Data Storage and Transfers

OLCF users have many options for data storage. Each user has multiple user-affiliated storage spaces, and each project has multiple project-affiliated storage spaces where data can be shared for collaboration. Below we give an overview and explain where each storage area is mounted.

Summary of Storage Areas

The storage area to use in any given situation depends upon the activity you wish to carry out. Storage areas are either user-centric or project-centric, and are further divided by the underlying storage type (e.g., Network File System (NFS), High Performance Storage System (HPSS), IBM Spectrum Scale). Each storage type has a different intended use as described below.

Each user has a User Home area on NFS, and a User Archive area on HPSS. For newer users, the User Archive area is not writable and is only a “link farm” to a user’s project areas on HPSS. For legacy users, the directory remains writable until files have been migrated to an appropriate project area. Each project has a Project Home area on NFS, multiple Work areas on Spectrum Scale, and multiple Archive areas on HPSS. The different storage areas are summarized in the list and table below.

  • User Home: Long-term data for routine access that is unrelated to a project. It is mounted on compute nodes of Summit as read only
  • User Archive: A “link farm” with symbolic links to a user’s project directories on HPSS. (Previously this was for non-project data on HPSS; such use is now deprecated)
  • Project Home: Long-term project data for routine access that’s shared with other project members. It is mounted on compute nodes of Summit as read only
  • Member Work: Short-term user data for fast, batch-job access that is not shared with other project members.
  • Project Work: Short-term project data for fast, batch-job access that’s shared with other project members.
  • World Work: Short-term project data for fast, batch-job access that’s shared with users outside your project.
  • Member Archive: Long-term project data for archival access that is not shared with other project members.
  • Project Archive: Long-term project data for archival access that’s shared with other project members.
  • World Archive: Long-term project data for archival access that’s shared with users outside your project.
Area Path Enclave Type Permissions Quota Backups Purged Retention On Compute Nodes
User Home /ccs/home/[userid] M1, M2 NFS User set 50 GB Yes No 90 days Read-only
User Archive [1] /home/[userid] M1 HPSS User set 2TB No No 90 days No
User Archive [2] /home/[userid] M1 HPSS 700 N/A N/A N/A N/A No
Project Home /ccs/proj/[projid] M1, M2 NFS 770 50 GB Yes No 90 days Read-only
Member Work /gpfs/alpine/[projid]/scratch/[userid] M1, M2 Spectrum Scale 700 [3] 50 TB No 90 days N/A [4] Read/Write
Project Work /gpfs/alpine/[projid]/proj-shared M1, M2 Spectrum Scale 770 50 TB No 90 days N/A [4] Read/Write
World Work /gpfs/alpine/[projid]/world-shared M1 Spectrum Scale 775 50 TB No 90 days N/A [4] Read/Write
Member Archive /hpss/prod/[projid]/users/$USER M1 HPSS 700 100 TB No No 90 days No
Project Archive /hpss/prod/[projid]/proj-shared M1 HPSS 770 100 TB No No 90 days No
World Archive /hpss/prod/[projid]/world-shared M1 HPSS 775 100 TB No No 90 days No
Moderate Enhanced User Home /gpfs/arx/[projid]/home/[userid] ME Spectrum Scale 700 50 TB No 90 days N/A [4] Read/Write
Moderate Enhanced Member Work /gpfs/arx/[projid]/scratch/[userid] ME Spectrum Scale 700 50 TB No 90 days N/A [4] Read/Write
Moderate Enhanced Project Work /gpfs/arx/[projid]/proj-shared/[userid] ME Spectrum Scale 770 50 TB No 90 days N/A [4] Read/Write
Open User Home /ccsopen/home/[userid] O NFS User set 50 GB Yes No 90 days Read-only
Open Project Home /ccsopen/proj/[projid] O NFS 770 50 GB Yes No 90 days Read-only
Open Member Work /gpfs/wolf/[projid]/scratch/[userid] O Spectrum Scale 700 [3] 50 TB No 90 days N/A [4] Read/Write
Open Project Work /gpfs/wolf/[projid]/proj-shared O Spectrum Scale 770 50 TB No 90 days N/A [4] Read/Write
Open World Work /gpfs/wolf/[projid]/world-shared O Spectrum Scale 775 50 TB No 90 days N/A [4] Read/Write
Area - The general name of the storage area.
Path - The path (symlink) to the storage area’s directory.
Enclave - The security enclave where the path is available. There are several security enclaves:
- Open (O) - Ascent and other OLCF machines accessible with a username/password
- Moderate Projects not subject to export control (M1) - These are projects on machines such as Summit or Andes that require 2-factor authentication but are not subject to export control restrictions.
- Moderate Projects subject to export control (M2) - Same as M1, but projects that are subject to export control restrictions.
- Moderated Enhanced (ME) - These are projects that might involve HIPAA or ITAR regulations. These projects utilize Summit compute resources but have extra security precautions and separate file systems.
Type - The underlying software technology supporting the storage area.
Permissions - UNIX Permissions enforced on the storage area’s top-level directory.
Quota - The limits placed on total number of bytes and/or files in the storage area.
Backups - States if the data is automatically duplicated for disaster recovery purposes.
Purged - Period of time, post-file-access, after which a file will be marked as eligible for permanent deletion.
Retention - Period of time, post-account-deactivation or post-project-end, after which data will be marked as eligible for permanent deletion.
On Compute Nodes - Is this filesystem available on compute nodes (no, available but read-only, and available read/write)

