HPSS

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Contents

High Performance Storage System

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

Since this system is intended for large data storage, it is accessible only to groups who have been awarded storage space at SciNet beyond 5TB in the yearly RAC resource allocation round. However, upon request, any user may be awarded access to HPSS, up to 2TB per group, so that you may get familiar with the system (just email support@scinet.utoronto.ca)

Access and transfer of data into and out of HPSS is done under the control of the user, whose interaction is expected to be scripted and submitted as a batch job, using one or more of the following utilities:

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

We're currently running HPSS v 7.3.3 patch 6, and HSI/HTAR version 4.0.1.2

Why should I use and trust HPSS?

  • 20+ years history, used by about 40 facilities in the “Top 500” HPC list
  • very reliable, data redundancy and data insurance built-in (we keep dual copies of everything on tapes)
  • over 1 ExaByte of combined storage world-wide.
  • The top 3 unclassified sites in the World report having 120PB, 86PB and 56PB in production.
  • highly scalable, reasonable performance at SciNet - Ingest: ~24 TB/day, Recall: ~12 TB/day (aggregated)
  • HSI/HTAR clients also very reliable and used on several HPSS sites. ISH was written at SciNet.
  • HPSS fits well with the Storage Capacity Expansion Plan at SciNet (pdf presentation)

Guidelines

  • Expanded storage capacity is provided on tape -- a media that is not suited for storing small files. Files smaller than ~200MB should be grouped into tarballs with tar or htar.
  • Optimal performance for aggregated transfers and allocation on tapes is obtained with tarballs of size 500GB or less, whether ingested by htar or hsi ( WHY?)
  • We strongly urge that you use the sample scripts we are providing as the basis for your job submissions.
  • Make sure to check the application's exit code and returned logs for errors after any data transfer or tarball creation process

New to the System?

The first step is to email scinet support and request an HPSS account (or else you will get "Error - authentication/initialization failed" and 71 exit codes).

THIS set of instructions on the wiki is the best and most compressed "manual" we have. It may seem a bit overwhelming at first, because of all the job script templates we make available below (they are here so you don't have to think too much, just copy and paste), but if you approach the index at the top as a "case switch" mechanism for what you intend to do, everything falls in place.

Try this sequence:

1) take a look around HPSS using an interactive HSI session

(most linux shell commands have an equivalent in HPSS)

2) archive a small test directory using HTAR

2a) use step 1) to see what happened

3) archive a file using hsi

3a) use step 1) to see what happened

4) archive a small test directory using HSI

4a) use step 1) to see what happened

5) now try the other cases and so on. In a couple of hours you'll be in pretty good shape.

Bridge between BGQ and HPSS

BGQ users may transfer material to/from HPSS via the GPC archive queue. On the HPSS gateway node (gpc-archive01), the BGQ GPFS file systems are mounted under a single mounting point /bgq (/bgq/scratch and /bgq/home).

Access Through the Queue System

All access to the archive system is done through the GPC queue system.

  • Job submissions should be done to the 'archive' queue
  • Short jobs are limited to 1H walltime by default. Long jobs (> 1H) are limited to 72H walltime.
  • Users are limited to only 1 long job and 1 short job at the same time.
  • There can only be 5 long jobs running at any given time overall. Remaining submissions will be placed on hold for the time being. So far we have not seen a need for overall limit on short jobs.

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

showq -w class=archiveshort
OR
showq -w class=archivelong

Access Through an Interactive HSI session

  • You may want to acquire an interactive shell, start an HSI session and navigate the archive naming-space. Keep in mind, you're restricted to 1H.
gpc-f103n084-$ qsub -q archive -I
qsub: waiting for job 11611291.gpc-sched to start
qsub: job 11611291.gpc-sched ready

----------------------------------------
Begin PBS Prologue Mon May 28 13:15:28 EDT 2012 1338225328
Job ID:		11611291.gpc-sched
Username:	pinto
Group:		scinet
Nodes:		gpc-archive01
End PBS Prologue Mon May 28 13:15:28 EDT 2012 1338225328
----------------------------------------

hpss-archive01-$ hsi    (DON'T FORGET TO START HSI)
******************************************************************
*     Welcome to HPSS@SciNet - High Perfomance Storage System    *
*                                                                *
*        Contact Information: support@scinet.utoronto.ca         *
*  NOTE: do not transfer SMALL FILES with HSI. Use HTAR instead  *
*              CHECK THE INTEGRITY OF YOUR TARBALLS              *
******************************************************************
Username: pinto  UID: 10010  Acct: 10010(10010) Copies: 2 Firewall: off [hsi.4.0.1 Thu Mar 22 11:44:03 EDT 2012] 
[HSI]/archive/s/scinet/pinto-> ls

[HSI]/archive/s/scinet/pinto-> cd <some directory>

take a look around HPSS using an interactive HSI session

Scripted File Transfers

File transfers in and out of the HPSS should be scripted into jobs and submitted to the archive queue. See generic example below.

