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Getting Started (Web-based)

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1. Get Duo

You must use Duo authentication to log on to the Beta OnDemand web service.  Get more details on the Safe Computing Two-Factor page and enroll here.

2. Get a Flux user login

All Flux users have access to Beta.  You must establish an account on Flux by filling out this form.

3. Connect to Beta OnDemand

You must be on campus or on the VPN to connect to Beta OnDemand.  If you are trying to log in from off campus or using an unauthenticated wireless network such as MGuest, you have a couple of options:

Once you are on the University network, follow these instructions to connect:

  1. Open your web browser (Firefox, Edge, or Chrome in incognito recommended) and navigate to lighthouse.arc-ts.umich.edu
  2. Log into cosign using your uniqname and password:
  3. Complete Duo authentication: 
  4. You should now be logged in.

4. Get files

At the top of the page, click “Files” and then “Home Directory”.  A new tab will be created that contains the File Explorer: 

Here you can navigate your home folder.  The buttons do the following:

  • “Go To…”: Navigate to a specified folder
  • “Open in Terminal”: Opens the active folder in a terminal session (new tab)
  • “New File”: Creates a new file in the active folder
  • “New Dir”: Creates a new folder in the active folder
  • “Upload”: Select files from your local machine to upload to the active folder
  • “Show Dotfiles”: Reveals hidden files (usually do not need to be changed)
  • “Show Owner/Mode”: Shows ownership and permission information
  • “View”: Shows file contents inside the current tab
  • “Edit”: Opens a file editor in a new tab
  • “Rename/Move”: Gives a file a new path and/or name
  • “Download”: Downloads the file or folder to your local machine
  • “Copy”: Copies selected files to the clipboard
  • “Paste”: Pastes files from the clipboard
  • “(Un)Select All”: Select or unselect all files/folders
  • “Delete”: Deletes selected files/folders

5. Submit a job

At the top of the home page, click “Jobs” and then “Job Composer”.  A new tab will be created that contains the Job Composer: 

Upon your first visit to this page, you’ll go through a helpful tutorial.  The buttons do the following:

  • “New Job”: Creates a new job…
    • “From Default Template”: Uses system defaults for a bare bones “Hello World” job on the Beta cluster.  Please note that you will still need to specify your account.
    • “From Specified Path”: Creates a job from a specified job script.  See the Slurm User Guide for Beta for information on writing this script.  Some attributes (name, account) can be set here if not set in the script.
    • “From Selected Job”: Creates a new job that is a copy of the selected job.
  • “Edit Files”: Opens a the project folder in a new File Explorer tab, allowing you to edit the files within (see “Get Files” above for File Explorer instructions).
  • “Job Options”: Allows for editing the Name, Cluster, Job Script, and Account fields.
  • “Open Terminal”: Opens a terminal session in a new tab, starting in the project folder.
  • “Submit”: Submits the selected job to the cluster.
  • “Stop”: Stops the selected job if it has been submitted.
  • “Delete”: Delete the selected job.

To view active job information, click “Jobs” and then “Active Jobs” from the home page.

This is a simple guide to get your jobs up and running. For more advanced Slurm features and job scripting information, see the Slurm User Guide for Beta. If you are familiar with using the resource manager Torque, you may find the migrating from Torque to Slurm guide useful.

Interactive Apps

At the top of the home page, click “Interactive Apps” and then select your desired application.

Beta Remote Desktop

Launches an interactive desktop in a new tab (uses noVNC).  Specify your account, hours, memory, cores, and partition:

Upon selecting “Launch”, your job will be queued on one of your nodes and shown on the “My Interactive Sessions” screen. As soon as the job’s status is “Running”, you can click on “Launch noVNC in New Tab”:

A remote desktop session will then be opened in a new tab for the requested amount of time.  If you finish early, return to the “My Interactive Sessions” tab and delete the job.

MATLAB

Launches an interactive desktop with MATLAB configured and running in a new tab (uses noVNC).  Specify your desired version, account, hours, and memory (4GB minimum):

Upon selecting “Launch”, your job will be queued on one of your nodes and shown on the “My Interactive Sessions” screen. As soon as the job’s status is “Running”, you can click on “Launch noVNC in New Tab”:

A remote desktop session running MATLAB will then be opened in a new tab for the requested amount of time. You may also use the terminal and other basic applications. If you finish early, return to the “My Interactive Sessions” tab and delete the job.

