Workspace Maker
Overview
Workspace Maker is a small utility used to manage access to scratch storage on Kamiak. In order to use any scratch storage, you’ll need to create what we call a “workspace” to store your data within. A workspace is simply a directory that expires and is automatically removed. The maximum lifetime of a scratch workspace on Kamiak is 2 weeks. Clearly, scratch storage is not intended for permanent data and users should consider project space for that use. To use a workspace you’ll need to know three commands: mkworkspace, lsworkspace, rmworkspace. Only the first is required since removal of a workspace is automatic if we let it expire. We recommend you remove workspaces as soon as they are no longer needed rather than allowing them to expire. That is so the system can promptly release the storage space for others to use.
Click each command below to see more information about it.
- mkworkspace: Create a workspace on the scratch storage of Kamiak
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$ mkworkspace --help Usage: mkworkspace [options] Options: -h, --help show this help message and exit -v, --verbose Enable verbose mode -n WORKSPACE_NAME, --name=WORKSPACE_NAME The name of the workspace to be created (defaults to user name + random number) -t TIMELIMIT, --timelimit=TIMELIMIT Time limit for the workspace to exist before its automatic removal. Syntax is DAYS-HOURS:MINUTES. Default: 14-00:00, Max: 14-00:00 -b BACKEND, --backend=BACKEND Storage backend to use for the workspace. Supported backends: '/scratch' (default), '/local' (compute nodes only; workspace will only be available on the node upon which it was created) -q, --quiet Output only the workspace created (useful in scripts)
- lsworkspace: List your workspaces
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$ lsworkspace --help Usage: lsworkspace [options] Options: -h, --help show this help message and exit -v, --verbose Enable verbose mode -b BACKEND, --backend=BACKEND Storage backend to use for the workspace. Supported backends: '/scratch' (default), '/local' (compute nodes only)
- rmworkspace: Remove workspaces
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$ rmworkspace --help Usage: rmworkspace [options] Options: -h, --help show this help message and exit -n WORKSPACE_NAME, --name=WORKSPACE_NAME The name of an individual workspace to remove -b BACKEND, --backend=BACKEND Storage backend to use for the workspace. Supported backends: '/scratch' (default), '/local' (compute nodes only) -a, --autoremove Remove workspace(s) without prompting for confirmation -f, --force Remove a workspace even if it is not expired (only valid with --name) -v, --verbose Enable verbose mode
Creating and Using Workspaces
Let’s look at an example of creating, using, and removing a workspace interactively:
$ mkworkspace
Successfully created workspace. Details:
Workspace: /scratch/my.NID_616253
User: my.NID
Group: its_p_sys_ur_kam-its
Expiration: 2017-08-20 16:21:30
Note that expiration date. Shortly after that time the workspace and all of the data within will be deleted. Now that the workspace has been created, we can use it and delete it when we’re done.
$ cd /scratch/my.NID_616253
[my.NID_616253]$ touch file.txt
[my.NID_616253]$ cd
$ lsworkspace
Workspace: /scratch/my.NID_616253
Creation host: login-p1n01
Creation time: 2017-08-6 16:21:30
User owner: my.NID
Group owner: its_p_sys_ur_kam-its
Expiration time: 2017-08-20 16:21:30
$ rmworkspace -n my.NID_616253 --force
Remove workspace '/scratch/my.NID_616253' (expired 2017-08-20 16:21:30)? y or n: y
Removing workspace /scratch/my.NID_616253
rmworkspace completed, total removed workspaces: 1
A workspace is a directory and you use it as you would any other. Let’s use a workspace in a batch job script:
#!/bin/bash #SBATCH --time=0-00:010:00 ### Wall clock time limit in Days-HH:MM:SS #SBATCH --ntasks-per-node=1 ### Number of tasks to be launched per Node my_workspace="$(mkworkspace --quiet)" echo "My workspace is: $my_workspace" cd $my_workspace echo 'Hello!' > file.txt
This job will simply create a workspace, place the text “Hello!” into a file in the workspace, and end the job. Let’s extend it slightly to use a Local Scratch workspace by using the option –backend to mkworkspace (see mkworkspace --help for all options):
#!/bin/bash #SBATCH --time=0-00:010:00 ### Wall clock time limit in Days-HH:MM:SS #SBATCH --ntasks-per-node=1 ### Number of tasks to be launched per Node my_workspace="$(mkworkspace --backend=/local)" echo "My workspace is: $my_workspace" cd $my_workspace echo 'Hello!' > file.txt
Workspaces in Compute Jobs
Let’s go through an example workflow of how we can utilize workspaces within compute jobs on Kamiak. Say we want to have a compute job:
- Create a workspace
- Run a computation using that workspace
- Write/copy final results to permanent storage, such as project space
- Remove the workspace when the job ends or is canceled (e.g. due to preemption)
We can use features of Workspace Maker and Kamiak’s scheduler, Slurm, to do exactly that.
#!/bin/bash
#SBATCH -n 1 # Number of cores
#SBATCH -t 0-00:10 # Runtime in D-HH:MM
my_workspace=$(mkworkspace --backend=/local --quiet)
function clean_up {
# Clean up. Remove temporary workspaces and the like.
rmworkspace --autoremove --force --name=$my_workspace
exit
}
# Call our clean_up function when we exit, even if SLURM cancels the job this should still run
trap 'clean_up' EXIT
echo "My current workspace is $my_workspace"
# Work happens here ...
In this job script we’re creating a workspace on Local Scratch storage. We’re also utilizing Unix process signals to remove the workspace when the job ends or is canceled (see here for more information). If that isn’t desired and you need to keep the workspace for further use, simply remove the function definition and “trap” command.
This job script is a simple example of how workspaces can be managed within a compute job. How to effectively use workspaces with your applications will depend on the application and your needs. Workspaces can be used as temp directories, buckets to download working datasets to, or -of course- as fast storage for general computation. Note: Scratch storage is faster than Project storage; Local Scratch storage is faster than Scratch.