#!/bin/bash
#PBS -l walltime=72:00:00
#PBS -q archive
#PBS -N htar_create_tarball_in_hpss
#PBS -j oe
#PBS -m e
 
echo "Creating a htar of finished-job1/ directory tree into HPSS"
 
trap "echo 'Job script not completed';exit 129" TERM INT
# Note that your initial directory in HPSS will be $ARCHIVE
 
DEST=$ARCHIVE/finished-job1.tar
 
# htar WILL overwrite an existing file with the same name so check beforehand.
 
hsi ls $DEST &> /dev/null
status=$?
 
if [ $status == 0 ]; then   
    echo 'File $DEST already exists. Nothing has been done'
    exit 1
fi
 
cd $SCRATCH/workarea/ 
htar -Humask=0137 -cpf $ARCHIVE/finished-job1.tar finished-job1/ 
status=$?
 
trap - TERM INT
 
if [ ! $status == 0 ]; then
   echo 'HTAR returned non-zero code.'
   /scinet/gpc/bin/exit2msg $status
   exit $status
else
   echo 'TRANSFER SUCCESSFUL'
fi

Note: Always trap the execution of your jobs for abnormal terminations, and be sure to return the exit code

Job Dependencies

Typically data will be recalled to /scratch when it is needed for analysis. Job dependencies can be constructed so that 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 archive recalling job that must finish successfully before the analysis job can start.

Here is a short cut for generating the dependency (lookup data-recall.sh samples):

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

HTAR

Please aggregate small files (<~200MB) into tarballs or htar files.

Keep your tarballs to size 500GB or less, whether ingested by htar or hsi ( WHY?)

HTAR is a utility that is used for aggregating a set of files and directories, by using a sophisticated multithreaded buffering scheme to write files directly from GPFS into HPSS, creating an archive file that conforms to the POSIX TAR specification, thereby achieving a high rate of performance. HTAR does not do gzip compression, however it already has a built-in checksum algorithm.

Caution

  • Files larger than 68 GB cannot be stored in an HTAR archive. If you attempt to start a transfer with any files larger than 68GB the whole HTAR session will fail, and you'll get a notification listing all those files, so that you can transfer them with HSI. unintentionally overwriting the htar destination file in HPSS
  • Files with pathnames too long will be skipped (greater than 100 characters), so as to conform with TAR protocol (POSIX 1003.1 USTAR) -- Note that the HTAR will erroneously indicate success, however will produce exit code 70. For now, you can check for this type of error by "grep Warning my.output" after the job has completed.
  • Unlike with cput/cget in HSI, "prompt before overwrite", this is not the default with (h)tar. Be careful not to unintentionally overwrite a previous htar destination file in HPSS. There could be a similar situation when extracting material back into GPFS and overwriting the originals. Be sure to double-check the logic in your scripts.
  • Check the HTAR exit code and log file before removing any files from the GPFS active filesystems.


=== HTAR Usage ===
  • To write the file1 and file2 files to a new archive called files.tar in the default HPSS home directory, and preserve mask attributes (-p), enter:
    htar -cpf files.tar file1 file2
OR
    htar -cpf $ARCHIVE/files.tar file1 file2
  • To write a subdirA to a new archive called subdirA.tar in the default HPSS home directory, enter:
    htar -cpf subdirA.tar subdirA
  • To extract all files from the archive file called proj1.tar in HPSS into the project1/src directory in GPFS, and use the time of extraction as the modification time, enter:
    htar -xpmf 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
  • To ensure that both the htar and the .idx files have read permissions to other members in your group use the umask option
    htar -Humask=0137 ....

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


Sample tarball create

#!/bin/bash
#PBS -l walltime=72:00:00
#PBS -q archive
#PBS -N htar_create_tarball_in_hpss
#PBS -j oe
#PBS -m e
 
trap "echo 'Job script not completed';exit 129" TERM INT
# Note that your initial directory in HPSS will be /archive/$(id -gn)/$(whoami)/
 
DEST=$ARCHIVE/finished-job1.tar
 
# htar WILL overwrite an existing file with the same name so check beforehand.
 
hsi ls $DEST &> /dev/null
status=$?
 
if [ $status == 0 ]; then   
    echo 'File $DEST already exists. Nothing has been done'
    exit 1
fi
 
cd $SCRATCH/workarea/ 
htar -Humask=0137 -cpf $DEST finished-job1/ 
status=$?
 
trap - TERM INT
 
if [ ! $status == 0 ]; then
   echo 'HTAR returned non-zero code.'
   /scinet/gpc/bin/exit2msg $status
   exit $status
else
   echo 'TRANSFER SUCCESSFUL'
fi

Note: If you attempt to start a transfer with any files larger than 68GB the whole HTAR session will fail, and you'll get a notification listing all those files, so that you can transfer them with HSI.

