... | ... | @@ -80,9 +80,9 @@ Check if your network configuration by pinging an outside host and your internal |
|
|
ping -c 1 www.google.com ; ping -c 1 192.168.62.7
|
|
|
|
|
|
Your result should look like this:
|
|
|
|
|
|
PING www.l.google.com (173.194.66.105) 56(84) bytes of data.
|
|
|
64 bytes from we-in-f105.1e100.net (173.194.66.105): icmp_seq=1 ttl=46 time=8.69 ms
|
|
|
```
|
|
|
PING www.l.google.com (173.194.66.105) 56(84) bytes of data.
|
|
|
64 bytes from we-in-f105.1e100.net (173.194.66.105): icmp_seq=1 ttl=46 time=8.69 ms
|
|
|
|
|
|
--- www.l.google.com ping statistics ---
|
|
|
1 packets transmitted, 1 received, 0% packet loss, time 0ms
|
... | ... | @@ -93,14 +93,14 @@ PING 192.168.62.7 (192.168.62.7) 56(84) bytes of data. |
|
|
--- 192.168.62.7 ping statistics ---
|
|
|
1 packets transmitted, 1 received, 0% packet loss, time 0ms
|
|
|
rtt min/avg/max/mdev = 0.036/0.036/0.036/0.000 ms
|
|
|
}}}
|
|
|
```
|
|
|
Edit your hosts file.
|
|
|
|
|
|
#!sh
|
|
|
sudo vi /etc/hosts
|
|
|
|
|
|
Your host file should look like this:
|
|
|
|
|
|
'''
|
|
|
127.0.0.1 localhost.localdomain localhost
|
|
|
10.160.12.60 shark.lumcnet.prod.intern shark
|
|
|
192.168.62.7 nurseshark.cluster.loc nurseshark nurse
|
... | ... | @@ -115,10 +115,10 @@ fe00::0 ip6-localnet |
|
|
ff00::0 ip6-mcastprefix
|
|
|
ff02::1 ip6-allnodes
|
|
|
ff02::2 ip6-allrouters
|
|
|
}}}
|
|
|
'''
|
|
|
|
|
|
Shark has a sdb disk we are going to use this as a /opt partition and use nfs to export this.
|
|
|
|
|
|
```
|
|
|
#!sh
|
|
|
sudo fdisk /dev/sdb
|
|
|
|
... | ... | @@ -140,7 +140,7 @@ The partition table has been altered! |
|
|
|
|
|
Calling ioctl() to re-read partition table.
|
|
|
Syncing disks.
|
|
|
}}}
|
|
|
```
|
|
|
Now format the new partition with ext4.
|
|
|
|
|
|
#!sh
|
... | ... | @@ -171,7 +171,7 @@ Auto mount the isilon nfs exports on every reboot edit your fstab file. |
|
|
sudo vi /etc/fstab
|
|
|
|
|
|
add these lines to your fstab file.
