 Apr 2026 08:57:08 Z Download the SSL-VPN client software "FortiClient" Click on the following URL to access the official... http://localhost/en/guides/FAQ/faq_personal_genome/ssl-vpn_config_file/pg_login_ssl-vpn_configure_file_linux/ http://localhost/en/guides/FAQ/faq_personal_genome/ssl-vpn_config_file/pg_login_ssl-vpn_configure_file_linux/ Fri, 03 Apr 2026 08:57:08 Z For Linux, configure the SSL-VPN client by creating and saving a configuration file 'config file' us... http://localhost/en/guides/FAQ/faq_personal_genome/ssl-vpn_config_file/pg_login_ssl-vpn_configure_file_mac/ http://localhost/en/guides/FAQ/faq_personal_genome/ssl-vpn_config_file/pg_login_ssl-vpn_configure_file_mac/ Fri, 03 Apr 2026 08:57:08 Z For Macs, use the FortiClient GUI to configure the SSL-VPN client. 1. Start FortiClient, select Remo... http://localhost/en/guides/FAQ/faq_personal_genome/ssl-vpn_config_file/pg_login_ssl-vpn_configure_file_win/ http://localhost/en/guides/FAQ/faq_personal_genome/ssl-vpn_config_file/pg_login_ssl-vpn_configure_file_win/ Fri, 03 Apr 2026 08:57:08 Z For Wondows, use the FortiClient GUI to configure the SSL-VPN client. 1. Start FortiClient, select R... http://localhost/en/guides/FAQ/faq_software/faq_archaea_tools/ http://localhost/en/guides/FAQ/faq_software/faq_archaea_tools/ Fri, 03 Apr 2026 08:57:08 Z When transferring files, do I always have to specify the transfer source and transfer destination wi... http://localhost/en/guides/FAQ/faq_software/faq_aspera/ http://localhost/en/guides/FAQ/faq_software/faq_aspera/ Fri, 03 Apr 2026 08:57:08 Z Unable to communicate. Since multiple ports (e.g. port 33001 in addition to the ssh port) are used f... http://localhost/en/guides/FAQ/faq_software/faq_bash/ http://localhost/en/guides/FAQ/faq_software/faq_bash/ Fri, 03 Apr 2026 08:57:08 Z What is the order in which shell configuration files such as are loaded? The official information so... http://localhost/en/guides/FAQ/faq_software/faq_scp/ http://localhost/en/guides/FAQ/faq_software/faq_scp/ Fri, 03 Apr 2026 08:57:08 Z I don't know how to transfer files stored on my personal laptop. To scp using PowerShell in Windows,... http://localhost/en/guides/FAQ/faq_software/faq_slurm/ http://localhost/en/guides/FAQ/faq_software/faq_slurm/ Fri, 03 Apr 2026 08:57:08 Z I requested to use 128 cores, but it appears that only 32 cores are actually being used. If no speci... http://localhost/en/guides/FAQ/faq_software/faq_ssh/ http://localhost/en/guides/FAQ/faq_software/faq_ssh/ Fri, 03 Apr 2026 08:57:08 Z Causes and Solutions for the SSH "Permission denied (publickey)" Error - "Client" means the user's l... http://localhost/en/guides/from_application_to_approval/ http://localhost/en/guides/from_application_to_approval/ Fri, 03 Apr 2026 08:57:08 Z To use the NIG supercomputer, you need to register your account application before you start using i... http://localhost/en/guides/hardware/ga_lustre/ http://localhost/en/guides/hardware/ga_lustre/ Fri, 03 Apr 2026 08:57:08 Z The home directories in both the general analysis division and the personal genome analysis division... http://localhost/en/guides/hardware/hardware/ http://localhost/en/guides/hardware/hardware/ Fri, 03 Apr 2026 08:57:08 Z Overview Classification Specifications Compute Nodes HPC CPU optimized nodes Total number of CPU cor... http://localhost/en/guides/old_docs/Rhelixa_RNAseq_Visualization/ http://localhost/en/guides/old_docs/Rhelixa_RNAseq_Visualization/ Fri, 03 Apr 2026 08:57:08 Z :::danger This is an old document This service ended on 31 October 2025 (Friday). For