High Performance Storage System

(Pilot usage phase to start in Jun/2011 with a select group of users. Deployment and configuration are still a work in progress)

The High Performance Storage System (HPSS) is a tape backed hierarchical storage system that will provide a significant portion of the allocated storage space at SciNet. It is a repository for archiving data that is not being actively used. Data will be returned to the active GPFS filesystem when it is needed.

Transfer of data into and out of the repository will be under the control of the user who will interact with the system using one or more of the following utilities:

HSI is a client with an ftp-like interface which can be used to archive and retrieve large files. It is also useful for browsing the contents of the repository.
HTAR is a utility that creates tar format archives resident in the repository. It also creates a separate index file (.idx) that can be accessed quickly.
ISH is a TUI utility that can perform an inventory of the files and directories in your tarballs.

User access will be controlled by the job scheduling system of the GPC. Transfer of data into or out of the repository is expected to be scripted and submitted as a batch job.

Guidelines

Expanded storage capacity is provided on tape -- a media that is not suited for storing small files. Files smaller than ~100MB should be grouped into tarballs with tar or htar.
The maximum size of a file that can be transferred into the repository is 1TB. However, optimal performance is obtained with file sizes <= 100 GB.
Make sure to check the application's exit code and the returned log file for errors after all data transfers and any tarball creation process.
Pilot users: DURING THE TESTING PHASE DO NOT DELETE THE ORIGINAL FILES FROM /scratch OR /project

Access Through the Queue System

All access to the archive system is through the GPC queue system documented here.

Scripted File Transfers

File transfers in and out of the repository should be scripted into jobs and submitted to the archive queue. Scripts should use the HSI and/or HTAR commands as in the example below.

#!/bin/env bash
#PBS -q archive
#PBS -N hsi_put_file_in_repo
#PBS -j oe
#PBS -me

/usr/local/bin/hsi  -v <<EOF
cput -p /scratch/$USER/workarea/finished-job1.tar.gz : finished-job1.tar.gz
EOF
status=$?
if [ ! $status == 0 ];then
   echo '!!! TRANSFER FAILED !!!'
fi
exit $status

The status of pending jobs can be monitored with showq specifying the archive queue:

showq -w class=archive

Recalling Data for Analysis

Typically, data will be recalled to the /scratch file system when it is needed for analysis. Job dependencies can be used to have analysis jobs wait in the queue for data recalls before starting. The qsub flag is

-W depend=afterok:<JOBID>

where JOBID is the job number of the staging job that must finish successfully before the analysis job can start.

Here is a short cut for generating the dependency:

gpc04 $ qsub $(qsub data-recall.sh | awk -F '.' '{print "-W depend=afterok:"$1}') job-to-work-on-recalled-data.sh

Using HSI

HSI is the primary client with which a user will interact with the archive system. It provides an ftp-like interface for archiving and retrieving files. In addition it provides a number of shell-like commands that are useful for examining and manipulating the contents of the repository. The most commonly used commands will be:

cput	Conditionally stores a file only if the file does not already exist in the repository
cget	Conditionally retrieves a copy of a file from the repository to your local storage only if a local copy does not already exist.
cd,mkdir,ls,rm,mv	Operate as one would expect on the contents of the repository.
lcd,lls	Local commands.

Simple commands can be executed on a single line.

   hsi "mkdir examples; cd examples; cput example_data.tgz"

More complex operations can be performed using a script such as this:

hsi <<EOF
  mkdir -p examples/201106
  cd examples
  mv example_data.tgz 201106/
  lcd /scratch/$USER/examples/
  cput -R -u * 
EOF
status=$?
if [ ! $status == 0 ];then
   echo '!!! TRANSFER FAILED !!!'
fi
exit status

HSI Documentation

Complete documentation of HSI is available on the Gleicher Enterprises web site.

Typical Usage

The most common interactions will be putting data into the repository, examining the contents of the repository (ls), and getting data back onto one of the active filesystems for inspection or analysis.

sample data offload

#!/bin/bash

# This script is named: data-offload.sh

#PBS -q archive
#PBS -N offload
#PBS -j oe
#PBS -me

date

# individual tarballs already exist
/usr/local/bin/hsi  -v <<EOF
mkdir put-away
cd put-away
cput /scratch/$USER/workarea/finished-job1.tar.gz : finished-job1.tar.gz
cput /scratch/$USER/workarea/finished-job2.tar.gz : finished-job2.tar.gz
EOF
status=$?
if [ ! $status == 0 ];then
   echo '!!! TRANSFER FAILED !!!'
fi
exit $status

sample data list

   - This example performs a recursive list of all files in a user's portion of the namespace. The list is placed in a dated file in the directory /home/$USER/repository.ix that can be inspected from the gpc-devel nodes.

