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:
- Allocate nodes using the system resource manager (i.e., start a job)
- Update any desired UnifyFS server configuration settings
- Start UnifyFS servers on each allocated node using
- Run one or more UnifyFS-enabled applications
- Terminate the UnifyFS servers using
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.
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
/etc/unifyfs/unifyfs.conf. See UnifyFS Configuration
for further details on customizing the UnifyFS runtime configuration.
1 2 3 4 5 6 7 8 9
#!/bin/bash # spillover data to node-local ssd storage export UNIFYFS_LOGIO_SPILL_DIR=/mnt/ssd/$USER/data # store server logs in job-specific scratch area export UNIFYFS_LOG_DIR=$JOBSCRATCH/logs unifyfs start --share-dir=/path/to/shared/file/system
unifyfs provides command-line options to choose the client mountpoint,
adjust the consistency model, 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": -C, --consistency=<model> [OPTIONAL] consistency model (NONE | LAMINATED | POSIX) -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 -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 -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.
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
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, and consequently required
-S|--share-dir, option to
unifyfs terminate to transfer files out of
$ unifyfs terminate --stage-out=/path/to/output/manifest/file --share-dir=/path/to/shared/file/system
A manifest file needs to be provided to the
terminate commands in
order to specify the desired transfers.
UnifyFS’s stage 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 unifyfs manifest file. Any other characters are allowed, including control characters. If a filename contains any characters that might be misinterpreted, then enclosing the filename in double-quotes is always a safe thing to do.
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 /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 one of two stand-alone applications.
The stand-alone applications 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¶
terminate transfer API stage functionality can also be used
via the stand-alone application
unifyfs-stage. This application is installed
in the same directory as the
unifyfs utility (
This application can be run at any time within a job to transfer new data into or results out of UnifyFS. 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 supported. Available options: -c, --checksum verify md5 checksum for each transfer -h, --help print this usage -m, --mountpoint=<mnt> use <mnt> as unifyfs mountpoint (default: /unifyfs) -p, --parallel transfer each file in parallel (experimental) -s, --share-dir=<path> directory path for creating status file -v, --verbose print noisy outputs Without the '-p, --parallel' option, a file is transferred by a single process. If the '-p, --parallel' option is specified, each file will be divided by multiple processes and transferred in parallel.
$ srun -N 1 -n 1 unifyfs-stage $MY_MANIFEST_FILE
$ srun -N 4 -n 8 unifyfs-stage --parallel $MY_MANIFEST_FILE
transfer-gotcha executable is currently unusable due to an issue
that is being tracked.
The transfer API can also be used during the job by invoking the stand-alone
transfer application. It works similarly to the Unix
cp command, with
source and destination, except being aware that it is copying files between an
external file system and internal UnifyFS.
[prompt]$ transfer-static --help Usage: transfer-static [options...] <source path> <destination path> Available options: -d, --debug pause before running test (handy for attaching in debugger) -h, --help help message -m, --mount=<mountpoint> use <mountpoint> for unifyfs (default: /unifyfs) -p, --parallel parallel transfer -r, --rank=<rank> use <rank> for transfer (default: 0)
Examples of using
$ srun -N 1 -n 1 $UNIFYFS_INSTALL/libexec/transfer-static /path/on/parallelfs/file.dat /unifyfs/file.dat $ srun -N 1 -n 1 $UNIFYFS_INSTALL/libexec/transfer-static /unifyfs/output.dat /scratch/my_output/output.dat
$ srun -N 4 -n 8 /path/to/libexec/transfer-static --parallel /path/on/parallelfs/file.dat /unifyfs/file.dat $ srun -N 4 -n 8 /path/to/libexec/transfer-static --parallel /unifyfs/output.dat /scratch/my_output/output.dat