----------------------------------------
INFO: File too large for htar to handle: finished-job1/file1 (86567185745 bytes)
INFO: File too large for htar to handle: finished-job1/file2 (71857244579 bytes)
ERROR: 2 oversize member files found - please correct and retry
ERROR: [FATAL] error(s) generating filename list 
HTAR: HTAR FAILED
###WARNING  htar returned non-zero exit status

Sample tarball list

#!/bin/bash
#PBS -l walltime=72:00:00
#PBS -q archive
#PBS -N htar_list_tarball_in_hpss
#PBS -j oe
#PBS -m e
 
trap "echo 'Job script not completed';exit 129" TERM INT
# Note that your initial directory in HPSS will be $ARCHIVE
 
DEST=$ARCHIVE/finished-job1.tar
 
 
htar -tvf $DEST
status=$?
 
trap - TERM INT
 
if [ ! $status == 0 ]; then
   echo 'HTAR returned non-zero code.'
   /scinet/gpc/bin/exit2msg $status
   exit $status
else
   echo 'TRANSFER SUCCESSFUL'
fi

Sample tarball extract

#!/bin/bash
#PBS -l walltime=72:00:00
#PBS -q archive
#PBS -N htar_extract_tarball_from_hpss
#PBS -j oe
#PBS -m e
 
trap "echo 'Job script not completed';exit 129" TERM INT
# Note that your initial directory in HPSS will be $ARCHIVE
 
cd $SCRATCH/recalled-from-hpss
htar -xpmf $ARCHIVE/finished-job1.tar
status=$?
 
trap - TERM INT
 
if [ ! $status == 0 ]; then
   echo 'HTAR returned non-zero code.'
   /scinet/gpc/bin/exit2msg $status
   exit $status
else
   echo 'TRANSFER SUCCESSFUL'
fi

HSI

HSI may be the primary client with which some users will interact with HPSS. It provides an ftp-like interface for archiving and retrieving tarballs or directory trees. In addition it provides a number of shell-like commands that are useful for examining and manipulating the contents in HPSS. The most commonly used commands will be:

cput Conditionally saves or replaces a HPSSpath file to GPFSpath if the GPFS version is new or has been updated
cput [options] GPFSpath [: HPSSpath]
cget Conditionally retrieves a copy of a file from HPSS to GPFS only if a GPFS version does not already exist.
cget [options] [GPFSpath :] HPSSpath
cd,mkdir,ls,rm,mv Operate as one would expect on the contents of HPSS.
lcd,lls Local commands to GPFS


  • There are 3 distinctions about HSI that you should keep in mind, and that can generate a bit of confusion when you're first learning how to use it:
    • HSI doesn't currently support renaming directories paths during transfers on-the-fly, therefore the syntax for cput/cget may not work as one would expect in some scenarios, requiring some workarounds.
    • HSI has an operator ":" which separates the GPFSpath and HPSSpath, and must be surrounded by whitespace (one or more space characters)
    • The order for referring to files in HSI syntax is different from FTP. In HSI the general format is always the same, GPFS first, HPSS second, cput or cget:
     GPFSfile : HPSSfile

For example, when using HSI to store the tarball file from GPFS into HPSS, then recall it to GPFS, the following commands could be used:

    cput tarball-in-GPFS : tarball-in-HPSS
    cget tarball-recalled : tarball-in-HPSS

unlike with FTP, where the following syntax would be used:

    put tarball-in-GPFS tarball-in-HPSS 
    get tarball-in-HPSS tarball-recalled
  • Simple commands can be executed on a single line.
    hsi "mkdir LargeFilesDir; cd LargeFilesDir; cput tarball-in-GPFS : tarball-in-HPSS"
  • More complex sequences can be performed using an except such as this:
    hsi <<EOF
      mkdir LargeFilesDir
      cd LargeFilesDir
      cput tarball-in-GPFS : tarball-in-HPSS
      lcd $SCRATCH/LargeFilesDir2/
      cput -Ruph *  
    end
    EOF
  • The commands below are equivalent, but we recommend that you always use full path, and organize the contents of HPSS, where the default HSI directory placement is $ARCHIVE:
    hsi cput tarball
    hsi cput tarball : tarball
    hsi cput $SCRATCH/tarball : $ARCHIVE/tarball
  • There are no known issues renaming files on-the-fly:
    hsi cput $SCRATCH/tarball1 : $ARCHIVE/tarball2
    hsi cget $SCRATCH/tarball3 : $ARCHIVE/tarball2
  • However the syntax forms such as the ones below will fail, since they rename the directory paths.
   hsi cput -Ruph $SCRATCH/LargeFilesDir : $ARCHIVE/LargeFilesDir     (FAILS)
OR
   hsi cget -Ruph $SCRATCH/LargeFilesDir : $ARCHIVE/LargeFilesDir2    (FAILS)
OR
   hsi cput -Ruph $SCRATCH/LargeFilesDir/* : $ARCHIVE/LargeFilesDir2  (FAILS)
OR
   hsi cget -Ruph $SCRATCH/LargeFilesDir : $ARCHIVE/LargeFilesDir     (FAILS)

One workaround is the following 2-steps process, where you do a "lcd " in GPFS first, and recursively transfer the whole directory (-R), keeping the same name. You may use '-u' option to resume a previously disrupted session, and the '-p' to preserve timestamp, and '-h' to keep the links.

    hsi <<EOF
      lcd $SCRATCH
      cget -Ruph LargeFilesDir
    end
    EOF

Another workaround is do a "lcd" into the GPFSpath first and a "cd" in the HPSSpath, but transfer the files individually with the '*' wild character. This option lets you change the directory name:

    hsi <<EOF
      lcd $SCRATCH/LargeFilesDir
      mkdir $ARCHIVE/LargeFilesDir2
      cd $ARCHIVE/LargeFilesDir2
      cput -Ruph *  
    end
    EOF

Documentation

Complete documentation on HSI is available from the Gleicher Enterprises links below. You may peruse those links and come with alternative syntax forms. You may even be already familiar with HPSS/HSI from other HPC facilities, that may or not have procedures similar to ours. HSI doesn't always work as expected when you go outside of our recommended syntax, so we strongly urge that you use the sample scripts we are providing as the basis for your job submissions

Note: HSI returns the highest-numbered exit code, in case of multiple operations in the same hsi session. You may use '/scinet/gpc/bin/exit2msg $status' to translate those codes into intelligible messages

Typical Usage Scripts

The most common interactions will be putting data into HPSS, examining the contents (ls,ish), and getting data back onto GPFS for inspection or analysis.

Sample data offload

#!/bin/bash
 
# This script is named: data-offload.sh
#PBS -l walltime=72:00:00
#PBS -q archive
#PBS -N offload
#PBS -j oe
#PBS -me
 
trap "echo 'Job script not completed';exit 129" TERM INT
# individual tarballs already exist
 
/usr/local/bin/hsi  -v <<EOF1
mkdir put-away
cd put-away
cput $SCRATCH/workarea/finished-job1.tar.gz : finished-job1.tar.gz
end
EOF1
status=$?
if [ ! $status == 0 ];then
   echo 'HSI returned non-zero code.'
   /scinet/gpc/bin/exit2msg $status
   exit $status
else
   echo 'TRANSFER SUCCESSFUL'
fi
 
/usr/local/bin/hsi  -v <<EOF2
mkdir put-away
cd put-away
cput $SCRATCH/workarea/finished-job2.tar.gz : finished-job2.tar.gz
end
EOF2
status=$?
if [ ! $status == 0 ];then
   echo 'HSI returned non-zero code.'
   /scinet/gpc/bin/exit2msg $status
   exit $status
else
   echo 'TRANSFER SUCCESSFUL'
fi
 
trap - TERM INT


Note: as in the above example, we recommend that you capture the (highest-numbered) exit code for each hsi session independently. And remember, you may improve your exit code verbosity by adding the excerpt below to your scripts:

if [ ! $status == 0 ];then
   echo 'HSI returned non-zero code.'
   /scinet/gpc/bin/exit2msg $status
   exit $status
else
   echo 'TRANSFER SUCCESSFUL'
fi

Sample data list

A very trivial way to list the contents of HPSS would be to just submit the HSI 'ls' command.

#!/bin/bash
 
# This script is named: data-list.sh
#PBS -l walltime=1:00:00
#PBS -q archive
#PBS -N hpss_ls
#PBS -j oe
#PBS -me
 
/usr/local/bin/hsi -v <<EOF
cd put-away
ls -R
end
EOF

Warning: if you have a lot of files, the ls command will take a long time to complete. For instance, about 400,000 files can be listed in about an hour. Adjust the walltime accordingly, and be on the safe side.

