Using Private Cluster

Using a Private Cluster allows you to exclusively use a specific node of the System B. To use a Private Cluster, you need to be a user of the Private Cluster course. Note that this Private Cluster course does not support batch processing.

To use a Private Cluster, log in to the login node dedicated to the Private Cluster through SSH with key authentication. The hostname (FQDN) is notified by email to the payment manager as well as the applicant who submitted the application. The hostname is in the format of:

GROUPNAME .kudpc.kyoto-u.ac.jp

The Private Cluster uses the same procedure as the other service courses. For details, see Logging In and Transferring Files.

The login node, connected to external networks, is configured using one of the nodes in the Private Cluster. To use other nodes for computation (computational nodes), log in via the dedicated login node through SSH with host-based authentication.

You can check the login node’s host name using the hostname command as below. The hostname is cXX-YYYY: XX means two digits of cluster-specific numbers, and YYYY means the login node number 0001 that is a serial number in the Private Cluster.

$ hostname
c01-0001

The computational node’s hostname is the serial number (YYYY) in the Private Cluster ranging from 0002 to the number of the nodes in use. For example, when the login node’s host name is “c01-0001”,and the number of the nodes in use is eight, the computational nodes’ hostnames are from “c01-0002” to “c01-0008”.

To log in to each computational node, log in to the login node dedicated to the Private Cluster, and then specify its hostname of the computational node using the ssh command as below:

$ ssh c01-0002

To execute a MPI program, create a host-definition file that describes the nodes’ hostname(s). In the example below, the file is created in ~/hydra.hosts.

$ cat ~/hydra.hosts
c01-0001
c01-0002
c01-0003
...
c01-0008

Use the mpiexec.hyrda command to execute a program.
To specify the host to be executed, specify the host-definition file that you created using the -machinefile or -hostfile option as below:

$ mpiexec.hydra -n 32 -machinefile ~/hydra.hosts ./a.out
rank= 6 machine=c01-0001 socket=0 start-core= 6 end-core= 6 size=32
.....

You can use /tmp as a temporary file area. Note that the files that are no longer used for ten days will be deleted.


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