MARS

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Massive Archive and Retrieval 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 SciNet Massive Archive and Retrieval System (MARS) is a tape backed hierarchical storage management 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.


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

  • HSI is a client with an ftp-like interface will 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 archive. It also creates a separate index file that can be accessed quickly.


User access will be controlled by the job scheduling system of the GPC. An interactive session can be requested that will allow a user to list, rearrange or remove files with the HSI client. Transfer of data into or out of the archive is expected to be scripted and submitted as a batch job.


Guidelines

  • HPSS storage space is provided on tape -- a media that is not suited for storing small files. Files smaller than ~100MB should be grouped into archive files with tar or htar.
  • The maximum size of a file that can be transferred into the archive is 1TB. However, optimal performance is obtained with file sizes <= 100 GB.
  • Make sure to check the application return code and check the log file for errors after all data transfers.
  • 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 queue system.

Scripted File Transfers

File transfers in and out of the archive should be scripted into jobs and submitted to the archive queue. 

#!/bin/env bash
#PBS -q archive
#PBS -N hsi_file_transfer
#PBS -j oe
#PBS -o hpsslogs/$PBS_JOBNAME.$PBS_JOBID

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

Staging Data for Analysis

Job dependencies can be used to make analysis jobs wait for data staging 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-restore.sh | awk -F '.' '{print "-W depend=afterok:"$1}') job-to-work-on-restored-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 archive. The most commonly used commands will be:

cput Conditionally stores a file only if the HPSS file does not exist
cget Conditionally retrieves a copy of a file from HPSS to your local file space on the host system only if a local copy does not already exist.
cd,mkdir,ls,rm,mv Operate as one would expect on the contents of the archive.
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 Here Document. 

hsi <<-EOF
  mkdir -p examples/201106
  cd examples
  mv example_data.tgz 201106/
  lcd /scratch/$USER/examples/
  cput -R -u * 
EOF

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 local files when storing files to HPSS or retrieving files from HPSS is different than FTP. With HSI, the syntax is always
     "local_file : HPSS_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 HPSS file "hpss_file1", then retrieve it back to the local filesystem as "file1.bak", the following commands could be used: 

    put file1 : hpss_file1
    get file1.bak : hpss_file1


  • With FTP, the following commands could be used:
    put file1 hpss_file1 
    get hpss_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.

HSI Documentation

Other 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 HPSS pathnames must be surrounded by whitespace (one or more space characters)

  • Restore 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

HTAR

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

HTAR is a utility that is used for aggregating a set of files from the local file system directly into HPSS, 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 HPSS, thereby achieving a high rate of performance.


  • 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 write the file1 and file2 files to a new archive called files.tar on a remote FTP server called "blue.pacific.llnl.gov", creating the tar file in the user’s remote FTP home directory, enter (bonus HTAR functionality to sites outside SciNet):
    htar -cf files.tar -F blue.pacific.llnl.gov file1 file2
  • 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

Submitting_A_Batch_Job

  • gpc-archive01 is part of the gpc queuing system under torque/moab
  • Currently it is setup to share the node with up to 12 jobs at one time
  • default parameters ( -l nodes=1:ppn=1,walltime=48:00:00)
showq -w class=archive

qsub -I -q archive
  • sample data offload
#!/bin/bash

# This script is named: data-offload.sh

#PBS -q archive
#PBS -N offload
#PBS -j oe
#PBS -o hpsslogs/$PBS_JOBNAME.$PBS_JOBID

date

# individual tarballs already exist
/usr/local/bin/hsi  -v <<EOF
mkdir put-away-and-forget
cd put-away-and-forget
put /scratch/$USER/workarea/finished-job1.tar.gz : finished-job1.tar.gz
put /scratch/$USER/workarea/finished-job2.tar.gz : finished-job2.tar.gz
EOF

# create a tarball on-the-fly of the finished-job3 directory
/usr/local/bin/htar -cf finished-job3.tar /scratch/$USER/workarea/finished-job3/

date
  • sample data list
  - Very painful without interactive browsing
      -Tentative solution: dump all user files to log file and use that as file index

#!/bin/bash

# This script is named: data-list.sh

#PBS -q archive
#PBS -N hpss_dump
#PBS -j oe
#PBS -o hpsslogs/$PBS_JOBNAME.$PBS_JOBID

date
echo ===========
echo
/usr/local/bin/hsi  -v <<EOF
ls -lUR
EOF
echo
echo ===========
date
  • sample data restore
#!/bin/bash

# This script is named: data-restore.sh

#PBS -q archive
#PBS -N restore
#PBS -j oe
#PBS -o hpsslogs/$PBS_JOBNAME.$PBS_JOBID

date

mkdir -p /scratch/$USER/restored-from-MARS

/usr/local/bin/hsi  -v << EOF
get /scratch/$USER/restored-from-MARS/Jan-2010-jobs.tar.gz : forgotten-from-2010/Jan-2010-jobs.tar.gz
get /scratch/$USER/restored-from-MARS/Feb-2010-jobs.tar.gz : forgotten-from-2010/Feb-2010-jobs.tar.gz
EOF

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

date
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