|
|
|
|
|
|
```
|
|
|
research.isilon.lumcnet.prod.intern:/ifs/exports/home /home/ nfs rw,hard,intr,rsize=32768,wsize=32768,tcp,vers=3,noatime 0 2
|
|
|
research.isilon.lumcnet.prod.intern:/ifs/exports/system /share/isilon/system/ nfs rw,hard,intr,rsize=32768,wsize=32768,tcp,vers=3,noatime 0 2
|
|
|
research.isilon.lumcnet.prod.intern:/ifs/exports/UCSC-bam /bam-export nfs rw,hard,intr,rsize=32768,wsize=32768,tcp,vers=3,noatime 0 2
|
... | ... | @@ -179,7 +179,7 @@ add these lines to your fstab file. |
|
|
research.isilon.lumcnet.prod.intern:/ifs/exports/data/MolEpi /data/MolEpi nfs rw,hard,intr,rsize=32768,wsize=32768,tcp,vers=3,noatime 0 2
|
|
|
research.isilon.lumcnet.prod.intern:/ifs/exports/data/DIV5/GoNL /data/DIV5/GoNL nfs rw,hard,intr,rsize=32768,wsize=32768,tcp,vers=3,noatime 0 2
|
|
|
research.isilon.lumcnet.prod.intern:/ifs/exports/data/DIV5/HumGen /data/DIV5/HumGen nfs rw,hard,intr,rsize=32768,wsize=32768,tcp,vers=3,noatime 0 2
|
|
|
|
|
|
```
|
|
|
To mount all type:
|
|
|
|
|
|
#!sh
|
... | ... | @@ -255,7 +255,7 @@ Edit the named.conf.options file: |
|
|
sudo vi /etc/bind/named.conf.options
|
|
|
|
|
|
Make sure the file looks like this:
|
|
|
|
|
|
```
|
|
|
options {
|
|
|
directory "/var/cache/bind";
|
|
|
|
... | ... | @@ -274,14 +274,14 @@ Make sure the file looks like this: |
|
|
10.12.1.9;
|
|
|
};
|
|
|
};
|
|
|
}}}
|
|
|
```
|
|
|
Edit the named.conf.local file:
|
|
|
|
|
|
#!sh
|
|
|
sudo vi /etc/bind/named.conf.local
|
|
|
|
|
|
To look like this:
|
|
|
|
|
|
```
|
|
|
zone "cluster.loc" {
|
|
|
type master;
|
|
|
file "/etc/bind/db.cluster.loc";
|
... | ... | @@ -291,7 +291,7 @@ zone "62.168.192.in-addr.arpa" { |
|
|
type master;
|
|
|
file "/etc/bind/db.62.168.192";
|
|
|
};
|
|
|
}}}
|
|
|
```
|
|
|
### Configure the Forward DNS Records
|
|
|
Create the file db.cluster.loc :
|
|
|
|
... | ... | @@ -299,7 +299,7 @@ Create the file db.cluster.loc : |
|
|
sudo vi /etc/bind/db.cluster.loc
|
|
|
|
|
|
Edit the file to look like this:
|
|
|
|
|
|
```
|
|
|
$TTL 24h
|
|
|
|
|
|
cluster.loc. IN SOA nurseshark.cluster.loc. root.cluster.loc (
|
... | ... | @@ -341,7 +341,7 @@ greenlandshark.cluster.loc. IN A 192.168.62.34 |
|
|
whorltoothshark.cluster.loc. IN A 192.168.62.35
|
|
|
camouflageshark.cluster.loc. IN A 192.168.62.36
|
|
|
megalodonshark.cluster.loc. IN A 192.168.62.37
|
|
|
}}}
|
|
|
```
|
|
|
|
|
|
### Configure the Reverse DNS Records
|
|
|
Create the file db.62.168.192
|
... | ... | @@ -350,7 +350,7 @@ Create the file db.62.168.192 |
|
|
sudo vi /etc/bind/db.62.168.192
|
|
|
|
|
|
Edit the file to look like this:
|
|
|
|
|
|
``
|
|
|
$TTL 24h
|
|
|
|
|
|
62.168.192.in-addr.arpa. IN SOA nurseshark.cluster.loc. root.cluster.loc (
|
... | ... | @@ -393,7 +393,7 @@ Edit the file to look like this: |
|
|
35.62.168.192.in-addr.arpa. IN PTR whorltoothshark.cluster.loc.
|
|
|
36.62.168.192.in-addr.arpa. IN PTR camouflageshark.cluster.loc.
|
|
|
37.62.168.192.in-addr.arpa. IN PTR megalodonshark.cluster.loc.
|
|
|
}}}
|
|
|
```
|
|
|
|
|
|
Restart BIND :
|
|
|
|
... | ... | @@ -420,9 +420,9 @@ should give the following result back: |
|
|
host 192.168.62.7
|
|
|
|
|
|
returns
|
|
|
|
|
|
```
|
|
|
7.62.168.192.in-addr.arpa domain name pointer nursesharktest.cluster.loc.
