Using Armis2, HIPAA-aligned storage

Armis2 Cluster Defaults

Armis2 Partition Limits

1. Get Duo

You must use Duo authentication to log on to the Armis2 OnDemand web service.  Get more details on the Safe Computing Two-Factor page and enroll here.

2. Get a Armis2 user login

You must establish a user login on Armis2 by filling out this form.

3. Connect to Armis2 OnDemand

You must be on campus or on the VPN to connect to Armis2 OnDemand.  If you are trying to log in from off campus or using an unauthenticated wireless network such as MGuest, you should install VPN software on your computer.

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:
   armis2.arc-ts.umich.edu
2. Log into cosign using your uniqname and password:
3. Complete Duo authentication: 
4. You should now be logged in.

If you receive a “Bad Request: Your browser sent a request that this server could not understand. Size of request header field exceeds server limit.” error, please clear your browser’s cookies and try to access Great Lakes OnDemand again.

This error can occur when the request header sent by the browser becomes too large. This is typically caused by accumulated cookies and cached data for a specific site; in some cases, corrupted cookies can also contribute to the problem.

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 Armis2 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 Armis2 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 Armis2. 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.

1. Get DUO

DUO two-factor authentication is required to access the majority of U-M services and all HPC services. If you need to set up DUO, visit the DUO page on the Safe Computing site for instructions to get started.

2. Get an Armis2 user login

You must establish user login on Armis2 by filling out this login request form. If you had a login on Armis, you should have one on Armis2.

3. Get an SSH Client & Connect to Armis2 Login Node

The login node (armis2.arc-ts.umich.edu) is the entry point into the cluster. It is accessible from the Ann Arbor, Dearborn, and Flint campus IP addresses and from the U-M VPN network only and require a valid user account and Duo authentication to log in. They are a shared resource and, as such, it is expected that users do not monopolize them.

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:

• Install VPN software on your computer
• SSH to login.itd.umich.edu and continue with the Linux instructions

See the policies below governing appropriate use of the login nodes.

Mac or Linux:

Open Terminal and type:

ssh uniqname@armis2.arc-ts.umich.edu

You will be required to enter your UMICH (Level-1) password to log in. Please note that as you type your password, nothing you type will appear on the screen; this is completely normal. Press “Enter/Return” key once you are done typing your password.

When you’re connecting for the first time, it’s not uncommon to see a message like this one:

The authenticity of host 'armis2-login1.arc-ts.umich.edu (141.211.19.11)' can't be established.
RSA key fingerprint is 6f:8c:67:df:43:4f:e0:fc:80:5b:49:1a:eb:81:cc:54.
Are you sure you want to continue connecting (yes/no)?

This is normal. By saying “yes” you’re accepting the public SSH key for the system. This key will be stored in a local known_hosts file on your system so you won’t be prompted in the future. The keys from Armis2 will NOT change. So, for example, if you get a new computer and SSH to Armis2, you’ll be prompted to add the key again.

We encourage you to compare the fingerprint you’re presented with, when connecting for the first time, to one of the fingerprints below. The format of the fingerprint you’re presented could be dictated by the SSH client on your machine.

In the example message given above, we are presented with the RSA key fingerprint and its MD5 value, which is the same value as in the above table.

If you’re NOT seeing one of these fingerprints, submit a ticket to arcts-support@umich.edu and do NOT connect to the server via SSH until discussing with an ARC staff member to determine if there is a security issue.

To avoid being prompted to accept the key on a new system you may choose to pre-populate your SSH known_hosts file with the pub keys from Armis2. The keys can be found in the FAQ.

Windows (using PuTTY)

Download and install PuTTY.

Launch PuTTY and enter armis2.arc-ts.umich.edu as the host name, then click open.

If you receive a “PuTTY Security Alert” pop-up, this is completely normal, click the “Yes” option. This will tell PuTTY to trust the host the next time you want to connect to it. From there, a terminal window will open; you will be required to enter your UMICH uniqname and then your UMICH (Level-1) password in order to log in. Please note that as you type your password, nothing you type will appear on the screen; this is normal. Press “Enter/Return” key once you are done typing your password.

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 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 “Armis2” or something similar
3. Select the “SFTP (SSH File Transfer Protocol)” option
4. In the Host field, type armis2-xfer.arc-ts.umich.edu
5. Select “Interactive” for Logon Type
6. In the User field, type your uniqname
7. Click “Connect”
8. Enter your UMICH (Level-1) 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.

SFTP: Mac or Linux using Terminal

To copy a single file, type:

scp localfile uniqname@armis2-xfer.arc-ts.umich.edu:./remotefile

To copy an entire directory, type:

scp -r localdir uniqname@armis2-xfer.arc-ts.umich.edu:./remotedir

These commands can also be reversed in order to copy files from Armis2 to your machine:

scp -r uniqname@armis2-xfer.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 Great Lakes is “umich#greatlakes”.

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#armis2 v2” 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#armis2 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 Armis2. 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 Armis2 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 Armis. 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.

Common Job Submission Options

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 Armis2.

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 salloc 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@armis2-login2 ~]$ salloc --account=test 
salloc: Granted job allocation 1001106
salloc: Waiting for resource configuration
salloc: Nodes armis20204 are ready for job
[user@armis20204 ~]$ hostname
armis20204.arc-ts.umich.edu
[user@armis20204 ~]$

Jobs submitted with salloc and no additional specification of resources will be assigned the cluster default values of 1 CPU and 768MB of memory. The account must be specified; the job will not run otherwise. If additional resources are required, they can be requested as options to the salloc command. The following example job would be appropriate for an MPI job where one wants two nodes with four MPI processes using one CPU on each node with one GB of memory for each CPU in each task. MPI programs run from jobs should be started with srun or one of the other commands that will start MPI programs. Note the --cpu-bind=none option, which is recommended unless you know what an efficient processor geometry for your job is.

[user@login ~]$ salloc --nodes=2 --ntasks-per-node=4 --mem-per-cpu=1GB
salloc: Granted job allocation 1001108
salloc: Waiting for resource configuration
salloc: Nodes armis[20303-20304] are ready for job
[user@armis20303 ~]$ srun --cpu-bind=none hostname
armis20303.arc-ts.umich.edu
armis20303.arc-ts.umich.edu
armis20303.arc-ts.umich.edu
armis20303.arc-ts.umich.edu
armis20304.arc-ts.umich.edu
armis20304.arc-ts.umich.edu
armis20304.arc-ts.umich.edu
armis20304.arc-ts.umich.edu
[user@armis20303 ~]$

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, though that is fairly uncommon. 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 a count option from the table below. All counts can be represented by gputype:number or just a number (default type will be used). Available GPU types can be found with the command sinfo -O gres -p <partition>. GPUs can be requested in both Batch and Interactive jobs.

Jobs can request nodes with large amounts of RAM with --partition=largemem.

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.