Jupyter Notebook Server

Launches a Jupyter Notebook Server in a new tab. Specify your desired version, project name, hours, memory, cores, runtime directory, and partition (usually your PI’s uniqname):

Upon selecting “Launch”, your job will be queued on one of your nodes and shown on the “My Interactive Sessions” screen. As soon as the job’s status is “Running”, you can click on “Connect to Jupyter”:

For instructions on using Jupyter Notebook, see the official documentation.

Policies

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Terms of Usage and User Responsibility

  1. Data is not backed up. None of the data on Beta is backed up. The data that you keep in your home directory, /tmp or any other filesystem is exposed to immediate and permanent loss at all times. You are responsible for mitigating your own risk. ARC-TS provides more durable storage on Turbo, Locker, and Data Den.  For more information on these, look here.
  2. Your usage is tracked and may be used for reports. We track a lot of job data and store it for a long time. We use this data to generate usage reports and look at patterns and trends. We may report this data, including your individual data, to your adviser, department head, dean, or other administrator or supervisor.
  3. Maintaining the overall stability of the system is paramount to us. While we make every effort to ensure that every job completes with the most efficient and accurate way possible, the stability of the cluster is our primary concern. This may affect you, but mostly we hope it benefits you. System availability is based on our best efforts. We are staffed to provide support during normal business hours. We try very hard to provide support as broadly as possible, but cannot guarantee support on a 24 hours a day basis. Additionally, we perform system maintenance on a periodic basis, driven by the availability of software updates, staffing availability, and input from the user community. We do our best to schedule around your needs, but there will be times when the system is unavailable. For scheduled outages, we will announce them at least one month in advance on the ARC-TS home page; for unscheduled outages we will announce them as quickly as we can with as much detail as we have on that same page. You can also track ARC-TS on Twitter (@ARC-TS ).
  4. Beta is intended only for non-commercial, academic research and instruction. Commercial use of some of the software on Beta is prohibited by software licensing terms. Prohibited uses include product development or validation, any service for which a fee is charged, and, in some cases, research involving proprietary data that will not be made available publicly. Please contact hpc-support@umich.edu if you have any questions about this policy, or about whether your work may violate these terms.
  5. You are responsible for the security of sensitive codes and data. If you will be storing export-controlled or other sensitive or secure software, libraries, or data on the cluster, it is your responsibility that is is secured to the standards set by the most restrictive governing rules.  We cannot reasonably monitor everything that is installed on the cluster, and cannot be responsible for it, leaving the responsibility with you, the end user.
  6. Data subject to HIPAA regulations may not be stored or processed on the cluster.

USER RESPONSIBILITIES

Users must manage data appropriately in their various locations:

  • /home
  • /scratch
  • /tmp and /var/tmp
  • customer-provided NFS

SECURITY ON BETA / USE OF SENSITIVE DATA

The Beta high-performance computing system at the University of Michigan has been built to provide a preview of the Great Lakes HPC cluster. Beta has the same security stance as the Flux cluster.

Applications and data are protected by secure physical facilities and infrastructure as well as a variety of network and security monitoring systems. These systems provide basic but important security measures including:

  • Secure access – All access to Beta is via ssh or Globus. Ssh has a long history of high-security.
  • Built-in firewalls – All of the Beta computers have firewalls that restrict access to only what is needed.
  • Unique users – Beta adheres to the University guideline of one person per login ID and one login ID per person.
  • Multi-factor authentication (MFA) – For all interactive sessions, Beta requires both a UM Kerberos password and Duo authentication. File transfer sessions require a Kerberos password.
  • Private Subnets – Other than the login and file transfer computers that are part of Beta, all of the computers are on a network that is private within the University network and are unreachable from the Internet.
  • Flexible data storage – Researchers can control the security of their own data storage by securing their storage as they require and having it mounted via NFSv3 or NFSv4 on Beta. Another option is to make use of Beta’s local scratch storage, which is considered secure for many types of data. Note: Beta is not considered secure for data covered by HIPAA.

Software

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Software modules

The Beta cluster uses the Lmod modules system to provide access to centrally installed software. If you used a cluster at UM previously, then you should review the documentation for the module system as we have changed the configuration to match that used at most national clusters and most other university clusters.

In particular, you should use the command module keyword to look for a module and do not use module available to search for software, as module available will only show software for which all the dependencies (or prerequisites) are already loaded.