Important

Files within “Work” directories (i.e., Member Work, Project Work, World Work) are not backed up and are purged on a regular basis according to the timeframes listed above.

Note

Moderate Enhanced projects do not have access to HPSS.

Tip

If your home directory reaches its quota, your batch jobs might fail with the error cat: write error: Disk quota exceeded. This error may not be intuitive, especially if your job exclusively uses work areas that are well under quota. The error is actually related to your home directory quota. Sometimes, batch systems write temporary files to the home directory (for example, on Summit LSF writes temporary data in ~/.lsbatch), so if the home directory is over quota and that file creation fails, the job will fail with the quota error.

You can check your home directory quota with the quota command. If it is over quota, you need to bring usage under the quota and then your jobs should run without encountering the Disk quota exceeded error.

Footnotes

[1]This entry is for legacy User Archive directories which contained user data on January 14, 2020.
[2]User Archive directories that were created (or had no user data) after January 14, 2020. Settings other than permissions are not applicable because directories are root-owned and contain no user files.
[3](1, 2) Permissions on Member Work directories can be controlled to an extent by project members. By default, only the project member has any accesses, but accesses can be granted to other project members by setting group permissions accordingly on the Member Work directory. The parent directory of the Member Work directory prevents accesses by “UNIX-others” and cannot be changed.
[4](1, 2, 3, 4, 5, 6, 7, 8, 9) Retention is not applicable as files will follow purge cycle.

On Summit, Andes, and the DTNs, additional paths to the various project-centric work areas are available via the following symbolic links and/or environment variables:

  • Member Work Directory: /gpfs/alpine/scratch/[userid]/[projid] or $MEMBERWORK/[projid]
  • Project Work Directory: /gpfs/alpine/proj-shared/[projid] or $PROJWORK/[projid]
  • World Work Directory: /gpfs/alpine/world-shared/[projid] or $WORLDWORK/[projid]

Notes on User-Centric Data Storage

User Home Directories (NFS)

The environment variable $HOME will always point to your current home directory. It is recommended, where possible, that you use this variable to reference your home directory. In cases in which using $HOME is not feasible, it is recommended that you use /ccs/home/$USER (or /ccsopen/home/$USER for home directories in the open enclave).

Users should note that since this is an NFS-mounted filesystem, its performance will not be as high as other filesystems.

