Bridges-2 User Guide

Welcome to Bridges-2

We take security very seriously. Please take a minute now to read PSC policies on passwords, security guidelines, resource use, and privacy. You are expected to comply with these policies at all times when using PSC systems. If you have questions at any time, you can send email to help@psc.edu.

Are you new to HPC?

If you are new to high performance computing, please read Getting Started with HPC before you begin your research on Bridges-2. It explains HPC concepts which may be unfamiliar. You can also check the Introduction to Unix or the Glossary for quick definitions of terms that may be new to you.

We hope that that information along with the Bridges-2 User Guide will have you diving into your work on Bridges-2. But if you have any questions, don’t hesitate to email us for help at help@psc.edu.

Questions?

PSC support is here to help you get your research started and keep it on track. If you have questions at any time, you can send email to help@psc.edu.

Set your PSC password

Before you can connect to Bridges-2, you must have a PSC password.

If you have an active account on any other PSC system

PSC usernames and passwords are the same across all PSC systems. You will use the same username and password on Bridges-2 as for your other PSC account.

If you do not have an active account on any other PSC system:

You must create a PSC password. Go to the web-based PSC password change utility  at  apr.psc.edu  to set your PSC password.

PSC password policies

Computer security depends heavily on maintaining secrecy of passwords.

PSC uses Kerberos authentication on all its production systems, and your PSC password (also known as your Kerberos password) is the same on all PSC machines.

Set your initial PSC password

When you receive a PSC account, go to the web-based PSC password change utility to set your password.  For security, you should use a unique password for your PSC account, not one that you use for other sites.

Change your PSC password

Changing your password changes it on all PSC systems. To change your Kerberos password, use the web-based PSC password change utility .

PSC password requirements

Your password must:

• be at least eight characters long
• contain characters from at least three of the following groups:
  • lower-case letters
  • upper-case letters
  • digits
  • special characters, excluding apostrophes (') and quotes (")
• be different from the last three PSC passwords you have used
• not be re-used on other accounts
• remain private; it must not be shared with anyone
• be changed at least once per year

Password safety

Under NO circumstances does PSC reveal any passwords over the telephone, FAX them to any location, send them through email, set them to a requested string, or perform any other action that could reveal a password.

If someone claiming to represent PSC contacts you and requests information that in any manner would reveal a password, be assured that the request is invalid and do NOT comply.

It is strongly recommended to use a Password Manager to aid in generating secure passwords and managing accounts.

Security guidelines and policies

PSC policies regarding privacy, security and the acceptable use of PSC resources are documented here. Questions about any of these policies should be directed to PSC User Services.

See also policies for:

• Passwords
• User Accounts

Security measures

Security is very important to PSC. These policies are intended to ensure that our machines are not misused and that your data is secure.

What you can do:

You play a significant role in security!  To keep your account and PSC resources secure, please:

• Be aware of and comply with PSC’s policies on security, use and privacy found in this document
• Choose strong passwords and don’t share them between accounts or with others. More information can be found in the PSC password policies.
• Utilize your local security team for advice and assistance
• Keep your computer properly patched and protected
• Report any security concerns to the PSC help desk ASAP by calling the PSC hotline at: 412-268-4960 or email help@psc.edu

What we will never do:

• PSC will never send you unsolicited emails requesting confidential information.
• We will also never ask you for your password via an unsolicited email or phone call.

Remember that the PSC help desk is always a  phone call away to confirm any correspondence at  412-268-4960.

If you have replied to an email appearing to be from PSC and supplied your password or other sensitive information, please contact the help desk immediately.

What you can expect:

• We will send you email when we need to communicate with you about service outages, new HPC resources, and the like.
• We will send you email when your password is about to expire and ask you to change it by using the web-based PSC password change utility.

Other security policies

• PSC password policies
• Users must connect to PSC machines using ssh in order to avoid remote logins with clear text passwords.
• We vigilantly monitor our computer systems and network connections for security violations
• We are in close contact with the CERT Coordination Project with regard to possible Internet security violations

Reporting security incidents

To report a security incident you should contact our Hotline at 412-268-4960. To report non-emergency security incidents you can send email to help@psc.edu.

PSC acceptable use policy

PSC’s resources are vital to the scientific community, and we have a responsibility to ensure that all resources are utilized in a responsible manner. PSC has legal and other obligations to protect its services, resources, and the intellectual property of users. Users share this responsibility by observing the rules of acceptable use that are outlined in this document. Your on-line assent to this Acceptable Use Policy is your acknowledgment that you have read and understand your responsibilities as a user of PSC Services and Resources, which refers to all computers owned or operated by PSC and all hardware, data, software, storage systems and communications networks associated with these computers. If you have questions, please contact PSC User Services at 412-268-4960 or email help@psc.edu.

By using PSC Services and Resources associated with your allocation, you agree to comply with the following conditions of use:

1. You will protect any access credentials (e.g., private keys, tokens & passwords) that are issued for your sole use by PSC and not knowingly allow any other person to impersonate or share any of your identities.
2. You will not use PSC Services and Resources for any unauthorized purpose, including but not limited to:
   1. Financial gain
   2. Tampering with or obstructing PSC operations
   3. Breaching, circumventing administrative, or security controls
   4. Inspecting, modifying, distributing, or copying privileged data or software without proper authorization, or attempting to do so
   5. Supplying, or attempting to supply, false or misleading information or identification in order to access PSC Services and Resources
3. You will comply with all applicable laws and relevant regulations, such as export control law or HIPAA.
4. You will immediately report any known or suspected security breach or misuse of PSC access credentials to help@psc.edu.
5. Use of PSC Services and Resources is at your own risk. There are no guarantees that PSC Services and Resources will be available, that they will suit every purpose, or that data will never be lost or corrupted. Users are responsible for backing up critical data.
6. Logged information, including information provided by you for registration purposes, will be used solely for administrative, operational, accounting, monitoring and security purposes.
7. Violations of this Acceptable Use Policy and/or abuse of PSC Services and Resources may result in loss of access to PSC Services and Resources. Abuse will be referred to the PSC User Services manager and/or the appropriate local, state and federal authorities, at PSC's discretion.
8. PSC may terminate or restrict any user's access to PSC Services and Resources, without prior notice, if such action is necessary to maintain computing availability and security for other users of the systems.
9. Allocations are awarded solely for open research, intended for publication. You will only use PSC Computing Resources to perform work consistent with the stated allocation request goals and conditions of use as defined by your approved PSC project and this Acceptable Use Policy.
10. PSC is entitled to regulate, suspend or terminate your access, and you will immediately comply with their instructions.

Privacy

Pittsburgh Supercomputing Center is committed to preserving your privacy. This privacy policy explains exactly what information is collected when you visit our site and how it is used.

This policy may be modified as new features are added to the site. Any changes to the policy will be posted on this page.

• Any data automatically collected from our site visitors - domain name, browser types, etc. - are used only in aggregate to help us better meet site visitors' needs.
• There is no identification of individuals from our aggregate data. Therefore, unless you choose otherwise, you are totally anonymous when visiting our site.
• We do not share data with anyone for commercial purposes.
• If you choose to submit personally identifiable information to us electronically via the PSC feedback page, email, etc., we will treat it with the same respect for privacy afforded to mailed submissions. Submission of such information is always optional.

PSC respects individual privacy and takes great effort in supporting web site privacy policy outlined above. Please be aware, however, that we may publish URLs of other sites on our web site that may not adhere to the same policy.

Reporting a problem

To report a problem on Bridges-2, please email help@psc.edu. Please report only one problem per email; it will help us to track and solve any issues more quickly and efficiently.

Be sure to include

• an informative subject line
• your username

If the question concerns a particular job, include these in addition:

• the JobID
• any error messages you received
• the date and time the job ran
• link to job scripts, output and data files
• the software being used, and versions when appropriate
• a screenshot of the error or the output file showing the error, if possible

Connecting to Bridges-2

Bridges-2 contains two broad categories of nodes: compute nodes, which handle the production research computing, and login nodes, which are used for managing files, submitting batch jobs and launching interactive sessions. Login nodes are not suited for production computing.

When you connect to Bridges-2, you are connecting to a Bridges-2 login node. You can connect to Bridges-2 via a web browser or through a command line interface.

See the Running Jobs section of this User Guide for information on production computing on Bridges-2.

Connect in a web browser

You can access Bridges-2 through a web browser by using the OnDemand software. You will still need to understand Bridges-2’s partition structure and the options which specify job limits, like time and memory use, but OnDemand provides a more modern, graphical interface to Bridges-2.

See the OnDemand section for more information.

Connect to a command line interface

You can connect to a traditional command line interface by logging in via ssh, using an ssh client from your local machine to connect to Bridges-2 using your PSC credentials.

SSH  is a program that enables secure logins over an unsecure network. It encrypts the data passing both ways so that if it is intercepted it cannot be read.

SSH is client-server software, which means that both the user’s local computer and the remote computer must have it installed. SSH server software is installed on all the PSC machines. You must install SSH client software on your local machine.

Free ssh clients for  Macs, Windows machines and many versions of Unix are available. Popular ssh clients (GUI) include PuTTY for Windows. A command line version of ssh is installed on Macs  by default; if you prefer that, you can use it in the Terminal application. You can also check with your university to see if there is an ssh client that they recommend.

Once you have an ssh client installed, you can use  your PSC credentials to connect to Bridges-2. Note that you must have created your PSC password before you can use ssh to connect to Bridges-2.

1. Using your ssh client, connect to hostname bridges2.psc.edu  using the default port (22).
2. Enter your PSC username and password when prompted.

Read more about using SSH to connect to PSC systems

Public-private keys

You can also use public-private key pairs to connect to Bridges-2. To do so, you must first fill out this form to register your keys with PSC.

Account administration

Changing your PSC password

There are two ways to change or reset your PSC password:

• Use the web-based PSC password change utility
• Use the kpasswd command when logged into a PSC system.  Do not use the passwd command.

When you change your PSC password, whether you do it via the online utility or via the kpasswd command on one PSC system, you change it on all PSC systems.

See PSC password policies.

Monitor your usage

The projects command

The projects command will help you monitor your allocation on Bridges-2. You can determine what Bridges-2 resources you have been allocated, your remaining balance, your charge id (used to track usage), and more. Typing projects at the command prompt will show all your charge ids.

This user has two Bridges-2 grants. The default grant, abc000000p, includes an allocation on Bridges-2 Regular Memory and Bridges-2 GPU resources for computing and Bridges-2 Ocean for file storage. The second one, xyz000000p, includes allocations on Bridges-2 Regular Memory nodes and Ocean for storage.

Accounting for Bridges-2 use

Accounting for Bridges-2 use varies with the type of node used, which is determined by the type of allocation you have: “Bridges-2 Regular Memory”, for Bridges-2’s RSM (256 and 512GB) nodes); “Bridges-2 Extreme Memory”, for  Bridges-2 4TB nodes; and “Bridges-2 GPU”, for Bridges-2’s GPU nodes.

For all allocations and all node types, usage is defined in terms of “Service Units” or SUs.  The definition of an SU varies with the type of node being used.

Bridges-2 Regular Memory

The  RM nodes are allocated as “Bridges-2 Regular Memory”.  This does not include Bridges-2’s GPU nodes.  Each RM node has 128 cores, each of which can be allocated separately. Service Units (SUs) are defined in terms of “core-hours”: the use of one core for 1 hour.

