HPC/FAQ

Access and proposals

The HPC Carbon cluster may be accessed, like any tool at the CNM, by one of two routes: either under a proposal within the CNM User Program or by being an employee of the CNM's hosting institution, Argonne's NST division. Your starting point is to become a CNM user. At the end of this process you will be able to log in using your existing or newly created individual Argonne computer user account.

The following is a summary of the main points as they pertain to Carbon.

Getting started on a proposal

To get a proposal started once it has been granted, Action is required for each proposal by the proposal spokesperson (usually the Principal Investigator,PI), regardless of any previous proposals with us. At this stage, we collect and update information about each proposal for reporting purposes to our funding agencies, and ensure that safety and training requirements are met by all participating users.

To get started as spokesperson or delegate

• Locate the email that we sent to you with subject User Proposal Status Notification, and follow the instructions therein. Some steps are needed only once because they pertain to your institution. Your key action, for each proposal, will be to fill in the Safety and Data form – follow the User Work Submittal (UWS) link given in the email.
• Remind participating users to review their individual access requirements.
• Please be patient. Processing typically takes at least one business day, as both our User Office staff and your Scientific Contact need to attend to your submission in person.

The User Office will notify the spokesperson once work on a proposal may begin.

To get started as participating user

For new proposals:

• Gently remind your spokesperson/PI to submit the UWS as shown above, or ask this person to nominate you via an email to the CNM User Office.
• Enter, review, or update your User Registration. We will notify you once your account is ready and added to the respective proposals.

For proposals already in progress, see the next section.

Adding users to a proposal

Most users are nominated to work on a proposal when it is first submitted. Additional users can be authorized to work under a proposal at any time after acceptance. Actions are needed from both the user and the proposal spokesperson.

Actions required by the User

1. Enter or review your registration as facility user and update as necessary.

–  Continued below.

Actions required by the PI or spokesperson

2. Confirm that the user has entered or reviewed their registration, and determine their badge number(s).

3. Have the user added to the proposal. How to do this depends on whether the proposal has already started or not (see above).

• For proposals that have already started, submit the users' names and badge numbers to the proposal's Scientific Contact at the CNM.
• If the proposal hasn't started yet, add the users yourself when you initially fill in the User Work Submittel (UWS) as part of the regular proposal startup process. The UWS can and must be submitted by the spokesperson, once only, to start a proposal. To make changes after your submission, ask your Scientific Contact at the CNM.

Your Scientific Contact and the link to the UWS for each proposal are shown in our email to you with the subject containing User Proposal Status Notification.

Actions required by the Scientific Contact

4. Add users in the section "Participating Personnel" in the UWS-SciCon form. Ensure badge numbers are present and correct for users to be working on Carbon and on mega.

• Some users' badge numbers can and may have been left empty in earlier UWS submissions, which happens by necessity for very newly registered users.

Follow-up actions required by the User

5. Complete required training courses as instructed by the User Office.

6. Have your Argonne computer accout name and password ready.

• New users: You will get those assigned by the User Office. You will need to personalize both name and password, following instructions sent to you by email.

• Existing users: Check for and if necessary renew your expired password.

Ongoing user access requirements

For you to log into Carbon and its mega SSH gateway, a number of criteria must be met, most of which are subject to expiration dates and require action from you for renewal.

• Review and update your User Registration.

  Your Argonne computer account will be disabled upon expiration of certain registration items. Notably, if you are not a US citizen, you will require a current US visa or related work permit to access Argonne computers, just as if you were to visit in person. This will very likely happen in the middle of your proposal's lifetime. For some of these expirations, no notice will be sent to you (for varying reasons), and you will suddenly find that you can no longer access mega.

  After you updated your user registration, contact the CNM User Office to have your Argonne account re-instated.

• Renew your User Courses.

  For remote users, the ESH223 course "Cybersecurity Annual Education and Awareness" is the one most likely in need of renewal.

• You must be a participant in at least one active or recently expired User Proposal.

