Link to section 'File Storage and Transfer for Gilbreth' of 'File Storage and Transfer' File Storage and Transfer for Gilbreth

Link to section 'Archive and Compression' of 'Archive and Compression' Archive and Compression

There are several options for archiving and compressing groups of files or directories on ITaP research systems. The mostly commonly used options are:

Link to section 'tar' of 'Archive and Compression' tar

See the official documentation for tar for more information.

Saves many files together into a single archive file, and restores individual files from the archive. Includes automatic archive compression/decompression options and special features for incremental and full backups.

Examples:


  (list contents of archive somefile.tar)
$ tar tvf somefile.tar

  (extract contents of somefile.tar)
$ tar xvf somefile.tar

  (extract contents of gzipped archive somefile.tar.gz)
$ tar xzvf somefile.tar.gz

  (extract contents of bzip2 archive somefile.tar.bz2)
$ tar xjvf somefile.tar.bz2

  (archive all ".c" files in current directory into one archive file)
$ tar cvf somefile.tar *.c

  (archive and gzip-compress all files in a directory into one archive file)
$ tar czvf somefile.tar.gz somedirectory/

  (archive and bzip2-compress all files in a directory into one archive file)
$ tar cjvf somefile.tar.bz2 somedirectory/

Other arguments for tar can be explored by using the man tar command.

Link to section 'gzip' of 'Archive and Compression' gzip

  (more information)

The standard compression system for all GNU software.

Examples:


  (compress file somefile - also removes uncompressed file)
$ gzip somefile

  (uncompress file somefile.gz - also removes compressed file)
$ gunzip somefile.gz

Link to section 'bzip2' of 'Archive and Compression' bzip2

See the official documentation for bzip for more information.

Strong, lossless data compressor based on the Burrows-Wheeler transform. Stronger compression than gzip.

Examples:


  (compress file somefile - also removes uncompressed file)
$ bzip2 somefile

  (uncompress file somefile.bz2 - also removes compressed file)
$ bunzip2 somefile.bz2

There are several other, less commonly used, options available as well:

  • zip
  • 7zip
  • xz

Link to section 'Environment Variables' of 'Environment Variables' Environment Variables

Several environment variables are automatically defined for you to help you manage your storage. Use environment variables instead of actual paths whenever possible to avoid problems if the specific paths to any of these change.

Some of the environment variables you should have are:
Name Description
HOME path to your home directory
PWD path to your current directory
RCAC_SCRATCH path to scratch filesystem

By convention, environment variable names are all uppercase. You may use them on the command line or in any scripts in place of and in combination with hard-coded values:

$ ls $HOME
...

$ ls $RCAC_SCRATCH/myproject
...

To find the value of any environment variable:

$ echo $RCAC_SCRATCH
 /scratch/gilbreth/myusername 

To list the values of all environment variables:

$ env
USER=myusername
HOME=/home/myusername
 RCAC_SCRATCH=/scratch/gilbreth/myusername 
...

You may create or overwrite an environment variable. To pass (export) the value of a variable in bash:

$ export MYPROJECT=$RCAC_SCRATCH/myproject

To assign a value to an environment variable in either tcsh or csh:

$ setenv MYPROJECT value

Storage Options

File storage options on ITaP research systems include long-term storage (home directories, Fortress) and short-term storage (scratch directories, /tmp directory). Each option has different performance and intended uses, and some options vary from system to system as well. ITaP provides daily snapshots of home directories for a limited time for accidental deletion recovery. ITaP does not back up scratch directories or temporary storage and regularly purges old files from scratch and /tmp directories. More details about each storage option appear below.

Home Directory

ITaP provides home directories for long-term file storage. Each user has one home directory. You should use your home directory for storing important program files, scripts, input data sets, critical results, and frequently used files. You should store infrequently used files on Fortress. Your home directory becomes your current working directory, by default, when you log in.

