1. Install Oracle Java 6:
   • download the .bin JDK from here;
   • run the following commands:

     chmod +x jdk-6u31-linux-x64.bin
     ./jdk-6u31-linux-x64.bin
     sudo chown root. -R jdk1.6.0_31/
     sudo mv jdk1.6.0_31/ /usr/lib/jvm/
     
     sudo update-alternatives --install "/usr/bin/java" "java" \
     "/usr/lib/jvm/jdk1.6.0_31/bin/java" 1
     sudo update-alternatives --install "/usr/bin/javac" "javac" \
     "/usr/lib/jvm/jdk1.6.0_31/bin/javac" 1
     sudo update-alternatives --install "/usr/bin/javaws" "javaws" \
     "/usr/lib/jvm/jdk1.6.0_31/bin/javaws" 1
     
     sudo update-alternatives --config java
     sudo update-alternatives --config javac
     sudo update-alternatives --config javaws

2. Install Eclipse by running:

   sudo apt-get install eclipse-platform -y

3. If you are running a 64-bit distribution run:

   sudo apt-get install ia32-libs -y

4. Start Eclipse, then select Help > Install New Software:
   • add the following repositories:
     • Name: Eclipse Indigo
       Location: http://download.eclipse.org/releases/indigo/
     • Name: ADT Plugin
       Location: https://dl-ssl.google.com/android/eclipse/
   • select the checkbox next to “Developer Tools” and click next, next, accept the terms and finish; press OK at the secirity warning; at the end restart Eclipse;
   • at the “Welcome to Android Development” dialog select “Install new SDK” option and press Next, and then Finish;
   • at the “Choose packages to install” press “Accept All” and press “Install”;

Globus Toolkit 5.2 promises to greatly enhance the ability to install, setup and update the GT client and service components. This has been achieved by providing binary native packages Red Hat, Fedora, Debian, Ubuntu, Scientific Linux, and CentOS. Globus developers will maintain a Globus repository containing all packages.

GT 5.2 includes the latest versions of all components: GRAM, GridFTP, MyProxy and GSISSH. This latest version of GRAM includes a number of scalability and reliability improvements found from working with Open Science Grid (OSG) that are not in the 5.0 series. GridFTP added support for the DCSC command, which allows the client to specify credentials used to secure the data channel connection. Globus Online utilizes this command for seamless data movement across multiple security domains.

GT 5.2 is protocol and client API compatible with GT 5.0 (e.g. 5.2 clients will work with GT 5.0 services, and visa versa.)

For more information about GT 5.2 visit http://www.globus.org/toolkit/docs/5.2/5.2.0/rn/

Disclosure: this troubleshooting 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.

~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~

ERROR service.ReliableFileTransferImpl [main,<init>:76] Unable to setup database driver with pooling.Connection refused. Check that the hostname and port are correct and that the postmaster is accepting TCP/IP connections

• open /etc/postgresql/X.Y/main/postgresql.conf(where X.Y is current PostgreSQL version) and check that the line beginning with “listen_addresses” is not commented (i.e. the line should not begin with a #) and is set to listen to all addresses, in the following way:

  listen_addresses = '*'

• open /etc/postgresql/X.Y/main/pg_hba.conf” and check that the last line looks like:

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

  where “x.x.x.x” is your public IP address. If you are using Globus Toolkit on your local machine for testing purposes then using 127.0.0.1 should be fine, although in this case you won’t be able to access Globus services outside your machine;

• check that PostgreSQL is up and running and on which port:

  sudo netstat -tulpn | grep postgres

• PostgreSQL should run on port 5432. The default port number may be automatically changed (usually to 5433) as result of a version upgrade. To change it back to 5432 edit the /etc/postgresql/X.Y/main/postgresql.conf and the stop and start the service (warning: a restart won’t be enough) with:

  sudo service postgresql stop
  sudo service postgresql start

• to check whether PostgreSQL is running properly on the 5432 port run:

  telnet localhost 5432

• the message “telnet: Unable to connect to remote host: Connection refused” would mean either PostgreSQL is not running, or is running on the wrong port. If you get “Connected to localhost.localdomain. Escape character is ‘^]’.” then PostgreSQL is fine.