However, we provide a much more useful and convenient way to explore the contents of HPSS with the inventory shell ISH. This example creates an index of all the files in a user's portion of the namespace. The list is placed in the directory /home/$(whoami)/.ish_register that can be inspected from the gpc-devel nodes.

#!/bin/bash
 
# This script is named: data-list.sh
#PBS -l walltime=1:00:00
#PBS -q archive
#PBS -N hpss_index
#PBS -j oe
#PBS -me
 
INDEX_DIR=$HOME/.ish_register
if ! [ -e "$INDEX_DIR" ]; then
  mkdir -p $INDEX_DIR
fi
 
export ISHREGISTER="$INDEX_DIR"
/scinet/gpc/bin/ish hindex

Note: the above warning on collecting the listing for many files applies here too.

This index can be browsed or searched with ISH on the development nodes.

gpc-f104n084-$ /scinet/gpc/bin/ish ~/.ish_register/hpss.igz 
[ish]hpss.igz> help

ISH is a powerful tool that is also useful for creating and browsing indices of tar and htar archives, so please look at the documentation or built in help.

Sample data recall

#!/bin/bash
 
# This script is named: data-recall.sh
#PBS -l walltime=72:00:00
#PBS -q archive
#PBS -N recall_files
#PBS -j oe
#PBS -me
 
trap "echo 'Job script not completed';exit 129" TERM INT
 
mkdir -p $SCRATCH/recalled-from-hpss
 
# individual tarballs previously organized in HPSS inside the put-away-on-2010/ folder
hsi  -v << EOF
cget $SCRATCH/recalled-from-hpss/Jan-2010-jobs.tar.gz : $ARCHIVE/put-away-on-2010/Jan-2010-jobs.tar.gz
cget $SCRATCH/recalled-from-hpss/Feb-2010-jobs.tar.gz : $ARCHIVE/put-away-on-2010/Feb-2010-jobs.tar.gz
end
EOF
status=$?
 
trap - TERM INT
 
if [ ! $status == 0 ]; then
   echo 'HSI returned non-zero code.'
   /scinet/gpc/bin/exit2msg $status
   exit $status
else
   echo 'TRANSFER SUCCESSFUL'
fi


We should emphasize that a single cget of multiple files (rather than several separate gets) allows HSI to do optimization, as in the following example:

#!/bin/bash
 
# This script is named: data-recall.sh
#PBS -l walltime=72:00:00
#PBS -q archive
#PBS -N recall_files_optimized
#PBS -j oe
#PBS -me
 
trap "echo 'Job script not completed';exit 129" TERM INT
mkdir -p $SCRATCH/recalled-from-hpss
 
# individual tarballs previously organized in HPSS inside the put-away-on-2010/ folder
hsi  -v << EOF
lcd $SCRATCH/recalled-from-hpss/
cd $ARCHIVE/put-away-on-2010/
cget Jan-2010-jobs.tar.gz Feb-2010-jobs.tar.gz
end
EOF
status=$?
 
trap - TERM INT
 
if [ ! $status == 0 ]; then
   echo 'HSI returned non-zero code.'
   /scinet/gpc/bin/exit2msg $status
   exit $status
else
   echo 'TRANSFER SUCCESSFUL'
fi

Sample transferring directories

Remember, it's not possible to rename directories on-the-fly:

hsi cget -Ruph $SCRATCH/LargeFiles-recalled : $ARCHIVE/LargeFiles    (FAILS)

One workaround is transfer the whole directory (and sub-directories) recursively:

#!/bin/bash
 
# This script is named: data-recall.sh
#PBS -l walltime=72:00:00
#PBS -q archive
#PBS -N recall_directories
#PBS -j oe
#PBS -me
 
trap "echo 'Job script not completed';exit 129" TERM INT
 
mkdir -p $SCRATCH/recalled
 
hsi  -v << EOF
lcd $SCRATCH/recalled
cd $ARCHIVE/
cget -Ruph LargeFiles
end
EOF
status=$?
 
trap - TERM INT
 
if [ ! $status == 0 ]; then
   echo 'HSI returned non-zero code.'
   /scinet/gpc/bin/exit2msg $status
   exit $status
else
   echo 'TRANSFER SUCCESSFUL'
fi


Another workaround is to transfer files and subdirectories individually with the "*" wild character:

