Category Archives: Linux

Install Globus Toolkit 4.0.8 on Ubuntu 10.04 LTS

October 10, 2010Grid, HowTos, LinuxMarco Lackovic

Disclosure: this tutorial is intended for legacy applications which mandatory need the version 4.0.x of Globus Toolkit. If you don’t have an impelling reason to install that particular version, it is highly recommended that you install the latest version available of Globus Toolkit from its official web site and follow the installation guide of the official documentation.

To install Ubuntu 10.04 server, download its iso from here and create a startup USB drive using UNetbootin (don’t use Startup Disk Creator, its latest version is not compatible with Ubuntu 10.04). Once booted from the USB drive, at the Unetbootin grub menu, scroll down to the same “Install Ubuntu server” option and press TAB. Bring your cursor to the end of this line and press space once, enter

cdrom-detect/try-usb=true

and press enter to start the installation.

(1) if you want to build Globus Toolkit download gt4.0.8-all-source-installer from:

http://www.globus.org/toolkit/downloads/4.0.8/

alternatively, if you want to save about one hour, you can use the prebuilt binary installer: you can find it in the right menu of this page. Either way proceed with the next step;

(2) run:

root@host:~#
apt-get update

apt-get install vim ant build-essential libpod-* postgresql 
xinetd zlib1g-dev libiodbc2 libiodbc2-dev libxml-parser-perl libxml2-dev

(3) install Oracle Java 6 JDK;
(4) add the following lines to your /etc/profile

export JAVA_HOME=/usr/lib/jvm/jdk1.6.0_34
export ANT_HOME=/usr/share/ant
export GLOBUS_LOCATION=/usr/local/globus-4.0.8
export GLOBUS_OPTIONS="-Xms512M -Xmx2048M"
source $GLOBUS_LOCATION/etc/globus-user-env.sh
export PATH=$ANT_HOME/bin:$JAVA_HOME/bin:$PATH:$GLOBUS_LOCATION/bin

then log out and back in;

(5) run:

root@host:~# service postgresql start

(6) open “/etc/postgresql/8.4/main/postgresql.conf”, uncomment the line beginning with “listen_addresses” and set it to listen to all addresses in the following way:

listen_addresses = '*'

(7) open “/etc/postgresql/8.4/main/pg_hba.conf” and add the following line at the bottom:

host rftDatabase "globus" "x.x.x.x" 255.255.255.255 md5

where “x.x.x.x” is your public IP address;

(8) add a non-privilged user with “globus” as username by runnng:

root@host:~# adduser globus

then add the globus group to all the users you want to use the globus container from:

root@host:~# adduser username globus

then log out and back in;

(9) run:

root@host:~# service postgresql restart

(10) if you have downloaded the binary installer then extract it into /usr/local/ and run:

root@host:~# chown globus. -R /usr/local/globus-4.0.8/

globus@host:~$ $GLOBUS_LOCATION/sbin/gpt-postinstall

and jump to step (17); if you have downloaded the source installer then proceed with the next step;

(11) run:

root@host:~# 
mkdir /usr/local/globus-4.0.8/
chown globus. /usr/local/globus-4.0.8/

(12) extract the content of gt4.0.8-all-source-installer you have downloaded into globus’ home directory;
(13) log in as globus user or run from terminal “su – globus”;
(14) enter the directory where you extracted the content of gt4.0.8-all-source-installer and run:

globus@host:~$ 
./configure --prefix=/usr/local/globus-4.0.8/ --with-iodbc=/usr/lib
make | tee installer.log

this process may take a few hours, depending on your hardware configuration (about one hour on an Intel Core 2 Duo CPU T6500 at 2.10GHz);

(15) make a tarfile of /usr/local/globus-4.0.8/ so that you won’t have to rebuild it to install it on other machines; you can untar it on other machines and run $GLOBUS_LOCATION/sbin/gpt-postinstall
(16) run:

globus@host:~$ make install

(17) get the “distribution package” (a tar.gz file) from your Certification Authority (CA). If you don’t have one you will need to set up a CA in one of your machine following these instructions. Once you have the distribution package copy it on all your server machines and run the following four commands:

root@host:~#
$GLOBUS_LOCATION/sbin/gpt-build your_ca.tar.gz
$GLOBUS_LOCATION/sbin/gpt-postinstall
$GLOBUS_LOCATION/setup/your_ca/setup-gsi
$GLOBUS_LOCATION/bin/grid-default-ca