  To review the dates for your proposals, ask your PI to search their email archive for mails with "Work Approval Received" or "Proposal Expiration" in the subject.

  • You may run compute jobs under a given proposal while it is active, i.e., within the dates stated in the Work Approval (UWA) notice.
  • For up to 30 days after your last active proposal has expired you may access only the mega and login nodes, according to CNM's Data Retention Policy.
  • While you still have access, offload from Carbon all your files that you need to keep. The CNM cannot be expected or held responsible to store your data beyond your access window.

Practical hints

• Set yourself calendar entries about one year into the future to remind yourself to renew any of your user registration or training requirements.
• After you were added to a user proposal, wait at least an hour or more before trying to access mega, preferably until the next morning.

  Updates of your status need to be propagated through a handful of systems, each being done about hourly, so it may take several cycles, for your status change to reach mega.

Proposal troubleshooting

Email the CNM User Office or call us if you have any questions or concerns, such as:

• about proposals,
• about users, or
• you find that responding to any of your submissions or previous communications takes longer than a few business days.

Only our User Office staff is able to review all aspects of your proposal or your user access requirements, and determine any steps that have yet to be taken or need to be refreshed.

Include in your message:

• Proposal number(s),
• Name of the Principal Investigator (PI),
• Names and badge numbers of participants.

Login issues

When you ask "I cannot log in" or "My password does not work", consider the following sections:

Review your access requirements

See section #Ongoing user access requirements above.

Review host names

Connect to the correct host names:

• When connecting from outside Argonne:
  • mega.cnm.anl.gov – the SSH tunnel setup connection.
  • clogin – one or more SSH "payload" connections.
• When onsite or using VPN:
  • carbon.cnm.anl.gov. The previous name clogin. … will continue to work.

To learn more, read HPC/Network Access.

Verify or change your password

• Visit https://credentials.anl.gov/ and verify that your username and password are correct.
• Visit https://mypassword.anl.gov/changepassword.aspx to change your password. You may not succeed if your account is disabled as such.
• You may also change an expired password by logging in to our SSH gateway host mega. It will accept your old password, and will ask for a new one.

Request a password reset

• To have your password reset, email the CNM User Office, at [email protected].
• When you connect to mega with still your temporary password in place, mega will ask for a new password. You can safely change your password at this point.
• You can also change your password at https://credentials.anl.gov/ - However, a change there will take a few hours to become active on mega.

Review network configuration

• Read again HPC/Network Access, and follow the instructions for your platform.

Mailing lists

Announcements about Carbon are made on the cnm-hpc-announce mailing list, hosted at Argonne. These list pages and the archive are, unfortunately, only accessible from onsite or via VPN.

• To update your email address on the list, simply unsubscribe as shown in the next item, then re-subscribe by sending a blank message to cnm-hpc-announce-join@lists.anl.gov.
• To unsubscribe from the mailing list, send a blank message to cnm-hpc-announce-leave@lists.anl.gov and follow up on the confirmation notice.

  See the GNU Mailman documenation for background.

Applications

I'd like to use application X

Check if the application is already available on Carbon

Either:

• Browse the Application Catalog, or
• View the catalog on the Carbon command line:

module avail
module -l avail 2>&1 | less

The second form gives you browsable output.

If you cannot find the application on Carbon

• Submit a support request.
  • Provide one or more URLs relevant to software you have in mind – be specific.
  • Describe the problem you are trying to solve – it may well be that we can suggest an alternative solution.
  • Give the extent of your planned use.

If you see the application on Carbon but you cannot access it

• Existing license agreements may cover only a subset of users (typically Argonne employees).
• If you feel you are eligible, submit a support request.

If a version newer than the installed one on Carbon is available

• Submit a support request.
• Include a URL to information about the new version.

How do I run application X?

• Customize your shell environment to load the application module.
• Learn about module conventions on Carbon.
• To determine the names of a package's executable scripts and binaries, load the application module (if you have not yet done so in your shell setup), then inspect the module's $NAME_HOME/bin directory. For instance, for the Quantum-ESPRESSO package:

module load quantum_espresso
ls $QUANTUM_ESPRESSO_HOME/bin

• Learn how to submit and manage jobs.

