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Introduction(The General Analysis Section)

System configuration of the general analysis section

The general analysis section of NIG supercomputer is a cluster configuration of bundling of many computers called nodes.

A job scheduler is a program that assigns an appropriate computer on a cluster computer system to a computation request from a user. The NIG supercomputer uses the Univa Grid Engine (UGE), the successor to Sun Grid Engine, which has been widely used in bioinformatics, as a job scheduler.

All nodes managed by UGE mounts a Large capacity high speed storage system (Lustre FS) and users' home directories are equally accessible from all nodes.

UGE Queue Type

Compute nodes managed by the UGE are broadly devided into login nodes and compute nodes.

  • Login nodes(login node) are calculators to develop users' programs or perform small, quick calculations interactively on the spot.
  • Compute nodes(compute node) are compute node to perform calculations that take a long time or use a large amount of CPU or memory.

Compute requests called jobs to login and compute nodes are managed in UGE with queues. Jobs wait in queue and are automatically executed by UGE as soon as a computer is available if calculation requirements exceed computer resources.

In the general analysis section of the NIG supercomputer, there is a UGE queue for each type of compute node.

Compute nodes TypeUGE queue nameHardware typeNumber of computers and total cores
Login NodesloginThin nodes Type1b
(AMD EPYC7702, 128 CPU cores/node,
4GB memory/CPU core)
three computers
login_gpuThin nodes Type2b
(Intel Xeon Gold 6136, 24 CPU cores/node,
16GB memory/CPU core)
one computer
Compute NodesepycThin nodes Type1b
(AMD EPYC7702, 128 CPU cores/node,
4GB memory/CPU core)
Thin nodes Type1a
(AMD EPYC7501, 64 CPU cores/node,
8GB memory/CPU core)
 
intelThin nodes Type2a
(Intel Xeon Gold 6130, 32 CPU cores/node,
12GB memory/CPU core)
gpuThin nodes Type2b
(Intel Xeon Gold 6136, 24 CPU cores/node,
16GB memory/CPU core)
shortThin nodes Type2b
(Intel Xeon Gold 6136, 24 CPU cores/node,
16GB memory/CPU core)
mediumMedium nodes
(Intel Xeon Gold 6148, 80 CPU cores/node,
38.4GB moemory/CPU core)
nine computers