Run UnifyFS

This section describes the mechanisms to start and stop the UnifyFS server processes within a job allocation.

Overall, the steps to run an application with UnifyFS include:

  1. Allocate nodes using the system resource manager (i.e., start a job)

  2. Update any desired UnifyFS server configuration settings

  3. Start UnifyFS servers on each allocated node using unifyfs

  4. Run one or more UnifyFS-enabled applications

  5. Terminate the UnifyFS servers using unifyfs

Start UnifyFS

First, one must start the UnifyFS server process (unifyfsd) on the nodes in the job allocation. UnifyFS provides the unifyfs command line utility to simplify this action on systems with supported resource managers. The easiest way to determine if you are using a supported system is to run unifyfs start within an interactive job allocation. If no compatible resource management system is detected, the utility reports an error message to that effect.

In start mode, the unifyfs utility automatically detects the allocated nodes and launches a server on each node. For example, the following script could be used to launch the unifyfsd servers with a customized configuration. On systems with resource managers that propagate environment settings to compute nodes, the environment variables override any settings in /etc/unifyfs/unifyfs.conf. See UnifyFS Configuration for further details on customizing the UnifyFS runtime configuration.

1#!/bin/bash
2
3# spillover data to node-local ssd storage
4export UNIFYFS_LOGIO_SPILL_DIR=/mnt/ssd/$USER/data
5
6# store server logs in job-specific scratch area
7export UNIFYFS_LOG_DIR=$JOBSCRATCH/logs
8
9unifyfs start --share-dir=/path/to/shared/file/system

unifyfs provides command-line options to select the shared file system path, choose the client mountpoint, and control stage-in and stage-out of files. The full usage for unifyfs is as follows:

[prompt]$ unifyfs --help

Usage: unifyfs <command> [options...]

<command> should be one of the following:
  start       start the UnifyFS server daemons
  terminate   terminate the UnifyFS server daemons

Common options:
  -d, --debug               enable debug output
  -h, --help                print usage

Command options for "start":
  -e, --exe=<path>           [OPTIONAL] <path> where unifyfsd is installed
  -m, --mount=<path>         [OPTIONAL] mount UnifyFS at <path>
  -s, --script=<path>        [OPTIONAL] <path> to custom launch script
  -t, --timeout=<sec>        [OPTIONAL] wait <sec> until all servers become ready
  -S, --share-dir=<path>     [REQUIRED] shared file system <path> for use by servers
  -c, --cleanup              [OPTIONAL] clean up the UnifyFS storage upon server exit
  -i, --stage-in=<manifest>  [OPTIONAL] stage in file(s) listed in <manifest> file
  -P, --stage-parallel       [OPTIONAL] use parallel stage-in
  -T, --stage-timeout=<sec>  [OPTIONAL] timeout for stage-in operation

Command options for "terminate":
  -o, --stage-out=<manifest> [OPTIONAL] stage out file(s) listed in <manifest> on termination
  -P, --stage-parallel       [OPTIONAL] use parallel stage-out
  -T, --stage-timeout=<sec>  [OPTIONAL] timeout for stage-out operation
  -s, --script=<path>        [OPTIONAL] <path> to custom termination script
  -S, --share-dir=<path>     [REQUIRED for --stage-out] shared file system <path> for use by servers

After UnifyFS servers have been successfully started, you may run your UnifyFS-enabled applications as you normally would (e.g., using mpirun). Only applications that explicitly call unifyfs_mount() and access files under the specified mountpoint prefix will utilize UnifyFS for their I/O. All other applications will operate unchanged.

Stop UnifyFS

After all UnifyFS-enabled applications have completed running, use unifyfs terminate to terminate the servers. Pass the --cleanup option to unifyfs start to have the servers remove temporary data locally stored on each node after termination.

Resource Manager Job Integration

UnifyFS includes optional support for integrating directly with compatible resource managers to automatically start and stop servers at the beginning and end of a job when requested by users. Resource manager integration requires administrator privileges to deploy.

Currently, only IBM’s Platform LSF with Cluster System Manager (LSF-CSM) is supported. LSF-CSM is the resource manager on the CORAL2 IBM systems at ORNL and LLNL. The required job prologue and epilogue scripts, along with a README documenting the installation instructions, is available within the source repository at util/scripts/lsfcsm.

Support for the SLURM resource manager is under development.

Transferring Data In and Out of UnifyFS

Data can be transferred in/out of UnifyFS during server startup and termination, or at any point during a job using two stand-alone applications.

