KIGI DevOps

July. 15th, 2014

,
GIST (Gwangju Institute of Science & Technology),
SCENT (Super Computing CENTer)
http://scent.gist.ac.kr

Youngbin Im

ybim@nm.gist.ac.kr

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GIST (KIGI)

Intel compiler 9.1 / Intel compiler 10.1 / GNU 4.1.2

MPICH-GM

MKL / FFTW 3.2 / FFTW 3.2.2 / FFTW 2.1.5 / netcdf 4.7 / lapack 3.0-37
VASP 4.6.38 (VASP_Param )
VASP 5.2.12 (VASP_Param )
VASP 5.3.2 (VASP_Param )

GAMESS(2009-01-21 R3)
Crystal 09
Gaussian 09

Lammps (2009-07-07), Lammps (2010-04-18)

Lammps (2013-06-07), Lammps (2013-08-21)
Lammps(2013-09-09)

WRF 3.0.1
NAMD 2.8b1
P4VASP 0.3.23
VESTA 3.1.7 ()

Gnuplot 4.6.4 ()
/home01/applic/lammps/intel/ssh/
/home01/applic/lammps/lammps-18Apr10/intel/ssh
/home01/applic/name/2.7b1/intel/ssh/
/home01/applic/gamess

LAMMPS
/home01/applic/lammps
lammps-23Sep13 (9Sep13, 21Aug13, 7Jun13)
VASP
/home01/applic/vasp
5.2.12, 5.3.3 (vasp/vasp.5.2.12 )

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PLSI (14/07/10)

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.
.
.

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:
kernel update, GPFS , Loadleveler , LDAP , Module
, Myrinet , NAGIOS , pdsh , syslog-ng , ntp
1. Kernel update
2. GPFS
3. Loadleveler
4. ldap
5. module
6. myrinet
7. gm
8. gm
9. ping
10. nagios
11. pdsh
12. syslog-ng
13. ntp

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KIGI

[ ]

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Script version
1. script1.sh
2. script2.sh
3. script3.sh
4. script4.sh
5. script5.sh
6. script6.sh
7. script7.sh

1. Kernel update
2. GPFS
3. Loadleveler
4. ldap
5. module
6. myrinet
7. gm
8. gm
9. ping
10.
11.
12.
13.

nagios
pdsh
syslog-ng
ntp

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Source code

Script1.sh

Script2.sh

Script5.sh

Script3.s
h

Script6.sh

Script4.sh

Script7.sh

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Chef

http://www.getchef.com/chef/
2009 1

(https://supermarket.getchef.com/cookbooks)
Automation platform for the coded business

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Chef ?

Chef is an automation platform for developers & systems engineers to

continuously define, build, and manage infrastructure.

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Chef

Workstation : (OS: win, mac, linux)

Server : Chef-Server
Node : Chef-Client

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Chef Components
Nodes
Workstations
- Knife
- Repository

The Hosted Server

- Cookbooks
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Recipes & Cookbooks

Recipes are collections of

Resources
Cookbooks contain
recipes, templates, files,
custom resources, etc
Code re-use and
modularity

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Resources

http://docs.opscode.com/

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Resources - bash

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Resources - package

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Resources - template

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Resources

http://docs.opscode.com/

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(Small) HPC over Cloud Test-bed

HPC over Cloud Test-bed

KIGI Box
(8core, 12GB mem)
GPU node

CPU : Intel Xeon 2.4 GHz x 1

OS : Cent OS 5.3
Memory : 8GB
HDD: 1TB

GPU (Nvidia K5000)