1 core-hour = 1 SU

Because the RM nodes each hold 128 cores, if you use one entire RM node for one hour, 128 SUs will be deducted from your allocation.

128 cores x 1 hour =128 core-hours = 128 SUs

If you don’t need all 128 cores, you can use just part of an RM node by submitting to the RM-shared partition. See more about the partitions on Bridges-2 below.

Using the RM-shared partition, if you use 2 cores on a node for 30 minutes, 1 SU will be deducted from your allocation.

2 cores x 0.5 hours = 1 core-hour = 1 SU

Bridges-2 Extreme Memory

The 4TB nodes on Bridges-2 are allocated as “Bridges-2 Extreme Memory”.  Accounting is done by the cores requested for the job. Service Units (SUs) are defined in terms of “core-hours”: the use of 1 core for one hour.

1 core-hour = 1 SU

If your job requests one node (96 cores) and runs for 1 hour, 96 SUs will be deducted from your allocation.

1 node x 96 cores/node x 1 hour = 96 core-hours = 96 SUs

If your job requests 3 nodes and runs for 6 hours, 1728 SUs will be deducted from your allocation.

3 nodes x 96 cores/node x 6 hours = 1728 core-hours = 1728 SUs

Bridges-2 GPU

Bridges-2 Service Units (SUs) for GPU nodes are defined in terms of “gpu-hours”: the use of one GPU Unit for one hour.

These nodes hold 8 GPU units each, each of which can be allocated separately.  Service Units (SUs) are defined in terms of GPU-hours.

1 GPU-hour = 1 SU

If you use an entire V100 GPU node for one hour, 8 SUs will be deducted from your allocation.

8 GPU units/node x 1 node x 1 hour = 8 gpu-hours = 8 SUs

If you don’t need all 8 GPUs, you can use just part of a GPU node by submitting to the GPU-shared partition. See more about the partitions on Bridges-2 below.

If you use the GPU-shared partition and use 4 GPU units for 48 hours, 196 SUs will be deducted from your allocation.

4 GPU units x 48 hours = 192 gpu-hours = 192 SUs

Accounting for file space

Every Bridges-2 grant has a storage allocation associated with it on the Bridges-2 file system, Ocean.  There are no SUs deducted from your allocation for the space you use, but if you exceed your storage quota, you will not be able to submit jobs to Bridges-2.

Each grant has a Unix group associated with it. Every file is “owned” by a Unix group, and that file ownership determines which grant is charged for the file space.  See “Managing multiple grants” for a further explanation of Unix groups, and how to manage file ownership if you have more than one grant.

You can check your Ocean usage with the projects command.

Managing multiple grants

If you have multiple grants on Bridges-2, you should ensure that the work you do for each grant is assigned correctly to that grant. The files created under or associated with that grant should belong to it, to make them easier to find and use by others on the same grant. There are two ids associated with each grant for these purposes: a SLURM charge id and a Unix group id. SLURM charge ids determine which grant your Bridges-2 (computational) use is deducted from. Unix group ids determine which Ocean allocation the storage space for files is deducted from, and who owns and can access files or directories. For a given grant, the SLURM charge id and the Unix group id are identical strings. One of your grants has been designated as your default grant, and the charge id and Unix group id associated with that grant are your default charge id and default Unix group id. When a Bridges-2 job runs, any SUs it uses are deducted from the default grant.  Any files created by that job are owned by the default Unix group.

Find your default charge id and Unix group

To find your SLURM charge ids, use the projects command.  It will display all the grants you belong to.  It will also list your default SLURM charge id in the projects output at the top. Your default Unix group id is an identical string. In this example, the user has two grants with SLURM charge ids abc000000p and xyz000000p.  The default charge id is abc000000p.

Use a secondary (non-default) grant

To  use a grant other than your default grant on Bridges-2, you must specify the appropriate charge id  with the -A option to the SLURM sbatch command.   See the Running Jobs section of this Guide for more information on batch jobs, interactive sessions and SLURM. NOTE that using the -A option does not change your default Unix group. Any files created during a job are owned by your default Unix group, no matter which charge id is used for the job, and the space they use will be deducted from the Ocean allocation for the default Unix group.

Change your Unix group for a login session

To temporarily change your Unix group, use the newgrp command. Any files created subsequently during this login session will be owned by the new group you have specified.  Their storage will be deducted from the Ocean allocation of the new group. After logging out of the session, your default Unix group will be in effect again.

newgrp unix-group

NOTE that the newgrp command has no effect on the charge id in effect.  Any Bridges-2 usage will be deducted from the default charge id or the one specified with the -A option to sbatch.

Change your default charge id and Unix group permanently

You can permanently change your default charge id and your default Unix group id with the change_primary_group command.  Type:

change_primary_group -l

to see all your groups.  Then type

change_primary_group account-id

to set account-id as your default.

Your default charge id changes immediately.  Bridges-2 use by any batch jobs or interactive sessions following this command are deducted from the new account by default.

Your default Unix group does not change immediately.  It takes about an hour for the change to take effect.  You must log out and log back in after that window for the new Unix group to be the default.

Tracking your usage

There are several ways to track your Bridges-2 usage:  the projects command and the Grant Management System.

The projects  command shows information on all Bridges-2 grants, including usage and the Ocean directories associated with the grant.

For more detailed accounting data you can use the Grant Management System.   You can also track your usage through the ACCESS Allocations Portal.  Be aware that the Grant Management System may not reflect the impact of a Grant Renewal.

Managing your ACCESS allocation

Most account management functions for your ACCESS (formerly XSEDE) grant are handled through the ACCESS Allocations Portal.  See the Manage Allocations tab for your usage. Be sure to check the RAMPS/Policies FAQ page for answers for many common questions.

Changing your default shell

The change_shell command allows you to change your default shell. This command is only available on the login nodes.

To see which shells are available, type

change_shell -l

To change your default shell, type

change_shell newshell

where newshell is one of the choices output by the change_shell -l command. You must log out and back in again for the new shell to take effect.

PSC account policies

The policies documented here are evaluated regularly to assure adequate and responsible administration of PSC systems for users. As such, they are subject to change at any time.

File retention

PSC provides storage resources, for long-term storage and file management.

Files in a PSC storage system are retained for 3 months after the affiliated grant has expired.

Requesting a refund

When appropriate, PSC provides refunds for jobs that failed due to circumstances beyond your control.

To request a refund, contact a PSC consultant or email help@psc.edu. In the case of batch jobs, we require the standard error and output files produced by the job. These contain information needed in order to refund the job.

File spaces

There are several distinct file spaces available on Bridges-2, each serving a different function.

• $HOME, your home directory on Bridges-2
• $PROJECT, persistent file storage on Ocean. $PROJECT is a larger space than $HOME.
• $LOCAL, Scratch storage on local disk on the node running a job
• $RAMDISK, Scratch storage in the local memory associated with a running job

File expiration

See PSC polices for user accounts for information about file expiration for Bridges-2 grants.

File permissions

Access to files in any Bridges-2 space is governed by Unix file permissions. If  your data has additional security or compliance requirements, please contact compliance@psc.edu.

Unix file permissions

For detailed information on Unix file protections, see the man page for the chmod (change mode) command.

To share files with your group, give the group read and execute access for each directory from your top-level directory down to the directory that contains the files you want to share.

chmod g+rx directory-name

Then give the group read and execute access to each file you want to share.

chmod g+rx filename

To give the group the ability to edit or change a file, add write access to the group:

chmod g+rwx filename

Access Control Lists

If you want more fine-grained control than Unix file permissions allow —for example, if you want to give only certain members of a group access to  a file, but not all members—then you need to use Access Control Lists (ACLs). Suppose, for example, that you want to give janeuser read access to a file in a directory, but no one else in the group.

Use the setfacl (set file acl) command to give janeuser read and execute access on the directory:

setfacl -m user:janeuser:rx directory-name

for each directory from your top-level directory down to the directory that contains the file you want to share with janeuser. Then give janeuser access to a specific file with

setfacl -m user:janeuser:r filename

User janeuser will now be able to read this file, but no one else in the group will have access to it.

To see what ACLs are set on a file, use the getfacl (get file acl) command.

There are man pages for chmod, setfacl and getfacl.

$HOME

This is your Bridges-2 home directory. It is the usual location for your batch scripts, source code and parameter files. Its path is /jet/home/username, where  username is your PSC username. You can refer to your home directory with the environment variable $HOME. Your home directory is visible to all of Bridges-2’s nodes.

Your home directory is backed up daily, although it is still a good idea to store copies of your important  files in another location, such as the Ocean file system or on a local file system at your site. If you need to recover a home directory file from backup send email to help@psc.edu. The process of recovery will take 3 to 4 days.

$HOME quota

Your home directory has a 25GB quota. You can check your home directory usage using the my_quotas command. To improve the access speed to your home directory files you should stay as far below your home directory quota as you can.

File expiration

See PSC polices for user accounts for information about file expiration for Bridges-2 grants.

$PROJECT

$PROJECT is persistent file storage. It is larger than your space in $HOME. Be aware that $PROJECT is NOT backed up.

The path of your Ocean home directory is /ocean/projects/groupname/username, where groupname is the Unix group id associated with your grant. Use the id command to find your group name.

The command id -Gn will list all the Unix groups you belong to.

The command id -gn will list the Unix group associated with your current session.

If you have more than one grant, you will have a $PROJECT directory for each grant. Be sure to use the appropriate directory when working with multiple grants.

File expiration

See PSC polices for user accounts for information about file expiration for Bridges-2 grants.

$PROJECT quota

Storage quota

Your usage quota for each of your grants is the Ocean storage allocation you received when your proposal was approved. If your total use in Ocean exceeds this quota you won’t be able to run jobs on Bridges-2 until you are under quota again.

Use the my_quotas  or projects command to check your Ocean usage.

If you have multiple grants, it is very important that you store your files in the correct $PROJECT directory.

Inode quota

In order to best serve all Bridges-2 users, an inode allocation has been established for $PROJECT. It will be enforced in addition to the storage quota for your grant. The inode allocation is proportional to the size of your storage quota, and is set at 6070 inodes per GB of storage allocated. There is currently no inode quota on home directories in the Jet file system.

Inodes are data structures that contain metadata about a file, such as the file size, user and group ids associated with the file, permission settings, time stamps, and more. Each file has at least one inode associated with it.

To view your usage on Bridges-2, use the my_quotas command which shows your limits as well as your current usage.

[user@bridges2-login013 ~]$ my_quotas
The quota for project directory /ocean/projects/abcd1234
Storage quota: 9.766T
 Storage used: 1.384T
 Inode quota: 60,700,000
 Inodes used: 453,596

Tips to reduce your inode usage:

• Delete files which are no longer needed
• Combine small files into one larger file via tools such as zip or tar

Should you need to increase your storage allocation or inode limit, please submit a supplement via the ACCESS allocation system. If you have questions, please email help@psc.edu.

$LOCAL

Each of Bridges-2’s nodes has a local file system attached to it. This local file system is only visible to the node to which it is attached, and provides fast access to local storage.

In a running job, this file space is available as $LOCAL.

If your application performs a lot of small reads and writes, then you could benefit from using this space.

Node-local storage is only available when your job is running, and can only be used as working space for a running job. Once your job finishes, any files written to $LOCAL are inaccessible and deleted. To use local space, copy files to it at the beginning of your job and back out to a persistent file space before your job ends.