~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~

ERROR service.ReliableFileTransferImpl [main,<init>:76] Unable to setup database driver with pooling.A connection error has occurred: FATAL:  password authentication failed for user “root”

• open $GLOBUS_LOCATION/etc/globus_wsrf_rft/jndi-config.xmland look into the “dbConfiguration” section:
  • make sure the userName value is not “root” but “globus”;
  • make sure the “password” value is not “foo” but the password for the globus user you have previously set in postgres;
  • make sure the “connectionString” value contains the fully qualified domain name of your host (e.g. “jdbc:postgresql://your.host.full.domain.com/rftDatabase”).
• make sure you are running globus-start-container as globus user

gt4.0.8-all-source-installer.tar.bz2 da
# http://www.globus.org/toolkit/downloads/4.0.8/

~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~

/O=YourCA/CN=Name Surname” is not authorized to use operation: http://www.globus.org/08/2004/delegationService}requestSecurityToken on this service

• ensure that in your /etc/grid-security/grid-mapfile there is a line containing the Subject of your usercert.pem (note that you need to change the ‘, ‘ with ‘/’), followed by a user on the server machine (you can use globus if you don’t have a user account on that machine). For example:

  "O=YourCA/CN=Name Surname" globus

  Stop and restart your Globus container for changes to take effect.

The 5.2 release is protocol and source compatible with Globus Toolkit 5.0.

Major Changes between 5.0 and 5.2:

• Native packaging for linux distributions based on RPM and Debian package managers
• The concept of “flavors” of Globus libraries has been obsoleted
• Elimination of the compile-time distinction between threaded and non-threaded builds. All libraries are built to be thread-safe, but most applications and services will run by default without threads. The GLOBUS_THREAD_MODEL environment variable can be used to select between “none” (nothreads) and “pthreads” event-handling model.
• The toolkit has been reorganized to be compliant with the Filesystem Hierarchy Standard.
• The environment variable GLOBUS_LOCATION is no longer required to be set at runtime (though it is still honored to allow non-native packages to be relocated).
• Shared library versioning to allow different versions of libraries to coexist.
• Simplified configuration: more default values for Globus service configurations (especially GRAM5), more admin tools for interacting with tools (GRAM gatekeeper, audit)
• Cleaner separate of configuration file and implementation for GRAM LRM modules.
• Elimination of GPT setup packages as a way to create default configuration files
• Much simplified globus-simple-ca package for managing a CA, including tools for distributing RPM and debian packages containing CA certificate and policy files.
• More user-installable documentation and man pages for tools and libraries
• Many bug fixes

For more information about GT 5.2 visit http://dev.globus.org/wiki/Globus_Toolkit/5.2

Highlights of this release include:

• Several bug fixes on GridFTP and a couple of extra options
• Added RSL attributes and unique job manager log file names to GRAM5
• Updated MyProxy to version 5.4
• Updated gsissh to version 5.3

[Release notes] – [Software] – [Documentation] -[Support]

Highlights of this release include:

• GridFTP
  • Added new command: Data Channel Security Context (DCSC)
    • Useful for 3rd party transfers between GridFTP servers that use different CA certificates
  • Added gridftp server chrooting
    • Allows admin to limit the directories a gridftp server can access
  • Added command strings for ‘-disable-command-list’ option for gridftp server configuration
  • Added Progress markers for stream mode
• Fixed a variety of bugs on GRAM5 related with PBS, Condor and Solaris
• Updated MyProxy to version v5.3
• Updated gsissh to version 5.2

[Release notes] – [Software] – [Documentation] -[Support]

The cloud-hosted, secure file transfer service, is now available for general use. Globus Online enables researchers and other end users to move and synchronize files reliably between multiple locations without configuring servers or installing complex software. Details are available here and here (from Ian Foster’s blog).

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.