|
|
|
|
|
|
```
|
|
|
|
|
|
## Install DHCP
|
|
|
|
... | ... | @@ -436,7 +436,7 @@ Edit the dhcpd.conf file: |
|
|
|
|
|
Make sure the file looks like this, the mac addresses should reflect the mac addresses for the blade servers!!!
|
|
|
in the file are the current mac addresses, these could change!!!
|
|
|
|
|
|
```
|
|
|
default-lease-time 900;
|
|
|
max-lease-time 900;
|
|
|
option subnet-mask 255.255.255.0;
|
... | ... | @@ -587,7 +587,7 @@ subnet 192.168.62.0 netmask 255.255.255.0 { |
|
|
# option host-name "megalodonshark";
|
|
|
}
|
|
|
}
|
|
|
}}}
|
|
|
```
|
|
|
Restart your DHCP server:
|
|
|
|
|
|
#!sh
|
... | ... | @@ -626,9 +626,9 @@ Edit the file /etc/inetd.conf: |
|
|
sudo vi /etc/inetd.conf
|
|
|
|
|
|
add the line :
|
|
|
|
|
|
```
|
|
|
tftp dgram udp4 wait root /usr/sbin/in.tftpd /usr/sbin/in.tftpd -s /var/lib/tftpboot
|
|
|
|
|
|
```
|
|
|
Now we need to create the tftboor Dir:
|
|
|
|
|
|
#!sh
|
... | ... | @@ -646,13 +646,13 @@ Edit the boot menu config file txt.cfg |
|
|
#!sh
|
|
|
sudo vi /tftpboot/ubuntu-installer/amd64/boot-screens/txt.cfg
|
|
|
|
|
|
Add the following lins to this file:
|
|
|
|
|
|
Add the following links to this file:
|
|
|
```
|
|
|
LABEL Shark execute Node Precise server auto install
|
|
|
menu default
|
|
|
kernel ubuntu-installer/amd64/linux
|
|
|
append ramdisk_size=14984 locale=en_US console-setup/ask_detect=false keyboard-configuration/layoutcode=us netcfg/wireless_wep= netcfg/choose_interface=eth0 netcfg/get_hostname= preseed/url=http://shark.lumcnet.prod.intern/preseed.cfg vga=normal initrd=ubuntu-installer/amd64/initrd.gz --
|
|
|
|
|
|
```
|
|
|
edit the file /tftpboot/ubuntu-installer/amd64/pxelinux.cfg/default :
|
|
|
|
|
|
#!sh
|
... | ... | @@ -695,7 +695,7 @@ Add the tftp service to your xinetd config |
|
|
sudo vi /etc/xinetd.d/tftp
|
|
|
|
|
|
add the following:
|
|
|
|
|
|
```
|
|
|
# TFTP configuration
|
|
|
service tftp
|
|
|
{
|
... | ... | @@ -708,7 +708,7 @@ add the following: |
|
|
server_args = -s /tftpboot
|
|
|
disable = no
|
|
|
}
|
|
|
}}}
|
|
|
```
|
|
|
Restart xinetd service:
|
|
|
|
|
|
#!sh
|
... | ... | @@ -749,12 +749,12 @@ make sure the home dir is owned by the nodeinstaller user: |
|
|
|
|
|
### Install Open Grid Sheduler
|
|
|
Get compile dependencies:
|
|
|
|
|
|
```
|
|
|
#!sh
|
|
|
sudo apt-get build-dep gridengine-common gridengine-client gridengine-exec gridengine-master gridengine-qmon
|
|
|
sudo apt-get install -y pvm-dev csh libpam0g-dev libxt-dev libmotif-dev x11proto-fixes-dev x11proto-randr-dev x11proto-xinerama-dev libxft-dev libxp-dev libxp6
|
|
|