Transfer at Server Start/Terminate

The transfer subsystem within UnifyFS can be invoked by providing the -i|--stage-in option to unifyfs start to transfer files into UnifyFS:

$ unifyfs start --stage-in=/path/to/input/manifest/file --share-dir=/path/to/shared/file/system

and/or by providing the -o|--stage-out option to unifyfs terminate to transfer files out of UnifyFS:

$ unifyfs terminate --stage-out=/path/to/output/manifest/file --share-dir=/path/to/shared/file/system

The argument to both staging options is the path to a manifest file that contains the source and destination file pairs. Both stage-in and stage-out also require passing the -S|--share-dir=<path> option.

Manifest File

UnifyFS’s file staging functionality requires a manifest file in order to move data.

The manifest file contains one or more file copy requests. Each line in the manifest corresponds to one transfer request, and it contains both the source and destination file paths. Directory copies are currently not supported.

Each line is formatted as: <source filename> <whitespace> <destination filename>.

If either of the filenames contain whitespace or special characters, then both filenames should be surrounded by double-quote characters (”) (ASCII character 34 decimal). The double-quote and linefeed end-of-line characters are not supported in any filenames used in a manifest file. Any other characters are allowed, including control characters. If a filename contains any characters that might be misinterpreted, we suggest enclosing the filename in double-quotes. Comment lines are also allowed, and are indicated by beginning a line with the # character.

Here is an example of a valid stage-in manifest file:

$ [prompt] cat example_stage_in.manifest

/scratch/users/me/input_data/input_1.dat /unifyfs/input/input_1.dat
# example comment line
/home/users/me/configuration/run_12345.conf /unifyfs/config/run_12345.conf
"/home/users/me/file with space.dat" "/unifyfs/file with space.dat"

Transfer During Job

Data can also be transferred in/out of UnifyFS using the unifyfs-stage helper program. This is the same program used internally by unifyfs to provide file staging during server startup and termination.

The helper program can be invoked at any time while the UnifyFS servers are up and responding to requests. This allows for bringing in new input and/or transferring results out to be verified before the job terminates.

UnifyFS Stage Executable

The unifyfs-stage program is installed in the same directory as the unifyfs utility (i.e., $UNIFYFS_INSTALL/bin).

A manifest file (see above) needs to be provided as an argument to use this approach.

[prompt]$ unifyfs-stage --help

Usage: unifyfs-stage [OPTION]... <manifest file>

Transfer files between unifyfs volume and external file system.
The <manifest file> should contain list of files to be transferred,
and each line should be formatted as

  /source/file/path /destination/file/path

OR in the case of filenames with spaces or special characters:

  "/source/file/path" "/destination/file/path"

One file per line; Specifying directories is not currently supported.

Available options:
  -c, --checksum           Verify md5 checksum for each transfer
                           (default: off)
  -h, --help               Print usage information
  -m, --mountpoint=<mnt>   Use <mnt> as UnifyFS mountpoint
                           (default: /unifyfs)
  -p, --parallel           Transfer all files concurrently
                           (default: off, use sequential transfers)
  -s, --skewed             Use skewed data distribution for stage-in
                           (default: off, use balanced distribution)
  -S, --status-file=<path> Create stage status file at <path>
  -v, --verbose            Print verbose information
                           (default: off)

By default, each file in the manifest will be transferred in sequence (i.e.,
only a single file will be in transfer at any given time). If the
'-p, --parallel' option is specified, files in the manifest will be
transferred concurrently. The number of concurrent transfers is limited by
the number of parallel ranks used to execute unifyfs-stage.

Examples:

Sequential Transfer using a Single Client
$ srun -N 1 -n 1 unifyfs-stage $MY_MANIFEST_FILE
Parallel Transfer using 8 Clients (up to 8 concurrent file transfers)
$ srun -N 4 -n 8 unifyfs-stage --parallel $MY_MANIFEST_FILE

UnifyFS LS Executable

The unifyfs-ls program is installed in the same directory as the unifyfs utility (i.e., $UNIFYFS_INSTALL/bin). This tool will provide information about any files the local server process knows about. Users may find this helpful when debugging their applications and want to know if the files they think are being managed by UnifyFS really are.

[prompt]$ unifyfs-ls --help
Usage:
  unifyfs-ls [ -v | --verbose ] [ -m <dir_name> | --mount_point_dir=<dir_name> ]

  -v | --verbose: show verbose information(default: 0)
  -m | --mount_point: the location where unifyfs is mounted (default: /unifyfs)