All the grid nodes on which you want to be able to submit jobs must have installed the public key file (e.g. 0a298c77.0) and the policy file (e.g. 0a298c77.signing_policy) of the CA into the directory /etc/grid-security/certificates;

(18) run:

root@host:~#
cd /etc/grid-security/
cp hostcert.pem containercert.pem
cp hostkey.pem containerkey.pem
chown globus. container*
chown root. hostcert.pem hostkey.pem
chmod 644 containercert.pem hostcert.pem
chmod 400 containerkey.pem hostkey.pem

(19) still in the /etc/grid-security/ directory create a file named “grid-mapfile” and paste into it the users and hosts of your grid, like in the following example:

"/O=Grid/OU=Monty Python/CN=Graham Chapman" graham
"/O=Grid/OU=Monty Python/CN=John Cleese" john
"/O=Grid/OU=Monty Python/CN=Terry Gilliam" terry
"/O=Grid/OU=Monty Python/CN=Eric Idle" eric
"/O=Grid/OU=Monty Python/CN=Terry Jones" terry
"/O=Grid/OU=Monty Python/CN=Michael Palin" michael

"/O=Grid/CN=host/mercury.domain.com" globus
"/O=Grid/CN=host/venus.domain.com" globus
"/O=Grid/CN=host/earth.domain.com" globus
"/O=Grid/CN=host/mars.domain.com" globus

then run:

root@host:~# 
chown globus. /etc/grid-security/grid-mapfile
chmod 660 /etc/grid-security/grid-mapfile
grid-mapfile-check-consistency

(20) make sure your hostname is associated with your public IP. The following entry which is created by default in your /etc/hosts:

127.0.1.1 hostname

should be removed, if your hostname is already mapped to an IP in your DNS server; if it’s not mapped then it should be modified into:

x.x.x.x hostname

where x.x.x.x is your public IP. Furthermore, make sure your parent domain is listed and your DNS servers are properly set in your /etc/resolv.conf

(21) create the file /etc/xinetd.d/gridftp and paste into it the following code:

service gsiftp
{
instances       = 100
socket_type     = stream
wait            = no
user            = root
env             += GLOBUS_LOCATION=/usr/local/globus-4.0.8
env             += LD_LIBRARY_PATH=/usr/local/globus-4.0.8/lib
env             += GLOBUS_TCP_PORT_RANGE=50000,55000
server          = /usr/local/globus-4.0.8/sbin/globus-gridftp-server
server_args     = -i
log_on_success  += DURATION
nice            = 10
disable         = no
}

(22) run:

root@host:~# service xinetd restart

(23) now to configure RFT run:

root@host:~# su postgres -c "createuser -P globus"

enter the globus user password when prompted and then answer in the following way to the following questions:

Shall the new role be a superuser? (y/n) n
Shall the new role be allowed to create databases? (y/n) y
Shall the new role be allowed to create more new roles? (y/n) n

(24) run:

globus@host:~$
createdb rftDatabase
psql -d rftDatabase -f $GLOBUS_LOCATION/share/globus_wsrf_rft/rft_schema.sql

(25) open $GLOBUS_LOCATION/etc/globus_wsrf_rft/jndi-config.xml (if it’s missing run as user globus the command $GLOBUS_LOCATION/sbin/gpt-postinstall). Look into the “dbConfiguration” section: make sure the userName value is not “root” but “globus”, then change the content of “password” from “foo” to the password for the globus user you have previously set in postgres. Also ensure that “connectionString” contains the fully qualified domain name of your host (e.g. “jdbc:postgresql://your.host.full.domain.com/rftDatabase”).
(26) to check whether RFT is working, start a globus container with:

globus@host:~$ globus-start-container

and leave it running. In a separate terminal run:

user@host:~$ vim /tmp/rft.xfr

Copy and paste the following code, making sure to modify “container.hostname” with your container hostname or IP:

true
16000
16000
false
1
true
1
null
null
false
10
gsiftp://container.hostname:2811/etc/group
gsiftp://container.hostname:2811/tmp/rftTest_Done.tmp

then run:

user@host:~$
grid-proxy-init
rft -h container.hostname -f /tmp/rft.xfr

To check whether the transfer has been correctly performed run:

user@host:~$ diff /etc/group /tmp/rftTest_Done.tmp

(27) now to configure GRAM run:

globus@host:~$
vim /usr/local/globus-4.0.8/lib/perl/Globus/GRAM/ExtensionsHandler.pm

and remove the % character in front of $attributes at lines 161 and 174.