So, to search for the software package FFTW, use

$ module keyword fftw

That will show which versions are installed and provide a command to determine what is needed to load it.

Please see our page on using the Lmod modules system for more details and examples.

There are two main categories of software available on the system: software that is installed as part of the installation of the operating system and software that is installed separately. No special action is needed to use the software installed with the operating system. The separately installed software is set up so that you will use a module to use it. The module will set up the environment and make the software available. We do it this way to enable having multiple versions of the same package and to avoid having conflicts between software packages that have mutually exclusive system requirements.

Requesting software licenses

Many of the software packages that are licensed for use on ARC clusters are licensed for a limited number of concurrent uses. If you will use one of those packages, then you must request a license or licenses in your submission script. As an example, to request one Stata license, you would use

#SBATCH --licenses=stata@slurmdb:1

The list of software can be found from Beta by using the command

$ scontrol show licenses

Getting Started (Command Line)

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1. Get Duo

You must use Duo authentication to log on to Beta.  Get more details on the Safe Computing Two-Factor page and enroll here.

2. Get a Flux user account

All Flux users have access to Beta.  You must establish an account on Flux by filling out this form.

3. Get an SSH Client & Connect to Beta

You must be on campus or on the VPN to connect to Beta.  If you are trying to log in from off campus, or using an unauthenticated wireless network such as MGuest, you have a couple of options:

Mac or Linux:

Open Terminal and type:

ssh uniqname@beta.arc-ts.umich.edu

Windows (using PuTTY):

Download and install PuTTY here.

Launch PuTTY and enter beta.arc-ts.umich.edu as the host name, then click open.

All Operating Systems:

At the “Enter a passcode or select one of the following options:” prompt, type the number of your preferred choice for Duo authentication.

4. Get files

You can use SFTP (best for simple transfers of small files) or Globus (best for large files or a commonly used endpoint) to transfer data to your /home directory.

SFTP: Mac or Windows using FileZilla
  1. Open FileZilla and click the “Site Manager” button
  2. Create a New Site, which you can name “Beta” or something similar
  3. Select the “SFTP (SSH File Transfer Protocol)” option
  4. In the Host field, type beta.arc-ts.umich.edu
  5. Select “Interactive” for Logon Type
  6. In the User field, type your uniqname
  7. Click “Connect”
  8. Enter your Kerberos password
  9. Select your Duo method (1-3) and complete authentication
  10. Drag and drop files between the two systems
  11. Click “Disconnect” when finished

On Windows, you can also use WinSCP with similar settings, available alongside PuTTY here.

SFTP: Mac or Linux using Terminal

To copy a single file, type:

scp localfile uniqname@beta.arc-ts.umich.edu:~/remotefile

To copy an entire directory, type:

scp -r localdir uniqname@beta.arc-ts.umich.edu:~/remotedir

These commands can also be reversed in order to copy files from Beta to your machine:

scp -r uniqname@beta.arc-ts.umich.edu:~/remotedir localdir

You will need to authenticate via Duo to complete the file transfer.

Globus: Windows, Mac, or Linux

Globus is a reliable high performance parallel file transfer service provided by many HPC sites around the world. It enables easy transfer of files from one system to another, as long as they are Globus endpoints.

  • The Globus endpoint for Beta is “umich#beta”.
How to use Globus

Globus Online is a web front end to the Globus transfer service. Globus Online accounts are free and you can create an account with your University identity.

  • Set up your Globus account and learn how to transfer files using the Globus documentation.  Select “University of Michigan” from the dropdown box to get started.
  • Once you are ready to transfer files, enter “umich#beta” as one of your endpoints.
Globus Connect Personal

Globus Online also allows for simple installation of a Globus endpoint for Windows, Mac, and Linux desktops and laptops.

  • Follow the Globus instructions to download the Globus Connect Personal installer and set up an endpoint on your desktop or laptop.
Batch File Copies

A non-standard use of Globus Online is that you can use it to copy files from one location to another on the same cluster. To do this use the same endpoint (umich#beta as an example) for both the sending and receiving machines. Setup the transfer and Globus will make sure the rest happens. The service will email you when the copy is finished.

Command Line Globus

There are Command line tools for Globus that are intended for advanced users. If you wish to use these, contact HPC support.