How do I use application X?

Read the package's documentation, using one or more of the following:

• Inspect the package's $NAME_HOME/share or $NAME_HOME/doc directory on Carbon (see module conventions).
• Browse the package's web page, generally mentioned in the module help text or the application catalog entry.
• Consult a package's man pages. Few packages have them. Man page files are generally installed under $NAME_HOME/man or $NAME_HOME/share/man and if so, will be made available automatically to the man command.

What's my account balance?

Simple answer: mybalance

To find out how many core-hours you have available, the simplest command to run is:

mybalance -h

Project  Machines Balance    
-------- -------- ---------- 
user     ANY         993.26
cnm34567 ANY       158760.93
cnm31234 ANY      -148893.62

The table gives all the Projects you have access to (for use with the qsub -A argument), and their balance. Machine lists all systems that can book jobs against your allocations. Carbon is currently the only machine that can do so. Balance is your account balance, in core-hours, as selected by the -h command option. This is the most useful and recommended unit. Without -h, you get core-seconds, which are integers but rather more unwieldy numbers.

• The "user" project provides you with a small initial startup allocation of typically 1000 core-hours.
• When a Balance is reported as negative, that account typically has a CreditLimit assigned, which permits the balance to dip below zero. These details, however, are not shown by mybalance.

Complete answer: gbalance

To get allocation details for accounts that have CreditLimits, run the gbalance command. Pass on -u username or -p projectname to select your allocations:

gbalance -h -u $USER

Use the literal string $USER which makes the shell fill in your actual username.

The ouput looks like:

Id  Name     Amount     Reserved Balance    CreditLimit Available
--- -------- ---------- -------- ---------- ----------- --------- 
100 cnm31234 -148893.62     0.00 -148893.62   150000.00   1106.38
217 kpelzer      993.26     0.00     993.26        0.00    993.26 
123 cnm34567  166440.93  7680.00  158760.93        0.00 158760.93 

The most relevant column for you is Available. The units, given the -h option, are again core-hours.

The colums and their meanings are:

Id

an internal number for the account.

Name

The project name (for use with qsub -A or #PBS -A).

Amount

Amount for transactions completely on the books for the project account; does not include running jobs or credits. Deposits are allocated by the User Office and implemented by the Carbon administrator.

Reserved

Amounts held in reserve by all running jobs using this account. The reserve ensures that a job does not cause an overdraft when it finishes and when its actual use will be booked. The quantity is calculated by walltime * number of cores blocked. When a job terminates, the charge according to the actual time used will be subtracted from Amount, and the unused quantities will be re-added to Available.

Balance

Available for new jobs; may go negative if CreditLimits are in place.

Balance = Amount - Reserved

CreditLimit

Amount by which Balance may go negative; assigned by the Carbon administrator.

Available

Relevant quantity for new jobs. Must be positive for a new job to start, and large enough to Reserve the entire job.

Available = Balance + CreditLimit

My account balance suddenly dropped

The compute time physically available by Carbon's processors is a perishable resource. Hence, your allocations are time-restricted in a use-it-or-lose-it manner. This is done to encourage consistent use of the machine throughout allocation cycles.

The expiration schedule is as follows:

• Your allocation is provided in three equal-sized installments.
• All installments are active from the beginning.
• Installments expire in a staggered fashion, currently after 4, 8, and 12 months, respectively. A diagram might illuminate this:

Installment
       |
    (3)|########################....
       |
    (2)|################............
       |                                           KEY
    (1)|########....................
       |                                           .  Installment is inactive
       |-------|-------|-------|------> Time       #  Installment is active
       0       4       8       12      (months)
    proposal                 proposal
     start                     end

• Your jobs will, sensibly, be booked against the installments that expire the earliest.

My question is not answered here

See HPC/Support.