more informati... http://localhost/en/guides/old_docs/general_analysis_division/ga_grid_engine_queue_old/ http://localhost/en/guides/old_docs/general_analysis_division/ga_grid_engine_queue_old/ Fri, 03 Apr 2026 08:57:08 Z :::danger This is an outdated document This document pertains to the former NIG Supercomputer (2019)... http://localhost/en/guides/old_docs/hardware/hardware2019/ http://localhost/en/guides/old_docs/hardware/hardware2019/ Fri, 03 Apr 2026 08:57:08 Z :::danger This is an old document This document is a former NIG supercomputer (2019) document and is... http://localhost/en/guides/old_docs/personal_genome_division/Parabricks_old/ http://localhost/en/guides/old_docs/personal_genome_division/Parabricks_old/ Fri, 03 Apr 2026 08:57:08 Z :::danger This is an outdated document This document pertains to the former NIG Supercomputer (2019)... http://localhost/en/guides/old_docs/resource_extension/ http://localhost/en/guides/old_docs/resource_extension/ Fri, 03 Apr 2026 08:57:08 Z :::danger This is an old document This document is a former NIG supercomputer (2019) document and is... http://localhost/en/guides/old_docs/software/CopyTool/CentOS/install_HCPtools_002/ http://localhost/en/guides/old_docs/software/CopyTool/CentOS/install_HCPtools_002/ Fri, 03 Apr 2026 08:57:08 Z :::danger This is an old document This document is a former NIG supercomputer (2019) document and is... http://localhost/en/guides/old_docs/software/CopyTool/hcptools_conf/ http://localhost/en/guides/old_docs/software/CopyTool/hcptools_conf/ Fri, 03 Apr 2026 08:57:08 Z Configuration file types There is a configuration file for each of the HCP tools commands. | #| comm... http://localhost/en/guides/old_docs/software/JobScheduler/grid_engine/ http://localhost/en/guides/old_docs/software/JobScheduler/grid_engine/ Fri, 03 Apr 2026 08:57:08 Z :::danger This is an old document This document is a former NIG supercomputer (2019) document and is... http://localhost/en/guides/old_docs/software/JobScheduler/grid_engine/array_jobs/ http://localhost/en/guides/old_docs/software/JobScheduler/grid_engine/array_jobs/ Fri, 03 Apr 2026 08:57:08 Z :::danger This is an old document This document is a former NIG supercomputer (2019) document and is... http://localhost/en/guides/old_docs/software/JobScheduler/grid_engine/batch_job2/ http://localhost/en/guides/old_docs/software/JobScheduler/grid_engine/batch_job2/ Fri, 03 Apr 2026 08:57:08 Z :::danger This is an old document This document is a former NIG supercomputer (2019) document and is... http://localhost/en/guides/old_docs/software/JobScheduler/grid_engine/batch_jobs/ http://localhost/en/guides/old_docs/software/JobScheduler/grid_engine/batch_jobs/ Fri, 03 Apr 2026 08:57:08 Z :::danger This is an old document This document is a former NIG supercomputer (2019) document and is... http://localhost/en/guides/old_docs/software/JobScheduler/grid_engine/interactive_jobs/ http://localhost/en/guides/old_docs/software/JobScheduler/grid_engine/interactive_jobs/ Fri, 03 Apr 2026 08:57:08 Z :::danger This is an old document This document is a former NIG supercomputer (2019) document and is... http://localhost/en/guides/old_docs/software/JobScheduler/grid_engine/other_commands/ http://localhost/en/guides/old_docs/software/JobScheduler/grid_engine/other_commands/ Fri, 03 Apr 2026 08:57:08 Z :::danger This is an old document This document is a former NIG supercomputer (2019) document and is... http://localhost/en/guides/old_docs/software/JobScheduler/grid_engine/parallel_jobs/ http://localhost/en/guides/old_docs/software/JobScheduler/grid_engine/parallel_jobs/ Fri, 03 Apr 2026 08:57:08 Z :::danger This is an old document This document is a former NIG supercomputer (2019) document and is... http://localhost/en/guides/old_docs/terms_of_use_2019/ http://localhost/en/guides/old_docs/terms_of_use_2019/ Fri, 03 Apr 2026 08:57:08 Z :::danger This is an old document This document is a former NIG supercomputer (2019) document and is... http://localhost/en/guides/overview/ http://localhost/en/guides/overview/ Fri, 03 Apr 2026 08:57:08 Z The NIG supercomputer system started its sixth phase of operation in March 2025. This system is inte... http://localhost/en/guides/security-policy/ http://localhost/en/guides/security-policy/ Fri, 03 Apr 2026 08:57:08 Z The official version of this document is the Japanese text. The English translation is provided only... http://localhost/en/guides/security_policy/ISMS_Certificate/ http://localhost/en/guides/security_policy/ISMS_Certificate/ Fri, 03 Apr 2026 08:57:08 Z Division of High Performance Computing and Division of Internal Affairs in Bioinformation and DDBJ C... http://localhost/en/guides/software/ http://localhost/en/guides/software/ Fri, 03 Apr 2026 08:57:08 Z Refer to the links for each software for detailed usage instructions. Job Scheduler A job scheduler ... http://localhost/en/guides/software/AnalysisPipeline/ http://localhost/en/guides/software/AnalysisPipeline/ Fri, 03 Apr 2026 08:57:08 Z area name the general analysis division the personal genome analysis division DFAST available availa... http://localhost/en/guides/software/Container/Apptainer/ http://localhost/en/guides/software/Container/Apptainer/ Fri, 03 Apr 2026 08:57:08 Z (Singularity has been renamed Apptainer.) Introduction Apptainer (Sigularity) containers are availab... http://localhost/en/guides/software/Container/BioContainers/ http://localhost/en/guides/software/Container/BioContainers/ Fri, 03 Apr 2026 08:57:08 Z Introduce Biocontainers Singularity Images Singularity container images created by the BioContainers... http://localhost/en/guides/software/Container/spack/install_spack/ http://localhost/en/guides/software/Container/spack/install_spack/ Fri, 03 Apr 2026 08:57:08 Z Spack is a package manager available with user permission. For example, spack allows installation an... http://localhost/en/guides/software/Container/spack/use_spack/ http://localhost/en/guides/software/Container/spack/use_spack/ Fri, 03 Apr 2026 08:57:08 Z Spack is a package manager available with user permission. References: - Spack Official Web Site - S... http://localhost/en/guides/software/CopyTool/Archaea_tools/ http://localhost/en/guides/software/CopyTool/Archaea_tools/ Fri, 03 Apr 2026 08:57:08 Z To upload and download files to and from the NIG supercomputer, you can generally use widely-used fi... http://localhost/en/guides/software/CopyTool/aspera_client/ http://localhost/en/guides/software/CopyTool/aspera_client/ Fri, 03 Apr 2026 08:57:08 Z Overview Aspera is a high-speed data transfer software. It can be used to download data from major r... http://localhost/en/guides/software/CopyTool/sratoolkit/ http://localhost/en/guides/software/CopyTool/sratoolkit/ Fri, 03 Apr 2026 08:57:08 Z Introduction prefetch is par of the SRA Tools provided by NCBI and is a command line tool for pre-do... http://localhost/en/guides/software/DevelopmentEnvironment/R/ http://localhost/en/guides/software/DevelopmentEnvironment/R/ Fri, 03 Apr 2026 08:57:08 Z This article explains the methods for installing the R environment on the user environment of the