User Home Quotas

Quotas are enforced on user home directories. To request an increased quota, contact the OLCF User Assistance Center. To view your current quota and usage, use the quota command:

$ quota -Qs
Disk quotas for user usrid (uid 12345):
     Filesystem  blocks   quota   limit   grace   files   quota   limit   grace
nccsfiler1a.ccs.ornl.gov:/vol/home
                  4858M   5000M   5000M           29379   4295m   4295m

Note

Moderate enhanced projects home directores are located in GPFS. There is no enforced quota, but it is recommended that users not exceed 50 TB. These directories are subject to the 90 day purge.

User Home Permissions

The default permissions for user home directories is shown in the Filesystem Summary Table. Users have the ability to change permissions on their home directories, although it is recommended that permissions be set to as restrictive as possible (without interfering with your work).

Note

Moderate enhanced projects have home directory permissions set to 0700 and are automatically reset to that if changed by the user.

User Home Backups

If you accidentally delete files from your home directory, you may be able to retrieve them. Online backups are performed at regular intervals. Hourly backups for the past 24 hours, daily backups for the last 7 days, and once-weekly backups are available. It is possible that the deleted files are available in one of those backups. The backup directories are named hourly.*, daily.*, and weekly.* where * is the date/time stamp of backup creation. For example, hourly.2020-01-01-0905 is an hourly backup made on January 1st, 2020 at 9:05 AM.

The backups are accessed via the .snapshot subdirectory. Note that ls alone (or even ls -a) will not show the .snapshot subdirectory exists, though ls .snapshot will show its contents. The .snapshot feature is available in any subdirectory of your home directory and will show the online backups available for that subdirectory.

To retrieve a backup, simply copy it into your desired destination with the cp command.

Note

There are no backups for moderate enhanced project home directories.

User Website Directory

Users interested in sharing files publicly via the World Wide Web can request a user website directory be created for their account. User website directories (~/www) have a 5GB storage quota and allow access to files at http://users.nccs.gov/~user (where user is your userid). If you are interested in having a user website directory created, please contact the User Assistance Center at help@olcf.ornl.gov.

User Archive Directories (HPSS)

Note

Use of User Archive areas for data storage is deprecated as of January 14, 2020. The user archive area for any user account created after that date (or for any user archive directory that is empty of user files after that date) will contain only symlinks to the top-level directories for each of the user’s projects on HPSS. Users with existing data in a User Archive directory are encouraged to move that data to an appropriate project-based directory as soon as possible.

The information below is simply for reference for those users with existing data in User Archive directories.

The High Performance Storage System (HPSS) at the OLCF provides longer-term storage for the large amounts of data created on the OLCF compute systems. The mass storage facility consists of tape and disk storage components, servers, and the HPSS software. After data is uploaded, it persists on disk for some period of time. The length of its life on disk is determined by how full the disk caches become. When data is migrated to tape, it is done so in a first-in, first-out fashion.

User archive areas on HPSS are intended for storage of data not immediately needed in either User Home directories (NFS) or User Work directories (GPFS). User Archive directories should not be used to store project-related data. Rather, Project Archive directories should be used for project data.

User Archive Access

Users are granted HPSS access if they are members of projects with Project Archive areas. Users can transfer data to HPSS from any OLCF system using the HSI or HTAR utilities. For more information on using HSI or HTAR, see the HPSS Data Archival System section.

User Archive Accounting

Each file and directory on HPSS is associated with an HPSS storage allocation. Storage allocations are normally associated with one of the user’s projects; however, legacy usage (from files stored to User Archive areas prior to January 14, 2020) may instead be associated with the user or a ‘legacy’ project. To check storage allocation usage, use the comand showusage -s hpss from an OLCF resource such as Summit or Andes.

For information on usage and best practices for HPSS, please see the HPSS Data Archival System section.