#!/bin/bash
 
# This script is named: data-recall.sh
#PBS -l walltime=72:00:00
#PBS -q archive
#PBS -N recall_directories
#PBS -j oe
#PBS -me
 
trap "echo 'Job script not completed';exit 129" TERM INT
 
mkdir -p $SCRATCH/LargeFiles-recalled
 
hsi  -v << EOF
lcd $SCRATCH/LargeFiles-recalled
cd $ARCHIVE/LargeFiles
cget -Ruph *
end
EOF
status=$?
 
trap - TERM INT
 
if [ ! $status == 0 ]; then
   echo 'HSI returned non-zero code.'
   /scinet/gpc/bin/exit2msg $status
   exit $status
else
   echo 'TRANSFER SUCCESSFUL'
fi


ISH

Documentation and Usage

File and directory management

Moving/renaming

  • you may use 'mv' or 'cp' in the same way as the linux version.
#!/bin/bash
#PBS -l walltime=72:00:00
#PBS -q archive
#PBS -N deletion_script
#PBS -j oe
#PBS -m e
 
echo "HPSS file and directory management"
 
trap "echo 'Job script not completed';exit 129" TERM INT
 
/usr/local/bin/hsi -v <<EOF1
    mkdir $ARCHIVE/2011
    mv $ARCHIVE/oldjobs $ARCHIVE/2011
    cp -r $ARCHIVE/almostfinished/*done $ARCHIVE/2011
end
EOF1
status=$?
 
trap - TERM INT
 
if [ ! $status == 0 ]; then
   echo 'HSI returned non-zero code.'
   /scinet/gpc/bin/exit2msg $status
   exit $status
else
   echo 'TRANSFER SUCCESSFUL'
fi

Deletions

Recommendations

  • Be careful with the use of 'cd' commands to non-existing directories before the 'rm' command. Results may be unpredictable
  • Avoid the use of the stand alone wild character *. If necessary, whenever possible have it bound to common patterns, such as '*.tmp', so to limit unintentional mis-happens
  • Avoid using relative paths, even the env variable $ARCHIVE. Better to explicitly expand the full paths in your scripts
  • Avoid using recursive/looped deletion instructions on $SCRATCH contents from the archive job scripts. Even on $ARCHIVE contents, it may be better to do it as an independent job submission, after you have verified that the original ingestion into HPSS finished without any issues.

Typical example

#!/bin/bash
#PBS -l walltime=72:00:00
#PBS -q archive
#PBS -N deletion_script
#PBS -j oe
#PBS -m e
 
echo "Deletion of an outdated directory tree into HPSS"
 
trap "echo 'Job script not completed';exit 129" TERM INT
# Note that the initial directory in HPSS ($ARCHIVE) has the path explicitly expanded
 
/usr/local/bin/hsi -v <<EOF1
    rm /archive/s/scinet/pinto/*.tmp
    rm -R /archive/s/scinet/pinto/obsolete
end
EOF1
status=$?
 
trap - TERM INT
 
if [ ! $status == 0 ]; then
   echo 'HSI returned non-zero code.'
   /scinet/gpc/bin/exit2msg $status
   exit $status
else
   echo 'TRANSFER SUCCESSFUL'
fi

Deleting with an interactive HSI session

  • You may feel more comfortable acquiring an interactive shell, starting an HSI session and proceeding with your deletions that way. Keep in mind, you're restricted to 1H.
gpc-f103n084-$ qsub -q archive -I
qsub: waiting for job 11611291.gpc-sched to start
qsub: job 11611291.gpc-sched ready

----------------------------------------
Begin PBS Prologue Mon May 28 13:15:28 EDT 2012 1338225328
Job ID:		11611291.gpc-sched
Username:	pinto
Group:		scinet
Nodes:		gpc-archive01
End PBS Prologue Mon May 28 13:15:28 EDT 2012 1338225328
----------------------------------------
hpss-archive01-$ hsi
******************************************************************
*     Welcome to HPSS@SciNet - High Perfomance Storage System    *
*                                                                *
*        Contact Information: support@scinet.utoronto.ca         *
*  NOTE: do not transfer SMALL FILES with HSI. Use HTAR instead  *
*              CHECK THE INTEGRITY OF YOUR TARBALLS              *
******************************************************************
Username: pinto  UID: 10010  Acct: 10010(10010) Copies: 2 Firewall: off [hsi.4.0.1 Thu Mar 22 11:44:03 EDT 2012] 
[HSI]/archive/s/scinet/pinto-> rm -R junk

HPSS for the 'Watchmaker'

Efficient alternative to htar

#!/bin/bash
#PBS -l walltime=72:00:00
#PBS -q archive
#PBS -N tar_create_tarball_in_hpss_with_hsi_by_piping
#PBS -j oe
#PBS -m e
 
trap "echo 'Job script not completed';exit 129" TERM INT
# Note that your initial directory in HPSS will be $ARCHIVE
 