Na... http://localhost/en/guides/software/DevelopmentEnvironment/R/r_studio_server/ http://localhost/en/guides/software/DevelopmentEnvironment/R/r_studio_server/ Fri, 03 Apr 2026 08:57:08 Z How to Use RStudio Server in a User Environment RStudio Server is a web server-based RStudio environ... http://localhost/en/guides/software/DevelopmentEnvironment/Rust/rust/ http://localhost/en/guides/software/DevelopmentEnvironment/Rust/rust/ Fri, 03 Apr 2026 08:57:08 Z Installing the Rust processor Rust can be installed with user permission, so install the version you... http://localhost/en/guides/software/DevelopmentEnvironment/TypeScript/typescript/ http://localhost/en/guides/software/DevelopmentEnvironment/TypeScript/typescript/ Fri, 03 Apr 2026 08:57:08 Z How to use TypeScript Installing the Node.js processor Node.js, the server-side JavaScript processor... http://localhost/en/guides/software/DevelopmentEnvironment/cuda/ http://localhost/en/guides/software/DevelopmentEnvironment/cuda/ Fri, 03 Apr 2026 08:57:08 Z Reference: - Official documentation: https://docs.nvidia.com/cuda/ :::info Currently, the number of ... http://localhost/en/guides/software/DevelopmentEnvironment/gcc/ http://localhost/en/guides/software/DevelopmentEnvironment/gcc/ Fri, 03 Apr 2026 08:57:08 Z GCC version: status of support for C and C++ language standards The GCC versions and the conforming ... http://localhost/en/guides/software/DevelopmentEnvironment/go/ http://localhost/en/guides/software/DevelopmentEnvironment/go/ Fri, 03 Apr 2026 08:57:08 Z Go is not installed on the NIG supercomputer. You need to install Go by yourself. The following desc... http://localhost/en/guides/software/DevelopmentEnvironment/intel_compiler/ http://localhost/en/guides/software/DevelopmentEnvironment/intel_compiler/ Fri, 03 Apr 2026 08:57:08 Z The NIG supercomputer system has installed the Intel oneAPI Base & HPC Toolkit Multi-node, enabling ... http://localhost/en/guides/software/DevelopmentEnvironment/intel_compiler/intel_compiler_AILib/ http://localhost/en/guides/software/DevelopmentEnvironment/intel_compiler/intel_compiler_AILib/ Fri, 03 Apr 2026 08:57:08 Z Intel OneCCL (Collective Communications Library) A high-performance communication library for distri... http://localhost/en/guides/software/DevelopmentEnvironment/intel_compiler/intel_compiler_NumCalc/ http://localhost/en/guides/software/DevelopmentEnvironment/intel_compiler/intel_compiler_NumCalc/ Fri, 03 Apr 2026 08:57:08 Z Intel oneMKL (Math Kernel Library) The NIG supercomputer allows the use of the Intel Math Kernel Lib... http://localhost/en/guides/software/DevelopmentEnvironment/intel_compiler/intel_compiler_OtherLanguages/ http://localhost/en/guides/software/DevelopmentEnvironment/intel_compiler/intel_compiler_OtherLanguages/ Fri, 03 Apr 2026 08:57:08 Z Intel Fortran Compiler Intel's Fortran compiler. - Added support for the Fortran 2023 standard. - En... http://localhost/en/guides/software/DevelopmentEnvironment/intel_compiler/intel_compiler_ParallelComLib/ http://localhost/en/guides/software/DevelopmentEnvironment/intel_compiler/intel_compiler_ParallelComLib/ Fri, 03 Apr 2026 08:57:08 Z Intel MPI Library Intel's MPI implementation. - Product page by the distributor - Developer's guide ... http://localhost/en/guides/software/DevelopmentEnvironment/intel_compiler/intel_compiler_debugger/ http://localhost/en/guides/software/DevelopmentEnvironment/intel_compiler/intel_compiler_debugger/ Fri, 03 Apr 2026 08:57:08 Z Intel Distribution for GDB A version of GDB that includes additional features for debugging on