(28) to give the user globus the privileges to run tasks on behalf of another user run:

root@host:~# visudo

and paste at the bottom the following two lines:

globus  ALL=(username1,username2) NOPASSWD: 
/usr/local/globus-4.0.8/libexec/globus-gridmap-and-execute -g 
/etc/grid-security/grid-mapfile 
/usr/local/globus-4.0.8/libexec/globus-job-manager-script.pl *

globus  ALL=(username1,username2) NOPASSWD: 
/usr/local/globus-4.0.8/libexec/globus-gridmap-and-execute -g 
/etc/grid-security/grid-mapfile 
/usr/local/globus-4.0.8/libexec/globus-gram-local-proxy-tool *

where the user names “username1” and “username2” are to be substituted with a comma-separated list of usernames that you actually want the user “globus” to be able to sudo to (that is all the users of your grid). Also, make sure these two entries are each on a single line. If there are any line breaks within an entry then it won’t work;

(29) to check whether GRAM is working, start a globus container with:

globus@host:~$ globus-start-container

and leave it running. In a separate terminal run:

user@host:~$ globusrun-ws -submit -c /bin/true
Submitting job...Done.
Job ID: uuid:3304e3f2-55f2-11da-8b8f-00d0b7b7c0bc
Termination time: 11/16/2005 16:09 GMT
Current job state: Active
Current job state: CleanUp
Current job state: Done
Destroying job...Done.

user@host:~$ echo $? 
0

user@host:~$ globusrun-ws -submit -c /bin/false
Submitting job...Done.
Job ID: uuid:456b7c9a-55f2-11da-9b0d-00d0b7b7c0bc
Termination time: 11/16/2005 16:09 GMT
Current job state: Active
Current job state: CleanUp
Current job state: Done
Destroying job...Done.

user@host:~$ echo $? 
1

Useful Linux howtos

February 9, 2010HowTos, Linux, TipsMarco Lackovic

Applications

to install Oracle Java JDK follow these instructions;
to compare files or directories use “Meld Diff Viewer”. You can install it by running:
```
sudo apt-get install meld
```

to install Microsoft’s Core Font package run:

sudo apt-get install ttf-mscorefonts-installer

to synchronize folders, files and make backups use “Conduit Synchronizer”. You can install it by running:
```
sudo apt-get install conduit
```
to change grub settings (e.g. to change your default operating system, etc) install “StartUp Manager” by running:
```
sudo apt-get install startupmanager
```
to automatically mount at boot your NTFS partitions install “Storage Device Manager” by running:
```
sudo apt-get install pysdm
```
to set up a repository cache on your network so that once a package is downloaded from an official repository, all other machines will download it from your local area network, install squid-deb-proxy (and its client so the server downloaded updates get cached by the squid proxy and will also allow the server to install already-fetched updates via the proxy) on your server machine by running:
```
sudo apt-get install squid-deb-proxy squid-deb-proxy-client
```
then reboot your server machine. Clients can auto-discover caching-enabled machines in the local network by having the squid-deb-proxy-client package installed. To do that simply run:
```
sudo apt-get install squid-deb-proxy-client
```

Information

to know your IP address:
```
ifconfig | grep Bcast
```
to know your hardware details and save them in an html page run:
```
lshw -html > your-file-name.html
```
(a good idea is to generate one for each of your computers and save them up for future reference)
to check whether a certain package is installed:
```
dpkg -l | grep packagename
```
to know whether you need to reboot a machine after updating the system via terminal check if the following file exists:
```
/var/run/reboot-required
```
to test the speed of your hard drive run:
```
sudo hdparm -t /dev/sd?
```
to list running services run:
```
sudo netstat -tulpn
```
to check RAM speed, size and frequency:
```
sudo dmidecode --type 17 | more
```
to know your processor details run:
```
cat /proc/cpuinfo | grep name
```

to know the bios version of your motherboard run:

sudo apt-get install smbios-utils
sudo smbios-sys-info

to know the name of the Linux distribution installed on your machine run:
```
lsb_release -a
```
or, if that doesn’t work then run:
```
cat /etc/issue
```
to have some system information of your machine run:
```
uname -a
```
to see if your operating system architecture is 32-bit or 64-bit run:
```
file /sbin/init
```
to list all users in your system from terminal, run:
```
cat /etc/passwd | grep "/home" |cut -d: -f1
```