If a node crashes all the node-local files are lost. You should checkpoint theses files by copying them to Ocean during long runs.

$LOCAL size

The maximum amount of local space varies by node type.

To check on your local file space usage type:

du -sh

No Service Units accrue for the use of $LOCAL.

Using $LOCAL

To use $LOCAL you must first copy your files to $LOCAL at the beginning of your script, before your executable runs. The following script is an example of how to do this

RC=1
 n=0
 while [[ $RC -ne 0 && $n -lt 20 ]]; do
     rsync -aP $sourcedir $LOCAL/
     RC=$?
     let n = n + 1
     sleep 10
 done

Set $sourcedir to point to the directory that contains the files to be copied before you call your executable. This code will try at most 20 times to copy your files. If it succeeds, the loop will exit. If an invocation of rsync was unsuccessful, the loop will try again and pick up where it left off.

At the end of your job you must copy your results back from $LOCAL or they will be lost. The following script will do this.

mkdir $PROJECT/results
 RC=1
 n=0
 while [[ $RC -ne 0 && $n -lt 20 ]]; do
     rsync -aP $LOCAL/ $PROJECT/results
     RC=$?
     let n = n + 1
     sleep 10
 done

This code fragment copies your files to a directory in your Ocean file space named results, which you must have created previously with the mkdir command. It will loop at most 20 times and stop if it is successful.

$RAMDISK

You can use the memory allocated for your job for IO rather than using disk space. In a running job, the environment variable $RAMDISK will refer to the memory associated with the nodes in use.

The amount of memory space available to you depends on the size of the memory on the nodes and the number of nodes you are using. You can only perform IO to the memory of nodes assigned to your job.

If you do not use all of the cores on a node, you are allocated memory in proportion to the number of cores you are using. Note that you cannot use 100% of a node’s memory for IO; some is needed for program and data usage.

This space is only available to you while your job is running, and can only be used as working space for a running job. Once your job ends this space is inaccessible and files there are deleted. To use $RAMDISK, copy files to it at the beginning of your job and back out to a permanent space before your job ends. If your job terminates abnormally, files in $RAMDISK are lost.

Within your job you can cd to $RAMDISK, copy files to and from it, and use it to open files.  Use the command du -sh to see how much space you are using.

If you are running a multi-node job the $RAMDISK variable points to the memory space on the node that is running your rank 0 process.

Transferring files

Several methods are available to transfer files into and from Bridges-2.

Please note that only small file transfers (up to 100MB) can be initiated from the Bridges-2 login nodes. Larger file transfers should use the Data Transfer Nodes (DTN), data.bridges2.psc.edu, which are specifically built to be high-speed data connectors.

 

Using the DTNs prevents file transfers from disrupting interactive use on Bridges-2’s login nodes.

Paths for Bridges-2 file spaces

To copy files into any of your Bridges-2 spaces, you need to know the path to that space on Bridges-2. The start of the full paths for your Bridges-2 directories are:

Home directory     /jet/home/username

Ocean directory   /ocean/projects/groupname/username

To find your groupname, use the command id -Gn. All of your valid groupnames will be listed. You have an Ocean directory for each grant you have.

Transfers into your Bridges-2 home directory

Your home directory quota is 25GB. More space is available in your $PROJECT file space in Ocean. Exceeding your home directory quota will prevent you from writing more data into your home directory and will adversely impact other operations you might want to perform.

Commands to transfer files

You can use rsync, scp, sftp or Globus to copy files to and from Bridges-2.

rsync

You can use the rsync command to copy files to and from Bridges-2. A sample rsync command to copy to a Bridges-2 directory is

rsync -rltpDvp -e 'ssh -l username' source_directory data.bridges2.psc.edu:target_directory

Substitute your username for ‘username‘. Make sure you use the correct groupname in your target directory. By default, rsync will not copy older files with the same name in place of newer files in the target directory. It will overwrite older files.

We recommend the rsync options -rltDvp. See the rsync man page for information on these options and other options you might want to use. We also recommend the option

-oMACS=umac-64@openssh.com

If you use this option, your transfer will use a faster data validation algorithm.

You may want to put your rsync command in a loop to insure that it completes. A sample loop is

RC=1
 n=0
 while [[ $RC -ne 0 && $n -lt 20 ]] do
     rsync source-file target-file
     RC = $?
     let n = n + 1
     sleep 10
 done

This loop will try your rsync command 20 times. If it succeeds it will exit. If an rsync invocation is unsuccessful the system will try again and pick up where it left off. It will copy only those files that have not already been transferred. You can put this loop, with your rsync command, into a batch script and run it with sbatch.

scp

To use scp for a file transfer you must specify a source and destination for your transfer. The format for either source or destination is

username@machine-name:path/filename

For transfers involving Bridges-2,  username is your PSC username. Use data.bridges2.psc.edu for the machine-name. This is the name for the Data Transfer Node,  a high-speed data connector at PSC. We recommend using it for all file transfers using scp involving Bridges-2. Using it prevents file transfers from disrupting interactive use on Bridges-2’s login nodes.

File transfers using scp must specify full paths for Bridges-2 file systems. See Paths for Bridges-2 file spaces for details.

sftp

To use sftp, first connect to the remote machine:

sftp username@machine-name

When  Bridges-2 is the remote machine, use your PSC userid as  username. The Bridges-2 machine-name should be specified as data.bridges2.psc.edu. This is the name for the Data Transfer Nodes (DTN), a high-speed data connector at PSC.  We recommend using it for all file transfers using sftp involving Bridges-2. Using it prevents file transfers from disrupting interactive use on Bridges-2’s login nodes.

You will be prompted for your password on the remote machine. If Bridges-2 is the remote machine, enter your PSC password.

You can then enter sftp subcommands, like put to copy a file from the local system to the remote system, or get to copy a file from the remote system to the local system.

To copy files into Bridges-2, you must either cd to the proper directory or use full pathnames in your file transfer commands. See Paths for Bridges-2 file spaces for details.

Globus

Globus can be used for any file transfer to Bridges-2. It tracks the progress of the transfer and retries when there is a failure; this makes it especially useful for transfers involving large files or many files.

To use Globus to transfer files you must authenticate either via a Globus account or with InCommon credentials.

To use a Globus account for file transfer, set up a Globus account at the Globus site.

To use InCommon credentials to transfer files to/from Bridges-2, you must first provide your  ePPN information to PSC. Follow these steps:

1. Find your ePPN
   1. Navigate your web browser to https://cilogon.org/.
   2. Select your institution from the ‘Select an Identity Provider’ list.
   3. Click the ‘Log On’ button.  You will be taken to the web login page for your institution.
   4. Login with your username and password for your institution.
      • If your institution has an additional login requirement (e.g., Duo), authenticate to that as well.
   5. After successfully authenticating to your institution’s web login interface, you will be returned to the CILogon webpage.
   6. Click on the User Attributes drop down link to find the ‘ePPN’.
2. Send your ePPN to PSC
   1.  From the User Attributes dropdown on the CILogon webpage, select and copy the ePPN text field, which is typically formmated like an e-mail address, with an account name @ some domain. If your CILogon User Attributes ePPN is blank, please let us know.
   2. Send email to help@psc.edu.  Paste your Certificate Subject field into the message, asking that it be mapped to your PSC username for GridFTP data transfers.

Your CILogon information will be added within one business day, and you will be able to begin transferring files to and from Bridges-2.

Globus endpoints

Once you have the proper authentication you can initiate file transfers from the Globus site. A Globus transfer requires a Globus endpoint, a file path and a file name for both the source and destination.

When using Globus GridFTP for data transfers to/from Bridges-2, please select the endpoint labelled: “PSC Bridges-2 /ocean and /jet filesystems”.

These endpoints are owned by psc@globusid.org. You must always specify a full path for the Bridges-2 file systems. See Paths for Bridges-2 file spaces for details.

Moving files between Bridges-2 grants

You can transfer files from a Bridges-2 grant that is expiring to a new grant by moving files to a directory belonging to the new grant and changing the file ownership.

Move the files to a new directory

Use the mv, rsync, or scp commands to move files from one directory to another.

To move a file from a directory test in the $PROJECT directory of your expiring grant to directory previous-results of of your $PROJECT space under your new grant, type:

mv /ocean/projects/old-groupid/username/test/file1  /ocean/projects/new-groupid/username/previous-results/file1

If you are in the test directory of the expiring grant, the command may be simplified to

mv file1 /ocean/projects/new-groupid/username/previous-results/file1

Note that this will remove the file from your expiring grant’s file space, rather than make a copy.

See the Transferring Files section of this User Guide for information on the rsync and scp commands.

Change the file ownership

You must also change the Unix group of any files moved into a different grant’s file space in order to access them under the new grant. Use the chgrp command to do this.  Type:

chgrp new-group filename

To change the group ownership of an entire directory, type:

chgrp -R new-group directory-name

See the Managing Multiple Grants section of this User Guide for an explanation of charge ids and Unix groups and how to find them.

Programming environment

Bridges-2 provides a rich programming environment for the development of applications.

C, C++ and Fortran

AMD (AOCC), Intel, Gnu and NVIDIA HPC compilers for C, C++ and Fortan are available on Bridges-2.  Be sure to load the module for the compiler set that you want to use.  Once the module is loaded,  you will have access to the compiler commands:

Compiler options

AMD provides a Compiler Options Quick Reference Guide for AMD, Gnu and Intel compilers on their EPYC processors.

There are man pages for each of the compilers.

See also:

• AMD Optimizing C/C++ Compiler (AOCC)
• NVIDIA compilers web site
• GNU compilers web site
• Module documentation for information on what modules are available and how to use them.

OpenMP programming

To compile OpenMP programs you must add an option to your compile command:

See also:

• OpenMP web site

MPI programming

Three types of MPI are supported on Bridges-2: MVAPICH2, OpenMPI and Intel MPI. The three MPI types  may perform differently on different problems or in different programming environments. If you are having trouble with one type of MPI, please try using another type. Contact help@psc.edu for more help.

To compile an MPI program, you must:

• load the module for the compiler that you want
• load the module for the MPI type you want to use – be sure to choose one that uses the compiler that you are using.   The module name will distinguish between compilers.
• issue the appropriate MPI wrapper command to compile your program

To run your previously compiled MPI program, you must load the same MPI module that was used in compiling.

To see what MPI versions are available, type module avail mpi  or module avail mvapich2. Note that the module names include the MPI family and version (“openmpi/4.0.2”),  followed by the associated compiler and version (“intel20.4”).  (Modules for other software installed with MPI are also shown.)

Wrapper commands

Custom task placement with Intel MPI

If you wish to specify custom task placement with Intel MPI (this is not recommended),  you must set the environment variable I_MPI_JOB_RESPECT_PROCESS_PLACEMENT to 0. Otherwise the mpirun task placement settings you give will be ignored. The command to do this is:

For the BASH shell:

export I_MPI_JOB_RESPECT_PROCESS_PLACEMENT=0

For the CSH shell:

setenv I_MPI_JOB_RESPECT_PROCESS_PLACEMENT 0

See also:

• Intel MPI web site
• MVAPICH2 web site
• OpenMPI web site
• Module documentation for information on what modules are available and how to use them.

Other languages

Other languages, including Java, Python, R,  and MATLAB, are available. See the software page for information.