Notes on Project-Centric Data Storage

Project directories provide members of a project with a common place to store code, data, and other files related to their project.

Project Home Directories (NFS)

Open and Moderate Projects are provided with a Project Home storage area in the NFS-mounted filesystem. This area is intended for storage of data, code, and other files that are of interest to all members of a project. Since Project Home is an NFS-mounted filesystem, its performance will not be as high as other filesystems.

Note

Moderate Enhanced projects are not provided with Project Home spaces, just Project Work spaces.

Project Home Path, Quota, and Permissions

The path, quota, and permissions for Project Home directories are summarized in the Filesystem Summary Table.

Quotas are enforced on Project Home directories. To check a Project Home directory’s usage, run df -h /ccs/proj/[projid] (where [projid] is the project ID). Note, however, that permission settings on some subdirectories may prevent you from accessing them, and in that case you will not be able to obtain the correct usage. If this is the case, contact help@olcf.ornl.gov for the usage information.

Project Home directories are root-owned and are associated with the project’s Unix group. Default permissions are set such that only members of the project can access the directory, and project members are not able to change permissions of the top-level directory.

Project Home Backups

If you accidentally delete files from your project home directory, you may be able to retrieve them. Online backups are performed at regular intervals. Hourly backups for the past 24 hours, daily backups for the last 7 days, and once-weekly backups are available. It is possible that the deleted files are available in one of those backups. The backup directories are named hourly.*, daily.*, and weekly.* where * is the date/time stamp of backup creation. For example, hourly.2020-01-01-0905 is an hourly backup made on January 1st, 2020 at 9:05 AM.

The backups are accessed via the .snapshot subdirectory. Note that ls alone (or even ls -a) will not show the .snapshot subdirectory exists, though ls .snapshot will show its contents. The .snapshot feature is available in any subdirectory of your project home directory and will show the online backups available for that subdirectory.

To retrieve a backup, simply copy it into your desired destination with the cp command.

Project Work Areas

Three Project Work Areas to Facilitate Collaboration

To facilitate collaboration among researchers, the OLCF provides (3) distinct types of project-centric work storage areas: Member Work directories, Project Work directories, and World Work directories. Each directory should be used for storing files generated by computationally-intensive HPC jobs related to a project.

Note

  • Moderate enhanced projects do not have World Work directories and the filesystem is called “arx” rather than “alpine”
  • Moderate projects subject to export control do not have World Work directories
  • Open projects’ work areas are in the “wolf” filesystem rather than “alpine”

The difference between the three storage areas lies in the accessibility of the data to project members and to researchers outside of the project. Member Work directories are accessible only by an individual project member by default. Project Work directories are accessible by all project members. World Work directories are potentially readable by any user on the system.

Permissions

UNIX Permissions on each project-centric work storage area differ according to the area’s intended collaborative use. Under this setup, the process of sharing data with other researchers amounts to simply ensuring that the data resides in the proper work directory.

  • Member Work Directory: 700
  • Project Work Directory: 770
  • World Work Directory: 775

For example, if you have data that must be restricted only to yourself, keep them in your Member Work directory for that project (and leave the default permissions unchanged). If you have data that you intend to share with researchers within your project, keep them in the project’s Project Work directory. If you have data that you intend to share with researchers outside of a project, keep them in the project’s World Work directory.

Backups

Member Work, Project Work, and World Work directories are not backed up. Project members are responsible for backing up these files, either to Project Archive areas (HPSS) or to an off-site location.

Project Archive Directories

Moderate projects without export control restrictions are also allocated project-specific archival space on the High Performance Storage System (HPSS). The default quota is shown on the table at the top of this page. If a higher quota is needed, contact the User Assistance Center.

Note

There is no HPSS storage for Moderate Enhanced Projects, Moderate Projects subject to export control, or Open projects.