5. Submit a job

This is a simple guide to get your jobs up and running. For more advanced Slurm features, see the Slurm User Guide for Beta. If you are familiar with using the resource manager Torque, you may find the migrating from Torque to Slurm guide useful.

Batch Jobs

Most work will be queued to be run on Beta and is described through a batch script. The sbatch command is used to submit a batch script to Slurm. To submit a batch script simply run the following from a shared file system; those include your home directory, /scratch, and any directory under /nfs that you can normally use in a job on Flux. Output will be sent to this working directory (jobName-jobID.log). Do not submit jobs from /tmp or any of its subdirectories.

$ sbatch myJob.sh

The batch job script is composed of three main components:

  • The interpreter used to execute the script
  • #SBATCH directives that convey submission options
  • The application(s) to execute along with its input arguments and options

Example:

#!/bin/bash
# The interpreter used to execute the script

#“#SBATCH” directives that convey submission options:

#SBATCH --job-name=example_job
#SBATCH --mail-type=BEGIN,END
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --mem-per-cpu=1000m 
#SBATCH --time=10:00
#SBATCH --account=test
#SBATCH --partition=standard

# The application(s) to execute along with its input arguments and options:

/bin/hostname
sleep 60

How many nodes and processors you request will depend on the capability of your software and what it can do. There are four common scenarios:

Example: One Node, One Processor

This is the simplest case and is shown in the example above. The majority of software cannot use more than this. Some examples of software for which this would be the right configuration are SAS, Stata, R, many Python programs, most Perl programs.

NOTE If you will be using licensed software, for example, Stata, SAS, Abaqus, Ansys, etc., then you may need to request licenses. See below table of common submission options for the syntax; in the Software section, we show the command to see which software requires you to request a license.

#!/bin/bash
#SBATCH --job-name JOBNAME
#SBATCH --nodes=1
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=1g
#SBATCH --time=00:15:00
#SBATCH --account=test
#SBATCH --partition=standard
#SBATCH --mail-type=NONE

srun hostname -s

Example: One Node, Multiple Processors

This is similar to what a modern desktop or laptop is likely to have. Software that can use more than one processor may be described as multicore, multiprocessor, or mulithreaded. Some examples of software that can benefit from this are MATLAB and Stata/MP. You should read the documentation for your software to see if this is one of its capabilities.

#!/bin/bash
#SBATCH --job-name JOBNAME
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=4
#SBATCH --mem-per-cpu=1g
#SBATCH --time=00:15:00
#SBATCH --account=test
#SBATCH --partition=standard
#SBATCH --mail-type=NONE

srun hostname -s

Example: Multiple Nodes, One Process per CPU

This is the classic MPI approach, where multiple machines are requested, one process per processor on each node is started using MPI. This is the way most MPI-enabled software is written to work.

#!/bin/bash
#SBATCH --job-name JOBNAME
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=4
#SBATCH --mem-per-cpu=1g
#SBATCH --time=00:15:00
#SBATCH --account=test
#SBATCH --partition=standard
#SBATCH --mail-type=NONE

srun hostname -s

Example: Multiple Nodes, Multiple CPUs per Process

This is often referred to as the “hybrid mode” MPI approach, where multiple machines are requested and multiple processes are requested. MPI will start a parent process or processes on each node, and those in turn will be able to use more than one processor for threaded calculations.

#!/bin/bash
#SBATCH --job-name JOBNAME
#SBATCH --nodes=2
#SBATCH --ntasks-per-node=4
#SBATCH --cpus-per-task=4
#SBATCH --mem-per-cpu=1g
#SBATCH --time=00:15:00
#SBATCH --account=test
#SBATCH --partition=standard
#SBATCH --mail-type=NONE

srun hostname -s
Common Job Submission Options
Description Slurm directive (#SBATCH option) Beta Usage
Job name --job-name=<name> --job-name=betajob1
Account --account=<account> --account=test
Queue --partition=<partion_name> --partition=standard

Available partitions: standard, gpu (GPU jobs only), largemem (large memory jobs only), debug

Wall time limit --time=<hh:mm:ss> --time=02:00:00

(default is 15 minutes if not specified)

Node count --nodes=<count> --nodes=2
Process count per node --ntasks-per-node=<count> --ntasks-per-node=1
Minimum memory per processor --mem-per-cpu=<memory> --mem-per-cpu=1000m
Request software license(s) --licenses=<application>@slurmdb:<N> --licenses=stata@slurmdb:1
requests one license for Stata
Request event notification

--mail-type=<events>

Note: multiple mail-type requests may be specified in a comma separated list:

--mail-type=BEGIN,END,NONE,FAIL,REQUEUE

--mail-type=BEGIN,END,FAIL

Please note that if your job is set to utilize more than one node, make sure your code is MPI enabled in order to run across these nodes and you must use srun rather then mpirun or mpiexec. More advanced job submission options can be found in the Slurm User Guide for Beta.

