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[[IT memo/linuxmemo4]]

- [[IT memo/linuxmemo]] for fuyu.ucsd.edu
- [[IT memo/linuxmemo2]] for isotope.ccsr.u-tokyo.ac.jp
- [[IT memo/linuxmemo3]] for isotope2.iis.u-tokyo.ac.jp->decomposed
*Setting up isotope2.ccsr.u-tokyo.ac.jp [#n1343bf2]
*Setting up isotope2.aori.u-tokyo.ac.jp [#n1343bf2]

**specification [#od3291a8]
 Name: isotope2
 Name: isotope2 (renewed on 2016)
 Cluster system
 Headnode: Xeon X5680 (3.3GHz, hexa core) x2
 Compute node: [Xeon X5690 (3.46GHz, hexa core)x2]x12
 Storage: /data:8TB, /data1-6:11TBx6
// Headnode: Xeon X5680 (3.3GHz, hexa core) x2
 Headnode: Xeon E5-2640 V4 2.4GHz 10Core×2
 Compute node: 
  Xeon X5690 (3.46GHz, hexa core) x2x12
  Xeon E5-2697V2 (2.7GHz, 12Core) x2x2
 Network: InfiniBand QDR (MPI/NFS)
 OS: RedHat Enterprise Linux 5 (Server)

** OS [#oc0ca5f6]

** softwares [#o93ecf92]
大抵はisotope2からそのまま引き継げでいる。詳しくは[IT memo/linuxmemo3]参照。

** ganglia [#s0a3fe41]
- ノード負荷状況のモニター。 から見れる(CCSR内のみ)。

* Basic rules [#qb8c8ad5]
- Use /dataX directories. Minimize to use /home directory.
- Use PBS (computing nodes) for long job. Head node (isotope2) is interactive use only. 

* Getting start [#k0cbab80]
- change your password ($ passwd)
- change your login shell to /bin/tcsh ($ chsh)
- copy /home/kei/.cshrc in your home directory ($ cp /home/kei/.cshrc ~/)
‐ go to your working directory (/dataX/yyyy) and work. ($ cd /dataX/yyyy)
- change your password
 $ passwd
- change your login shell to /bin/tcsh (if your default is bash)
 $ chsh
- copy /home/kei/.cshrc in your home directory 
 $ cp /home/kei/.cshrc ~/
- make your public key for isotope2
 $ ssh-keygen -t rsa
 (do not input passphrase)
- save your id_rsa.pub as authorized_keys
 $ cat ~/.ssh/id_rsa.pub >> ~/.ssh/authorized_keys
 $ chmod 600 ~/.ssh/authorized_keys
- go to your working directory (/dataX/yyyy) and work. 
 $ cd /dataX/yyyy

* Manuals [#rbdbd6cc]

* Benchmark [#af5ded83]
** NCEP/SIO GSM [#ka320ddd]
-http://http://g-rsm.wikispaces.com のグローバルモデルのテスト。
 Run1 (headnode only): 30.9s
 Run2 (node=1:ppn=8):  30.4s
 Run3 (node=2:ppn=4):  26.3s
 Run4 (node=4:ppn=2):  23.9s

** NCEP/SIO RSM [#gfcc5d91]
 Run1 (node=2:ppn=12): 536.2s
 Run2 (node=3:ppn=8):  518.6s
 Run3 (node=4:ppn=6):  510.5s

** NICAM [#y0e400b8]
- GL5RL0, Isotope/River入り実験。10並列、72時間。
- mvapich2だとノードをまたぐジョブがうまく走らない。
 Run1 mvapich2 (node=1:ppn=10): 404s
 Run2 mpich1 (node=1:ppn=10): 401s
 Run3 mpich1 (node=2:ppn=5): 336s

** MIROC5 offline MATSIRO [#z57fcfe5]
- AR5用のMIROC5陸面のみ。1ヶ月計算。
 Run1 mvapich2-1.6 (node=2:ppn=10) 82s
 Run2 mvapich2-1.6 (node=4:ppn=5) 76s
 Run3 openmpi-1.5.4 (node=2:ppn=10) 83s
 Run4 openmpi-1.5.4 (node=4:ppn=5) 70s
mpich2だとcannot connect to local mpdというエラーが出て止まる。