Introductory Site Guide
Table of Contents
- 1. Introduction
- 1.1. Purpose of this document
- 1.2. About the ERDC DSRC
- 1.3. Who our services are for
- 1.4. How to get an account
- 1.5. Visiting the ERDC DSRC
- 2. Policies
- 2.1. Baseline Configuration (BC) policies
- 2.2. Login node abuse policy
- 2.3. File space management policy
- 2.3.1. $WORKDIR
- 2.3.2. $CENTER
- 2.4. Maximum session lifetime policy
- 2.5. Batch use policy
- 2.6. Special request policy
- 2.7. Account removal policy
- 2.8. Communications policy
- 2.9. Account sharing policy
- 3. Available resources
- 3.1. HPC systems
- 3.2. Data storage
- 3.2.1. File systems
- 3.2.2. Archive system
- 3.3. Computing environment
- 3.3.1. Software
- 3.3.2. Bring your own code
- 3.3.3. Batch schedulers
- 3.3.4. Advance Reservation Service (ARS)
- 3.4. HPC Portal
- 3.5. Secure Remote Desktop (SRD)
- 3.6. Network connectivity
- 4. How to access our systems
- 5. How to get help
- 5.1. Productivity Enhancement and Training (PET)
- 5.2. User Advocacy Group (UAG)
- 5.3. Baseline Configuration Team (BCT)
- 5.4. Computational Research and Engineering Acquisition Tools and Environments (CREATE)
- 5.5. Data Analysis and Assessment Center (DAAC)
1.1. Purpose of this document
This document introduces users to the U.S. Engineer Research & Development Center (ERDC) DoD Supercomputing Resource Center(DSRC). It provides an overview of available resources, links to important documentation, important policies governing the use of our systems, and other information to help you make efficient and effective use of your allocated hours.
1.2. About the ERDC DSRC
The ERDC DSRC is one of five DSRCs managed by the DoD High Performance Computing Modernization Program (HPCMP). The DSRCs deliver a range of compute-intensive and data-intensive capabilities to the DoD science and technology, test and evaluation, and acquisition engineering communities. Each DSRC operates and maintains major High Performance Computing (HPC) systems and associated infrastructure, such as data storage, in both unclassified and classified environments. The HPCMP provides user support through a centralized help desk and data analysis/visualization group.
The ERDC DSRC is physically located in the Information Technology Laboratory (ITL) at ERDC. ERDC is the premier research and development laboratory complex for the U.S. Army Corps of Engineers. ERDC conducts critical research in the Tri-Service Reliance areas of Civil Engineering, Environmental Quality, and Environmental Sciences.
1.3. Who our services are for
The HPCMP's services are available to Service and Agency researchers in the Research, Development, Test, and Evaluation (RDT&E) and acquisition engineering communities of the DoD and its respective Services and Agencies, DoD contractors, and University staff working on a DoD research grant.
For more details, see HPCMP Presentation " Who may run on HPCMP Resources?"
1.4. How to get an account
Anyone meeting the above criteria may request an HPCMP account. A Help Desk video is available to guide you through the process of getting an account. To begin the account application process, visit HPC Centers: Obtaining an Account, and follow the instructions presented there.
1.5. Visiting the ERDC DSRC
If you need to travel to the ERDC DSRC, there are security procedures that must be completed BEFORE planning your trip. Please visit our Planning a Visit page and coordinate with your Service/Agency Approval Authority (S/AAA) to ensure that all requirements are met.
2.1. Baseline Configuration (BC) policies
The Baseline Configuration Team sets policies that apply to all HPCMP HPC systems. The BC Policy Compliance Matrix provides an index of all BC policies and compliance status of systems at each DSRC.
2.2. Login node abuse policy
The login nodes provide login access to the systems and support such activities as compiling, editing, debugging, job preparation and submission, and other general interactive use by all users. Memory or CPU-intensive programs running on the login nodes can significantly affect all users of the system. Therefore, only small applications requiring less than 10 minutes of runtime and less than 8 GB of memory are allowed on the login nodes. The preferred method to run resource intensive executions such as pre- and post-processing of data is to use a compute node within an interactive batch session (see Batch use policy).
Use of programs such as watch to automatically run queue status commands, for example, should have an execution interval of no shorter than one minute.
You are encouraged to use the transfer batch queue for file packaging and unpackaging (i.e. tar, gzip) and for frequent or lengthy file transfers to and from $ARCHIVE_HOME and $CENTER.
Failure to abide by these limitations can result in your account being disabled.
2.3. File space management policy
$WORKDIR is the local temporary file system (i.e., local high-speed disk) that is available on all ERDC DSRC HPC systems and is available to all users.
$WORKDIR is intended to be used for executing programs and performing file I/O local to that system. $WORKDIR doesn’t have space restrictions, such as your home ($HOME) or /tmp directories, but $WORKDIR is not intended for use as a permanent file storage area.
