Getting Started Guide

The ALCF operates an IBM Blue Gene/P system used for scientific computing, application porting, system software development and scaling studies. The following content is meant to provide a jump-start for new ALCF users and more detailed information for experienced ALCF users. Links to additional documents on specific topics of interest are also provided. 

Contacting Us

ALCF Service Desk staff are available from 9:00 am through 5:00 pm (Central Time), Monday through Friday for phone-based support. Email support is the preferred method of requesting assistance and covers standard hours (9:00 - 5:00) as well emergency response for after-hours and weekend support.

Email:

support@alcf.anl.gov

Telephone:
630-252-3111
866-508-9181

Service Desk Office:
Building 240, 2-D.21
Argonne National Laboratory
9700 South Cass Avenue
Argonne, IL 60439

How to get an Allocation

All ALCF accounts must be associated with an allocated project. The majority of ALCF resources are allocated through DOE programs: INCITE and ALCC. For information on the INCITE program, see the DOE INCITE website. For information on ALCC, see the DOE ALCC website.

Scientists seeking a Director's Discretionary Allocation of CPU time on one of the ALCF systems must provide the following:

  • Description of the science and expected achievements.
  • Description of any previous applications for an INCITE allocation; description of future plans for applying for an INCITE allocation.
  • If applying for an allocation on the Intrepid system, application scaling results up to at least one rack of BG/P, on either Surveyor or another BG/P system.

If you would like to apply for a Director's Discretionary Allocation, please fill out a request form for the system(s) you wish to use.

You may be contacted and asked to provide additional information. You should receive a confirmation of your application within several days, and your request may take 4 to 6 weeks to approve.

If you have any questions, please contact us at support@alcf.anl.gov.

How to get an Account

Requesting an ALCF BG/P Account

Access to the machine is limited to users with an ALCF allocation through the INCITE program or from Director's Discretionary resources. If you have an ALCF allocation, apply for an ALCF account at https://accounts.alcf.anl.gov/accounts/request.php. Please fill out the forms as completely as possible.

  • Your contact information, including mailing address, phone number, and e-mail address
  • Your project information. If you do not belong to an ALCF or Magellan project with an active allocation, please skip the account request and proceed to the section at the bottom of the page titled "Requesting a Project"
  • Your sponsor's full name and e-mail address -- your project's PI (Principal Investigator) will serve as your sponsor (if you are the PI, your primary ALCF contact should be your sponsor)
  • A security question and answer: these may be used by our Help Desk to verify your identity if you contact us about account issues; therefore, please phrase it in the form of a question whose answer you will remember, that someone else won't be able to guess, and that we can read back to you for your answer.

If you are not a U.S. citizen, ANL policies require that we collect additional information from you:

  • Your city of birth and country (or countries) of citizenship
  • Your complete collegiate educational background including year(s) of graduation
  • The type of organization where you're currently employed or studying (e.g., university, government contractor, etc.), and your research field
  • Your passport information
  • Your Legal Permanent Resident information (if applicable)
  • Your visa information (if applicable).

If you don't provide complete information, or if your INS documentation has expired, there may be significant delays in processing your account request.

If you have any questions or concerns, please contact us at support@alcf.anl.gov.Access to the machine is limited to users with an ALCF allocation through the INCITE program or from Director's Discretionary resources. If you have an ALCF allocation, apply for an ALCF account at https://accounts.alcf.anl.gov/accounts/request.php. Please fill out the forms as completely as possible.

Connect & Login

SSH (and scp) access to the BG/P systems requires SSH keys or a one-time password generated by a CRYPTOCard token

  • Surveyor.alcf.anl.gov (cryptocard or ssh key)
  • Intrepid.alcf.anl.gov (cryptocard only)

Once you have an account and have set up your SSH keys and/or CRYPTOCard token, you may log onto the BG/P systems. Use the following login hosts: surveyor.alcf.anl.gov intrepid.alcf.anl.gov. The login hostnames refer to all currently available user login hosts. Users are placed onto the real hosts in round-robin fashion. As a result, they may end up on a different host from one login to the next. Because the real hosts may change without notice, we suggest that you use the alias and not the real hostnames to log onto the system.

Using SSH on the ALCF BG/P Surveyor System

Accessing the ALCF BG/P system Surveyor via SSH can be done with any SSH software package. Before logging in, you will need to generate an SSH public key and send it to support@alcf.anl.gov for verification and installation.    

Generating a Key

If you have not yet generated an SSH key, you can do so by running:

ssh-keygen -t rsa -b 2048

Input a secure passphrase that you don't use anywhere else when requested, and then send the

~/.ssh/id_rsa.pub

file that is created afterward to support@alcf.anl.gov with the request to have it added to your account.