ITaP provides daily snapshots of your home directory for a limited period of time in the event of accidental deletion. For additional security, you should store another copy of your files on more permanent storage, such as the Fortress HPSS Archive.

Your home directory physically resides on a GPFS storage system in the Research Computing data center. To find the path to your home directory, first log in then immediately enter the following:

$ pwd
/home/myusername

Or from any subdirectory:

$ echo $HOME
/home/myusername

Your home directory and its contents are available on all ITaP research computing machines, including front-end hosts and compute nodes.

Your home directory has a quota limiting the total size of files you may store within. For more information, refer to the Storage Quotas / Limits Section.

Link to section 'Lost File Recovery' of 'Home Directory' Lost File Recovery

ITaP maintains daily snapshots of your home directory for seven days in the event of accidental deletion. Cold storage backups of snapshots are kept for 90 days. For additional security, you should store another copy of your files on more permanent storage, such as the Fortress HPSS Archive.

Link to section 'Performance' of 'Home Directory' Performance

Your home directory is medium-performance, non-purged space suitable for tasks like sharing data, editing files, developing and building software, and many other uses.

Your home directory is not designed or intended for use as high-performance working space for running data-intensive jobs with heavy I/O demands.

Link to section 'Long-Term Storage' of 'Long-Term Storage' Long-Term Storage

Long-term Storage or Permanent Storage is available to ITaP research users on the High Performance Storage System (HPSS), an archival storage system, called Fortress. Program files, data files and any other files which are not used often, but which must be saved, can be put in permanent storage. Fortress currently has over 10PB of capacity.

For more information about Fortress, how it works, and user guides, and how to obtain an account:

Scratch Space

ITaP provides scratch directories for short-term file storage only. The quota of your scratch directory is much greater than the quota of your home directory. You should use your scratch directory for storing temporary input files which your job reads or for writing temporary output files which you may examine after execution of your job. You should use your home directory and Fortress for longer-term storage or for holding critical results. The hsi and htar commands provide easy-to-use interfaces into the archive and can be used to copy files into the archive interactively or even automatically at the end of your regular job submission scripts.

Files in scratch directories are not recoverable. ITaP does not back up files in scratch directories. If you accidentally delete a file, a disk crashes, or old files are purged, they cannot be restored.

ITaP purges files from scratch directories not accessed or had content modified in 60 days. Owners of these files receive a notice one week before removal via email. Be sure to regularly check your Purdue email account or set up mail forwarding to an email account you do regularly check. For more information, please refer to our Scratch File Purging Policy.

All users may access scratch directories on Gilbreth. To find the path to your scratch directory:

$ findscratch
/scratch/gilbreth/myusername

The value of variable $RCAC_SCRATCH is your scratch directory path. Use this variable in any scripts. Your actual scratch directory path may change without warning, but this variable will remain current.

$ echo $RCAC_SCRATCH
/scratch/gilbreth/myusername

All scratch directories are available on each front-end of all computational resources, however, only the /scratch/gilbreth directory is available on Gilbreth compute nodes. No other scratch directories are available on Gilbreth compute nodes.

Your scratch directory has a quota capping the total size and number of files you may store in it. For more information, refer to the section Storage Quotas / Limits .

Link to section 'Performance' of 'Scratch Space' Performance

Your scratch directory is located on a high-performance, large-capacity parallel filesystem engineered to provide work-area storage optimized for a wide variety of job types. It is designed to perform well with data-intensive computations, while scaling well to large numbers of simultaneous connections.

/tmp Directory

ITaP provides /tmp directories for short-term file storage only. Each front-end and compute node has a /tmp directory. Your program may write temporary data to the /tmp directory of the compute node on which it is running. That data is available for as long as your program is active. Once your program terminates, that temporary data is no longer available. When used properly, /tmp may provide faster local storage to an active process than any other storage option. You should use your home directory and Fortress for longer-term storage or for holding critical results.