Three Project Archive Areas Facilitae Collaboration on Archival Data

To facilitate collaboration among researchers, the OLCF provides (3) distinct types of project-centric archival storage areas: Member Archive directories, Project Archive directories, and World Archive directories. These directories should be used for storage of data not immediately needed in either the Project Home (NFS) areas or Project Work (Alpine) areas and to serve as a location to store backup copies of project-related files.

As with the three project work areas, the difference between these three areas lies in the accessibility of data to project members and to researchers outside of the project. Member Archive directories are accessible only by an individual project member by default, Project Archive directories are accessible by all project members, and World Archive directories are readable by any user on the system.

Permissions

UNIX Permissions on each project-centric archive storage area differ according to the area’s intended collaborative use. Under this setup, the process of sharing data with other researchers amounts to simply ensuring that the data resides in the proper archive directory.

  • Member Archive Directory: 700
  • Project Archive Directory: 770
  • World Archive Directory: 775

For example, if you have data that must be restricted only to yourself, keep them in your Member Archive directory for that project (and leave the default permissions unchanged). If you have data that you intend to share with researchers within your project, keep them in the project’s Project Archive directory. If you have data that you intend to share with researchers outside of a project, keep them in the project’s World Archive directory.

Project Archive Access

Project Archive directories may only be accessed via utilities called HSI and HTAR. For more information on using HSI or HTAR, see the HPSS Data Archival System section.

Data Policies

Information

Although there are no hard quota limits for project storage, an upper storage limit should be reported in the project request. The available space of a project can be modified upon request.

Purge

To keep the Spectrum Scale file system exceptionally performant, files that have not been accessed (e.g. read) or modified in the project and user areas are purged at the intervals shown in the Filesystem Summary Table above. Please make sure that valuable data is moved off of these systems regularly. See HPSS Data Archival System for information about using the HSI and HTAR utilities to archive data on HPSS.

Special Requests

If you need an exception to the limits listed in the table above, such as a higher quota in your User/Project Home or a purge exemption in a Member/Project/World Work area, contact help@olcf.ornl.gov with a summary of the exception that you need.

Data Retention

By default, the OLCF does not guarantee lifetime data retention on any OLCF resources. Following a user account deactivation or project end, user and project data in non-purged areas will be retained for 90 days. After this timeframe, the OLCF retains the right to delete data. Data in purged areas remains subject to normal purge policies.

Alpine IBM Spectrum Scale Filesystem

Summit mounts a POSIX-based IBM Spectrum Scale parallel filesystem called Alpine. Alpine’s maximum capacity is 250 PB. It is consisted of 77 IBM Elastic Storage Server (ESS) GL4 nodes running IBM Spectrum Scale 5.x which are called Network Shared Disk (NSD) servers. Each IBM ESS GL4 node, is a scalable storage unit (SSU), constituted by two dual-socket IBM POWER9 storage servers, and a 4X EDR InfiniBand network for up to 100Gbit/sec of networking bandwidth. The maximum performance of the final production system will be about 2.5 TB/s for sequential I/O and 2.2 TB/s for random I/O under FPP mode, which means each process, writes its own file. Metada operations are improved with around to minimum 50,000 file access per sec and aggregated up to 2.6 million accesses of 32KB small files.

../_images/summit_nds_final.png

Figure 1. An example of the NDS servers on Summit

Performance under non-ideal workloads

The I/O performance can be lower than the optimal one when you save one single shared file with non-optimal I/O pattern. Moreover, the previous performance results are achieved under an ideal system, the system is dedicated, and a specific number of compute nodes are used. The file system is shared across many users; the I/O performance can vary because other users that perform heavy I/O as also executing large scale jobs and stress the interconnection network. Finally, if the I/O pattern is not aligned, then the I/O performance can be significantly lower than the ideal one. Similar, related to the number of the concurrent users, is applied for the metadata operations, they can be lower than the expected performance.