Operations

to configure your terminal commands history add one or more of the following lines to your ~/.bashrc file:
- to change name of the file in which command history is saved:
```
export HISTFILE=
```
  (the default value is ~/.bash_history)
- to not save in the history certain command lines add them as a colon-separated list:
```
export HISTIGNORE=
```
- to not save a line matching any other previous entry in the history:
```
export HISTCONTROL=ignoreboth
```
- to change the number of commands to remember in the command history:
```
export HISTSIZE=500
```
  (the default value is 500)

to add aliases system-wide you need to edit the file /etc/bash.bashrc For example, the following alias will provide a comprehensive update and clean operation:

alias apt-update='sudo apt-get -f install
&& sudo apt-get autoremove -y
&& sudo apt-get autoclean -y
&& sudo apt-get clean -y
&& sudo apt-get update 
&& sudo apt-get upgrade -y --fix-missing'

to boot in text mode instead of graphical mode (GUI) open the /etc/default/grub file, locate the following line:
```
GRUB_CMDLINE_LINUX_DEFAULT=”quiet splash“
```
and change it to:
```
GRUB_CMDLINE_LINUX_DEFAULT=”quiet splash text“
```
and don’t forget to run ‘update-grub’ afterwards to update. If you need the graphical interface you can still have it by simply running “startx” once logged in.
to keep your computer’s time accurate follow these instructions;

to install fonts for system-wide run:

mkdir /usr/share/fonts/truetype/myfonts
cp [fonts] /usr/share/fonts/truetype/myfonts
fc-cache -f -v

to add a new user via terminal run:
```
sudo adduser username
```
to add a group to a userrun:
```
sudo adduser username groupname
```

to modify the groups of a userrun:

sudo usermod -G comma,separated,list,of,groupnames username

some useful command line shortcuts:
- Ctrl-D: exit from the current session;
- Ctrl-R: searching through the command history;
- Ctrl-A: moves the cursor to the beginning of the command line;
- Ctrl-E: moves the cursor to the end of the command line;
- Ctrl-W: deletes the word immediately before the cursor;
- Ctrl-K: deletes everything immediately after the cursor;
- Ctrl-Y: undo a deletion.
to start a terminal maximized use the command
```
gnome-terminal --window --maximize
```
to start a terminal in full screen use the command
```
gnome-terminal --full-screen
```
to copy multiple files using scp use it like showed below:
```
scp {file1,file2,file3} user@destination:~/
```
to speed up the ssh connection add “UseDNS no” (without quotation marks) at the end of your /etc/ssh/sshd_config and then run:
```
sudo /etc/init.d/ssh reload
```
to add a new resolution to your monitor/display/screen run (assuming you want to add 1600×900):
```
cvt 1600 900
```
that will output something like this:
```
Modeline "1600x900_60.00" 118.25 1600 1696 1856 2112 900 903 908 934 -hsync +vsync
```
Copy the text following Modeline and paste it in the following command:
```
xrandr --newmode "1600x900_60.00" 118.25 1600 1696 1856 2112 900 903 908 934 -hsync +vsync
```
Then run the command xrandr alone:
```
xrandr
```
and note down the connected primary video source (should something like VGA-0, or VGA1). Supposing it’s VGA-0 then run:
```
xrandr --addmode VGA-0 "1600x900_60.00"
```
to open/extract an eml file install munpack:
```
sudo apt-get install mpack
```
then run:
```
munpack filename.eml -t
```

to chmod 775 sub-directories, files excluded:

find /path/to/base/dir -type d -exec chmod 775 {} +

to chmod 664 files recursively, sub-directories excluded:

find /path/to/base/dir -type f -exec chmod 664 {} +