Debugging and performance analysis

DDT is a debugging tool for C, C++ and Fortran 90 threaded and parallel codes. It is client-server software. Install the client on your local machine and then you can access the GUI on Bridges-2 to debug your code.

See the DDT page for more information.

Collecting performance statistics

In order to collect performance statistics, you must use the -C PERF option to the sbatch command. Note that this can only be done in RM partitions in which jobs do not share a node with other jobs: RM  and RM-512 partitions. See the sbatch section of this User Guide for more information on the options available with the sbatch command.

Software

Bridges-2 has a broad collection of applications installed.  See the list of software installed on Bridges-2.

Typing bioinformatics on Bridges-2 will list all of the biological science software that is installed .

PSC has built some environments which provide a rich, unified, Anaconda-based environment for AI, Machine Learning, and Big Data applications. Each environment includes several popular AI/ML/BD packages, selected to work together well. See the section on AI software environments in this User Guide for more information. 

Additional software may be installed by request. If you feel that you need particular software for your research, please send a request to help@psc.edu.

Running jobs

All production computing must be done on Bridges-2's compute nodes, NOT on Bridges-2's login nodes. The SLURM scheduler (Simple Linux Utility for Resource Management) manages and allocates all of Bridges-2's compute nodes. Several partitions, or job queues, have been set up in SLURM to allocate resources efficiently.

To run a job on Bridges-2, you need to decide how you want to run: interactively, in batch, or through OnDemand;  and where to run - that is, which partitions you are allowed to use.

What are the different ways to run a job?

You can run jobs in Bridges-2 in several ways:

• interactive sessions - where you type commands and receive output back to your screen as the commands complete
• batch mode - where you first create a batch (or job) script which contains the commands to be run, then submit the job to be run as soon as resources are available
• through OnDemand - a browser interface that allows you to run interactively, or create, edit and submit batch jobs and also provides a graphical interface to tools like RStudio, Jupyter notebooks, and IJulia,  More information about OnDemand is in the OnDemand section of this user guide.

Regardless of which way you choose to run your jobs, you will always need to choose a partition to run them in.

Which partitions can I use?

Different partitions control different types of Bridges-2's resources; they are configured by the type of node they control, along with other job requirements like how many nodes or how much time or memory is needed.  Your access to the partitions is based on the type of Bridges-2 allocation that you have: "Bridges-2 Regular Memory", "Bridges-2 Extreme Memory",  or “Bridges-2 GPU". You may have more than one type of allocation; in that case, you will have access to more than one set of partitions.

You can see which of Bridges-2's resources that you have been allocated with the projects command. See section "The projects command" in the Account Administration section of this User Guide for more information.

Interactive sessions

You can do your production work interactively on Bridges-2, typing commands on the command line, and getting responses back in real time.  But you must  be allocated the use of one or more Bridges-2's compute nodes by SLURM to work interactively on Bridges-2.  You cannot use Bridges-2's login nodes for your work.

You can run an interactive session in any of the RM or GPU partitions.  You will need to specify which partition you want, so that the proper resources are allocated for your use.

Note
You cannot run an interactive session in the EM partition.

If all of the resources set aside for interactive use are in use, your request will wait until the resources you need are available. Using a shared partition (RM-shared, GPU-shared) will probably allow your job to start sooner.

The interact command

To start an interactive session, use the command interact.  The format is:

interact -options

The simplest interact command is

interact

This command will start an interactive job using the defaults for interact, which are

Partition: RM-shared

Cores: 1

Time limit: 60 minutes

If you want to run in a different partition, use more than one core, multiple nodes, or set a different time limit, you will need to use options to the interact command.   See the Options for interact section of this User Guide below.

Once the interact command returns with a command prompt you can enter your commands. The shell will be your default shell. When you are finished with your job, type CTRL-D.

[user@bridges2-loginr01 ~]$ interact
A command prompt will appear when your session begins
"Ctrl+d" or "exit" will end your session
[user@r004 ~]

Notes:

• Be sure to use the correct charge id for your job if you have more than one grant. See "Managing multiple grants".
• Service Units (SU) accrue for your resource usage from the time the prompt appears until you type CTRL-D, so be sure to type CTRL-D as soon as you are done.
• The maximum time you can request is 8 hours. Inactive interact jobs are logged out after 30 minutes of idle time.
• By default, interact uses the RM-shared partition.  Use the -p option for interact to use a different partition.

Options for interact

If you want to run in a different partition, use more than one core or set a different time limit, you will need to use options to the interact command.   Available options are given below.

-p partition

-t HH:MM:SS

-N n

--ntasks-per-node=n
Note the "--" for this option

-n NTasks

--gres=gpu:type:n
Note the "--" for this option

-A charge id

-R reservation-name

-h

See also

• Bridges-2 partitions
• How to determine your valid SLURM charge ids and Unix groups and change your default, in the Account Adminstration section of this User Guide
• Managing multiple grants
• The srun command, for more complex control over your interactive job

Batch jobs

Instead of working interactively on Bridges-2, you can instead run in batch. This means you will

• create a file called a batch or job script
• submit that script to a partition (queue) using the sbatch command
• wait for the job's turn in the queue
• if you like, check on the job's progress as it waits in the partition and as it is running
• check the output file for results or any errors when it finishes

A simple example

This section outlines an example which submits a simple batch job. More detail on batch scripts, the sbatch command and its options follow.

Create a batch script

Use any editor you like to create your batch scripts. A simple batch script named hello.job which runs a "hello world" command is given here. Comments, which begin with '#', explain what each line does.

The first line of any batch script must indicate the shell to use for your batch job.

#!/bin/bash
# use the bash shell
set -x 
# echo each command to standard out before running it
date
# run the Unix 'date' command
echo "Hello world, from Bridges-2!"
# run the Unix 'echo' command

Submit the batch script to a partition

Use the sbatch command to submit the hello.job script.

[joeuser@login005 ~]$ sbatch hello.job
Submitted batch job 7408623

Note the jobid that is echoed back to you when the job is submitted.  Here it is 7408623.

Check on the job progress

You can check on the job's progress in the partition by using the squeue command. By default you will get a list of all running and queued jobs. Use the -u option with your username to see only your jobs.  See the squeue command for details.

[joeuser@login005 ~]$ squeue -u joeuser
 JOBID   PARTITION NAME     USER    ST TIME NODES NODELIST(REASON)
 7408623 RM        hello.jo joeuser PD 0:08 1     r7320:00

The status "PD" (pending) in the output here shows that job 7408623 is waiting in the queue.  See more about the squeue command below.

When the job is done, squeue will no longer show it:

[joeuser@login005 ~]$ squeue -u joeuser
 JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)

Check the output file when the job is done

By default, the standard output and error from a job are saved in a file with the name slurm-jobid.out, in the directory that the job was submitted from.

[joeuser@login005 ~]$ more slurm-7408623.out
+ date
Sun Jan 19 10:27:06 EST 2020
+ echo 'Hello world, from Bridges-2!'
Hello world, from Bridges-2!
[joeuser@login005 ~]$

The sbatch command

To submit a batch job, use the sbatch command.  The format is

sbatch -options batch-script

The options to sbatch can either be in your batch script or on the sbatch command line.  Options in the command line override those in the batch script.

Note:

• Be sure to use the correct charge id  if you have more than one grant. Please see the -A option for sbatch to change the SLURM charge id for a job. Information on how to determine your valid charge ids and change your default charge id is in the Account adminstration section of this User Guide.
• In some cases, the options for sbatch differ from the options for interact or srun.
• By default, sbatch submits jobs to the RM partition.  Use the -p option for sbatch to direct your job to a different partition

Options to the sbatch command

For more information about these options and other useful sbatch options see the sbatch man page.

-p partition

-t HH:MM:SS

-N n

-n n

--ntasks-per-node=n
Note the "--" for this option

-o filename

--gpus=type:n
Note the "--" for this option

-A charge id

-C constraints

--res reservation-name
Note the "--" for this option

--mail-type=type
Note the "--" for this option

--mail-user=username

Note the "--" for this option

-d=dependency-list

--no-requeue
Note the "--" for this option

--time-min=HH:MM:SS
Note the "--" for this option.

-h

See also

• Bridges-2 partitions
• How to determine your valid charge ids and change your defaults, in the Account administration section of this User Guide
• Managing multiple grants

Managing multiple grants

If you have more than one grant, be sure to use the correct SLURM charge id and Unix group when running jobs.

See "Managing multiple grants" in the Account Administration section of this User Guide to see how to find your charge ids and Unix groups and determine or change your defaults.

Permanently change your default SLURM charge id and Unix group

See the change_primary_group command in the "Managing multiple grants" in the Account Administration section of this User Guide to permanently change your default SLURM charge id and Unix group.

Temporarily change your SLURM charge id or Unix group

See the -A option to the sbatch or interact commands to set the SLURM charge id for a specific job.

The newgrp command will change your Unix group for that login session only. Note that any files created by a job are owned by the Unix group in effect when the job is submitted, which is not necessarily the same as the charge id used for the job.  See the newgrp command in the Account Administration section of this User Guide to see how to change the Unix group currently in effect.

Bridges-2 partitions

Each SLURM partition manages a subset of Bridges-2's resources.  Each partition allocates resources to interactive sessions, batch jobs, and OnDemand sessions that request resources from it.

Not all partitions may be open to you. Your Bridges-2 allocations determine which partitions you can submit jobs to.

A "Bridges-2 Regular Memory" allocation allows you to use Bridges-2's RM (256 and 512GB) nodes.   The RM, RM-shared and RM-512 partitions handle jobs for these nodes.

A "Bridges-2 Extreme Memory" allocation allows you to use  Bridges-2’s 4TB EM nodes.  The EM partition handles jobs for these nodes.

A "Bridges-2 GPU" allocation allows you to use Bridges-2's GPU nodes. The GPU and GPU-shared partitions handle jobs for these nodes.

All the partitions use FIFO scheduling. If the top job in the partition will not fit, SLURM will try to schedule the next job in the partition. The scheduler follows policies to ensure that one user does not dominate the machine. There are also limits to the number of nodes and cores a user can simultaneously use. Scheduling policies are always under review to ensure best turnaround for users.

Partitions for Bridges-2 “Regular memory” allocations

The RM, RM-shared, and RM-512 partitions can be used for Bridges-2 “Regular memory” allocations.

Use the appropriate charge id for your jobs: If you have more than one Bridges-2 grant, be sure to use the correct SLURM charge id for each job.  See “Managing multiple grants”.

For information on requesting resources and submitting  jobs see the discussion of the interact or sbatch commands.

Jobs in the RM and RM-shared partitions run on Bridges-2 256GB RM  nodes.  Jobs in the RM-512 partition run on Bridges-2 512GB RM nodes.

• Jobs in the RM partition use one or more full nodes. However, the memory space of  all the nodes is not integrated. The cores within a node access a shared memory space, but cores in different nodes do not.
• Jobs in the RM-shared partition use only part of one node. Because SUs are calculated using how many cores are used, using only part of a node will result in a smaller SU charge.
• Jobs in the RM-512 partition can use one or more full 512GB nodes. These nodes cannot be shared.

RM partition

When submitting a job to the RM partition, you can request:

• the number of  nodes
• the walltime limit

If you do not specify the number of nodes or time limit, you will get the defaults.  See the summary table for the RM partition below for the defaults.