ITaP does not perform backups for the /tmp directory and removes files from /tmp whenever space is low or whenever the system needs a reboot. In the event of a disk crash or file purge, files in /tmp are not recoverable. You should copy any important files to more permanent storage.

Storage Quota / Limits

ITaP imposes some limits on your disk usage on research systems. ITaP implements a quota on each filesystem. Each filesystem (home directory, scratch directory, etc.) may have a different limit. If you exceed the quota, you will not be able to save new files or new data to the filesystem until you delete or move data to long-term storage.

Link to section 'Checking Quota' of 'Storage Quota / Limits' Checking Quota

To check the current quotas of your home and scratch directories check the My Quota page or use the myquota command:

$ myquota
Type        Filesystem          Size    Limit  Use         Files    Limit  Use
==============================================================================
home        myusername         5.0GB   25.0GB  20%             -        -   -
scratch     /scratch/gilbreth/    8KB  476.8GB   0%             2  100,000   0%

The columns are as follows:

  • Type: indicates home or scratch directory.
  • Filesystem: name of storage option.
  • Size: sum of file sizes in bytes.
  • Limit: allowed maximum on sum of file sizes in bytes.
  • Use: percentage of file-size limit currently in use.
  • Files: number of files and directories (not the size).
  • Limit: allowed maximum on number of files and directories. It is possible, though unlikely, to reach this limit and not the file-size limit if you create a large number of very small files.
  • Use: percentage of file-number limit currently in use.

If you find that you reached your quota in either your home directory or your scratch file directory, obtain estimates of your disk usage. Find the top-level directories which have a high disk usage, then study the subdirectories to discover where the heaviest usage lies.

To see in a human-readable format an estimate of the disk usage of your top-level directories in your home directory:

$ du -h --max-depth=1 $HOME >myfile
32K /home/myusername/mysubdirectory_1
529M    /home/myusername/mysubdirectory_2
608K    /home/myusername/mysubdirectory_3

The second directory is the largest of the three, so apply command du to it.

To see in a human-readable format an estimate of the disk usage of your top-level directories in your scratch file directory:

$ du -h --max-depth=1 $RCAC_SCRATCH >myfile
160K    /scratch/gilbreth/myusername

This strategy can be very helpful in figuring out the location of your largest usage. Move unneeded files and directories to long-term storage to free space in your home and scratch directories.

Link to section 'Increasing Quota' of 'Storage Quota / Limits' Increasing Quota

Link to section 'Home Directory' of 'Storage Quota / Limits' Home Directory

If you find you need additional disk space in your home directory, please first consider archiving and compressing old files and moving them to long-term storage on the Fortress HPSS Archive. Unfortunately, it is not possible to increase your home directory quota beyond it's current level.

Link to section 'Scratch Space' of 'Storage Quota / Limits' Scratch Space

If you find you need additional disk space in your scratch space, please first consider archiving and compressing old files and moving them to long-term storage on the Fortress HPSS Archive. If you are unable to do so, you may ask for a quota increase at rcac-help@purdue.edu.

Link to section 'Sharing Files from Gilbreth' of 'Sharing' Sharing Files from Gilbreth

Gilbreth supports several methods for file sharing. Use the links below to learn more about these methods.

Link to section 'Sharing Data with Globus' of 'Globus' Sharing Data with Globus

Data on any Research Computing resource can be shared with other users within Purdue or with collaborators at other institutions. Globus allows convenient sharing of data with outside collaborators. Data can be shared with collaborators' personal computers or directly with many other computing resources at other institutions.

To share files, login to https://transfer.rcac.purdue.edu, navigate to the endpoint (collection) of your choice, and follow instructions as described in Globus documentation on how to share data:

File Transfer

Gilbreth supports several methods for file transfer. Use the links below to learn more about these methods.

SCP

SCP (Secure CoPy) is a simple way of transferring files between two machines that use the SSH protocol. SCP is available as a protocol choice in some graphical file transfer programs and also as a command line program on most Linux, Unix, and Mac OS X systems. SCP can copy single files, but will also recursively copy directory contents if given a directory name.

