last updated on 23 April 2021

Configuring Host

This page explains how to configure the information of a computational host.


How a job is submitted to a computational host

Generally speaking, we need to use a job scheduler, such as Torque, to submit a job to High-Performance Computers (HPCs) or CPU clusters. When submitting a job to a job scheduler, we usually need to specify various parameters such as the number of nodes required for the job, the maximum elapsed time, and the number of CPU cores.

The problem is that the specifications of these job schedulers are different from each other, showing a wide variety. Therefore, OACIS uses a small script, called XSUB to absorb the difference between schedulers. XSUB must be prepared in the computational hosts before you register the host information on OACIS.

About the installation procedure of XSUB, please refer to the official document. After you install XSUB properly, the commands xsub, xstat, and xdel became available.

(Note) OACIS runs these command from bash launched as a login-shell. Therefore, please set the environment variables required to use XSUB, such as PATH, in .bash_profile file, not in .bashrc.

About XSUB

The parameters required to specify when submitting a job are called “host parameters”. Required host parameters are different depending on the specification of the job schedulers. OACIS retrieves the information of the required host parameters using the “xsub” command. Hence, XSUB must be setup before registering the host information on OACIS. When you create a run, fields for the host parameters are shown in the page as shown in the figure below.

Creating a run specifying host parameters

Specification of Host

We will explain the list of information which you need to specify when registering a host.

field explanation
Name The name used in “~/.ssh/config” file.
Work base dir The path to the work directory. The work directory is the place where jobs are executed. Please specify the directory dedicated to OACIS jobs.
Mounted work base dir If the work base dir is directly accessible from OACIS, specify the path which is accessible from OACIS. See the notes below this table.
Max num jobs The maximum number of concurrent jobs. Jobs are queued until the number of running jobs becomes this number.
Polling interval Time interval to check the status of the computational host. With this interval, SSH connection is made to check the status. The default value is 60 seconds.
MPI processes The available range of the number of MPI processes. If you specify a number out of this range when making a run, you will get an error.
OMP threads The available range of the number of OpenMP threads.
Executable simulators List of executable simulators on that host.
Executable analyzers List of executable analyzers on that host.

The SSH setting must be written in “~/.ssh/config” file. For instance, setting of “MyHost” may be written as the following.

Host MyHost
  HostName example.com
  User user_ABC
  IdentityFile ~/.ssh/id_rsa
  port 22
Tips
If you specify *"Mounted work base dir"*, OACIS uses copy instead of SFTP to download the results from the computational host. This may significantly improve the performance of the file transfer. For "localhost", always specify the same value as "Work base dir". The performance will be much improved. If the "Work base dir" on the computational host is mounted by NFS, specify the mounted path. If the directory is not accessible from OACIS, leave it blank.
Tips
From OACIS version 3, "Hostname, "User", "Port" fields are removed. Instead, OACIS refers to "~/.ssh/config" file.

If you find an error like “no such command: xsub” when registering a host, please check if XSUB is properly installed.

[Advanced] Using the K-computer

In addition to the SSH and XSUB configurations, a special configuration is needed for the K-computer because of the staging functionality.

Since the executable file is also copied by staging, you can not specify the path to the executable by absolute path. The path changes after staging-in. Use “preprocess” to copy the executable to the current directory and specify the simulation command using the relative path from the current directory.

Suppose your executable file is located at ~/path/to/simulator.out. Please set the preprocess of the simulator as follows.

cp ~/path/to/simulator.out .

When you execute a job via xsub, the temporary directory prepared for the job is going to be staged-in. So, copy all the necessary files to the current directory in the pre-process.

Set the execution command as follows.

./simulator.out

By setting “command” and “pre-process” like these, we can submit jobs to the K-computer. All the simulation results are properly staged-out if all the output files are generated in the current directory because all the files in the current directory are staged-out.

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