# When using a pipeline like this
set -o pipefail 
 
# to put (cput will fail)
tar -c $SCRATCH/mydir | hsi put - : $ARCHIVE/mydir.tar
status=$?
if [ ! $status == 0 ]; then
   echo 'TAR+HSI+piping returned non-zero code.'
   /scinet/gpc/bin/exit2msg $status
   exit $status
else
   echo 'TRANSFER SUCCESSFUL'
fi
 
# to immediately generate an index
ish hindex $ARCHIVE/mydir.tar
status=$?
if [ ! $status == 0 ]; then
   echo 'ISH returned non-zero code.'
   /scinet/gpc/bin/exit2msg $status
   exit $status
else
   echo 'TRANSFER SUCCESSFUL'
fi
 
# to get
#cd $SCRATCH
#hsi cget - : $ARCHIVE/mydir.tar | tar -xv 
#status=$?
# if [ ! $status == 0 ]; then
#   echo 'TAR+HSI+piping returned non-zero code.'
#   /scinet/gpc/bin/exit2msg $status
#   exit $status
#else
#   echo 'TRANSFER SUCCESSFUL'
#fi
 
trap - TERM INT

Notes:

  • Combining commands in this fashion, besides being HPSS-friendly, should not be that noticeably slower than the recursive put with HSI that stores each file one by one. However, reading the files back from tape in this format will be many times faster. It would also overcome the current 68GB limit on the size of stored files that we have with htar.
  • To top things off, we recommend indexing with ish (in the same script) immediately after the tarball creation , while it resides in the HPSS cache. It would be as if htar was used.
  • To ensure that an error at any stage of the pipeline shows up in the returned status use: set -o pipefail (The default is to return the status of the last command in the pipeline and this is not what you want.)
  • Optimal performance for aggregated transfers and allocation on tapes is obtained with tarballs of size 500GB or less, whether ingested by htar or hsi ( WHY?). Be sure to check the contents of the directory tree with 'du' for the total amount of data before sending them to the tar+HSI piping.

Multi-threaded gzip'ed compression with pigz

We compiled multi-threaded implementation of gzip called pigz (http://zlib.net/pigz/). It's now part of the "extras" module. It can also be used on any compute or devel nodes. This makes the execution of the previous version of the script much quicker than if you were to use 'tar -cfz'. In addition, by piggy-backing ISH to the end of the script, it will know what to do with the just created mydir.tar.gz compressed tarball.

#!/bin/bash
#PBS -l walltime=72:00:00
#PBS -q archive
#PBS -N tar_create_compressed_tarball_in_hpss_with_hsi_by_piping
#PBS -j oe
#PBS -m e
 
trap "echo 'Job script not completed';exit 129" TERM INT
# Note that your initial directory in HPSS will be $ARCHIVE
 
# When using a pipeline like this
set -o pipefail 
 
load module extras
 
# to put (cput will fail)
tar -c $SCRATCH/mydir | pigz | hsi put - : $ARCHIVE/mydir.tar.gz
status=$?
if [ ! $status == 0 ]; then
   echo 'TAR+PIGZ+HSI+piping returned non-zero code.'
   /scinet/gpc/bin/exit2msg $status
   exit $status
else
   echo 'TRANSFER SUCCESSFUL'
fi

Content Verification

HTAR CRC checksums

Specifies that HTAR should generate CRC checksums when creating the archive.

#!/bin/bash
#PBS -l walltime=72:00:00
#PBS -q archive
#PBS -N htar_create_tarball_in_hpss_with_checksum_verification
#PBS -j oe
#PBS -m e
 
trap "echo 'Job script not completed';exit 129" TERM INT
# Note that your initial directory in HPSS will be $ARCHIVE
 
cd $SCRATCH/workarea
 
# to put
htar -Humask=0137 -cpf $ARCHIVE/finished-job1.tar -Hcrc -Hverify=1 finished-job1/
 
# to get
#mkdir $SCRATCH/verification
#cd $SCRATCH/verification
#htar -Hcrc -xvpmf $ARCHIVE/finished-job1.tar 
 
status=$?
 
trap - TERM INT
 
if [ ! $status == 0 ]; then
   echo 'HTAR returned non-zero code.'
   /scinet/gpc/bin/exit2msg $status
   exit $status
else
   echo 'TRANSFER SUCCESSFUL'
fi

Current HSI version - Checksum built-in

More usage details here

MD5 is the standard Hashing Algorithm for the HSI build at SciNet.

