Hardware

Overview

Classification			Specifications
Compute Nodes 15,424 CPU cores 933.560 TFLOPS (CPU: 434.360 TFLOPS, GPU: 499.2 TFLOPS) 153.088 TB total memory	Thin nodes Total: 232 units Total number of CPU cores: 14,336 Total computing performance: 844.472 TFLOPS (CPU: 345.272 TFLOPS, GPU: 499.2 TFLOPS) Total memory capacity 110.080 TB	Type 1a AMD EPYC 7501 CPU.	136 nodes 8,704 CPU cores 139.264 TFLOPS 69.632 TB total memory（8GB memory/CPU core）
		Type 1b AMD EPYC 7702 CPU. (Expansion in April 2020)	28 nodes 3,584 CPU cores 57.344 TFLOPS 14.336 TB total memory (4GB memory/CPU core)
		Type 2a Intel Xeon Gold 6130 CPU	52 nodes 1,664 CPU cores 111.800 TFLOPS 19.968 TB total memory (12GB memory/CPU core)
		Type 2b GPU installed	16 nodes 384 CPU cores 64GPUs (4 GPU/node) 536.064 TFLOPS (CPU: 36.864 TFLOPS, GPU: 499.2 TFLOPS) 6.144 TB total memory (16GB moemory/CPU core)
	Medium node 3TB of shared memory installed		10 nodes 800 CPU cores 61.440 TFLOPS 30.72 TB total memory (38.4GB memory/CPU core)
	Fat node 12TB of shared memory		1 node 288 CPU cores 27.648 TFLOPS 12.288 TB total memory (42.7GB memory/CPU core)
Storage Total storage capacity: 57.6PB	Analysis storage(*1) For user home directories in the general analysis division and personal genome analysis division.		Lustre file system 13.3PB
	Database storage For DDBJ database including DRA		Lustre file system 40.5PB
Inter-node interconnect network			InfiniBand 4×EDR 100Gbps fat tree (For storage, full bi-division; for compute nodes, connection bandwidth to upstream SW : connection bandwidth to downstream SW = 1:4)

Compute nodes

Thin compute node Type 1a (HPE ProLiant DL385 Gen10; 136 computers)

Compute nodes with AMD EPYC 7501 processors.

HPE ProLiant DL385 Gen10 (host name: at001 -- at136)

component	model number	number of computation	performance per node, etc
CPU	AMD EPYC 7501 (32 cores) Base 2.0GHz, Max 3.0GHz	2	Total 64 cores
Memory	32GB DDR4-2666	16	Total 512GB (8GB per CPU core)
Storage	1.6TB NVMe SSD x1, 3.2TB NVMe SSDx1
Network	InfiniBand 4xEDR	1	100Gbps

Thin compute node Type 1b (DELL PowerEdge R6525; 28 computers)

Compute nodes with AMD EPYC 7702 processors.

DELL PowerEdge R6525 (host name: at137 -- at164)

component	model number	number of computation	performance per node, etc
CPU	AMD EPYC 7702 (64 cores) Base 2.0GHz, Max 3.35GHz	2	Total 128 cores
Memory	32GB DDR4-2666	16	Total 512GB (4GB per CPU core)
Storage	1.6TB NVMe SSD x1, 900GB SAS HDDx1
Network	InfiniBand 4xEDR	1	100Gbps

Thin compute node Type 2a (HPE Apollo 2000 Gen10; 52 computers)

Compute nodes with Intel Xeon processors.

HPE Apollo 2000 Gen10 (host name: it001 -- it052)

component	model number	number of computation	performance per node, etc
CPU	Intel Xeon Gold 6130 (16 cores) Base 2.1GHz, Max 3.7GHz	2	Total 32 cores
Memory	32GB DDR4-2666	12	Total 386GB (12GB per CPU core )
Storage	1.6TB NVMe SSD x1, 3.2TB NVMe SSDx1
Network	InfiniBand 4xEDR	1	100Gbps

Thin compute node Type 2b (HPE Apollo 6500 Gen10; 16 computers)

Compute nodes with four GPUs on each node.

HPE Apollo 6500 Gen10 (host name: igt001 -- igt016)

component	model number	number of computation	performance per node, etc
CPU	Intel Xeon Gold 6136 (12 cores) Base 3.0GHz, Max 3.7GHz	2	Total 24 cores
Memory	32GB DDR4-2666	12	Total 386GB (16GB per CPU core)
GPU	NVIDIA Tesla V100 SXM2	4
Storage	1.6TB NVMe SSD x1, 3.2TB NVMe SSDx1
Network	InfiniBand 4xEDR	1	100Gbps

(Reference) GPU Specifications

Properties	Value
name	NVIDIA Tesla V100 SXM2
number of core	640
clock speed	1,455MHz
peak performance of single precision floating point number	15TFLOPS
peak performance of double precision floating point number	7.5TFLOPS
single core theoretical performance	1.3GLOPS
memory size	16GB(GDDR5)
memory bandwidth	900GB/sec
memory bandwidth per 1GFLOPS	266GB/sec
connection bandwidth	8 (PCIe2.0 x16)GB/sec

Medium compute node (HPE ProLiant DL560 Gen10; 10 computers)

The Medium node has been partially migrated to Ubuntu Linux and a new Gride Engine queue (medium-ubuntu.q) has been established. For more information, see the announcement.

These nodes are compute nodes with 80 cores with 3 TB of physical memory, suitable for running large memory intensive programs such as de novo assembler, etc. You can use it by job submission under Grid Engine.

HPE ProLiant DL560 Gen10 (host name: m01 -- m10)

component	model number	number of computation	performance per node, etc
CPU	Intel Xeon Gold 6148 (20 cores) Base 2.4GHz, Max 3.7GHz	4	Total 80 cores
Memory	32GB DDR4-2666	48	Total 3,072GB (38.4GB per CPU core)
Storage	1TB SATA HDD	2	1TB (RAID1)
Network	InfiniBand 4xEDR	1	100Gbps

Fat compute node (HPE Superdome Flex; one computer)

The fat node hardware (that is, HPE ProLiant DL560 Gen10 and HPE Superdome Flex) do not support Ubuntu Linux and could not be migrated from Cent OS 7.9 to Ubuntu Linux 22.04 at the scheduled maintenance in November 2023.

A total of 12 TB of shared memory compute nodes are configured by connecting HPE Superdome Flex 2 chassis with Superdome Flex grid interconnects.

You can use FAT nodes by application only.

HPE Superdome Flex (host name: fat1)

component	model number	number of computation	performance per node, etc
CPU	Intel Xeon Gold 6154 (18 cores) Base 3.0GHz, Max 3.7GHz	16	Total 288 cores
Memory	32GB DDR4-2666	192	Total 12,288GB (47.2GB per CPU core)
Storage	1.2TB SAS HDD	4	2.4TB (RAID1)
Network	InfiniBand 4xEDR	1	100Gbps

Storage

Analysis storage

access path	Effective Capacity	Usage	Peak Performance	Configuration
/lustre7	8.0PB	home directories in the general analysis division	35GB/sec or more	DDN SFA14KXE+SS9012, DDN 1U server, DDN SFA7700X
/lustre8	5.3PB	home directories in the personal genome analysis division	35GB/sec or more	DDN SFA14KXE+SS9012, DDN 1U server, DDN SFA7700X

Database storage

access path	Effective Capacity	Usage	Peak Performance	Configuration
/lustre9	40.5PB	DDBJ work	150GB/sec	DDN ES400NVX2 + DDN SS9024