If you already have an SSH key, just send the public key part to the above address.

NOTE: Do NOT send id_rsa to us, only id_rsa.pub.

Logging In

To log in to Surveyor from a Unix machine, ssh to surveyor.alcf.anl.gov:

ssh surveyor.alcf.anl.gov

If your username on your local machine is different from your username on Surveyor, you will need specify your ALCF account username within the SSH command. This can be done two ways: by using the -l option or by prepending your username to the hostname.

ssh -l alcf_username surveyor.alcf.anl.gov

ssh alcf_username@surveyor.alcf.anl.gov

Once you have connected, you will be prompted for your SSH passphrase. "Accessed Denied" error messages at login usually mean there is a passphrase or username problem. If you are experiencing this problem, use the -vv option to ssh (or scp) to get diagnostic output and send that output, along with your username on both systems, to the ALCF help desk.   

Copying Files

Copying files to and from Surveyor can be accomplished with the scp command. The format of the scp command is very similar to the format of using ssh:    

scp localfile surveyor.alcf.anl.gov:/path/to/remote/file

If you wish to copy an entire directory, use the -r option:

scp -r localdir surveyor.alcf.anl.gov:path-to-remotedir

Once again, if your local username differs from your ALCF account username, you will need to specify the ALCF account username within the scp command. The -l option will not work, so you must prepend the username:

scp localfile alcf_username@surveyor.alcf.anl.gov:path-to-remotefile

The method used to copy files to and from Surveyor may need to take into account any firewalls between your local machine and Surveyor. It is possible that there is a firewall that will prevent access to your local machine from the Argonne LCF BG/P network. This can make copying files from Surveyor to your local machine seem difficult. If you are logged onto one of the front-ends and you are unable to scp files to your local machine using the standard scp format, try pulling the Surveyor files using scp on your local machine:

scp surveyor.alcf.anl.gov:path-to-remotefile localfile

Notice that you are simply swapping the local and remote filenames. The prepending of the username and use of the -r option will work with this format as well.

Extra Information

The surveyor.alcf.anl.gov name refers to all currently available user login hosts. Users are placed onto the real hosts in round-robin fashion. As a result you may end up on a different host from one login to the next. Because the real hosts may change without notice, we suggest that you use the alias and not the real hostnames to log onto the cluster.

For more information on using ssh and how to obtain a version for your local machine, please read the MCS Offsite Access document. This document also contains information on why ssh is necessary and pointers to other useful sources of information on ssh and scp.

 

Cryptocard Token

Your CRYPTOCard token should be protected by you as carefully as your credit cards or house keys. If your token is lost, stolen, or damaged, please contact us immediately so that we can deactivate the token and prevent unauthorized access. Sharing of tokens is strictly forbidden. Please do not mark on the token or alter it in any way.

When you receive your token, it will be initialized, but it will have no access privileges until you have contacted us to verify your identity and that you have received the correct token.

SSH Keys

Using SSH on the ALCF BG/P Surveyor System

Accessing the ALCF BG/P system Surveyor via SSH can be done with any SSH software package. Before logging in, you will need to generate an SSH public key and send it to support@alcf.anl.gov for verification and installation.

GENERATING A KEY

If you have not yet generated an SSH key, you can do so by running:

ssh-keygen -t rsa -b 2048

Input a secure passphrase that you don't use anywhere else when requested, and then send the ~/.ssh/id_rsa.pub file that is created afterward to support@alcf.anl.gov with the request to have it added to your account.

If you already have an SSH key, just send the public key part to the above address.

NOTE: Do NOT send id_rsa to us, only id_rsa.pub.

LOGGING IN

To log in to Surveyor from a Unix machine, ssh to surveyor.alcf.anl.gov:

ssh surveyor.alcf.anl.gov

If your username on your local machine is different from your username on Surveyor, you will need specify your ALCF account username within the SSH command. This can be done two ways: by using the -l option or by prepending your username to the hostname.

ssh -l alcf_username surveyor.alcf.anl.gov

ssh alcf_username@surveyor.alcf.anl.gov

Set-up Your Environment

Once you are logged onto the BG/P system, you will be sitting at a UNIX shell prompt in your home ($HOME) directory. If you have never used UNIX before, you will need to learn some basic commands before you will be able to submit jobs. A number of links to tutorial information may be found at the Unix Guru Universe Beginners' Pages (external link), particularly the "Getting Started" section. Your account will be set up with the default shell bash, unless you requested a different shell in your account request.

Two other shells are also provided.

  • tcsh  
  • zsh  

You can change your shell by logging in to your account web page. Scroll down to the "Unix Shell" section and choose your new shell.

