9.6. Launching with SSH

When launching jobs in a non-scheduled environment, ssh is typically used to launch commands on remote nodes. As listed in the quick start section, successfully launching MPI applications with ssh requires the following:

1. You must be able to non-interactively login — without entering a password or passphrase — to all remote nodes from all remotes nodes.

2. PRRTE’s daemon executablesmust be findable (e.g., in your PATH).

3. PRRTE’s libraries must be findable (e.g., in your LD_LIBRARY_PATH).

9.6.1. Specifying the hosts for a job

There are three mechanisms for specifying the hosts that an job will run on:

1. The --hostfile option to prterun.

   Use this option to specify a list of hosts on which to run. Note that for compatibility with other launchers, --machinefile is a synonym for --hostfile.

2. The --host option to prterun.

   This option can be used to specify a list of hosts on which to run on the command line.

3. Running in a scheduled environment.

   If you are running in a scheduled environment (e.g., in a Slurm, Torque, or LSF job), PRRTE will automatically get the lists of hosts from the scheduler. See the next subsections for details about launching jobs in supported scheduled environements.

Important

The specification of hosts using any of the above methods has nothing to do with the network interfaces that are used for application traffic. The list of hosts is only used for specifying which hosts on which to launch processes.

9.6.2. Non-interactive ssh logins

SSH keys must be setup such that the following can be executed without being prompted for password or passphrase:

shell$ ssh othernode echo hello
hello
shell$

Consult instructions and tutorials from around the internet to learn how to setup SSH keys. Try Google search terms like “passwordless SSH” or “SSH key authentication”.

For simplicity, it may be desirable to configure your SSH keys without passphrases. This adds some risk, however (e.g., if your SSH keys are compromised). But it simplifies your SSH setup because you will not need to use ssh-agent. Evaluate the risk level you are comfortable with.

Important

PRRTE uses a tree-based pattern to launch processes on remote nodes. This means that PRRTE must be able to non-interactively login — without being prompted for password or passphrase — to any node in the host list from any node in the host list.

It may not be sufficient to only setup an SSH key from the node where you are invoking prterun to all other nodes.

If you have a shared $HOME filesystem between your nodes, you can setup a single SSH key that is used to login to all nodes.

9.6.3. Finding the PRRTE daemon executable and libraries

Once PRRTE is able to use ssh to invoke executables on a remote node, it must be able to find its daemon executable and shared libraries on that remote node.

If PRRTE is installed in a system-level folder (e.g., in /usr/bin), PRRTE will likely be able to find its daemon and libraries on the remote node with no additional assistance.

If, however, PRRTE is installed into a path that is not searched by default, you will need to provide assistance so that PRRTE can find its daemon and libraries.

Important

For simplicity, it is strongly recommended that you install PRRTE in the same location on all nodes in your job.

You can do this in one of two ways.

9.6.3.1. Use “prefix” behavior

Note

“Prefix” behavior is only available with prterun; it is not available via resource manager direct launch mechanisms. However, this section is about using ssh to launch jobs, which means that there is no resource manager, and therefore there is no direct launch mechanism available.

When “prefix” behavior is enabled, PRRTE will automatically set the $PATH and $LD_LIBRARY_PATH on remote nodes before executing remote commands.

Important

PRRTE assumes that the installation prefix, bindir, and libdir are the same on the remote node as they are on the local node. If they are not, then you should not use the “prefix” behavior.

You can enable “prefix” behavior in one of three ways:

1. Use an absolute path name to invoke prterun.

   shell$ $HOME/my-prrte/bin/prterun --hostfile my-hostfile.txt mpi-hello-world
   

   Simply using the absolute path name to prterun tells PRRTE to enable “prefix” mode.

2. Use the --prefix option to prterun.

  shell$ $HOME/my-prrte/bin/prterun --hostfile my-hostfile.txt \
      --prefix $HOME/my-prrte \
      mpi-hello-world

The ``--prefix`` option takes a single argument: the prefix path to
use for the bindir and libdir on the remote node.

1. Configure PRRTE with --enable-prterun-prefix-by-default.

   If PRRTE is built this way, prterun will always enable “prefix” behavior.

9.6.3.2. Set the PATH and LD_LIBRARY_PATH in your shell startup files

Consider the case where PRRTE was configured with:

shell$ ./configure --prefix=$HOME/my-prrte ...

In this cause, PRRTE will be installed into $HOME/my-prrte. This path is almost certainly not in any system-default search paths, so it must be added to the $PATH and $LD_LIBRARY_PATH environment variables.

Specifically: the goal is that the following non-interactive commands must be able to execute without error:

# First, ensure that this command returns the correct prte_info
# instance (i.e., $HOME/my-prrte/bin/prte_info).
shell$ ssh remotenode which prte_info
/home/myusername/my-prrte/bin/prte_info

# Next, ensure that you can run that prte_info command without
# error
shell$ ssh remotenode prte_info

# ... lots of output ...

Ensure that you do not see any errors about libraries that cannot be found.

All shells have some kind of script file that is executed at login time perform environmental setup tasks. This startup file is the one that needs to be edited to:

1. Add PRRTE’s daemon executable path (which is likely $prefix/bin, or $HOME/my-prrte/bin in this example) to the $PATH environment variable.

2. Add PRRTE’s library path (which is likely $prefix/lib, or $HOME/my-prrte/lib in this example) to the $LD_LIBRARY_PATH environment variable.

You probably want to add PRRTE’s libraries to the front of $PATH and $LD_LIBRARY_PATH to ensure that this PRRTE installation’s files are found first.

Consult the manual page for your shell for specific details (some shells are picky about the permissions of the startup file, for example). The list below contains some common shells and the startup files that they read/execute upon login:

Shell	Non-interactive login	Interactive login
bash or zsh	$HOME/.bashrc if it exists.	$HOME/.bash_profile if it exists, or $HOME/.bash_login if it exists, or $HOME/.profile if it exists (in that order). Note that some Linux distributions automatically come with $HOME/.bash_profile scripts for users that automatically execute $HOME/.bashrc as well. Consult the bash man page for more information.
sh	This shell does not execute any file automatically, so PRRTE will execute the $HOME/.profile script before invoking PRRTE executables on remote nodes	$HOME/.profile
csh	$HOME/.cshrc	$HOME/.cshrc followed by $HOME/.login
tcsh	$HOME/.tcshrc if it exists, or $HOME/.cshrc if it does not	$HOME/.tcshrc if it exists, or $HOME/.cshrc if it does not Afterwards, execute $HOME/.login