The $WORKDIR file system is NOT backed up or exported to any other system. In the event of file or directory structure deletion or a catastrophic disk failure, such files and directory structures are lost. It is your responsibility to transfer files that need to be saved to a location that allows for long-term storage, such as your archival ($ARCHIVE_HOME) or, for smaller files, home ($HOME) directory locations. Please note that your archival storage area has no disk quota assigned to it, while your home directory area has a disk quota assigned.
In order to provide sufficient free $WORKDIR disk space to all users, all files in the $WORKDIR file system that have not been accessed in more than 30 days are subject to deletion.
$CENTER refers to the directory that each user has on the Center-Wide File System (CWFS). The CWFS provides file storage that is accessible from the login nodes of each HPC system and from the HPC Portal. The CWFS allows file transfers and other file and directory operations from these systems using standard Linux commands.
$CENTER is to be used for short-term file storage and to enable shared file access among the ERDC DSRC HPC systems. All files in the CWFS that have not been accessed in more than 120 days are subject to deletion.
2.4. Maximum session lifetime policy
To provide users with a more secure high performance computing environment, the ERDC DSRC has implemented a limit on the lifetime of all terminal/window sessions. Regardless of activity, any terminal or window session connections to the ERDC DSRC will automatically terminate after 24 hours.
2.5. Batch use policy
The batch queues and internal policies of the batch job scheduler have been configured to allow great flexibility in job execution. However, improper use of the queueing system can result in delayed or cancelled job execution and potential system issues.
The debug queue is reserved for small, short-running test and debug jobs. It should not be used for production-level work.
Application binaries on Cray systems should be launched from within a batch session onto one or more compute nodes with either the aprun or ccmrun commands. DO NOT execute application binaries directly on the batch nodes, which are shared service nodes similar to login nodes. Abuse of batch nodes by running incorrectly will result in your job being terminated, and you will be prevented from running additional jobs until you have taken corrective action.
You should carefully monitor any jobs you place on hold. Jobs still in the Hold state after 30 days may be removed from the queue by ERDC DSRC staff.
2.6. Special request policy
All special requests such as increased queue priority, increased maximum number of CPUs or wall time, or dedicated use should be directed to the HPC Help Desk at firstname.lastname@example.org. Documentation of the requirement and the associated justification will be required.
2.7. Account removal policy
The ERDC DSRC follows Baseline Configuration (BC) policy FY13-02 (Data Removal at Account Closure) for actions related to user account removal.
2.8. Communications policy
The ERDC DSRC is fully compliant with Baseline Configuration (BC) policy FY06-11 (Announcing and Logging Changes). The key methods that we use to communicate announcements and important information to our users about HPC systems and the environment include:
- Mass emails sent to all users or those assigned to a particular HPC system
- Maintenance notices posted on the ERDC DSRC public site at https://www.erdc.hpc.mil
- Maintenance notices posted on the HPC Centers public site at https://centers.hpc.mil
- System login messages posted to the appropriate HPC systems.
It is vital to the ERDC DSRC's communication process, and mutually beneficial to our users, to understand the responsibilities of being a good citizen of the ERDC DSRC. We ask that users:
- Please keep the ERDC DSRC apprised of current email addresses. This way we can assure that vital information about our Center reaches you. Please contact your S/AAA to have your email address updated. Please note that if the email address you give us is behind a firewall, you may need to arrange for your local system administrator to allow email from the ERDC DSRC to pass through the firewall boundary to your work site.
- Please check the website, which has up to date current news and information on topics such as HPC resource availability, upcoming training opportunities, or updates to our user guides and the policies and procedures documentation.
2.9. Account sharing policy
You are responsible for all passwords, accounts, YubiKeys, and associated Personal Identification Number (PINs) issued to you, and you are not to share them with any other individual for any reason. Doing so is a violation of the contract that you are required to sign in order to obtain access to HPCMP computational resources.
Upon discovery/notification of a violation of the above policy, your account will be disabled and access to your account assets will be restricted. Any executing jobs will be allowed to complete, but queued jobs will be deleted. The S/AAA who authorized your account will be notified of the policy violation and the actions taken.
3. Available resources
3.1. HPC systems
The ERDC DSRC unclassified HPC systems are accessible through the Defense Research and Engineering Network (DREN) to all active users. Our current HPC systems include:
Onyx is a Cray XC40/50 system. It has 4,810 standard compute nodes, 4 large-memory compute nodes, 32 GPU compute nodes, 32 Knights Landing (Phi) compute nodes, and 64 Machine Learning Accelerator (MLA) multi-GPGPU nodes (a total of 4,942 compute nodes or 217,128 compute cores). It is rated at 6.06 peak PFLOPS. For more information about Onyx, visit our hardware page.