The BG/P system uses the MCS SoftEnv package to manage access to applications on the machine. The first time a user logs on to BG/P, a '.softenvrc' configuration file will automatically be created in the user's home directory. This file will be set up with the default applications environment -- typically there will be a single line with '@default' in the file. Depending on the user's applications, further modifications to the .softenvrc file may be necessary.

SoftEnv man pages are available in the default environment (use 'man softenv'). The command 'softenv' will list all available applications. Users wishing to gain a more complete understanding of how softenv works may read the complete softenv documentation.

Bash Shell

A popular shell provided with the operating system, bash is available as a login shell. To change your login shell use your ALCF personal account page.

Version(s): 3.1.17

Package type: Shell

Known Problems: No known bugs.

Documentation

Man page (man bash ) - available on any ALCF BG/P system.

Bash online manual located at http://www.gnu.org/software/bash/manual/bashref.html

From the bash documentation:

When and how bash executes startup files.

For Login shells (subject to the -noprofile option):

   On logging in:

	If `/etc/profile' exists, then source it.
					
        If `~/.bash_profile' exists, then source it, else if `~/.bash_login' exists, then source it, else if `~/. profile' exists, then source it.

   On logging out: 

        If `~/.bash_logout' exists, source it.

        For non-login interactive shells (subject to the -norc and -rcfile options): On starting up: If `~/.bashrc' exists, then source it.

For non-interactive shells: On starting up: If the environment variable ENV is non-null, expand the variable and source the file named by the value. If Bash is not started in Posix mode, it looks for BASH_ENV before ENV.

Getting Started on ALCC

ASCR Leadership Computing Challenge (ALCC)

ALCC is open to scientists from the research community in national laboratories, academia and industry, the ALCC program allocates up to 30% of the computational resources at NERSC and the Leadership Computing Facilities at Argonne and Oak Ridge for special situations of interest to the Department’s energy mission, with an emphasis on high-risk, high-payoff simulations.

These special situations of interest are directly related the following:

  • Advancing the clean energy agenda.
  • Understanding the environmental impacts of global energy systems.
  • Responding to natural and man-made disasters or incidents; e.g., hurricanes, earthquakes, tsunamis, pandemics.
  • Broadening the community of researchers capable of using leadership computing resources.
  • Exploration of new frontiers in physical and biological sciences.

Submission to the 2012 ALCC will require a reviewable proposal that includes an abstract; identification of the computational resources requested, including the number of processor hours needed; a narrative of no longer than 15 pages describing the proposed research, computational approach code, including scaling studies; identification of funding source to support this work, CV of the PI and a bibliography. The ALCC proposals should not be resubmissions of INCITE proposals or ERCAP proposals.

Applications submitted will be subjected to scientific merit review (peer review) and will be evaluated against the following evaluation criteria, which are listed in descending order of importance codified at CFR 605.10(d):

  1. Scientific and/or Technical Merit of the Project
  2. Appropriateness of the Proposed Method or Approach
  3. Competency of Applicant's Personnel and Adequacy of Proposed Resources
  4. Reasonableness and Appropriateness of the Proposed allocation request
SUBMITTING AN APPLICATION

ALCC applications submitted from September 1, 2011 through February 14, 2012 will be considered for allocation in 2012. Please submit applications to the following email address:   ALCC@science.doe.gov

Reporting Requirements for ALCC projects

Quarterly Report Policy

Reporting your progress is of significant benefit to the ALCF and can help promote your work within the DOE. These reports are used to improve our service for your project and to trigger collaborating with you on highlights of your work. Please submit a quarterly report of your ALCC project's progress to the ALCF.

  • Q1: April 1st, 2012
  • Q2: July 1st, 2012
  • Q3: October 1st, 2012
  • Q4: January 1st, 2013

Quarterly Report Templates

PI-Name_2012QX_ALCC.docx

Please modify the file name to replace PI-Name with the last name of the PI of the ALCC project. Also, please modify the file name to replace the 'X' in QX with the quarter number that you will be submitting the report for. For example, for a project with PI 'Joe Smith' that is submitting the third quarter report for 2011, the file name will be Smith_ALCF_PI_QuarterlyReport_Form_Q3_CY2011.docx

Getting Started on Director's Discretionary

Start-Up Time (Director's Discretionary Allocation Program)

Start-up time is awarded by the ALCF through the Director's Discretionary program. Time is available to researchers in academia, industry, and other research institutions who can demonstrate a need for our leadership-class resources. Awards are available year round and are usually between three and six months in duration. Award sizes generally range from the low tens of thousands to the low millions of compute hours. Start-up time through the Director's Discretionary program is often a "first step" for projects working toward an INCITE allocation.