The checksum algorithm is very CPU-intensive. Although the checksum code is compiled with a high level of compiler optimization, transfer rates can be significantly reduced when checksum creation or verification is in effect. The amount of degradation in transfer rates depends on several factors, such as processor speed, network transfer speed, and speed of the local filesystem (GPFS).

#!/bin/bash
#PBS -l walltime=72:00:00
#PBS -q archive
#PBS -N MD5_checksum_verified_transfer
#PBS -j oe
#PBS -me
 
thefile=<GPFSpath>
storedfile=<HPSSpath>
 
# Generate checksum on fly (-c on)
hsi -q put -c on $thefile : $storedfile
pid=$!
 
# Check the exit code of the HSI process  
status=$?
 
if [ ! $status == 0 ]; then
   echo 'HSI returned non-zero code.'
   /scinet/gpc/bin/exit2msg $status
   exit $status
else
   echo 'TRANSFER SUCCESSFUL'
fi
 
# verify checksum
hsi lshash $storedfile
status=$?
 
if [ ! $status == 0 ]; then
   echo 'HSI returned non-zero code.'
   /scinet/gpc/bin/exit2msg $status
   exit $status
else
   echo 'TRANSFER SUCCESSFUL'
fi
 
# get the file back with checksum
hsi get -c on $storedfile
status=$?
 
if [ ! $status == 0 ]; then
   echo 'HSI returned non-zero code.'
   /scinet/gpc/bin/exit2msg $status
   exit $status
else
   echo 'TRANSFER SUCCESSFUL'
fi

Prior to HSI version 4.0.1.1

This will checksum the contents of the HPSSpath against the original GPFSpath after the transfer has finished.

#!/bin/bash
#PBS -l walltime=72:00:00
#PBS -q archive
#PBS -N checksum_verified_transfer
#PBS -j oe
#PBS -me
 
thefile=<GPFSpath>
storedfile=<HPSSpath>
 
# Generate checksum on fly using a named pipe so that file is only read from GPFS once
mkfifo /tmp/NPIPE
cat $thefile  | tee /tmp/NPIPE | hsi -q put - : $storedfile &
pid=$!
md5sum /tmp/NPIPE |tee /tmp/$fname.md5
rm -f  /tmp/NPIPE
 
# Check the exit code of the HSI process  
wait $pid
status=$?
 
if [ ! $status == 0 ]; then
   echo 'HSI returned non-zero code.'
   /scinet/gpc/bin/exit2msg $status
   exit $status
else
   echo 'TRANSFER SUCCESSFUL'
fi
 
# change filename to stdin in checksum file
sed -i.1 "s+/tmp/NPIPE+-+" /tmp/$fname.md5
 
# verify checksum
hsi -q get - : $storedfile  | md5sum -c  /tmp/$fname.md5
status=$?
 
if [ ! $status == 0 ]; then
   echo 'HSI returned non-zero code.'
   /scinet/gpc/bin/exit2msg $status
   exit $status
else
   echo 'TRANSFER SUCCESSFUL'
fi


Access to HPSS using Globus

  • You may now transfer data between SciNet's HPSS and an external source
  • Follow the link below
 https://globus.computecanada.ca
Enter your Compute Canada username and password.
  • In the 'File Transfer' tab, enter 'Compute Canada HPSS' as one of the Endpoints. To authenticate this endpoint, enter your SciNet username and password.
  • You may read more about Compute Canada's Globus Portal here:
 https://docs.computecanada.ca/wiki/Globus

Access to HPSS using SME

  • Storage Made Easy - SME - is an Enterprise Cloud Portal adopted by SciNet to allow our users to access HPSS
  • Best suitable for light transfers to/from your personal computer and to navigate your contents on HPSS
  • Follow the link below using a web browser and login with your SicNet UserID and password. Under File Manager you will find the "SciNet HPSS" folder.
 https://sme.scinet.utoronto.ca
  • SME can be configured as a DropBox. To download the Free Cloud File Manager native to your OS (Windows, Mac, Linux, mobile), follow the link below:
 https://www.storagemadeeasy.com/clients_and_tools/

Once you have downloaded and installed the Cloud Manager App, fill up the following information:

 Server location
 https://sme.scinet.utoronto.ca/api
  • You may learn more about SME capabilities and features here:
 https://www.storagemadeeasy.com/ownFileserver/
 https://www.storagemadeeasy.com/pricing/#features  (Enterprise)
 https://storagemadeeasy.com/faq/

User provided Content/Suggestions

Packing up large data sets and putting them on HPSS

(Pomés group recommendations)

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