A simple, straightforward way to archive and restore stuff to/from HPSS(SDA).
IU dc2 has been deprecated and replaced by Slate. To restore data archived in dc2 to slate, you will need to fool autohpss because it can only archive/restore on the same filepath.
You can do this by running autohpss via singularity and bind mounting slate as dc2/scratch, for example
singularity exec -B /N/slate:/N/dc2/scratch docker://soichih/autohpss restore /N/dc2/scratch/hayashis/sca
This system assumes you have HPSS(SDA) account.. If not, create it at
Undergraduate needs a faculty sponsor (see https://kb.iu.edu/d/aczn). If you are eligible but not seeing SDA account listed, please send email to [email protected] and ask them to give you access to SDA.
autohpss uses kerberos token to access HSI. If you don't know what it is, simply use kktgen command to setup your keytab.
$ module load nodejs
$ kktgen
IU username: hayashis
IU password:
Keytab successfully created.
autohpss is currently installed on Karst and BigRed2 as nodejs/npm module.
$ module load nodejs hpss
You are now ready to use autohpss commands!
In order to archive your files, directories, navigate to the directory where you want to archive all files and directories under it and run archive.
$ cd /N/dc2/projects/o3d/O3D_STN
$ archive
archive command will recursively walk through a specified directory and find
any files that are new, or modified since you previously run this command. It then creates batches of files that are roughtly 30GB in size
and transfer them to your SDA account using htar.
autohpss keeps up with list of files in local sqlite3 DB (~/.config/autohpss) along with modified data and which htar archive the files belongs.
You can run archive periodically by setting up a cron job which will 1) ssh to karst 2) run archive at desired interval. Please note that, the arhcive command will re-archive files if they are modified since they were last archived. If you have a files that are frequently modified, you should either not archive those files or archive them less frequently to prevent too many copies of those files to be created in HPSS.
In the future, I will provide a functionality to automatically purge older versions of the same file in HPSS (maybe only keep 3 latest copies?)
You can specify -d to do dry-run of archive to show which files needs to be archived.
You can also specify a Path that you'd like to archive
$ archive /N/dc2/projects/o3d/O3D_STN
Path can be a relative path (it will be automatically resolved to the absolute path)
$ cd /N/dc2/projects/o3d
$ archive O3D_STN
To restore files, simply run restore command with the directory / file path that you'd like to restore.
$ restore /N/dc2/projects/o3d/O3D_STN/derivatives/preprocess/sub-0001
restore command will only restore files that are missing. If archived file already exists, it will skip the file. You are safe to run this command as often as you'd like (like at top of your job script). If the file you have archived is locally modified (with newer timestamp), it will display warning - that you should re-archive those files.
You can specify -d option run a dry run to show which files needs to be restored without actually restoring.
For any workflow that read data from dc2, you should update it so that it will run restore command for each input file/directory that you use in your workflow (restore only files that you actually use!). Be sure to add extra walltime in case files don't exist on dc2 and need to pull from HPSS tape (2-3 hours?)
#!/bin/bash
#PBS -l nodes=1:ppn=16:dc2,walltime=6:00:00
#PBS -N app-dtiinit
#PBS -V
cd $PBS_O_WORKDIR
module load hpss nodejs
restore /N/dc2/scratch/hayashis/neuro/commondata
restore /N/dc2/scratch/hayashis/neuro/subject_111111
restore /N/dc2/scratch/hayashis/neuro/subject_222222
module load matlab
module load spm
module load fsl
... run your applicaiton using data restored above ...
#After successful completion of your job, archive any output files
archive /N/dc2/scratch/hayashis/neuro/derivatives
You could run archive command on your entire project directories, but you should avoid if if you could; archive command will archive all new/modified files under the specified directory recursively.
After successful archive, you can test to make sure that your files are safely archived by renaming a few files that you have archived, then running restore command on those files to see if the files with original filename re-appears. You can also run diff command betwen the renamed file and files that are restored to be sure that they are identical.