Install GLOBUS and SGE-Setup on rocks use VDT

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Contents

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Stop old globus

If you have an existing globus installation

  • Disable current globus/grid-ftp/gris if any is running. 
# service globus stop
# service globus-ws stop
# move /etc/init.d/globus <path-to-backup-dir>
# move /etc/init.d/globus-ws <path-to-backup-dir>

Comment-out the lines for gsigatekeeper, gsiftp, gris in /etc/services files. 

# move /etc/xinet.d/globus-gatekeeper <path-to-backup-dir>
# move /etc/xinet.d/grid-ftp <path-to-backup-dir>
# /etc/init.d/xinetd restart
  • Remove but save any system profile for globus 
# mv /etc/profile.d/globus.sh <path-to-backup-dir>
# mv /etc/profile.d/globus.csh <path-to-backup-dir>
  • Logoff and re-login to get a clean environment setup.
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Install Globus use VDT

  • Install pacman (this example is installing pacman in /opt) 
# wget http://physics.bu.edu/pacman/sample_cache/tarballs/pacman-latest.tar.gz
# cd /opt
# tar xvzf /root/pacman-latest.tar.gz
# ln -s pacman-3.26/ pacman
  • Install GLOBUS 
# cd pacman
# source ./setup.sh
# cd ..
# mkdir vdt
# cd vdt
# pacman -get http://vdt.cs.wisc.edu/vdt_1101_cache:Globus
# pacman -get http://vdt.cs.wisc.edu/vdt_1101_cache:Globus-WS

This example is based on answering "yes" to all questions during the Globus installation, except "No" for install certificates.

  • Post-install setup 
# cd /opt/vdt
# . setup.sh

See post-install/README for what need to be done. Here are some example actions:

  • If you answered "yes" for auto-update CA certificates and would like to use IGTF+PRAGMA combo distribution, add the line below in /opt/vdt/vdt/etc/vdt-update-certs.conf 
cacerts_url = http://rocks56.sdsc.edu/certs/igtf-pragma-ca-certs-version
  • run 
# . /opt/vdt/vdt-questions.sh
# /opt/vdt/vdt/sbin/vdt-setup-ca-certificates --root
  • Make sure the /opt/vdt/globus/TRUSTED-CA is a symbolic link which points to the desired certificates directory. If not, create it.
  • Add the following lines in /etc/sudoers 
Runas_Alias GLOBUSUSERS = user1, user2 
# VDT globus-ws
globus ALL=(GLOBUSUSERS) NOPASSWD: /opt/vdt/globus/libexec/globus-gridmap-and-execute -g /etc/grid-security/grid-mapfile /opt/vdt/globus/libexec/globus-job-manager-script.pl *
globus ALL=(GLOBUSUSERS) NOPASSWD: /opt/vdt/globus/libexec/globus-gridmap-and-execute -g /etc/grid-security/grid-mapfile /opt/vdt/globus/libexec/globus-gram-local-proxy-tool *
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Install Globus-SGE-Setup use VDT

  • Setup jobmanager for batch system 
# cd /opt/vdt
# pacman -get http://vdt.cs.wisc.edu/vdt_1101_cache:Globus-SGE-Setup
# pacman -get http://vdt.cs.wisc.edu/vdt_1101_cache:Globus-WS-SGE-Setup
  • If SGE_QMASTER_PORT is not defined in /opt/vdt/globus/lib/perl/Globus/GRAM/JobManager/sge.pm, back it up, then edit it according to the patch provided by AIST. But, note that the line numbers may not correspond to your version of sge.pm file.
  • If the sge jobmanager script still have problem, try more modifications in sge.pm
  • If encounter the error "$GLOBUS_LOCATION/libexec/globus-scheduler-provider-sge: not found" in $GLOBUS-LOCATION/var/container-real.log, create the file with the 2 lines: 
 echo "<Scheduler xmlns=\"http://mds.globus.org/batchproviders/2004/09\">"; 
 echo "</Scheduler>";

and make the file executable using the command 'chmod + x globus-scheduler-provider-sge'.

  • If encounter the error "sudo: sorry, you must have a tty to run sudo", then comment-out the line "Defaults requiretty" in /etc/sudoers.
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Activate and test

  • If /etc/grid-security/grid-mapfile does not exist, create it and add user entry in the file
  • copy host cert files to container cert files 
# cp /etc/grid-security/hostcert.pem /etc/grid-security/containercert.pem
# cp /etc/grid-security/hostkey.pem /etc/grid-security/containerkey.pem
# chown globus:globus /etc/grid-security/container*.pem
  • Make sure all VDT components are enabled 
# vdt-control --list

If not, enable it with "vdt-control --enable <component-name>".

  • Activate and verify all VDT components 
# vdt-control --on
  • Add VDT environment setup script to system profiles 
# cp /opt/vdt/setup.sh /etc/profile.d/vdt.sh
  • Test Globus

Login an user account with Globus certificates properly setup. Test pre-WS: 

$ grid-proxy-init
$ globusrun -a -r <the-gateway-system-FQDN>
$ globus-job-run <the-gateway-system-FQDN>/jobmanager-sge /bin/date

Test WS: (Note - VDT sets container port# to 9443) 

$ globusrun-ws -submit -factory <the-gateway-system-FQDN>:9443 -Ft SGE -J -S -s -c /bin/date
  • If you like to change the port# to standard default (8443)
    • Edit /etc/init.d/globus-ws, change port# 9443 to 8443
    • Edit /opt/vdt/post-install/globus-ws, change port# 9443 to 8443
    • Restart /etc/init.d/globus-ws
    • Test job submission without specifying port# 
$ globusrun-ws -submit -factory <the-gateway-system-FQDN> -Ft SGE -J -S -s -c /bin/date
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