Intel... http://localhost/en/guides/software/DevelopmentEnvironment/intel_compiler/intel_compiler_profiler/ http://localhost/en/guides/software/DevelopmentEnvironment/intel_compiler/intel_compiler_profiler/ Fri, 03 Apr 2026 08:57:08 Z Intel Advisor Intel Advisor is a high-performance vectorization and threading optimization tool for ... http://localhost/en/guides/software/DevelopmentEnvironment/java/ http://localhost/en/guides/software/DevelopmentEnvironment/java/ Fri, 03 Apr 2026 08:57:08 Z Java 処理系のインストール Java 処理系 (JDK)のイン--- id: java title: "Java" --- Installing the Java processor The Ja... http://localhost/en/guides/software/DevelopmentEnvironment/jupyter_lab/ http://localhost/en/guides/software/DevelopmentEnvironment/jupyter_lab/ Fri, 03 Apr 2026 08:57:08 Z Jupyter Lab was implemented based on Jupyter Notebook. Jupyter Lab provides better usability and sup... http://localhost/en/guides/software/DevelopmentEnvironment/jupyter_notebook/ http://localhost/en/guides/software/DevelopmentEnvironment/jupyter_notebook/ Fri, 03 Apr 2026 08:57:08 Z Jupyter Notebook is installed on the system. Follow the instruction below to use.[^1] [^1]:Jupyter L... http://localhost/en/guides/software/DevelopmentEnvironment/pgi_compiler/ http://localhost/en/guides/software/DevelopmentEnvironment/pgi_compiler/ Fri, 03 Apr 2026 08:57:08 Z As of February 2024, the genetic research supercomputer system has implemented NVIDIA HPC SDK 23.7. ... http://localhost/en/guides/software/DevelopmentEnvironment/python/ http://localhost/en/guides/software/DevelopmentEnvironment/python/ Fri, 03 Apr 2026 08:57:08 Z Python processors are installed from the outset on the NIG supercomputer. You can also install Pytho... http://localhost/en/guides/software/JobScheduler/Slurm/ http://localhost/en/guides/software/JobScheduler/Slurm/ Fri, 03 Apr 2026 08:57:08 Z Slurm is a type of program known as a job scheduler or resource scheduler, which automatically alloc... http://localhost/en/guides/software/JobScheduler/Slurm/array_jobs/ http://localhost/en/guides/software/JobScheduler/Slurm/array_jobs/ Fri, 03 Apr 2026 08:57:08 Z When you want to submit a large number of jobs (batch or parallel jobs) to the system at once, pleas... http://localhost/en/guides/software/JobScheduler/Slurm/batch_jobs/ http://localhost/en/guides/software/JobScheduler/Slurm/batch_jobs/ Fri, 03 Apr 2026 08:57:08 Z How to Use Batch Jobs Batch jobs should be executed as batch jobs when running a small number of pro... http://localhost/en/guides/software/JobScheduler/Slurm/interactive_jobs/ http://localhost/en/guides/software/JobScheduler/Slurm/interactive_jobs/ Fri, 03 Apr 2026 08:57:08 Z When you need an interactive job, for instance, to perform calculations using a large amount of memo... http://localhost/en/guides/software/JobScheduler/Slurm/other_commands/ http://localhost/en/guides/software/JobScheduler/Slurm/other_commands/ Fri, 03 Apr 2026 08:57:08 Z How to Use GPUs In the personal genome analysis section, GPU compute nodes are operated by allocatin... http://localhost/en/guides/software/JobScheduler/Slurm/parallel_jobs/ http://localhost/en/guides/software/JobScheduler/Slurm/parallel_jobs/ Fri, 03 Apr 2026 08:57:08 Z When running programs that utilize multiple CPU cores simultaneously for extended periods, please ex... http://localhost/en/guides/software/JobScheduler/Slurm/slurm_time/ http://localhost/en/guides/software/JobScheduler/Slurm/slurm_time/ Fri, 03 Apr 2026 08:57:08 Z Overview In Slurm, you need to specify the job time limit yourself. - If you do not specify the