Tips

  • For best performance on the IBM Spectrum Scale filesystem, use large page aligned I/O and asynchronous reads and writes. The filesystem blocksize is 16MB, the minimum fragment size is 16K so when a file under 16K is stored, it will still use 16K of the disk. Writing files of 16 MB or larger, will achieve better performance. All files are striped across LUNs which are distributed across all IO servers.

  • If your application occupies up to two compute nodes and it requires a significant number of I/O operations, you could try to add the following flag in your job script file and investigate if the total execution time is decreased. This flag could cause worse results, it depends on the application.

    #BSUB -alloc_flags maximizegpfs

Major difference between Lustre and IBM Spectrum Scale

The file systems have many technical differences, but we will mention only what a user needs to be familiar with:

  • On Summit, there is no concept of striping from the user point of view, the user uses the Alpine storage without the need to declare the striping for files/directories. The GPFS will handle the workload, the file system was tuned during the installation.

HPSS Data Archival System

There are two methods of moving data to/from HPSS. The more traditional method is via the command-line utilities hsi and htar. These commands are available from most OLCF systems. Recently, we added the capability of using Globus to move data to/from HPSS. HPSS is available via the “OLCF HPSS” Globus endpoint. By connecting to that endpoint and the “OLCF DTN” endpoint, you can transfer files between HPSS and other OLCF filesystems. By connecting to “OLCF HPSS” and some other endpoint, you can transfer files to/from an offsite location to HPSS. More details on various transfer methods are available in the Transferring Data section.

HPSS is optimized for large files. Ideally, we recommend sending files 768GB or larger to HPSS. HPSS will handle small files, but write and read performance will be negatively affected with files smaller than 512 MB. We recommend combining small files prior to tranfer. Alternatively you can use htar to combine them and create the .tar file directly on HPSS.

Transferring Data

Globus

Three Globus Endpoints have been established for OLCF resources. These are “OLCF DTN”, “OLCF HPSS”, and “NCCS Open DTN”. The “OLCF DTN” endpoint provides access to User/Project Home areas as well as the Alpine filesystem, the “OLCF HPSS” endpoint provides access to HPSS, and the “NCCS Open DTN” endpoint provides access to the Open User/Project Home areas and the Wolf filesystem. By selecting one of these endpoints and some offsite endpoint, you can use Globus to transfer data to/from that storage area at OLCF. By selecting the “OLCF DTN” and “OLCF HPSS” endpoints, you can transfer data between HPSS and one of our other filesystems. The example below shows the latter, although it should be relatively easy to adapt this example to a transfer from some other endpoint to “OLCF DTN” or “OLCF HPSS”.

Globus has restriction of 8 active transfers across all the users. Each user has a limit of 3 active transfers, so it is required to transfer a lot of data on each transfer than less data across many transfers. If a folder is constituted with mixed files including thousands of small files (less than 1MB each one), it would be better to tar the small files. Otherwise, if the files are larger, Globus will handle them.

Globus Example

  • Visit www.globus.org and login
../_images/globus_first_page.png
  • Then select the organization that you belong, if you don’t work for ORNL, do not select ORNL. If your organization is not in the list, create a Globus account
../_images/globus_organization.png
  • Search for the endpoint OLCF DTN
../_images/search_endpoint1.png ../_images/search_endpoint2.png
  • Declare path
../_images/globus_first_endpoint.png
  • Open a second panel to declare the new endpoint called OLCF HPSS and use the appropriate path for HPSS
../_images/globus_second_endpoint_hpss.png ../_images/globus_second_endpoint_hpss2.png
  • Select your file/folder and click start. Then an activity report will appear and you can click on it to see the status. When the transfer is finished or failed, you will receive an email
../_images/globus_select_start.png ../_images/globus_activity.png ../_images/globus_activity_information.png ../_images/globus_activity_done.png

Using Globus From Your Local Workstation

Globus is most frequently used to facilitate data transfer between two institutional filesystems. However, it can also be used to facilitate data transfer involving an individual workstation or laptop. The following instructions demonstrate creating a local Globus endpoint, and initiating a transfer from it to the OLCF’s Alpine GPFS filesystem.