#!/bin/bash

# This script is named: data-list.sh

#PBS -q archive
#PBS -N repository_dump
#PBS -j oe
#PBS -me

TODAY=$(date +%Y%m%d)
INDEX_DIR=/home/$USER/repository.ix
if [[ -! -e $INDEX_DIR ]];then
  mkdir $INDEX_DIR
fi

/usr/local/bin/hsi  <<EOF > $INDEX_DIR/contents-$TODAY
ls -lUR
EOF

sample data recall

  - This example should be modified to emphasize that a single cget of multiple files (rather than several separate gets) allows HSI to do optimization.

#!/bin/bash

# This script is named: data-recall.sh

#PBS -q archive
#PBS -N recall
#PBS -j oe
#PBS -me


mkdir -p /scratch/$USER/recalled-from-repository
hsi  -v << EOF
cget /scratch/$USER/recalled-from-repository/Jan-2010-jobs.tar.gz : put-away-on-2010/Jan-2010-jobs.tar.gz
cget /scratch/$USER/recalled-from-repository/Feb-2010-jobs.tar.gz : put-away-on-2010/Feb-2010-jobs.tar.gz
EOF
status=$?

exit $status

HSI vs. FTP

HSI syntax and usage is very similar to that of FTP. Please note the following information adapted from the HSI man page:

HSI supports several of the commonly used FTP commands, including "dir","get","ls","mdelete","mget","put","mput" and "prompt", with the following differences:

The "dir" command is an alias for "ls" in HSI. The "ls" command supports an extensive set of options for displaying files, including wildcard pattern-matching, and the ability to recursively list a directory tree
The "put" and "get" family of commands support recursion
There are "conditional put" and "conditional" get commands (cput, cget)

The syntax for renaming files during transfers with HSI is different from FTP. With HSI, the general format is always

     "local_file : repository_file"

and multiple such pairs may be specified on a single command line. With FTP, the local filename is specified first on a "put" command, and second on a "get" command.

For example, when using HSI to store the local file "file1" as "repository_file1" on the archival system, then retrieve it back to the local filesystem as "file1.bak", the following commands could be used:

    put file1 : repository_file1
    get file1.bak : repository_file1

With FTP, the following syntax would be used instead:

    put file1 repository_file1 
    get repository_file1 file1.bak

The "m" prefix is not needed for HSI commands; all commands that work with files accept multiple files on the command line. The "m" series of commands are intended to provide a measure of compatibility for FTP users.

Other HSI Examples

Creating tar archive on the fly by piping stdout:

   tar cf - *.[ch] | hsi put - : source.tar

Note: the ":" operator which separates the local and HSI pathnames must be surrounded by whitespace (one or more space characters)

Retrieve the tar file source kept above and extract all files:

    hsi get - : source.tar | tar xf -

The commands below are equivalent (the default HSI directory placement is /archive/<group>/<user>/):

    hsi put source.tar
    hsi put source.tar : /archive/<group>/<user>/source.tar

For more details please check the HSI Introduction, the HSI Man Page or the or the hsi help

HTAR

Please aggregate small files (<~100MB) into tarballs or htar files.

HTAR is a utility that is used for aggregating a set of files from the local filesystem directly into the repository, creating a file that conforms to the POSIX TAR specification. It does this without having to first create an intermediate file on the local filesystem; instead, it uses a sophisticated multithreaded buffering scheme to write files directly into the repository, thereby achieving a high rate of performance.

CAUTION

Files larger than 68 GB cannot be stored in an htar archive (you'll get an error message for the whole operation)
HTAR archives cannot contain more than 1 million files.
Check the HTAR exit code and log file before removing any files from the active filesystems.

HTAR Usage

To write the file1 and file2 files to a new archive called files.tar in the default HPSS home directory, enter:

    htar -cf files.tar file1 file2
OR
    htar -cf /archive/<group>/<user>/files.tar file1 file2

To write a subdirA to a new archive called subdirA.tar in the default HPSS home directory, enter:

    htar -cf subdirA.tar subdirA

To extract all files from the project1/src directory in the Archive file called proj1.tar, and use the time of extraction as the modification time, enter:

    htar -xm -f proj1.tar project1/src

To display the names of the files in the out.tar archive file within the HPSS home directory, enter (the out.tar.idx file will be queried):

    htar -vtf out.tar

For more details please check the HTAR - Introduction or the HTAR Man Page online

More detailed examples

create a tarball on-the-fly of the finished-job3 directory

/usr/local/bin/htar -cf finished-job3.tar /scratch/$USER/workarea/finished-job3/

cd /scratch/$USER/recalled-from-repository/usr/local/bin/htar -xf finished-job3.tar

HPSS

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