Backup diff of Linux/Install vs current(No. 2)

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*Installation [#g87845a1]

**/opt configuration [#g3950b46]

create /opt partion during installation.

 $ su
 password:
 $ cd /usr/local
 $ mv * /opt
 $ cd /usr
 $ rmdir /usr/local
 $ ln -s /opt local

Basic idea is that we are fond of having non-mandriva applications installed in /opt directory.  Those are Intel compiler, ncview, matlab, google-earth, and so on.  /opt directory / partition should have > 8GB (preferably > 16 GB).

/optに必要なソフトをコピーする。例えばsnapperにocean:/optを丸ごとコピーしてみよう。
まず、snapper上で、

 $ su
 password:
 $ chown yusuke:yusuke -R /opt

を実行して、/optに書き込み権限を与える（この場合、ユーザー「yusuke」はoptを改変できる）。
次にocean上で、

 $ su
 password:
 cd /opt
 $ rsync -av --progress * yusuke@snapper:/opt/

を実行し、ocean:/opt --> snapper:/optに同期させる。

続いてMatlab関連のファイルをコピーする。例えばtatsuya@oceanのホームディレクトリにあるmatlabディレクトリをyuki@snapperにコピーする場合は、

 $ su
 password:
 $ cd /home/tatsuya
 $ rsync -av --progress matlab yuki@snapper:~/

「.cshrc」ファイルを編集する。編集済みのものがyuki@snapper:/home/yukiにあるので、それをコピーすればよい。例えば、yellowtail上で、

 $ scp -pv yuki@snapper:/home/yuki/.cshrc .
 $ cd ~
 $ source .cshrc

最後にROMSのテストファイルをコピーする。ここではhideki@octopusにあるマダガスカルのサンプルをコピーする例を示す。

 $ ssh octopus
 $ cd ~/ROMS/test1
 $ rsync -av --progress code grid bry yuki@snapper:/home/yuki/ROMS/test1/

**NVIDIATM video driver [#z099fd2b]

Use mcc (Mandriva Control Center) to install linux kernel source, ld, binutils, make, gcc, gfortran, etc...

Leave x-window to get console mode

 su
 telinit 3

then

 sh NVIDIA-Linux-x86_64-260.19.44.run

from the appropriate directory where the driver file is saved.

Basically, video drivers must be merged with Linux kernel.  Nvidia drivers manage to re-compile the kernel from the kernel source file. (n.b., The student workstations are equipped with GeForce GT430.  Use the appropriate driver.)


**Failure in mounting a DVD drive during installation [#c0152804]

For workstations with ASUS P8H67-V mother board, a DVD drive is missing immediately after the linux kernel in the installation DVD (Mandriva 2010.2 Free) takes over the BIOS-level DVD controller.  This is true for the three BTO computers bought from Unitcom Inc. for the 2011 undergrads.

This is caused by incomplete packaging of the Mandriva 2010.2 distribution with the AHCI driver for SATA3 ports. The thing is that the DVD drive attached to a SATA3 port on M/B (the grayish connector) is inaccessible from the Linux kernel.  Another possible solution is to (update flush BIOS and) disable AHCI mode to revert back to IDE mode --- it was unfortunately not working with our PCs.

A (crude) solution is to detach the DVD data cable from a SATA3 port and then to plug in to a SATA2 port (the blueish connectors) before the installation.  This is totally OK because DVD drives do not require such a high speed accessibility.  Rather, SATA3 ports are reserved for extra HDD for future usage.


**Dropping NIC with a kernel message like "Disabling IRQ #xx"... [#w52e28db]

You should add "irqpoll" during booting your machine to prevent this issue. Make yourself root

 su
 vi /boot/grub/menu.lst
 kernel /vmlinuz ............ vga=788 irqpoll

and reboot your machine.


**Restart MATLAB license manually [#u123aad0]

As a user, go to /opt/MATLAB/R2011a/etc, then submit

 ./lmstart

This sequence should be done automatically upon booting.


**Fixing hostname of the machine [#ub373260]

Add your hostname in /etc/hosts

It reads:

 127.0.0.1       sardine
 127.0.0.1       localhost
    :                    :

Edit /etc/sysconfig/network

 NETWORKING=yes
 CRDA_DOMAIN=US
 HOSTNAME=sardine.dce.kobe-u.ac.jp

Restart network with 

 /etc/init.d/network restart

**Configure RAID 5 [#n75c81ac]
 
Go with mcc and do the followings:

-Local disks --> Manage disk partitions 
-sdb, sdc, sdd, sde --> Linux Raid
-add all 4 disks to RAID --> RAID 5, md0
-raid --> mount point (such as /snapper <-- you have to make it as root a priori)
-execute "format" command.

to check raid signature, submit

 mdadm --examine /dev/sdX1   (where X stands for b,c,d or e)

for all the disks to make sure if they have the same signature. It looks like
          Magic : a92b4aaa
        Version : 00.90.00
           UUID : 4b1175ca:a8baaaac:134a2d0d:3b22ab35
  Creation Time : Wed Feb 17 10:25:21 2010

UUID is the signature. Then copy & paste it to /etc/mdadm.conf

 [root@ainu etc]# vi /etc/mdadm.conf
 DEVICE /dev/sdb1 /dev/sdc1 /dev/sdd1 /dev/sde1 /dev/sdf1 /dev/sdg1 /dev/sdh1 /dev/sdi1
 ARRAY /dev/md0 UUID=ee47f80d:c8a96e63:d8dad40f:1b9552ad auto=no
 MAILADDR uchiyama@we.love.ocean

Then check the status of creation of your RAID volume.

 cat /proc/mdstat
 Personalities : [raid6] [raid5] [raid4]
 md0 : active raid5 sdb1[0] sdc1[1] sdd1[2] sde1[4]
       5860532352 blocks super 1.2 level 5, 128k chunk, algorithm 2 [4/3] [UUU_]
       [==========>..........]  recovery = 50.9% (994464644/1953510784) finish=122.2min speed=130700K/sec


That's all for now.  It may take up to several hours.  Go get a coffee.