Interactive Jobs

An interactive job is a job that returns a command line prompt (instead of running a script) when the job runs. Interactive jobs are useful when debugging or interacting with an application. The srun command is used to submit an interactive job to Slurm. When the job starts, a command line prompt will appear on one of the compute nodes assigned to the job. From here commands can be executed using the resources allocated on the local node.

[user@beta-login ~]$ srun --account=test --pty /bin/bash 
srun: job 309 queued and waiting for resources 
srun: job 309 has been allocated resources 
[user@bn01 ~]$ hostname 
bn01.stage.arc-ts.umich.edu 
[user@bn01 ~]$

Jobs submitted with srun –-pty /bin/bash will be assigned the cluster default values of 1 CPU, 1024MB of memory, and 15 minutes of walltime. If additional resources are required, they can be requested as options to the srun command. The following example job is assigned 2 nodes with 4 CPUS and 4GB of memory each:

[user@beta-login ~]$ srun --account=test --time=00:15:00 --nodes=2 --ntasks-per-node=4 --mem-per-cpu=1GB --pty /bin/bash
srun: job 894 queued and waiting for resources
srun: job 894 has been allocated resources
[user@bn01 ~]$ srun hostname
bn01.stage.arc-ts.umich.edu
bn02.stage.arc-ts.umich.edu
bn01.stage.arc-ts.umich.edu
bn01.stage.arc-ts.umich.edu
bn01.stage.arc-ts.umich.edu
bn02.stage.arc-ts.umich.edu
bn02.stage.arc-ts.umich.edu
bn02.stage.arc-ts.umich.edu

In the above example srun is used within the job from the first compute node to run a command once for every task in the job on the assigned resources. srun can be used to run on a subset of the resources assigned to the job. See the srun man page for more details.

GPU and Large Memory Jobs

Jobs can request GPUs with the job submission options --partition=gpu and --gres=gpu:<count>. GPUs can be requested in both Batch and Interactive jobs.

Similarly, jobs can request nodes with large amounts of RAM with --partition=largemem.  The largemem (and debug) partition’s nodes on Beta have the same configuration as standard nodes, so this partition is just for testing.  Great Lakes will have high-RAM nodes on this partition.

Job Status

Most of a job’s specifications can be seen by invoking scontrol show job <jobID>.  More details about the job can be written to a file by using  scontrol write batch_script <jobID> output.txt. If no output file is specified, the script will be written to slurm<jobID>.sh.

A job’s record remains in Slurm’s memory for 30 minutes after it completes.  scontrol show job will return “Invalid job id specified” for a job that completed more than 30 minutes ago.  At that point, one must invoke the sacct command to retrieve the job’s record from the Slurm database.

To view TRES (Trackable RESource) utilization by user or account, use the following commands (substitute your values for bolded parts):

Shows TRES usage by all users on account during date range:
sreport cluster UserUtilizationByAccount start=mm/dd/yy end=mm/dd/yy account=test --tres type
Shows TRES usage by specified user(s) on account during date range:
sreport cluster UserUtilizationByAccount start=mm/dd/yy end=mm/dd/yy users=un1,un2 account=test --tres type
Lists users alphabetically along with TRES usage and total during date range:
sreport cluster AccountUtilizationByUser start=mm/dd/yy end=mm/dd/yy tree account=test --tres type
Possible TRES types:

cpu
mem
node
gres/gpu

For more reporting options, see the Slurm sreport documentation.

System Overview

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Beta is a preview cluster that allows users to become familiar with SchedMD’s Slurm Workload Manager, which will be used in our upcoming Great Lakes cluster. All standard compute nodes in the Beta cluster have 16 core Intel(R) Xeon(R) CPU E5-2670 processors at 2.60GHz and 64GB memory. There is one GPU node with 8 K20x GPUs.  Beta will leverage some existing infrastructure (minimal software via modules, storage, etc).