time... http://localhost/en/guides/software/software_update_info/ http://localhost/en/guides/software/software_update_info/ Fri, 03 Apr 2026 08:57:08 Z Software update frequency - For shared nodes. - Twice a year, the software is updated. (around June ... http://localhost/en/guides/top_page/ http://localhost/en/guides/top_page/ Fri, 03 Apr 2026 08:57:08 Z The National Institute of Genetics (NIG) provides a cutting-edge supercomputer system equipped with ... http://localhost/en/guides/using_general_analysis_division/ http://localhost/en/guides/using_general_analysis_division/ Fri, 03 Apr 2026 08:57:08 Z System configuration of the general analysis division The general analysis division of NIG supercomp... http://localhost/en/guides/using_general_analysis_division/ga_advance_reservation/ http://localhost/en/guides/using_general_analysis_division/ga_advance_reservation/ Fri, 03 Apr 2026 08:57:08 Z Overview Advance Reservation is a service that users reserve a certain range of resources in the Gri... http://localhost/en/guides/using_general_analysis_division/ga_application/ http://localhost/en/guides/using_general_analysis_division/ga_application/ Fri, 03 Apr 2026 08:57:08 Z Steps from account application to start of use For issuance criteria of user account, check the 'Iss... http://localhost/en/guides/using_general_analysis_division/ga_grid_engine_queue/ http://localhost/en/guides/using_general_analysis_division/ga_grid_engine_queue/ Fri, 03 Apr 2026 08:57:08 Z :::danger This is an old document This document is a former NIG supercomputer (2019) document and is... http://localhost/en/guides/using_general_analysis_division/ga_interactive_login/ http://localhost/en/guides/using_general_analysis_division/ga_interactive_login/ Fri, 03 Apr 2026 08:57:08 Z Introduction :::caution The following procedure is temporary, due to the transition to the Next-Gene... http://localhost/en/guides/using_general_analysis_division/ga_login/ http://localhost/en/guides/using_general_analysis_division/ga_login/ Fri, 03 Apr 2026 08:57:08 Z Introduction SSH connection is used for logging in to the general analysis division of the NIG super... http://localhost/en/guides/using_general_analysis_division/ga_slurm_partition/ http://localhost/en/guides/using_general_analysis_division/ga_slurm_partition/ Fri, 03 Apr 2026 08:57:08 Z The compute nodes managed by the Slurm job scheduler are broadly categorised into interactive nodes ... http://localhost/en/guides/using_general_analysis_division/ga_transfer/ http://localhost/en/guides/using_general_analysis_division/ga_transfer/ Fri, 03 Apr 2026 08:57:08 Z In addition to commonly used protocols such as SCP and SFTP, the NIG supercomputer also supports Asp... http://localhost/en/guides/using_general_analysis_division/largescale_storage/ http://localhost/en/guides/using_general_analysis_division/largescale_storage/ Fri, 03 Apr 2026 08:57:08 Z When you start using this service, check Terms of Use and Appendix for Rules of Use (table of charge... http://localhost/en/guides/using_personal_genome_division/ http://localhost/en/guides/using_personal_genome_division/ Fri, 03 Apr 2026 08:57:08 Z About the Personal Genome Analysis division The NIG supercomputer delivers the personal genome analy... http://localhost/en/guides/using_personal_genome_division/CPU_nodes/ http://localhost/en/guides/using_personal_genome_division/CPU_nodes/ Fri, 03 Apr 2026 08:57:08 Z (This page is being prepared and will be available soon.) http://localhost/en/guides/using_personal_genome_division/GPU_nodes_type2/ http://localhost/en/guides/using_personal_genome_division/GPU_nodes_type2/ Fri, 03 Apr 2026 08:57:08 Z The Accelerator-Optimized Node Type 2 is a compute node equipped with eight NVIDIA L40S GPUs per nod... http://localhost/en/guides/using_personal_genome_division/Parabricks/ http://localhost/en/guides/using_personal_genome_division/Parabricks/ Fri, 03 Apr 2026 08:57:08 Z Overview This guide explains how to run genome analysis using Parabricks on the GPU nodes of the NIG... http://localhost/en/guides/using_personal_genome_division/Parabricks/parabricks_fq2bam/ http://localhost/en/guides/using_personal_genome_division/Parabricks/parabricks_fq2bam/ Fri, 03 Apr 2026 08:57:08 Z Application for Access To run Parabricks, GPU compute nodes are required. Currently, due to the limi... http://localhost/en/guides/using_personal_genome_division/Parabricks/parabricks_setup/ http://localhost/en/guides/using_personal_genome_division/Parabricks/parabricks_setup/ Fri, 03 Apr 2026 08:57:08 Z Applying for Access Parabricks requires access to GPU compute nodes. Due to the limited number of av... http://localhost/en/guides/using_personal_genome_division/group_cloud/ http://localhost/en/guides/using_personal_genome_division/group_cloud/ Fri, 03 Apr 2026 08:57:08 Z DDBJ Group Cloud is a service for sharing data that requires access restrictions, including personal... http://localhost/en/guides/using_personal_genome_division/job_submission_notes/ http://localhost/en/guides/using_personal_genome_division/job_submission_notes/ Fri, 03 Apr 2026 08:57:08 Z When using Parabricks (a job that utilizes GPUs) in the personal genome analysis division, even if t... http://localhost/en/guides/using_personal_genome_division/pg_application/ http://localhost/en/guides/using_personal_genome_division/pg_application/ Fri, 03 Apr 2026 08:57:08 Z Preparation of user's computer The personal genome analysis division of NIG supercomputer can be use... http://localhost/en/guides/using_personal_genome_division/pg_data_transfer/ http://localhost/en/guides/using_personal_genome_division/pg_data_transfer/ Fri, 03 Apr 2026 08:57:08 Z :::caution The Archaea tools server for the Personal Genome Analysis Division is currently being pre... http://localhost/en/guides/using_personal_genome_division/pg_login/ http://localhost/en/guides/using_personal_genome_division/pg_login/ Fri, 03 Apr 2026 08:57:08 Z Introduction SSL-VPN connection is used for login and file transfer to the personal genome analysis ... http://localhost/en/guides/using_personal_genome_division/pg_overview/ http://localhost/en/guides/using_personal_genome_division/pg_overview/ Fri, 03 Apr 2026 08:57:08 Z - For security reasons, users are generally required to use dedicated (exclusive) compute nodes in t... http://localhost/en/operation/job_queue_status/ http://localhost/en/operation/job_queue_status/ Fri, 03 Apr 2026 08:57:08 Z In the line graph below, queueing time is the waiting time until starting execution. - The waiting t... http://localhost/en/operation/power_consumption/ http://localhost/en/operation/power_consumption/ Fri, 03 Apr 2026 08:57:08 Z This graph shows the power consumption of the NIG supercomputer. - Top (yellow): Cooling System - Bo... http://localhost/en/report/institution/accounts_by_institution_2023/ http://localhost/en/report/institution/accounts_by_institution_2023/ Fri, 03 Apr 2026 08:57:08 Z Aggregated only for universities and public research institutions (companies are not dixcclosed). Na... http://localhost/en/report/institution/accounts_by_institution_2024/ http://localhost/en/report/institution/accounts_by_institution_2024/ Fri, 03 Apr 2026 08:57:08 Z Aggregated only for universities and public research institutions (companies are not dixcclosed). Na... http://localhost/en/report/institution/accounts_by_institution_2025/ http://localhost/en/report/institution/accounts_by_institution_2025/ Fri, 03 Apr 2026 08:57:08 Z Aggregated only for universities and public research institutions (companies are not disclosed). Nam... http://localhost/en/report/papers/papers_2012/ http://localhost/en/report/papers/papers_2012/ Fri, 03 Apr 2026 08:57:08 Z List of papers published by users January 1st, 2012 -- December 31st, 2012 Papers compiled at the en... http://localhost/en/report/papers/papers_2013/ http://localhost/en/report/papers/papers_2013/ Fri, 03 Apr 2026 08:57:08 Z List of papers published by users January 1st, 2013 -- December 31st, 2013 Papers compiled at the en... http://localhost/en/report/papers/papers_2014/ http://localhost/en/report/papers/papers_2014/ Fri, 03 Apr 2026 08:57:08 Z List of papers published by users January 1st, 2014 -- December 31st, 2014 Papers compiled at the en... http://localhost/en/report/papers/papers_2015/ http://localhost/en/report/papers/papers_2015/ Fri, 03 Apr 2026 08:57:08 Z List of papers published by users January 1st, 2015 -- December 31st, 2015 Papers compiled at the en... http://localhost/en/report/papers/papers_2016/ http://localhost/en/report/papers/papers_2016/ Fri, 03 Apr 2026 08:57:08 Z List of papers published by users January 1st, 2016 -- December 31st, 2016 Papers compiled at the en... http://localhost/en/report/papers/papers_2017/ http://localhost/en/report/papers/papers_2017/ Fri, 03 Apr 2026 08:57:08 Z List of papers published by users January 1st, 2017 -- December 31st, 2017 Papers compiled at the en... http://localhost/en/report/papers/papers_2018/ http://localhost/en/report/papers/papers_2018/ Fri, 03 Apr 2026 08:57:08 Z List of papers published by users January 1st, 2018 -- December 31st, 2018 Papers compiled at the en... http://localhost/en/report/papers/papers_2019/ http://localhost/en/report/papers/papers_2019/ Fri, 03 Apr 2026 08:57:08 Z List of papers published by users January 1st, 2019 -- December 31st, 2019 Papers compiled at the en... http://localhost/en/report/papers/papers_2020/ http://localhost/en/report/papers/papers_2020/ Fri, 03 Apr 2026 08:57:08 Z List of papers published by users January 1st, 2020 -- December 31st, 2020 Papers compiled at the en... http://localhost/en/report/papers/papers_2021/ http://localhost/en/report/papers/papers_2021/ Fri, 03 Apr 2026 08:57:08 Z List of papers published by users January 1st, 2021 -- December 31st, 2021 Papers compiled at the en... http://localhost/en/report/papers/papers_2022/ http://localhost/en/report/papers/papers_2022/ Fri, 03 Apr 2026 08:57:08 Z List of papers published by users January 1st, 2022 -- December 31st, 2022 Papers compiled at the en... http://localhost/en/report/papers/papers_2023/ http://localhost/en/report/papers/papers_2023/ Fri, 03 Apr 2026 08:57:08 Z List of papers published by users January 1st, 2023 -- December 31st, 2023 Papers compiled at the en... http://localhost/en/report/papers/papers_2024/ http://localhost/en/report/papers/papers_2024/ Fri, 03 Apr 2026 08:57:08 Z List of papers published by users January 1st, 2024 -- December 31st, 2024 Papers compiled at the en... http://localhost/en/report/statistics/ http://localhost/en/report/statistics/ Fri, 03 Apr 2026 08:57:08 Z Number of users Aggregate date login user (normal) login user (large scale) DDBJ SE Total 12-31-2012...