Command-line usage:


  (to a remote system from local)
$ scp sourcefilename myusername@gilbreth.rcac.purdue.edu:somedirectory/destinationfilename

  (from a remote system to local)
$ scp myusername@gilbreth.rcac.purdue.edu:somedirectory/sourcefilename destinationfilename

  (recursive directory copy to a remote system from local)
$ scp -r sourcedirectory/ myusername@gilbreth.rcac.purdue.edu:somedirectory/

Linux / Solaris / AIX / HP-UX / Unix:

  • The "scp" command-line program should already be installed.

Microsoft Windows:

  • MobaXterm
    Free, full-featured, graphical Windows SSH, SCP, and SFTP client.

Mac OS X:

  • You should have already installed the "scp" command-line program. You may start a local terminal window from "Applications->Utilities".
  • Cyberduck is a full-featured and free graphical SFTP and SCP client.

Globus

Globus, previously known as Globus Online, is a powerful and easy to use file transfer service for transferring files virtually anywhere. It works within ITaP's various research storage systems; it connects between ITaP and remote research sites running Globus; and it connects research systems to personal systems. You may use Globus to connect to your home, scratch, and Fortress storage directories. Since Globus is web-based, it works on any operating system that is connected to the internet. The Globus Personal client is available on Windows, Linux, and Mac OS X. It is primarily used as a graphical means of transfer but it can also be used over the command line.

Link to section 'Globus Web:' of 'Globus' Globus Web:

  • Navigate to http://transfer.rcac.purdue.edu
  • Click "Proceed" to log in with your Purdue Career Account.
  • On your first login it will ask to make a connection to a Globus account. If you already have one - sign in to associate with your Career Account. Otherwise, click the link to create a new account.
  • Now you are at the main screen. Click "File Transfer" which will bring you to a two-endpoint interface.
  • You will need to select one endpoint on one side as the source, and a second endpoint on the other as the destination. This can be one of several Purdue endpoints or another University or your personal computer (see Personal Client section below).

The ITaP Research Computing endpoints are as follows. A search for "Purdue" will give you several suggested results you can choose from, or you can give a more specific search.

  • Home Directory storage: "Purdue Research Computing - Home Directories", however, you can start typing "Purdue" or "Home Directories" and it will suggest appropriate matches.
  • Gilbreth scratch storage: "Purdue Gilbreth Cluster", however, you can start typing "Purdue" or "Gilbreth and it will suggest appropriate matches. From here you will need to navigate into the first letter of your username, and then into your username.
  • Research Data Depot: "Purdue Research Computing - Data Depot", a search for "Depot" should provide appropriate matches to choose from.
  • Fortress: "Purdue Fortress HPPS Archive", a search for "Fortress" should provide appropriate matches to choose from.

From here, select a file or folder in either side of the two-pane window, and then use the arrows in the top-middle of the interface to instruct Globus to move files from one side to the other. You can transfer files in either direction. You will receive an email once the transfer is completed.

Link to section 'Globus Personal Client setup:' of 'Globus' Globus Personal Client setup:

Globus Connect Personal is a small software tool you can install to make your own computer a Globus endpoint on its own. It is useful if you need to transfer files via Globus to and from your computer directly.

  • On the endpoint page from earlier, click "Get Globus Connect Personal" or download a version for your operating system it from here: Globus Connect Personal
  • Name this particular personal system and follow the setup prompts to create your Globus Connect Personal endpoint.
  • Your personal system is now available as an endpoint within the Globus transfer interface.

Link to section 'Globus Command Line:' of 'Globus' Globus Command Line:

Globus supports command line interface, allowing advanced automation of your transfers.