• (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;

• (2.1) install Oracle’s Sun Java 6 JDK;
  
• (2.2) run:

sudo apt-get update

sudo apt-get install vim ant \
build-essential libpod-\* libxml-parser-perl postgresql odbc-postgresql \
libodbcinstq1c2 xinetd zlib1g-dev libiodbc2 libiodbc2-dev postgresql

sudo ln -s /usr/lib/libodbc.so.1.0.0 /usr/lib/libodbc.so

• (3) add the following lines to your /etc/profile

export JAVA_HOME=/usr/lib/jvm/java-6-sun
export ANT_HOME=/usr/share/ant
export GLOBUS_LOCATION=/usr/local/globus-4.0.8
export GLOBUS_OPTIONS="-Xms256M -Xmx1024M"
source $GLOBUS_LOCATION/etc/globus-user-env.sh
export PATH=$ANT_HOME/bin:$JAVA_HOME/bin:$PATH:$GLOBUS_LOCATION/bin

• (4) log out and back in;
• (5) run:

sudo service postgresql start

• (6) open “/etc/postgresql/9.1/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/9.1/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 user with “globus” as username;
• (9) run:

sudo service postgresql restart

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

sudo chown globus. -R /usr/local/globus-4.0.8/
su - globus
$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:

sudo mkdir /usr/local/globus-4.0.8/

sudo 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 (as globus):
  

./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 a 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 (as globus):

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:

sudo $GLOBUS_LOCATION/sbin/gpt-build your_ca.tar.gz
sudo $GLOBUS_LOCATION/sbin/gpt-postinstall
sudo $GLOBUS_LOCATION/setup/your_ca/setup-gsi
sudo $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:

cd /etc/grid-security/
sudo cp hostcert.pem containercert.pem
sudo cp hostkey.pem containerkey.pem
sudo chown globus. container*
sudo chown root. hostcert.pem hostkey.pem
sudo chmod 644 containercert.pem hostcert.pem
sudo 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:

sudo chown globus. grid-mapfile
sudo chmod 660 grid-mapfile
grid-mapfile-check-consistency

• (20) 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
}

• (21) run:

sudo service xinetd restart

• (22) now to configure RFT run:

sudo 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

• (23) run:

su - globus
createdb rftDatabase
psql -d rftDatabase -f $GLOBUS_LOCATION/share/globus_wsrf_rft/rft_schema.sql

• (24) open $GLOBUS_LOCATION/etc/globus_wsrf_rft/jndi-config.xml and 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”).
• (25) now to configure GRAM run:

sudo 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;

• (26) since all users must have read permissions on the grid-mapfile you need to add the “globus” group to each user. First list all groups to which the user is already a member using the command:

groups <user id>

then add the “globus” group by adding it to the beginning of the user’s groups list (as the list in the command is absolute and not an addition) and running:

usermod -G globus,<comma separated group list> <user id>

log out from the user interface and log back in;

• (27) check that your /etc/hostname contains the fully qualified name of your machine (to change without a reboot run “sudo start hostname” after you have edited /etc/hostname);
• (28) finally you can start the Globus container by running as globus user:

globus-start-container

• (29) to check whether GRAM is working, run as normal user:

globusrun-ws -submit -c /bin/touch touched_it

if everything is working fine you should see something like this:

Submitting job...Done.
Job ID: uuid:6adb70fa-62d1-11dc-92fe-0013d46f2605
Termination time: 09/15/2007 14:47 GMT
Current job state: Active
Current job state: CleanUp
Current job state: Done
Destroying job...Done.

gt4.0.8-all-source-installer.tar.bz2 da
# http://www.globus.org/toolkit/downloads/4.0.8/

Highlights of this release include:

• GridFTP
  • Synchronization (globus-url-copy -sync) feature that transfers files only if they do not exist at the destination or differ from the source
  • An offline mode for the server
• GRAM5
  • Improvements have been made to address all the known blocker issues for production deployment on TeraGrid and OSG
• MyProxy
  • Updated to MyProxy v5.2

[Release notes] – [Software] – [Documentation] -[Support]

Highlights of the 5.0.1 release include:

• GridFTP
  • New globus-url-sync command for syncing individual files or directories
  • New server option to control the default permissions of created files
  • New server option to time out on slow or hanging filesystems
  • New server logging level to include transfer statistics
• GRAM5
  • Improved reliability with Condor-G clients
  • Fixed a number of bugs and memory leaks
• MyProxy
  • Updated to MyProxy v5.1
• GSI-OpenSSH
  • Updated to GSI-OpenSSH v5.2
• GSI
  • Added OpenSSL 1.0.0 Support

Also, a Windows installer for GT 5.0 is now available, and includes most standard Globus components like GSI and GridFTP.

Relevant 5.0.1 links:

[Release notes] – [Software] – [Documentation] -[Support]