  • Visit https://www.globus.org/globus-connect-personal and Install Globus Connect Personal, it is available for Windows, Mac, and Linux.
  • Make note of the endpoint name given during setup. In this example, the endpoint is laptop_gmarkom.
  • When the installation has finished, click on the Globus icon and select Web: Transfer Files as below
../_images/globus_personal1.png
  • Globus will ask you to login. If your institution does not have an organizational login, you may choose to either Sign in with Google or Sign in with ORCiD iD.
../_images/globus_google.png
  • In the main Globus web page, select the two-panel view, then set the source and destination endpoints. (Left/Right order does not matter)
../_images/globus_laptop_summit.png
  • Next, navigate to the appropriate source and destination paths to select the files you want to transfer. Click the “Start” button to begin the transfer.
../_images/globus_laptop_transfer.png
  • An activity report will appear, and you can click on it to see the status of the transfer.
../_images/globus_laptop_activity.png
  • Various information about the transfer is shown in the activity report. You will receive an email once the transfer is finished, including if it fails for any reason.
../_images/globus_laptop_activity_done.png

HSI

HSI (Hierarchial Storage Interface) is sued to transfer data to/from OLCF systems and HPSS. When retrieving data from a tar archive larger than 1 TB, we recommend that you pull only the files that you need rather than the full archive. Examples of this will be given in the htar section below. Issuing the command hsi will start HSI in interactive mode. Alternatively, you can use:

hsi [options] command(s)

…to execute a set of HSI commands and then return. To list you files on the HPSS, you might use:

hsi ls

hsi commands are similar to ftp commands. For example, hsi get and hsi put are used to retrieve and store individual files, and hsi mget and hsi mput can be used to retrieve multiple files. To send a file to HPSS, you might use:

hsi put a.out : /hpss/prod/[projid]/users/[userid]/a.out

To retrieve one, you might use:

hsi get /hpss/prod/[projid]/proj-shared/a.out

Here is a list of commonly used hsi commands.

Command Function
cd Change current directory
get, mget Copy one or more HPSS-resident files to local files
cget Conditional get - get the file only if it doesn’t already exist
cp Copy a file within HPSS
rm mdelete Remove one or more files from HPSS
ls List a directory
put, mput Copy one or more local files to HPSS
cput Conditional put - copy the file into HPSS unless it is already there
pwd Print current directory
mv Rename an HPSS file
mkdir Create an HPSS directory
rmdir Delete an HPSS directory

Additional HSI Documentation

There is interactive documentation on the hsi command available by running:

hsi help

Additional documentation can be found on the HPSS Collaboration website.

HTAR

HTAR is another utility to transfer data between OLCF systems and HPSS. The htar command provides an interface very similar to the traditional tar command found on UNIX systems. The primary difference is instead of creating a .tar file on the local filesystem, it creates that file directly on HPSS. It is used as a command-line interface. The basic syntax of htar is:

htar -{c|K|t|x|X} -f tarfile [directories] [files]

As with the standard Unix tar utility the -c, -x, and -t options, respectively, function to create, extract, and list tar archive files. The -K option verifies an existing tarfile in HPSS and the -X option can be used to re-create the index file for an existing archive. For example, to store all files in the directory dir1 to a file named /hpss/prod/[projid]/users/[userid]/allfiles.tar on HPSS, use the command:

htar -cvf /hpss/prod/[projid]/users/[userid]/allfiles.tar dir1/*

To retrieve these files:

htar -xvf  /hpss/prod/[projid]/users/[userid]/allfiles.tar

htar will overwrite files of the same name in the target directory. When possible, extract only the files you need from large archives. To display the names of the files in the project1.tar archive file within the HPSS home directory:

htar -vtf  /hpss/prod/[projid]/users/[userid]/project1.tar

To extract only one file, executable.out, from the project1 directory in the Archive file called `` /hpss/prod/[projid]/users/[userid]/project1.tar``:

htar -xm -f project1.tar project1/ executable.out

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

htar -xm -f  /hpss/prod/[projid]/users/[userid]/project1.tar project1/src

HTAR Limitations

The htar utility has several limitations.