To use the recommended standalone Globus CLI application (the globus command):

Link to section 'Sharing Data with Outside Collaborators' of 'Globus' Sharing Data with Outside Collaborators

Globus allows convenient sharing of data with outside collaborators. Data can be shared with collaborators' personal computers or directly with many other computing resources at other intstitutions. See the Globus documentation on how to share data:

For links to more information, please see Globus Support page.

Windows Network Drive / SMB

SMB (Server Message Block), also known as CIFS, is an easy to use file transfer protocol that is useful for transferring files between ITaP research systems and a desktop or laptop. You may use SMB to connect to your home, scratch, and Fortress storage directories. The SMB protocol is available on Windows, Linux, and Mac OS X. It is primarily used as a graphical means of transfer but it can also be used over the command line.

Note: to access Gilbreth through SMB file sharing, you must be on a Purdue campus network or connected through VPN.

Link to section 'Windows:' of 'Windows Network Drive / SMB' Windows:

  • Windows 7: Click Windows menu > Computer, then click Map Network Drive in the top bar
  • Windows 8 & 10: Tap the Windows key, type computer, select This PC, click Computer > Map Network Drive in the top bar
  • In the folder location enter the following information and click Finish:

    • To access your home directory, enter \\home.rcac.purdue.edu\myusername.
    • To access your scratch space on Gilbreth, enter \\scratch.gilbreth.rcac.purdue.edu\gilbreth. Once mapped, you will be able to navigate to your scratch directory.

  • Your home or scratch directory should now be mounted as a drive in the Computer window.

Link to section 'Mac OS X:' of 'Windows Network Drive / SMB' Mac OS X:

  • In the Finder, click Go > Connect to Server
  • In the Server Address enter the following information and click Connect:

    • To access your home directory, enter smb://home.rcac.purdue.edu/myusername.
    • To access your scratch space on Gilbreth, enter smb://scratch.gilbreth.rcac.purdue.edu/gilbreth. Once connected, you will be able to navigate to your scratch directory.

Link to section 'Linux:' of 'Windows Network Drive / SMB' Linux:

  • There are several graphical methods to connect in Linux depending on your desktop environment. Once you find out how to connect to a network server on your desktop environment, choose the Samba/SMB protocol and adapt the information from the Mac OS X section to connect.
  • If you would like access via samba on the command line you may install smbclient which will give you FTP-like access and can be used as shown below. For all the possible ways to connect look at the Mac OS X instructions.
    smbclient //home.rcac.purdue.edu/myusername -U myusername
    smbclient //scratch.gilbreth.rcac.purdue.edu/gilbreth -U myusername

FTP / SFTP

ITaP does not support FTP on any ITaP research systems because it does not allow for secure transmission of data. Use SFTP instead, as described below.

SFTP (Secure File Transfer Protocol) is a reliable way of transferring files between two machines. SFTP is available as a protocol choice in some graphical file transfer programs and also as a command-line program on most Linux, Unix, and Mac OS X systems. SFTP has more features than SCP and allows for other operations on remote files, remote directory listing, and resuming interrupted transfers. Command-line SFTP cannot recursively copy directory contents; to do so, try using SCP or graphical SFTP client.

Command-line usage:

$ sftp -B buffersize myusername@gilbreth.rcac.purdue.edu

      (to a remote system from local)
sftp> put sourcefile somedir/destinationfile
sftp> put -P sourcefile somedir/

      (from a remote system to local)
sftp> get sourcefile somedir/destinationfile
sftp> get -P sourcefile somedir/

sftp> exit
  • -B: optional, specify buffer size for transfer; larger may increase speed, but costs memory
  • -P: optional, preserve file attributes and permissions

Linux / Solaris / AIX / HP-UX / Unix:

  • The "sftp" command-line program should already be installed.

Microsoft Windows:

  • MobaXterm
    Free, full-featured, graphical Windows SSH, SCP, and SFTP client.

Mac OS X:

  • The "sftp" command-line program should already be installed. You may start a local terminal window from "Applications->Utilities".
  • Cyberduck is a full-featured and free graphical SFTP and SCP client.
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