Warning

Jobs in the RM partition are charged for all 128 cores on every node they use. For a job using one node, that is 128 SUs per hour. If you do not need 128 cores, you can use the RM-shared partition to request only the number of cores that you need. This will reduce the SU charges and your job may begin earlier.

Sample interact command for the RM partition

An example of an interact command for the RM partition, requesting the use of 2 nodes for 30 minutes is

interact -p RM -N 2 -t 30:00

where:

-p indicates the intended partition

-N is the number of nodes requested

-t is the walltime requested in the format HH:MM:SS

Sample sbatch command for the RM partition

An example of a sbatch command to submit a job to the RM partition, requesting one node for 5 hours is

sbatch -p RM -t 5:00:00 -N 1 myscript.job

where:

-p indicates the intended partition

-t is the walltime requested in the format HH:MM:SS

-N is the number of nodes requested

myscript.job is the name of your batch script

Sample job script for the RM partition

#!/bin/bash
#SBATCH -N 1
#SBATCH -p RM
#SBATCH -t 5:00:00
#SBATCH --ntasks-per-node=128

# type 'man sbatch' for more information and options
# this job will ask for 1 full RM node (128 cores) for 5 hours
# this job would potentially charge 640 RM SUs

#echo commands to stdout
set -x

# move to working directory
# this job assumes:
# - all input data is stored in this directory
# - all output should be stored in this directory
# - please note that groupname should be replaced by your groupname
# - username should be replaced by your username
# - path-to-directory should be replaced by the path to your directory where the executable is

cd /ocean/projects/groupname/username/path-to-directory

# run a pre-compiled program which is already in your project space

./a.out

RM-shared partition

You can only use part of one node in the RM-shared partition.

When submitting a job to the RM-shared partition, you can request:

• the number of  cores
• the walltime limit

If you do not specify the number of cores or time limit, you will get the defaults.  See the summary table for the RM partitions below for the defaults.

Jobs in the RM-shared partition cannot:

• span nodes
• specifically request memory. Jobs are alloted 2GB of memory per core that is requested. 
• request more than 64 cores

Sample interact command for the RM-shared partition

An example of an interact command for the RM-shared partition, requesting the use of 64 cores for 30 minutes is

interact -p RM-shared --ntasks-per-node=64 -t 30:00

where:

-p indicates the intended partition

–ntasks-per-node is the number of cores requested

-t is the walltime requested in the format HH:MM:SS

Sample sbatch command for the RM-shared partition

An example of a sbatch command to submit a job to the RM-shared partition, requesting 32 cores for 5 hours is

sbatch -p RM-shared -t 5:00:00 --ntasks-per-node=32 myscript.job

where:

-p asks for the RM-shared partition

-t requests 5 hours of walltime

–ntasks-per-node asks for 32 cores

myscript.job is the name of your batch script

Sample job script for the RM-shared partition

Summary of partitions for Bridges-2 RM nodes

Partitions for “Bridges-2 Extreme Memory” allocations

The EM partition should be used for “Bridges-2 Extreme Memory” allocations.

Use the appropriate charge id for your jobs: If you have more than one Bridges-2 grant, be sure to use the correct SLURM charge id for each job.  See “Managing multiple grants”.

For information on requesting resources and submitting  jobs see the discussion of the interact or sbatch commands.

Jobs in the EM partition

• run on Bridges-2’s EM  nodes, which have 4TB of memory and 96 cores per node
• can use at most one full EM node
• must specify the number of cores to use
• must use a multiple of 24 cores. A job can request 24, 48, 72 or 96 cores.

When submitting a job to the EM partition, you can request:

• the number of  cores
• the walltime limit

Your job will be allocated memory in proportion to the number of cores you request. Be sure to request enough cores to be allocated the memory that your job needs. Memory is allocated at about 1TB per 24 cores. As an example, if your job needs 2TB of memory, you should request 48 cores.

If you do not specify the number of cores or time limit, you will get the defaults.  See the summary table for the EM partition below for the defaults.

Note
You cannot submit an interactive job to the EM partition.

You cannot use the EM partition through OnDemand.

Sample sbatch command for the EM partition

An example of a sbatch command to submit a job to the EM partition, requesting an entire node for 5 hours is

sbatch -p EM -t 5:00:00 --ntasks-per-node=96 myscript.job

where:

-p indicates the intended partition

-t is the walltime requested in the format HH:MM:SS

--ntasks-per-node is the number of cores requested per node

myscript.job is the name of your batch script

Sample job script for the EM partition

#!/bin/bash
#SBATCH -N 1
#SBATCH -p EM
#SBATCH -t 5:00:00
#SBATCH -n 96

# type 'man sbatch' for more information and options
# this job will ask for 1 full EM node (96 cores) and 5 hours of runtime
# this job would potentially charge 480 EM SUs

# echo commands to stdout
set -x

# move to working directory
# this job assumes:
# - all input data is stored in this directory
# - all output should be stored in this directory
# - please note that groupname should be replaced by your groupname
# - username should be replaced by your username
# - path-to-directory should be replaced by the path to your directory where the executable is

cd /ocean/projects/groupname/username/path-to-directory

#run pre-compiled program which is already in your project space

./a.out

Summary of the EM partition

GPU and GPU-shared partitions

Jobs in the GPU and GPU-shared partitions run on the GPU nodes and are available for Bridges-2 GPU allocations .

For information on requesting resources and submitting  jobs see the interact or sbatch commands.

Use the appropriate charge id for your jobs: If you have more than one Bridges-2 grant, be sure to use the correct SLURM charge id for each job. See “Managing multiple grants”.

Jobs in the GPU partition can use more than one node. Jobs in the GPU partition do not share nodes, so jobs are allocated all the cores and all of the GPUs associated with the nodes assigned to them . Your job will incur SU costs for all of the cores on your assigned nodes. The memory space across nodes is not integrated. The cores within a node access a shared memory space, but cores in different nodes do not.

Jobs in the GPU-shared partition use only part of one node. Because SUs are calculated using how many gpus are used, using only part of a node will result in a smaller SU charge.

GPU types

Bridges-2 has two designations of GPU nodes, "v100-32", and v100-16". The "32" or "16" designation indicates the amount of GPU memory per GPU on the node. Both "v100-32" and "v100-16"  node types can be used in all GPU partitions.

v100-32 nodes

• There are 24 Tesla v100-32 nodes. Each has eight V100 GPUs and 32GB of GPU memory per GPU. These nodes have 512GB RAM per node.
• There is one DGX-2 node, with 16 V100 GPUs, each with 32GB of GPU memory. It has 1.5TB RAM.

v100-16 nodes

• There are 9 v100-16 nodes containing eight V100 GPUs, each with 16GB of GPU memory. These nodes have 192GB RAM per node.

The GPU partition

The GPU partition is for jobs that will use one or more entire GPU nodes.

When submitting a job to the GPU partition, you must use these options to specify the number of GPUs you want. Be aware that the way to request a number of GPUs is different, depending on whether you are using an interactive session or a batch job.

If you do not specify the number of GPUs or time limit, you will get the defaults.  See the summary table for the GPU partitions below for the defaults.

Interactive sessions

Use a command like

interact -p GPU --gres=gpu:type:n -N x

• In interactive use,  n is the number of GPUs you are requesting per node. Because you always use one or more entire nodes in the GPU partition,  n  must always be either  8 or 16.  To use the DGX-2,  n must be 16. For all other GPU nodes, n must be 8.
• type is one of "v100-16" or v100-32"
• x indicates the number of nodes you want to use.  If you only want one node, you can omit the -N option because it defaults to one.
  • Because there is only one DGX-2,  you cannot request more than one node with -N when using asking for 16 GPUs (i.e., --gres=gpu:v100-32:16).

See  interact command options for details on other options, such as the walltime limit.

Sample interact command for the GPU partition

An interact command to start a GPU job on 2 GPU v100-32 nodes for 30 minutes is

interact -p GPU --gres=gpu:v100-32:8 -N 2 -t 30:00

where:

-p indicates the intended partition
--gres=gpu:v100-32:8 requests the use of 8 GPUs on each v100-32 node
-N 2 requests the use of 2 nodes
-t 30:00 requests 30 minutes of walltime, in the format HH:MM:SS

Batch jobs

Use a command like

sbatch -p GPU --gpus=type:n -N x jobname

• In batch use, n is the total number of GPUs you are requesting for the job. Because you always use one or more entire nodes in the GPU partition, n must be a multiple of 8, either: 8, 16, 24 or 32, depending on how many nodes you are requesting. To use the DGX-2, use 16 for n and never ask for more than one node.
• type is one of "v100-16" or v100-32"
• x indicates the number of nodes you want to use, from 1-4.  If you only want one node, you can omit the -N option because it defaults to one.
• Valid options to use one node are
  •  --gpus=v100-32:16  to use the DGX-2
  • --gpus=v100-32:8, to use a V100-32 Tesla node
  • --gpus=v100-16:8, to use a Volta node
• jobname is the name of your job script

See the sbatch command options for more details on available options, such as the walltime limit.

Sample sbatch command for the GPU partition

A sample sbatch command to submit a job to the GPU partition to use 2 full GPU v100-16 nodes  and all 8 GPUs on each node for 5 hours is

sbatch -p GPU -N 2 --gpus=v100-16:16 -t 5:00:00 jobname

where:

-p indicates the intended partition
-N 2 requests two v100-16 GPU nodes
--gpus=v100-16:16  requests the use of all 8 GPUs on both v100-16 nodes, for a total of 16 for the job
-t is the walltime requested in the format HH:MM:SS
jobname is the name of your batch script

Sample job script for the GPU partition

#!/bin/bash
#SBATCH -N 1
#SBATCH -p GPU
#SBATCH -t 5:00:00
#SBATCH --gpus=v100-32:8

#type 'man sbatch' for more information and options
#this job will ask for 1 full v100-32 GPU node(8 V100 GPUs) for 5 hours
#this job would potentially charge 40 GPU SUs

#echo commands to stdout
set -x

# move to working directory
# this job assumes:
# - all input data is stored in this directory
# - all output should be stored in this directory
# - please note that groupname should be replaced by your groupname
# - username should be replaced by your username
# - path-to-directory should be replaced by the path to your directory where the executable is

cd /ocean/projects/groupname/username/path-to-directory

#run pre-compiled program which is already in your project space

./gpua.out

The GPU-shared partition

The GPU-shared partition is for jobs that will use part of one GPU node. You can request at most 4 GPUs from one node in the GPU-shared partition.

When submitting a job to the GPU-shared partition, you must use one of these options to specify the type of GPU node and the total number of GPUs you want, where type indicates what kind of node you want, and n is the number of GPUS you are requesting.

• for an interactive session, use --gres=gpu:type:n
• for a batch job, use --gpus=type:n

You can also request

• the walltime limit

See the GPU partitions section of this User Guide for information on the types of GPU nodes on Bridges-2.