Scientists on non-INCITE projects seeking start-up time must provide the following:

  • A description of the science and expected achievements.
  • A description of any previous applications for an INCITE allocation; a description of future plans for applying for an INCITE allocation.
  • If applying for an allocation on the Blue Gene/P (Intrepid) system, provide application scaling results up to at least one rack of Blue Gene/P, on either Surveyor or another Blue Gene/P system.

To apply for a start-up allocation, please fill out the request form.

You may be contacted and asked to provide additional information. You should receive a confirmation of your application within several days, and your request may take 4 to 6 weeks to approve.

If you have any questions, please contact us at support at alcf.anl.gov.

Getting Started on an INCITE Award

Welcome to INCITE at the Argonne Leadership Computing Facility

Here is some useful information you’ll need to get started at the ALCF. If you have questions, please contact our Help Desk.

If you don't currently have an INCITE award and would like additional information, please visit the INCITE Program webpage.

Obtaining a Master User Agreement

A Master User Agreement must be in place between an institution and Argonne before researchers from that institution may use Argonne resources and facilities. There are currently more than 600 institutions with signed Master User Agreements in place with Argonne. To see if your institution already has a Master User Agreement with Argonne, to initiate a new Master Agreement, or for a sample of the document, go to: http://www.aps.anl.gov/Users/User_Agreements.

Signing and Returning the Acknowledgement Form

Where a Master User Agreement exists between an institution and Argonne, each individual within that institution requesting an ALCF account must also sign and return an Acknowledgement Form, agreeing to the terms stated in the Master User Agreement. You can download the Acknowledgement Form or the form will be emailed to you once you request a user account. Argonne employees are not required to complete an acknowledgement form. Please direct questions to Margaret Kaczmarski.

Requesting User Accounts

The link to the account application is https://accounts.alcf.anl.gov.

Note: No accounts can be issued until the requisite Master User Agreement and Acknowledgement Form are received (see above). 

The ALCF solicits PI approval for all requested project accounts. If you have requested an account and have not received confirmation that it has been created, please verify with your PI that he or she has responded to our request for account approval. Requests from non-U.S. citizens may require special documentation and additional processing time.

Projects with Foreign Nationals

As required by the U.S. Department of Energy, foreign nationals must provide INS documentation before being given Argonne site, technology or equipment access. The ALCF collects this documentation (known as a 593) for each foreign national requesting access. If you are a foreign national, or if you are a PI with individuals on your project who are foreign nationals, please be advised that the 593 process generally takes 2-4 weeks to complete. Those who have completed the 593 process at Argonne previously may still be asked to provide copies of their INS documentation to the ALCF. Questions about the 593 process for foreign nationals should be directed to Margaret Kaczmarski.

CRYPTOCARD Tokens

Users with access to the ALCF resources will be mailed a CRYPTOCARD token to access these systems. If you have questions on how to use the CRYPTOCARD, including how to resynchronize it, please refer to our resource guide documentation page Using CRYPTOCARDS or contact our Help Desk. CRYPTOCARDS issued to users must be returned to the ALCF when no longer needed.

Help Desk

9 a.m. – 5 p.m. (U.S. Central Time), Monday through Friday

Email: support@alcf.anl.gov

Phone: 630-252-3111 or 866-508-9181 (For after hours or emergency support, please email.)

Walk-in Support: User Support Desk, Building 240, 2-D-27, Argonne National Laboratory, 9700 South Cass Avenue Argonne, IL 60439

Reporting Policy for INCITE projects

Quarterly Report Policy

The Department of Energy (DOE) requires the Argonne Leadership Computing Facility (ALCF) to provide quarterly reports on the progress of all INCITE projects. ALCF, in turn, requires PIs from all INCITE projects to complete a quarterly report and send it to their assigned Catalysts. Quarterly reports are due on or before the first day of the following quarter. Due dates for the 2012 INCITE Quarterly Reports are:

  • Q1: April 1st, 2012
  • Q2: July 1st, 2012
  • Q3: October 1st, 2012
  • Q4: January 1st, 2013

Penalties

If a report is more than 30 days late:

  • The ability to submit jobs for the PI and users of the late project will be disabled.

If a report is more than 90 days late:

  • The PI and users of the late project will have their accounts disabled.

When the quarterly report is submitted, the penalties will be removed within three business days.

Appeals

A PI or user may appeal a project or account suspension to the ALCF Director by a request to support at alcf.anl.gov.

Quarterly Report Templates

PI-Name_2012QX_INCITE.docx

Please modify the file name to replace PI-Name with the last name of the PI of the INCITE project. Also, please modify the file name to replace the 'X' in QX with the quarter number that you will be submitting the report for. For example, for a project with PI 'Joe Smith' that is submitting the third quarter report for 2012, the file name will be Smith_2012Q3_INCITE.docx