Vulcanite is a SuperMicro SuperServer MLA V100 system. It has 26 2-GPGPU nodes, 8 4-GPGPU nodes, and 5 8-GPGPU nodes (a total of 39 GPGPU nodes or 744 GPGPU cores). It is rated at n peak PFLOPS. For more information about Vulcanite, visit our hardware page.
3.2. Data storage
3.2.1. File systems
Each HPC system has several file systems available for storing user data. Your personal directories on these file systems are commonly referenced via the $HOME, $WORKDIR, $CENTER, and $ARCHIVE_HOME environment variables. Other file systems may be available as well.
|$HOME||Your home directory on the system|
|$WORKDIR||Your temporary work directory on a high-capacity, high-speed scratch file system used by running jobs|
|$CENTER||Your short-term (120-day) storage directory on the Center-Wide File System (CWFS)|
|$ARCHIVE_HOME||Your archival directory on the archive server|
For details about the specific file systems on each system, see the system user guides on the documentation page.
3.2.2. Archive system
All of our HPC systems have access to an online archival system,Gold, which provides long term storage for users' files on a petascale robotic tape library system. A 1.2-PB disk cache frontends the tape file system and temporarily holds files while they are being transferred to or from tape.
For information on using the archive server, see the Archive User Guide.
3.3. Computing environment
To ensure a consistent computing environment and user experience on all HPCMP HPC systems, all systems follow a standard configuration baseline. For more information on the policies defining the baseline configuration, see the Baseline Configuration Compliance Matrix. All systems run variants of the Linux operating system, but the computing environment varies by vendor and architecture due to vendor-specific enhancements.
Each HPC system hosts a large variety of compiler environments, math libraries, programming tools, and third-party analysis applications which are available via loadable software modules. A list of software is available on the software page, or for more up-to-date software information, use the module commands on the HPC systems. Specific details of the computing environment on each HPC system are discussed in the system user guides, available on the documentation page.
To request additional software or to request access to restricted software, please contact the HPC Help Desk at email@example.com.
3.3.2. Bring your own code
While all HPCMP HPC systems offer a diversity of open source, commercial and government software, there are times when we don't support the application codes and tools needed for specific projects. The following information describes a convenient way to utilize your own software on our systems.
Our HPC systems provide you with adequate file space to store your codes. Data stored in your home directory ($HOME) will be backed up on a periodic basis. If you need more home directory space, you may submit a request to the HPC Help Desk at firstname.lastname@example.org. For more details on home directories, see to the Baseline Configuration (BC) policy FY12-01 (Minimum Home Directory Size and Backup Schedule).
If you need to share an application among multiple users, BC policy FY10-07 (Common Location to Maintain Codes) explains how to create a common location on the $PROJECTS_HOME file system, to place applications and codes without using home directories or scrubbed scratch space. To request a new "project directory," please provide the following information to the HPC Help Desk:
- Desired DSRC system where a project directory is being requested.
- POC Information: Name of the sponsor of the project directory, user name, and contact information.
- Short Description of Project: Short summary of the project describing the need for a project directory.
- Desired Directory Name: This will be the name of the directory created under $PROJECTS_HOME.
- Is the code/data in the project directory restricted (e.g. ITAR, etc.)?
- Desired Directory Owner: The user name to be assigned ownership of the directory.
- Desired Directory Group: The group name to be assigned to the directory.
(New group names must be 8 characters or less)
- Additional users to be added to the group.
If the POC for the project directory ceases being an account holder on the system, project directories will be handled according to the user data retention policies of the center.
Once the project directory is created, you can install software (custom or open source) in this directory. Then, depending on requirements, you can set file and/or directory permissions to allow any combination of group read, write, and execute privileges. Since this directory is fully owned by the POC, he or she can even make use of different groups within subdirectories to provide finer granularity of permissions.
Users are expected to ensure that any software or data that is placed on HPCMP systems is protected according to any external restrictions on the data. Users are also responsible for ensuring no unauthorized or malicious software is introduced to the HPCMP environment.
For installations involving restricted software, it is your responsibility to set up group permissions on the directories and to protect the data. It is crucially important to note that there are users on the HPCMP systems who are not authorized to access restricted data. You may not run servers or use software that communicates to a remote system without prior authorization.
If you need help porting or installing your code, the HPC Help Desk provides a "Code Assist" team that specializes in helping users with installation and configuration issues for user supplied codes. To get help, simply contact the HPC Help Desk and open a ticket.
Please contact the HPC Help Desk email@example.com to discuss any special requirements.
3.3.3. Batch schedulers
Our HPC systems use various batch schedulers to manage user jobs and system resources. Basic instructions and examples for using the scheduler on each system can be found in the system user guides. More extensive information can be found in the Scheduler Guides. These documents are available on the documentation page.