Sample interact command for the GPU-shared partition

An interact command to start a GPU-shared job using 4 v100-32 GPUs for 30 minutes is

interact -p GPU-shared --gres=gpu:v100-32:4 -t 30:00

where:

-p indicates the intended partition
–gres=gpu:v100-32:4  requests the use of 4 GPUs on a v100-32 GPU node
-t is the walltime requested in the format HH:MM:SS

Sample sbatch command for the GPU-shared partition

A sample sbatch command to submit a job to the GPU-shared partition to use 2 v100-16 GPUs for 2 hours is

sbatch -p GPU-shared  --gres=gpu:v100-16:2 -t 2:00:00

where:

-p indicates the intended partition
–gpus=v100-16:2  requests the use of 2 GPUs on a v100-16 node
-t is the walltime requested in the format HH:MM:SS

Sample job script for the GPU-shared partition

#!/bin/bash
#SBATCH -N 1
#SBATCH -p GPU-shared
#SBATCH -t 5:00:00
#SBATCH --gpus=v100-32:4

#type 'man sbatch' for more information and options
#this job will ask for 4 V100 GPUs on a v100-32 node in GPU-shared for 5 hours
#this job would potentially charge 20 GPU SUs

#echo commands to stdout
set -x

# move to working directory
# this job assumes:
# - all input data is stored in this directory
# - all output should be stored in this directory
# - please note that groupname should be replaced by your groupname
# - username should be replaced by your username
# - path-to-directory should be replaced by the path to your directory where the executable is

cd /ocean/projects/groupname/username/path-to-directory

#run pre-compiled program which is already in your project space

./gpua.out

Summary of partitions for GPU nodes

Running benchmarking jobs

Benchmarking jobs require using one or more entire nodes. Use the RM, RM-512 or GPU partitions to ensure that no other jobs can run on any of the nodes your benchmarking job is using.

Using the DGX-2 for benchmarking

To use the entire DGX-2 node, submit a job to the GPU partition requesting 16 v100-32 GPUs. Use a command like

sbatch -p GPU --gpus=v100-32:16  jobname

Add any other options, like walltime, that you need.  See the section of this User Guide on sbatch options for descriptions of other available options.

Using other GPU nodes for benchmarking

To use the entire GPU node, submit a job to the GPU partition requesting 8 GPUs. Use a command like

sbatch -p GPU --gpus=v100-32:8 jobname

or

sbatch -p GPU --gpus=v100-16:8 jobname

depending on the type of GPU node you need.

Add any other options, like walltime, that you need.  See the section of this User Guide on sbatch options for descriptions of other available options.

Using RM nodes for benchmarking

You can use either the RM or RM-512 partitions for benchmarking.  Use a command like

sbatch -p RM jobname

or

sbatch -p RM-512 jobname

depending on how much memory you need.

Add any other options, like walltime, that you need.  See the section of this User Guide on sbatch options for descriptions of other available options.

Reservations

A Bridges-2 reservation dedicates nodes for your exclusive use for a specified time. So that the entire Bridges-2 community receives the best service possible, reservations are only granted for significant reasons. You will be charged for the entire reservation slot, whether you have jobs running or not.

Things to keep in mind when submitting a reservation request:

• State clearly the reason that you need the reservation.  Requesting a reservation is not a guarantee that you will receive one.
• Submit your request early, at least a week in advance.  It is not always possible to drain the nodes for a reservation on short notice. The nodes may already be busy with jobs that will run for several days.

Use the Bridges-2 Reservation Request form to ask for a reservation.

If your request is approved, you wil get email from PSC User Support with the details of your reservation, including the name of the reservation.

You can see and manage your reservation with these commands:

scontrol show reservation=reservation-name

Displays the details for the named reservation.

scontrol delete reservation=reservation-name

Ends the reservation. This will prevent you from being charged for the remaining time on the reservation.

[user@bridges2-login012 ~]$ scontrol show res=myreservation
ReservationName=myreservation StartTime=2021-08-17T09:10:53 EndTime=2021-08-17T10:10:53 Duration=01:00:00
   Nodes=v007 NodeCnt=1 CoreCnt=40 Features=(null) PartitionName=GPU-shared Flags=
   TRES=cpu=40
   Users=(null) Groups=(null) Accounts=pscstaff Licenses=(null) State=ACTIVE BurstBuffer=(null) Watts=n/a
   MaxStartDelay=(null)

[user@bridges2-login012 ~]$ scontrol delete res=myreservation
[user@bridges2-login012 ~]$ scontrol show res=myreservation
Reservation myreservation not found
[user@bridges2-login012 ~]$

Job status, node, and partition information

slurm-tool

The slurm-tool command can provide information about your running, queued or completed jobs. It can also show the jobs that are running or queued in a partition or give the limits on partitions.

For help on its options, type slurm-tool -h.

[user@bridges2-login011 ~]$ slurm-tool -h

Show or watch job queue:
 slurm-tool [watch] queue     show own jobs
 slurm-tool [watch] q   show user's jobs
 slurm-tool [watch] quick     show quick overview of own jobs
 slurm-tool [watch] shorter   sort and compact entire queue by job size
 slurm-tool [watch] short     sort and compact entire queue by priority
 slurm-tool [watch] full      show everything
 slurm-tool [w] [q|qq|ss|s|f] shorthands for above!

 slurm-tool qos               show job service classes
 slurm-tool top [queue|all]   show summary of active users

Show detailed information about jobs:
 slurm-tool prio [all|short]  show priority components
 slurm-tool j|job      show everything else
 slurm-tool steps      show memory usage of running srun job steps

Show usage and fair-share values from accounting database:
 slurm-tool h|history   show jobs finished since, e.g. "1day" (default)
 slurm-tool shares

Show nodes and resources in the cluster:
 slurm-tool p|partitions      all partitions
 slurm-tool n|nodes           all cluster nodes
 slurm-tool c|cpus            total cpu cores in use
 slurm-tool cpus   cores available to partition, allocated and free
 slurm-tool cpus jobs         cores/memory reserved by running jobs
 slurm-tool cpus queue        cores/memory required by pending jobs
 slurm-tool features          List features and GRES

Other:
 slurm-tool v|version         Print versions of slurm-tool tool and slurm itself

showuserjobs

The showuserjobs command allows you to see current queued and running jobs. It also allows you to see jobs sorted by account.  To get help, type showuserjobs -h.

[user@bridges2-login014 ~]$ showuserjobs -h
Usage: /opt/packages/interact/bin/showuserjobs [-u username] [-a account] [-p partition] [-q QOS] [-A] [-C] [-h]
where:
        -u username: Print only user 
        -a account: Print only jobs in Slurm account 
        -A: Print only ACCT_TOTAL lines
        -C: Print comma separated lines for Excel
        -p partition: Print only jobs in partition 
        -q qos-list: Print only jobs in QOS 
        -r: Print additional job Reason columns
        -h: Print this help information

sinfo

The sinfo command displays information about the state of Bridges-2's nodes. The nodes can have several states:

More information

• sinfo man page

squeue

The squeue command displays information about the jobs in the partitions. Some useful options are:

More information

• squeue man page for a discussion of the codes for job state, for why a job is waiting to run, and more options.

scancel

The scancel command is used to kill a job in a partition, whether it is running or still waiting to run.  Specify the jobid for the job you want to kill.  For example,

scancel 12345

kills job # 12345.

More information

• scancel man page

sacct

The sacct command can be used to display detailed information about jobs. It is especially useful in investigating why one of your jobs failed. The general format of the command is:

sacct -X -j nnnnnn -S MMDDYY --format parameter1,parameter2, ...

• For 'nnnnnn' substitute the jobid of the job you are investigating.
• The date given for the -S option is the date at which sacct begins searching for information about your job.
• The commas between the parameters in the --format option cannot be followed by spaces.

The --format option determines what information to display about a job. Useful parameters are

• JobID
• Partition
• Account - the charge id
• ExitCode - useful in determining why a job failed
• State - useful in determining why a job failed
• Start, End, Elapsed - start, end and elapsed time of the job
• NodeList - list of nodes used in the job
• NNodes - how many nodes the job was allocated
• MaxRSS - how much memory the job used
• AllocCPUs - how many cores the job was allocated

 More information

• sacct man page

job_info

The job_info command provides information on completed jobs.  It will display cores and memory allocated and SUs charged for the job.  Options to job_info can be used to get additional information, like the exit code, number of nodes allocated, and more.

Options for sinfo are:

-slurm, adds all slurm info for the job level as sacct output
--steps, adds all slurm info for the job and all job steps (this can be a LOT of output)

[joeuser@br012 ~]$ /opt/packages/allocations/bin/job_info 5149_24
CoresAllocated: 96
EndTime: 2021-01-06T14:32:00.000Z
GPUsAllocated: 0
JobId: 5149_24
MaxTaskMemory_MB: 1552505.0
MemoryAllocated_MB: 4128000
Project: abc123
StartTime: 2021-01-06T13:07:14.000Z
State: COMPLETED
SuCharged: 0.0
SuUsed: 135.627
Username: joeuser

Using the -slurm option will provide this output IN ADDTION:

[joeuser@br012 ~]$ /opt/packages/allocations/bin/job_info --slurm 5149_24

*** Slurm SACCT data ***
Account: abc123
AllocCPUS: 96
AllocNodes: 1
AllocTRES: billing=96,cpu=96,mem=4128000M,node=1
AssocID: 234
CPUTime: 5-15:37:36
CPUTimeRAW: 488256
Cluster: bridges2
DBIndex: 10092
DerivedExitCode: 0:0
Elapsed: 01:24:46
ElapsedRaw: 5086
Eligible: 2021-01-06T02:27:34
End: 2021-01-06T14:32:00
ExitCode: 0:0
Flags: SchedMain
GID: 15312
Group: abc123
JobID: 5149_24
JobIDRaw: 5196
JobName: run_velveth_gcc10.2.0_96threads_ocean.sbatch
NCPUS: 96
NNodes: 1
NodeList: e002
Partition: EM
Priority: 4294900776
QOS: lm
QOSRAW: 4
ReqCPUS: 96
ReqMem: 4128000Mn
ReqNodes: 1
ReqTRES: billing=96,cpu=96,node=1
Reserved: 10:39:40
ResvCPU: 42-15:28:00
ResvCPURAW: 3684480
Start: 2021-01-06T13:07:14
State: COMPLETED
Submit: 2021-01-06T02:27:33
Suspended: 00:00:00
SystemCPU: 52:13.643
Timelimit: 06:00:00
TimelimitRaw: 360
TotalCPU: 3-15:06:51
UID: 19178
User: joeuser
UserCPU: 3-14:14:37
WCKeyID: 0
WorkDir: /ocean/projects/abc123/joeuser/velvet

Monitoring memory usage

It can be useful to find the memory usage of your jobs. For example, you may want to find out if memory usage was a reason a job failed.

You can determine a job's memory usage whether it is still running or has finished. To determine if your job is still running, use the squeue command.

squeue -j nnnnnn -O state

where nnnnnn is the jobid.

For running jobs: srun and top or sstat

You can use the srun and top commands to determine the amount of memory being used.

srun --jobid=nnnnnn top -b -n 1 | grep userid

For nnnnnn substitute the jobid of your job. For 'userid' substitute your userid. The RES field in the output from top shows the actual amount of memory used by a process. The top man page can be used to identify the fields in the output of the top command.

• See the man pages for srun and top for more information.

You can also use the sstat command to determine the amount of memory being used in a running job

sstat -j nnnnnn.batch --format=JobID,MaxRss

where nnnnnn is your jobid.

More information

See the man page for sstat for more information.

For jobs that are finished: sacct or job_info

If you are checking within a day or two after your job has finished you can issue the command

sacct -j nnnnnn --format=JobID,MaxRss

If this command no longer shows a value for MaxRss, use the job_info command

job_info nnnnnn | grep max_rss

Substitute your jobid for nnnnnn in both of these commands.