sudo apt-get install -y xfs xfstt gsfonts gsfonts-x11 texlive-fonts-extra texlive-fonts-recommended xfonts-scalable cm-super cmap-adobe-cns1 cmap-adobe-gb1 dvi2ps-fontdata-three t1-cyrillic tex-gyre ttf-adf-ikarius libfreetype6 ttf-freefont ttf-uralic xfonts-mplus fgfs-base t1-xfree86-nonfree ttf-xfree86-nonfree ttf-xfree86-nonfree-syriac ttf-mscorefonts-installer dbus-x11 gnuplot-x11 gsfonts-x11 libx11-6 libx11-data libx11-dev libx11-protocol-perl x11-common x11-utils x11-xserver-utils x11proto-core-dev x11proto-fixes-dev x11proto-input-dev x11proto-kb-dev x11proto-print-dev x11proto-randr-dev x11proto-render-dev x11proto-xext-dev x11proto-xinerama-dev xfonts-base xfonts-100dpi xfonts-75dpi xfonts-100dpi-transcoded xfonts-75dpi-transcoded gsfonts-x11 lmodern texlive-fonts-recommended texlive-font-utils defoma fontconfig ttmkfdir cabextract ttmkfdir libmotif-dev libmotif3
|
|
|
|
|
|
```
|
|
|
Create the OpenGridScheduler directoryand change into this directory:
|
|
|
|
|
|
#!sh
|
... | ... | @@ -774,7 +774,7 @@ Get the Open Grid Scheduler source,extract and compile read http://gridscheduler |
|
|
|
|
|
|
|
|
Install the gridengine
|
|
|
|
|
|
```
|
|
|
#!sh
|
|
|
mkdir /usr/local/OpenGridScheduler/gridengine-GE2011.11
|
|
|
ln -s /usr/local/OpenGridScheduler/gridengine-GE2011.11 /usr/local/OpenGridScheduler/gridengine
|
... | ... | @@ -832,7 +832,7 @@ Install the gridengine |
|
|
Hit <RETURN> to continue >> <RETURN>
|
|
|
Configurations , 1) Normal, Default configuration is [1] >> 1
|
|
|
We're configuring the scheduler with >Normal< settings!, Do you agree? (y/n) [y] >> y
|
|
|
|
|
|
```
|
|
|
You should now enter the command:
|
|
|
|
|
|
source /usr/local/OpenGridScheduler/gridengine/default/common/settings.csh
|
... | ... | @@ -844,7 +844,7 @@ if you are a csh/tcsh user or |
|
|
if you are a sh/ksh user.
|
|
|
|
|
|
This will set or expand the following environment variables:
|
|
|
|
|
|
```
|
|
|
- $SGE_ROOT (always necessary)
|
|
|
- $SGE_CELL (if you are using a cell other than >default<)
|
|
|
- $SGE_CLUSTER_NAME (always necessary)
|
... | ... | @@ -857,7 +857,7 @@ Hit <RETURN> to see where Grid Engine logs messages >> <RETURN> |
|
|
Do you want to see previous screen about using Grid Engine again (y/n) [n] >> n
|
|
|
Please hit <RETURN> >> <RETURN>
|
|
|
|
|
|
}}}
|
|
|
```
|
|
|
Tight Integration of the MPICH2 library into SGE.
|
|
|
Remove libopenmpi1.3 openmpi-common:
|
|
|
|
... | ... | @@ -872,7 +872,7 @@ Add a new parallel environment mpich2. |
|
|
qconf -ap mpich2
|
|
|
|
|
|
Make sure it looks like this:
|
|
|
|
|
|
```
|
|
|
pe_name mpich2
|
|
|
slots 122
|
|
|
user_lists NONE
|
... | ... | @@ -884,7 +884,7 @@ Make sure it looks like this: |
|
|
job_is_first_task FALSE
|
|
|
urgency_slots min
|
|
|
accounting_summary FALSE
|
|
|
|
|
|
```
|
|
|
Add the new parallel environment to the queue you want mpich2 for.