Schedulers place user jobs into different queues based on the project associated with the user account. Most users only have access to the debug, standard, transfer, HIE, and background queues, but other queues may be available to you depending on your project. For more information about the queues on a system, see the Scheduler Guides.
3.3.4. Advance Reservation Service (ARS)
Another way to schedule jobs is through the Advance Reservation Service. This service allows users to reserve resources for use at specific times and for specific durations. The ARS works in tandem with the batch scheduler to ensure that your job runs at the scheduled time, and that all required resources (i.e., nodes, licenses, etc.) are available when your job begins. For information on using the ARS, see the ARS User Guide.
3.4. HPC Portal
The HPC Portal provides a suite of custom web applications, allowing you to access a command line, manage files, and submit and manage jobs from a browser. It also supports pre/post-processing and data visualization by making DSRC-hosted desktop applications accessible over the web. For more information about the HPC Portal, see the HPC Portal page on the HPC Centers website.
3.5. Secure Remote Desktop (SRD)
The Secure Remote Desktop enables users to launch a gnome desktop on an HPC system via a downloadable Java interface client. This desktop is then piped to the user's local workstation (Linux, Mac, or Windows) for display. Once the desktop is launched, a user may run any software application installed on the HPC system. For information on using SRD, or to download the client, see the Secure Remote Desktop page on the DAAC website.
3.6. Network connectivity
The ERDC DSRC is a primary node on the Defense Research and Engineering Network (DREN), which provides up to 40-Gb/sec service to DoD HPCMP centers nationwide across a 100-Gb/sec backbone. We connect to the DREN via a 10-Gb/sec circuit linking us to the DREN backbone.
The DSRC's local network consists of a 40-Gb/sec fault-tolerant backbone with 10-Gb/sec connections to the HPC and archive systems.
4. How to access our systems
The HPCMP uses a network authentication protocol called Kerberos to authenticate user access to our HPC systems. Before you can login, you must download and install an HPCMP Kerberos client kit on your local system. For information about downloading and using these kits, visit HPC Centers: Kerberos & Authentication, and click on the tab for your platform. There you will find instructions for downloading and installing the kit, getting a ticket, and logging in.
After installing and configuring a Kerberos client kit, you can access our HPC systems via standard Kerberized commands, such as ssh. File transfers between local and remote systems can be accomplished via the scp, mpscp, or scampi commands. For additional information on using the Kerberos tools, see the Kerberos User Guide or review the tutorial video on Logging into an HPC System. Instructions for logging into each system can be found in the system user guides on the documentation page.
Another way to access the HPC systems is through the HPC Portal. For information on using the portal, visit HPC Centers: HPC Portal. You may also wish to review the HPC Portal demonstration videos. To log into the portal, click on the link for the center where your account is located.
5. How to get help
For almost any issue, the first place you should turn for help is the HPC Help Desk. You can email the Help Desk at firstname.lastname@example.org. You can also contact the Help Desk via phone, fax, DSN, or even traditional mail. Full contact for the Help Desk is available on HPC Centers: Technical and Customer Support. The Help Desk can assist with a wide array of technical issues related to your account and your use of our systems. The Help Desk can also assist in connecting you with various special-purpose groups to address your particular need.
5.1. Productivity Enhancement and Training (PET)
The PET initiative gives users access to computational experts in many HPC technology areas. These HPC application experts help HPC users become more productive using HPCMP supercomputers. The PET initiative also leverages the expertise of academia and industry experts in new technologies and provides training on HPC-related topics. Help in specific computational technology areas is available providing a wide range of expertise including algorithm development and implementation, code porting and development, performance analysis, application and I/O optimization, accelerator programming, preprocessing and grid generation, workflows, in-situ visualization, and data analytics.
5.2. User Advocacy Group (UAG)
The UAG provides a forum for users of HPCMP resources to influence policies and practices of the Program; to facilitate the exchange of information between the user community and the HPCMP; to serve as an advocate for HPCMP users; and to advise the HPC Modernization Program Office on policy and operational matters related the HPCMP.
5.3. Baseline Configuration Team (BCT)
The BCT is tasked to define a common set of capabilities and functions so that users can work more productively and collaboratively when using the HPC resources at multiple computing centers. To accomplish this, the BCT passes policies which collectively create a configuration baseline for all HPC systems.
5.4. Computational Research and Engineering Acquisition Tools and Environments (CREATE)
The CREATE program provides tools to enhance the productivity of the DoD acquisition engineering workforce by providing high fidelity design and analysis tools with capabilities greater than today's tools, reducing the acquisition development and test process cycle. CREATE projects provide enhanced engineering design tools for the DoD HPC community.
5.5. Data Analysis and Assessment Center (DAAC)
The DAAC serves the needs of DoD HPCMP scientists to analyze an ever increasing volume and complexity of data. Their mission is to put visualization and analysis tools and services into the hands of every user.