Apending data

You cannot add or append files to an existing archive.

File Path Length

File path names within an htar archive of the form prefix/name are limited to 154 characters for the prefix and 99 characters for the file name. Link names cannot exceed 99 characters.

Size

There are limits to the size and number of files that can be placed in an HTAR archive.

Individual File Size Maximum 68GB, due to POSIX limit
Maximum Number of Files per Archive 1 million

For example, when attempting to HTAR a directory with one member file larger that 64GB, the following error message will appear:

$ htar -cvf  /hpss/prod/[projid]/users/[userid]/hpss_test.tar hpss_test/

INFO: File too large for htar to handle: hpss_test/75GB.dat (75161927680 bytes)
ERROR: 1 oversize member files found - please correct and retry
ERROR: [FATAL] error(s) generating filename list
HTAR: HTAR FAILED

Additional HTAR Documentation

For more information about htar, execute man htar.

Command-Line/Terminal Tools

Command-line tools such as scp and rsync can be used to transfer data from outside OLCF. In general, when transferring data into or out of OLCF from the command line, it’s best to initiate the transfer from outside OLCF. If moving many small files, it can be beneficial to compress them into a single archive file, then transfer just the one archive file. When using command-line tools, you should use the Data Transfer Nodes rather than systems like Summit or Andes.

  • scp - secure copy (remote file copy program)

    • Sending a file to OLCF
    scp yourfile $USER@dtn.ccs.ornl.gov:/path/
    
    • Retrieving a file from OLCF
    scp $USER@dtn.ccs.ornl.gov:/path/yourfile .
    
    • Sending a directory to OLCF
    scp -r yourdirectory $USER@dtn.ccs.ornl.gov:/path/
    
  • rsync - a fast, versatile, remote (and local) file-copying tool

    • Sync a directory named mydir from your local system to the OLCF
    rsync -avz mydir/ $USER@dtn.ccs.ornl.gov:/path/
    
    where:
    • a is for archive mode
    • v is for verbose mode
    • z is for compressed mode
    • Sync a directory from the OLCF to a local directory
    rsync -avz  $USER@dtn.ccs.ornl.gov:/path/dir/ mydir/
    
    • Transfer data and show progress while transferring
    rsync -avz --progress mydir/ $USER@dtn.ccs.ornl.gov:/path/
    
    • Include files or directories starting with T and exclude all others
    rsync -avz --progress --include 'T*' --exclude '*' mydir/ $USER@dtn.ccs.ornl.gov:/path/
    
    • If the file or directory exists at the target but not on the source, then delete it
    rsync -avz --delete $USER@dtn.ccs.ornl.gov:/path/ .
    
    • Transfer only the files that are smaller than 1MB
    rsync -avz --max-size='1m' mydir/ $USER@dtn.ccs.ornl.gov:/path/
    
    • If you want to verify the behavior is as intended, execute a dry-run
    rsync -avz --dry-run mydir/ $USER@dtn.ccs.ornl.gov:/path/
    

See the manual pages for more information:

$ man scp
$ man rsync
  • Differences:
    • scp cannot continue if it is interrupted. rsync can.
    • rsync is optimized for performance.
    • By default, rsync checks if the transfer of the data was successful.

Note

Standard file transfer protocol (FTP) and remote copy (RCP) should not be used to transfer files to the NCCS high-performance computing (HPC) systems due to security concerns.

Burst Buffer and Spectral Library

Summit has node-local NVMe devices that can be used as Burst Buffer by jobs, and the Spectral Library can help with some of these use cases.