|
|
|
|
|
|
qconf -mq para.q
|
... | ... | @@ -931,7 +931,7 @@ create the /etc/init.d/ganglia-start script: |
|
|
chmod a+x /etc/init.d/ganglia-monitor
|
|
|
|
|
|
edit the script to look like this:
|
|
|
|
|
|
```
|
|
|
#! /bin/sh
|
|
|
### BEGIN INIT INFO
|
|
|
# Provides: ganglia-monitor
|
... | ... | @@ -977,14 +977,14 @@ case "$1" in |
|
|
esac
|
|
|
|
|
|
exit 0
|
|
|
}}}
|
|
|
```
|
|
|
Create the /etc/init.d/gmetad start script:
|
|
|
|
|
|
#!sh
|
|
|
sudo vi /etc/init.d/gmetad
|
|
|
|
|
|
MAke sure it looks like this:
|
|
|
|
|
|
Make sure it looks like this:
|
|
|
```
|
|
|
#! /bin/sh
|
|
|
### BEGIN INIT INFO
|
|
|
# Provides: gmetad
|
... | ... | @@ -1030,8 +1030,8 @@ case "$1" in |
|
|
esac
|
|
|
|
|
|
exit 0
|
|
|
}}}
|
|
|
Majke the script executable:
|
|
|
```
|
|
|
Make the script executable:
|
|
|
|
|
|
chmod a+x /etc/init.d/gmetad
|
|
|
|
... | ... | @@ -1041,7 +1041,7 @@ Configure ganglia: |
|
|
cp ~/ganglia-3.3.7/web/debian/gmond.conf /etc/ganglia/
|
|
|
|
|
|
vi /etc/ganglia/gmond.conf, make sure the cluster part looks like this:
|
|
|
|
|
|
```
|
|
|
|
|
|
cluster {
|
|
|
name = "Shark Cluster"
|
... | ... | @@ -1049,18 +1049,17 @@ vi /etc/ganglia/gmond.conf, make sure the cluster part looks like this: |
|
|
latlong = "unspecified"
|
|
|
url = "unspecified"
|
|
|
}
|
|
|
}}}
|
|
|
```
|
|
|
add a UDP receive channel to the gmond.conf file :
|
|
|
|
|
|
|
|
|
```
|
|
|
udp_recv_channel {
|
|
|
#mcast_join = shark.lumcnet.prod.intern
|
|
|
port = 8649
|
|
|
#bind = shark.lumcnet.prod.intern
|
|
|
family = inet4
|
|
|
}
|
|
|
}}}
|
|
|
|
|
|
```
|
|
|
Install the ganglia web frontend:
|
|
|
|
|
|
#!sh
|
... | ... | @@ -1074,7 +1073,7 @@ Please edit the Makefile found in the tarball. Adjust the DESTDIR to where you c |
|
|
|
|
|
make install
|
|
|
chown -R www-data:www-data /var/www/ganglia-web-3.4.2
|
|
|
}}}
|
|
|
|
|
|
|
|
|
Make sure ganglia and gmetad start at boot time:
|
|
|
|
... | ... | @@ -1116,7 +1115,7 @@ Create a common-cluster-env.sh file: |
|
|
Make the file look like this:
|
|
|
|
|
|
#!/bin/bash
|
|
|
|
|
|
```
|
|
|
####add here system wide variables and PATH for all sharks
|
|
|
####this filexs will be loaded by the /etc/bash.bashrc script on all sharks.
|
|
|
|
... | ... | @@ -1154,7 +1153,7 @@ export TMOUT=1000 |
|
|
export readonly TMOUT=1000
|
|
|
|
|
|
unset MANPATH
|
|
|
}}}
|
|
|
```
|
|
|
make this file executable:
|
|
|
|
|
|
#!sh
|
... | ... | |