4GB GDDR5

1,536 CUDA Cores

Shader Model 5.0,
OpenGL 4.3, DirectX 11
CUDA, DirectCompute,
OpenCL

GPU node 1

kigi125

Node
GPU 11

kigi126
kigi127

GPU 2

kigi128

KIGI node

CPU : Intel Xeon 2.8 GHz x 2

OS : Cent OS 5.3 (32bit)
Memory : 3GB
HDD: 5TB

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HPC Box
Network Setting

SSH

4
Compute
nodes

IP: 203.x.x.x
ID : ybim
PW : ****

Node
Node
Node
Node

1
2
3
4

(kigi-lg) : 100.1.1.1 / kigi-lg.scent.or.kr

(kigi001) : 100.1.1.101 / kigi001.scent.or.kr
(kigi002) : 100.1.1.102 / kigi002.scent.or.kr
(kigi003) : 100.1.1.103 / kigi003.scent.or.kr

Node 1
Node 2
Node 3
Node 4

Kigi 125, 126, 127, 128

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GPU Box

node

CPU : Intel Xeon 2.4 GHz x 1

OS : Cent OS 5.3
Memory : 8GB
HDD: 1TB

GPU
4GB GDDR5
1,536 CUDA Cores
Shader Model 5.0,
OpenGL 4.3, DirectX 11
CUDA, DirectCompute,
OpenCL

1
Compute nod
e
Node 1
GPU 1
GPU 2

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Install Test Chef

1. Chef
4. Cookbook

5. Recipe

2. Repository

6. Chef Solo
3. Knife

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(Small) HPC over Cloud Test-bed

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Testbed for HPC over Cloud

SSH
203.x.x.x

IP: 203.x.x.x
ID : root
PW : ****

1
Compute
node
203.x.x.x

Node001
(64bit)

1. Network
(Public
private )
2. CPU bit
(64bit / 32bit)
3. O/S
(Ubuntu 12.04
/ Centos 5.3)
.
.
.

4
Compute
nodes
Kigi125
(32bit)
Kigi126
(32bit)
Kigi127
(32bit)
Kigi128
(32bit)

Network Setting

kigi125
kigi126
kigi127
kigi128

:
:
:
:

x.x.x.224
x.x.x.225
x.x.x.226
x.x.x.227

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Chef Installer FAQ

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Knife bootstrap
Knife bootstrap node x root P passwd
chef (client)
/etc/chef
chef-validator
chef-client client.rb
chef-client chef server

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error - Knife bootstrap

Error - Temporary failure in name resolution

Install - Chef-11.10.4-1.el5.i686.rpm (rpm/32bit)

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server - client
sudo chef-client --server http://x.x.x.228 N kigi126

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error client.rb
Did not find config file: /etc/chef/client.rb

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error - NTP
NTP time / 15 minute

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error - hostname

vi /etc/sysconfig/network

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recipe / run

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search node

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Chef Control Box

1. PLSI
(login01)
ssh 134.75.133.228

KIGI
(kigi-001~128)
ssh kigi128

2. KIGI
(kigi-lg01)
ssh kigi-lg01

3. Chef Control Box

(kigi-lg01)
ssh 134.75.133.228

Chef Control Box 3 SSH

kigi001~kigi128

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SCENT


:
kernel update, GPFS , Loadleveler , LDAP , Module
, Myrinet , NAGIOS , pdsh , syslog-ng , ntp
1. Kernel update
2. GPFS
3. Loadleveler
4. ldap
5. module
6. myrinet
7. gm
8. gm
9. ping
10. nagios
11. pdsh
12. syslog-ng
13. ntp

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Source code

recipe[kigi::automation]

- 88 / 2,770
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parallel / recovery-kigi125~7

case

kigi

run time

Serial

kigi128

436s

Parallel

Kigi125

405s

Parallel

Kigi126

395s

Parallel / idempotence

Kigi127

313s

Average / 412s / 6m 8s

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Thank you!
Sent Inquiry to ybim@nm.gist.ac.kr
http://scent.gist.ac.kr
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Contact Us

http://scent.gist.ac.kr

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Add: 261 ()
C 206, () 500-712
E-mail: mail@scent.gist.ac.kr
Tel: 062-715-3149
Fax: 062-715-3155
, ybim@nm.gist.ac.kr, 062-715-3135
, jykim@nm.gist.ac.kr, 062-715-2276

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