• See the man page for sacct for more information.

More information

• Online documentation for SLURM, including man pages for all the SLURM commands

Sample batch scripts

Both sample batch scripts for some popular software packages and sample batch scripts for general use on Bridges-2 are available.

For more information on how to run a job on Bridges-2, what partitions are available, and how to submit a job, see the Running Jobs section of this user guide.

Sample batch scripts for popular software packages

Sample scripts for some popular software packages are available on Bridges-2 in the directory /opt/packages/examples.  There is a subdirectory for each package, which includes the script along with input data that is required and typical output.

See the documentation for a particular package for more information on using it and how to test any sample scripts that may be available.

Sample batch scripts for common types of jobs

Sample Bridges-2 batch scripts for common job types are given below.

Note that in each sample script:

• The bash shell is used, indicated by the first line ‘!#/bin/bash’.  If you use a different shell some Unix commands will be different.
• For username and groupname you must substitute your username and your appropriate Unix group.

Sample scripts are available for

• Jobs for Bridges-2’s RM partition
• Jobs for Bridges-2’s RM-shared partition
• Jobs for Bridges-2’s RM-512 partition
• Jobs for Bridges-2’s EM partition
• Jobs for Bridges-2’s GPU partition
• Jobs for Bridges-2’s GPU-shared partition

Sample batch script for a job in the RM partition

#!/bin/bash
#SBATCH -N 1
#SBATCH -p RM
#SBATCH -t 5:00:00
#SBATCH --ntasks-per-node=128

# type 'man sbatch' for more information and options
# this job will ask for 1 full RM node (128 cores) for 5 hours
# this job would potentially charge 640 RM SUs

#echo commands to stdout
set -x

# move to working directory
# this job assumes:
# - all input data is stored in this directory
# - all output should be stored in this directory
# - please note that groupname should be replaced by your groupname
# - username should be replaced by your username
# - path-to-directory should be replaced by the path to your directory where the executable is

cd /ocean/projects/groupname/username/path-to-directory

# run a pre-compiled program which is already in your project space

./a.out

#!/bin/bash
#SBATCH -N 1
#SBATCH -p EM
#SBATCH -t 5:00:00
#SBATCH -n 96

# type 'man sbatch' for more information and options
# this job will ask for 1 full EM node (96 cores) and 5 hours of runtime
# this job would potentially charge 480 EM SUs

# echo commands to stdout
set -x

# move to working directory
# this job assumes:
# - all input data is stored in this directory
# - all output should be stored in this directory
# - please note that groupname should be replaced by your groupname
# - username should be replaced by your username
# - path-to-directory should be replaced by the path to your directory where the executable is

cd /ocean/projects/groupname/username/path-to-directory

#run pre-compiled program which is already in your project space

./a.out

#!/bin/bash
#SBATCH -N 1
#SBATCH -p GPU
#SBATCH -t 5:00:00
#SBATCH --gpus=v100-32:8

#type 'man sbatch' for more information and options
#this job will ask for 1 full v100-32 GPU node(8 V100 GPUs) for 5 hours
#this job would potentially charge 40 GPU SUs

#echo commands to stdout
set -x

# move to working directory
# this job assumes:
# - all input data is stored in this directory
# - all output should be stored in this directory
# - please note that groupname should be replaced by your groupname
# - username should be replaced by your username
# - path-to-directory should be replaced by the path to your directory where the executable is

cd /ocean/projects/groupname/username/path-to-directory

#run pre-compiled program which is already in your project space

./gpua.out

#!/bin/bash
#SBATCH -N 1
#SBATCH -p GPU-shared
#SBATCH -t 5:00:00
#SBATCH --gpus=v100-32:4

#type 'man sbatch' for more information and options
#this job will ask for 4 V100 GPUs on a v100-32 node in GPU-shared for 5 hours
#this job would potentially charge 20 GPU SUs

#echo commands to stdout
set -x

# move to working directory
# this job assumes:
# - all input data is stored in this directory
# - all output should be stored in this directory
# - please note that groupname should be replaced by your groupname
# - username should be replaced by your username
# - path-to-directory should be replaced by the path to your directory where the executable is

cd /ocean/projects/groupname/username/path-to-directory

#run pre-compiled program which is already in your project space

./gpua.out

OnDemand

The OnDemand interface allows you to conduct your research on Bridges-2 through a web browser. You can manage files – create, edit and move them – submit and track jobs, see job output, check the status of the queues, run a Jupyter notebook through JupyterHub and more, without logging in to Bridges-2 via traditional interfaces.

OnDemand was created by the Ohio Supercomputer Center (OSC). In addition to this document, you can check the extensive documentation for OnDemand created by OSC, including many video tutorials, or email help@psc.edu.

Note
You cannot use OnDemand to submit a job to the EM partition.

Connect  to Bridges-2 using OnDemand

To connect to Bridges-2 via OnDemand, point your browser to https://ondemand.bridges2.psc.edu.

• You will be prompted for a username and password.  Enter your PSC username and password.
• The OnDemand Dashboard will open.  From this page, you can use the menus across the top of the page to manage files and submit jobs to Bridges-2.

To end your OnDemand session, choose Log Out at the top right of the Dashboard window and close your browser.

Manage files

To create, edit or move files, click on the Files menu from the Dashboard window. A dropdown menu will appear, listing all your file spaces on Bridges-2: your home directory and the Ocean directories for each of your Bridges-2 grants.

Choosing one of the file spaces opens the File Explorer in a new browser tab. The files in the selected directory are listed.  No matter which directory you are in, your home directory is displayed in a panel on the left.

There are two sets of buttons in the File Explorer.

Buttons on the top left just below the name of the current directory allow you to View, Edit, Rename, Download, Copy or Paste (after you have moved to a different directory) a file, or you can toggle the file selection with (Un)Select All.

Buttons on the top of the window on the right perform these functions:

Create and edit jobs

You can create new job scripts, edit existing scripts, and submit those scripts to Bridges-2 through OnDemand.

From the top menus in the Dashboard window, choose Jobs > Job Composer. A Job Composer window will open.

There are two tabs at the top: Jobs and Templates.

In the Jobs tab, a listing of your previous jobs is given.

Create a new job script

To create a new job script:

1. Select a template to begin with
2. Edit the job script
3. Edit the job options

Select a template

1. Go to the Jobs tab in the Jobs Composer window. You have been given a default template, named Simple Sequential Job.
2. To create a new job script,  click the blue New Job > From Default Template button in the upper left. You will see a green message at the top of the window, “Job was successfully created”.

At the right of the Jobs window, you will see the Job Details, including the location of the script and the script name (by default, main_job.sh). Under that, you will see the contents of the job script in a section titled Submit Script.

Edit the job script

Edit the job script so that it has the commands and workflow that you need.

If you do not want the default settings for a job, you must include options to change them in the job script. For example, you may need more time or more than one node. For the GPU partitions, you must specify the number of GPUs per node that you want. Use an SBATCH directive in the job script to set these options.

• See the default settings for all partitions
• See how to use SBATCH directives

There are two ways to edit the job script: using the Edit Files button or the Open Editor button. First, go to the Jobs tab in the Jobs Composer window.

Find the blue Edit Files tab at the top of the window

Find the Submit Script section at the bottom right.  Click the blue Open Editor button.

In either case, an Editor window opens. Make the changes you want and click the blue Save button.

After you save the file, the editor window remains open, but if you return to the Jobs Composer window, you will see that the content of  your script has changed.

Edit the job options

In the Jobs tab in the Jobs Composer window, click the blue Job Options button.

The options for the selected job such as name, the job script to run, and the account to run it under are displayed and can be edited. Click Reset to revert any changes you have made. Click Save or Back to return to the job listing (respectively saving or discarding your edits).

Submit jobs to Bridges-2

Select a job in the Jobs tab in the Jobs Composer window. Click the green Submit button to submit the selected job. A message at the top of the window shows whether the job submission was successful or not.  If it is not, you can edit the job script or options and resubmit. When the job submits successfully, the status of the job in the Jobs Composer window will change to Queued or Running. When  the job completes, the status will change to Completed.

Running Jupyter Notebooks through OnDemand

You can run Jupyter Notebooks through OnDemand.

1. Select Interactive Apps > Jupyter Notebook from the top menu in the Dashboard window.
2. In the screen that opens, specify the timelimit, number of nodes, and partition to use. If you have mutiple grants on Bridges2, you can also designate the account to deduct this usage from.
3. Use the Extra Slurm Args field to specify the number of cores or number of GPUs you want.
   • If you will use the RM-shared or EM partition, use the --ntasks-per-node=n flag to indicate that you want to use n cores. Note that there are two hyphens preceding ‘ntasks-per-node’.
   • If you will use one of the GPU partitions, use the --gpus=n flag to indicate that you want to use n GPUs per node. Note that there are two hyphens preceding ‘gpus’.
     See the Running jobs section of this User Guide for more information on Bridges-2 partitions and the options available.
   • Use the Extra Jupyter Args field to pass arguments to your Jupyter notebook.
4. Click the blue Launch button to start your JupyterHub session.  You may have to wait in the queue for resources to be available.
5. When your session starts, click the blue Connect to Jupyter button.  The Dashboard window now displays information about your JupyterHub session including which node it is running on, when it began, and how much time remains. A new window running JupyterHub also opens.  Note the three tabs: Files, Running and Clusters.

   By default you are in the Files tab, and it displays the contents of your Bridges home directory.  You can navigate through your home directory tree.

   Running

   Under the Running tab, you will see listed any notebooks or terminal sessions that you are currently running.

6. Now you can start a Jupyter notebook:
   1. To start a Jupyter notebook which is stored in your home directory space, in the Files tab, click on its name.  A new window running the notebook opens.
   2. To start a Jupyter notebook which is stored in your ocean directory, you must first create a symbolic link to it from your home directory. While in your home directory, use a command like

      ln -s /ocean/projects/yourgroup/youruserid OCEANDIR

      When you enter JuypterHub, you will see the entry OCEANDIR in your list of files under the Files tab. Click on this to be moved to your  directory.

Errors

If you get an “Internal Server Error” when starting a JupyterHub session, you may be over your home directory quota. Check the Details section of the error for a line like:

#<ActionView::Template::Error: Disk quota exceeded @ dir_s_mkdir - /home/joeuser/ondemand/data/sys/dashboard/batch_connect/sys/jupyter_app...............

You can confirm that you are over quota by opening a Bridges-2 shell access window and typing

du -sh

This command shows the amount of storage in your home directory.  Home directory quotas are 10GB. If du -sh shows you are near 10GB, you should delete or move some files out of your home directory.  You can do this in OnDemand in the File Explorer window or in a shell access window.

When you are under quota, you can try starting a JupyterHub session again.

Stopping your JupyterHub session

In the Dashboard window, click the red Delete button.

GPU nodes

Bridges-2’s GPU nodes provide substantial, complementary computational power for deep learning, simulations and other applications.

A standard NVIDIA accelerator environment is installed on  Bridges-2’s GPU nodes. If you have programmed using GPUs before, you should find this familiar. Please contact help@psc.edu for more help.

