CentOS 7.x Rocks cluster 7.0 Reinstall OS on compute node

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Reinstall OS on one specific compute node

To reinstall OS on compute node use:

rocks list host boot
rocks set host boot <hostname> action=install
ssh <hostname> "shutdown -r now" 

This assumes that the boot order on compute node is properly set to boot from network.

By default there is /state/partition1 partition created on compute nodes. This partition is not affected during the reinstall process. Any data on this partition remains as it is after the reinstallation.

Refer:

• http://central-7-0-x86-64.rocksclusters.org/roll-documentation/base/7.0/x2105.html

Reinstall OS on all compute nodes

If the reinstallation has to be done on all compute nodes then use:

1. You must have a non-root user. If not there create one with useradd

   Note we cannot run sge jobs as root user

2. The non-root user must have manager privilege. If not there add via:

   qconf -am <username>

   This is required because jobs with positive priority can be submitted only by managers.

3. Edit '/opt/gridengine/examples/jobs/sge-reinstall.sh' and replace the qsub line with (might have been split into two lines):

   runuser -l <non-root-username> -c "qsub -p 1024 -pe mpi $numprocs -q all.q@$TARGETHOST /opt/gridengine/examples/jobs/reboot.qsub"

4. Now run the script to submit job that configures each node host action as install

   /opt/gridengine/examples/jobs/sge-reinstall.sh

5. Validate that host action has updated properly

   rocks list host boot

6. Restart the nodes using:

   for A in $(rocks list host | cut -f 1 -d ' ' | grep -v HOST | sed 's/.$//' | grep -v <master-hostname>); do ssh $A "shutdown -r now"; done

   Ensure to replace <master-hostname> with proper name to avoid rebooting of master itself

7. If for one or two nodes reinstallation is not desired we can always change their boot action using:

   rocks set host boot <hostname> action=os
   rocks list host boot

Refer:

• http://central-7-0-x86-64.rocksclusters.org/roll-documentation/base/7.0/sge-cluster-reinstall.html
• https://docs.oracle.com/cd/E19957-01/820-0698/6ncdvjclp/index.html
• https://stackoverflow.com/questions/37733095/unable-to-run-jobs-on-cfncluster
• https://stackoverflow.com/questions/30645020/what-does-sge-mean-by-positive-submission-priority-requires-operator-privileges

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