The GPU nodes on Bridges-2 are available to those with a Bridges-2 “GPU” allocation. You can see which of Bridges-2’s resources that you have been allocated with the projects command. See “The projects command” section in the Account Administration section of this User Guide for more information.

Hardware description

See the System configuration section of this User Guide for hardware details for all GPU node types.  Bridges’ GPU-AI resources have been migrated to Bridges-2, adding the DGX-2 and nine more V100 GPU nodes to Bridges-2’s GPU resources.

File systems

The $HOME (/jet/home) and Ocean file systems are available on all of these nodes.  See the File Spaces section of this User Guide for more information on these file systems.

Compiling and running jobs

After your codes are compiled, use the GPU partition, either in batch or interactively, to run your jobs. See the Running Jobs section of this User Guide for more information on Bridges-2’s partitions and how to run jobs.

CUDA

More information on using CUDA on Bridges-2 can be found in the CUDA document.

To use CUDA, first you must load the CUDA module. To see all versions of CUDA that are available, type:

module avail cuda

Then choose the version that you need and load the module for it.

module load cuda

loads the default CUDA.   To load a different version, use the full module name.

module load cuda/8.0

OpenACC

Our primary GPU programming environment is OpenACC.

The NVIDIA compilers are available on all GPU nodes. To set up the appropriate environment for the NVIDA compilers, use the  module  command:

module load nvhpc

Read more about the module command at PSC.

If you will be using these compilers often, it will be useful to add this command to your shell initialization script.

There are many options available with these compilers. See the online NVIDIA documentation for detailed information.  You may find these basic OpenACC options a good place to start:

nvcc –acc yourcode.c  
nvfortran –acc yourcode.f90

Adding the “-Minfo=accel” flag to the compile command (whether nvfortran, nvcc or nvc++) will provide useful feedback regarding compiler errors or success with your OpenACC commands.

nvfortran -acc -Minfo=accel yourcode.f90

Hybrid MPI/GPU jobs

To run a hybrid MPI/GPU job use the following commands for compiling your program. Use module spider cuda and  module spider openmpi to see what the module versions are.

module load cuda
module load openmpi/version-nvhpc-version  
mpicc -acc yourcode.c

When you execute your program you must first issue the above two module load commands.

Profiling and debugging

For CUDA codes, use the command line profiler nvprof. See the CUDA document for more information.

For OpenACC codes, the environment variables NV_ACC_TIME, NV_ACC_NOTIFY and NV_ACC_DEBUG can provide profiling and debugging information for your job. Specific commands depend on the shell you are using.

Conda best practices

Environments for AI software

PSC has built some environments which provide a rich, unified, Anaconda-based environment for AI, Machine Learning, and Big Data applications. Each environment includes several popular AI/ML/BD packages, selected to work together well.

The AI environments are built for the GPU nodes on Bridges-2. Be sure to use one of the GPU partitions. See the Bridges-2 User  Guide for information on Bridges-2 partitions and how to choose one to use.

See also:

• the python documentation, for a description of the ways to use python on Bridges-2
• the Anaconda modules, for information on creating, editing and storing anaconda environments on Bridges-2

Using the AI environments on Bridges-2

Typing module spider AI will list the available AI environments.

module spider AI

----------------------------------------------------------------------------
  AI:
----------------------------------------------------------------------------
    Description:
      TensorFlow 2.10.0 AI development environment

     Versions:
        AI/anaconda2-tf1.2019.10
        AI/anaconda3-tf1.2020.11
        AI/anaconda3-tf2.2020.11
        AI/pytorch_22.07-1.12-py3
        AI/pytorch_23.02-1.13.1-py3
        AI/tensorflow_22.07-2.8-py3
        AI/tensorflow_23.02-2.10.0-py3

Note that AI/anaconda2 environments use python2, while AI/anaconda3 environments use python3.

For additional help, type module help AI/package-version.

 module help AI/tensorflow_23.02-2.10.0-py3

---------- Module Specific Help for "AI/tensorflow_23.02-2.10.0-py3" -----------
TensorFlow 2.10.0
-----------------------------

Description
-----------
The modulefile AI/tensorflow_23.02-2.10.0-py3 provides a TensorFlow 2.10.0 devel
opment environment for Artificial Intelligence(AI)/Machine Learning(ML)/Big Data
(BD) on top of Python 3.

Module contents
---------------
Several popular libraries are included in this environment, such as:
    bokeh, matplotlib, mkl, numba, numpy, pandas, pillow, scikit-learn, theano,
tensorflow.

To check the full list of available packages in this environment, first activate
 it and then run the command
    conda list

* bokeh                     3.0.3
* cudnn                     8.2.1
.
.
.

See what the PSC defined AI environment contains

To see the full list of software included in a given environment, first load the module and activate the environment. Then type

conda list

Customize the PSC defined AI environment

If you need software that is not in the pre-built environment, you can create a new environment by cloning the PSC defined one and then customizing it. First load the module and activate the PSC defined environment, as above, then  clone it with

conda create --name your-new-environment-name --clone $AI_ENV

Then you can activate the new environment and proceed with your customization.

Example

In this example, the user installs the h5py package in a new environment they are creating. Use the following commands.

Note:

• The conda list command shows what packages are currently installed. Check to see if what you need is already available.  The conda list command also shows the version number of the installed packages.
• The conda create command clones $AI_ENV to create a new environment.  This can take a long time, so ask for an hour of time with the interact command.
• Here, the new environment is named clone-env-1, and is stored in the user's ocean directory.  The --prefix flag names the full path to the where the environment will be stored. You can name the environment anything you like and store it in any directory you like.

interact -gpu -t 01:00:00
 module load AI    # loads the default AI module
 source activate $AI_ENV
 conda list 
 conda create --name clone-env-1 --clone $AI_ENV
 conda activate clone-env-1
 conda install h5py

The conda install command will install the newest version of the package. If you want to install a version of the package not available in the public installations use the --revision option to the conda install command.

Containers

Containers are stand-alone packages holding the software needed to create a very specific computing environment. If you need a very specialized environment, you can create  your own container or use one that is already installed on Bridges-2. Singularity is the only type of container supported on  Bridges-2.

Creating a container

Singularity is the only container software supported on Bridges-2. You can create a Singularity container, copy it to Bridges-2 and then execute your container on Bridges-2, where it can use Bridges-2’s compute nodes and filesystems. In your container you can use any software required by your application: a different version of CentOS,  a different Unix operating system, any software in any specific version needed. You can install your Singularity container without any intervention from PSC staff.

See the PSC documentation on Singularity for more details on producing your own container and Singularity use on Bridges-2.

However, Bridges-2 may have all the software you will need.  Before creating a container for your work, check the extensive list of software that has been installed on Bridges-2.   While logged in to Bridges-2, you can also get a list of installed packages by typing

module avail

If you need a package that is not available on Bridges-2 you can request that it be installed by emailing help@psc.edu.  You can also install software packages in your own file spaces and, in some cases, we can provide assistance if you encounter difficulties.

Publicly available containers on Bridges-2

We have installed many containers from the NVIDIA GPU Cloud (NGC) on Bridges-2. These containers are fully optimized, GPU-accelerated environments for AI, machine learning and HPC. They can only be used on the Bridges-2 GPU nodes.

These include containers for:

• Caffe and Caffe2
• Microsoft Cognitive Toolkit
• DIGITS
• Inference Server
• MATLAB
• MXNet
• PyTorch
• Tensorflow
• TensorRT
• Theano
• Torch

See the PSC documentation on Singularity for more details on Singularity use on Bridges-2.

Public datasets

A community dataset space allows Bridges-2 users from different grants to share data in a common space. Bridges-2 hosts both community (public) and private datasets, providing rapid access for individuals, collaborations and communities with appropriate protections.

You can ask that PSC install a community dataset on Bridges-2 by submitting the Community Dataset Request form.

These datasets are available to anyone with a Bridges-2 account:

2019nCoVR: 2019 Novel Coronavirus Resource

The 2019 Novel Coronavirus Resource concerns the outbreak of novel coronavirus in Wuhan, China since December 2019. For more details about the statistics, metadata, publications, and visualizations of the data, please visit https://ngdc.cncb.ac.cn/ncov/.

Available on Bridges-2 at /ocean/datasets/community/genomics/2019nCoVR.

AlphaFold

The AlphaFold protein structure database contains over 990,00 protein structure predictions for the human proteome and other key proteins of interest. For more information, see https://alphafold.ebi.ac.uk/.

Available on Bridges-2 at /ocean/datasets/community/alphafold.

CIFAR-10

The CIFAR-10 dataset is a subset of the 8 million tiny images dataset, which contains 60,000 images in ten classes. See https://www.cs.toronto.edu/~kriz/cifar.html for more details.

Available on Bridges-2 at /ocean/datasets/community/cifar.

COCO

COCO (Common Objects in Context) is a large scale image dataset designed for object detection, segmentation, person keypoints detection, stuff segmentation, and caption generation. Please visit http://cocodataset.org/ for more information on COCO, including details about the data, paper, and tutorials.

Available on Bridges-2 at /ocean/datasets/community/COCO.

CosmoFlow

CosmoFlow consists of data from around 10,000 cosmological N-body dark matter simulations.  Anyone with a Bridges-2 grant can use CosmoFlow data, but you must request access via the CosmoFlow request form. 

Please visit the CosmoFlow site at https://portal.nersc.gov/project/m3363/ for more information about this dataset.

Available on Bridges-2 at /ocean/datasets/community/cosmoflow.

ImageNet

ImageNet is an image dataset organized according to WordNet hierarchy. See the ImageNet website for complete information.

Available on Bridges-2 at /ocean/datasets/community/imagenet.

MNIST

Dataset of handwritten digits used to train image processing systems.

Available on Bridges-2 at /ocean/datasets/community/mnist.

Natural Languge Tool Kit Data

NLTK comes with many corpora, toy grammars, trained models, etc. A complete list of the available data is posted at: http://nltk.org/nltk_data/.

Available on Bridges-2 at /ocean/datasets/community/nltk.

OpenWebText

Available on Bridges-2 at  /ocean/datasets/community/openwebtext.

PREVENT-AD

The PREVENT-AD (Pre-symptomatic Evaluation of Experimental or Novel Treatments for Alzheimer Disease) cohort is composed of cognitively healthy participants over 55 years old, at risk of developing Alzheimer Disease (AD) as their parents and/or siblings were/are affected by the disease. These ‘at-risk’ participants have been followed for a naturalistic study of the presymptomatic phase of AD since 2011 using multimodal measurements of various disease indicators. Two clinical trials intended to test pharmaco-preventive agents have also been conducted. The PREVENT-AD research group is now releasing data openly with the intention to contribute to the community’s growing understanding of AD pathogenesis.

Available on Bridges-2 at /ocean/datasets/community/prevent_ad.

TCGA Images

Available on Bridges-2 at /ocean/datasets/community/tcga_images.

Genomics datasets

These datasets  are available to anyone with a Bridges-2 allocation. They are stored under /ocean/datasets/community/genomics.

Gateways

Bridges-2 hosts a number of gateways – web-based, domain-specific user interfaces to applications, functionality and resources that allow users to focus on their research rather than programming and submitting jobs. Gateways  provide intuitive, easy-to-use interfaces to complex functionality and data-intensive workflows.

Gateways can manage large numbers of jobs and provide collaborative features, security constraints and provenance tracking, so that you can concentrate on your analyses instead of on the mechanics of accomplishing them.