Getting Started on GannettPeak
GannettPeak is a Specialty Cluster and therefore subject to a number of differences from standard ARCC Systems and Services.
Steps to get started on GannettPeak
1. Apply for Access:
ACCESS IS SUBJECT TO APPROVAL
The fundamental difference between the GannettPeak Service and other UW ARCC services is that at this time, PIs MUST be invited or granted approval from the GannettPeak review committee before they're granted access to use the GannettPeak cluster.
We are not providing general access to all UW researchers. This policy also applies to any changes associated with additional billing or costs on GannettPeak projects.
Requestors MUST fill out a project request form on the ARCC Service Portal in order to request GannettPeak allocations. Please be sure to write in the computational requirements section to indicate your request for GannettPeak.
Upon request approval, you are automatically granted an allocated project on the GannettPeak cluster.
There are several differences between the GannettPeak cluster and other UW ARCC Services & Resources
Requestors should be aware of these differences:
1. Requestors will not be able to specify their project names. Allocated projects are configured using a systematic naming convention and project names may not be changed.
2. All projects are subject to expiration after 1 year. Projects must be renewed or re-requested which, like initial applications for access, are subject to approval by the GannettPeak review committee.
3. All requests for new allocations, adjustments to existing allocations, or any allocation renewal are subject to approval by the GannettPeak review committee.
When your allocated project is set up on GannettPeak, accounts associated with your project are created for you and your project members, based upon the information you entered in the request form. Should you need anything changed, you will need to reach out to ARCC-help@uwyo.edu for those changes, and depending upon the degree of the change, you may be subject to additional approval from the review committee.
2. Log into the GannettPeak Web Portal
ARCC uses Open OnDemand to provide the gateway to GannettPeak. Please use a web browser and navigate to https://ai4wy.arcc.uwyo.edu.
Enter your UWyo username and password into the associated textboxes, then click 'sign in'.
Invalid Username or Password
If you get this error, it may not actually be your username or password. If you do not have Duo configured to automatically send apush notification then this is second factor authentication timeout error.
To force a push notification, please enter your password with this format:
password,push
With a comma after your password and the word "push" and no spaces in between.
- Click the button at the bottom of the that says "ARCC-Only/Wildiris" to be redirected to the ARCC-Only sign-in portal.
- Next follow the setup instructions to complete account setup.
If you're unable to login to the system, please contact arcc-help@uwyo.edu for assistance.
2a. (Optional) Set up SSH Login
This should only be done after you've successfully logged in through the web portal.
See Logging into ARCC HPC Systems for step-by-step instructions.
3. Setup Computation(s)
This is a shared resource
A key principle of any shared computing environment is that resources are shared among users and therefore must be scheduled. Please DO NOT simply log into the HPC and run your computations without requesting or scheduling resources from Slurm through a batch script or Interactive job.
3a. Get Access to Software
There are two options for using software on the GannettPeak system:
1. Users can utilize preinstalled modules on the cluster.
2. User can install their own software.
Please choose the tab for the option that applies best to your specific use case.
The Module System: LMOD
LMOD is very useful software on a HPC cluster that is leveraged to maintain a number of dynamic user environments and allow users to switch between software stacks and packages on HPC resources. You may check to see if software is available as a module by running a module spider in the following expandable example.
LMOD Spider
The spider subcommand is a great search tool to find out if the software package has been installed as a system package. From the command line, run the module spider command to output a list of the available software for the entire system:
module spider
To search for specific packages and/or versions, you can supply the names/arguments to the command:
module spider samtools
If there is only one version, the output will contain information regarding which compilers are required to be loaded before the package can be loaded as well as provide a brief segment on the help of the module. If there are multiple versions available, the output contains which versions are available and instructions to get more information on the individual version.
To get information regarding a specific version of the package, include the version as part of the argument: module spider samtools/1.6
There are opportunities to use regular expressions to search for modules. See output from the command: module --help for more information.
For example, when specifying all apps you want to load the general process is:
1. Find versions
2. Find a version’s dependencies.
3. Check what is already loaded and what is missing.
4. Load required (missing) dependencies.
5. Load application
If you have a software package that is not installed as a module, but you think it would be widely utilized on the cluster, You can make a request through our service portal for installation.
Learn more about using LMOD on our tutorials here.
Install software on your own
If your software packages are somewhat research specific, you may install them to your project. Information on installing software on your own will vary depending on the software. General instructions may be found here.
3b. Transfer Data on and off HPC
Data transfer can be performed between HPC resources using a number of methods. The two easiest ways to transfer data are detailed below. A cumulative list of methods to transfer data on or off of ARCC Resources are detailed here.
Access Files using OnDemand
Instructions for accessing your files
Note: The current max file size is limit is set to 5GB
- After connecting, click on the home directory from your GannettPeak OnDemand dashboard or click on files in the drop down menu.
- You should then see your home directory on GannettPeak, but may also access your project or gscratch space
- File and directory modification options are available along the top of this window
- The “show owner/mode” option show who owns the file/directory (often helpful in shared Project directories).
- The “show DotFiles” option shows hidden files within the current directory.
- The Files drop down allows you to see your different storage space that you have access to. After selecting a storage space, you will be shown the files in that area. You can then:
a. Create a new directory
b. Create a new file
c. Download/Upload files to the current directory
d. Copy and Move files to a new location
e. Rename Files
f. Delete Files
g. Edit Files
Configuring Globus Online
- Login to Globus Web Access here
a. Click “Login” on the top right corner of the webpage.
b. To use your UWYO organizational login, search for ‘University of Wyoming’.
It should autofill as shown in the screenshot below.
c. Hit 'Continue' to continue setting up your globus account, then click 'Allow' as shown below to allow globus to manage your groups search data using your ID and groups, and manage transfers:
d. Note that the sign up and setup may be skipped if you’ve already logged into Globus and Globus still has you cached. - On the left side of your browser window will be a file manager menu.
- Select this menu then type: uw-arcc in the Collection field to pull up ARCC storage spaces you have access to.
ARCC manages several data storage endpoints so be sure you pick the one associated with your storage and HPC cluster (if applicable). You may have access to multiple ARCC endpoints/collections.
GannettPeak and Data-Alcova are accessible and under the GCSv5.4 endpoint name Medbow.
- GannettPeak data (/gscratch, /home, and /project) are under /cluster/medbow
- When you get to the folder you’re looking for you can save it for future access by adding it to your bookmarks. To do that, once you’re in the folder you’re looking for click on the bookmark icon to the right of the path text box.
- When you wish to come back to your saved bookmarks, you can go to the bookmarks option on the very left side of the screen to get back to your bookmarked locations easily.
- If you wish to copy, sink or share, select the files/folders you wish to copy, transfer or share, and click ‘Start’, and choose a location or e-mail with which to transfer or sync.
- Click ‘Activity’ in the left pane to observe the transfer progress.
3c. View Visual Data or Access HPC with Graphical/Visual Interface
If you want to view visual output you’ve created on the cluster or just need access to a GUI (Graphical User Interface), please use OnDemand and launch an XFCE Desktop. This allows you to launch a job on the cluster using an interface similar to that of your standard workstation, shown in the image below:
Additional pages have been created for accessing GannettPeak over OnDemand. General OnDemand documentation can be found.
Want to learn more or need help on something specific?
- Links to ARCCs HPC Training: Access our in-depth training pages on for using our cluster resources.
- Link to Frequently Asked Questions (FAQs)
Links to wiki subpages with more detailed documentation:
- HPC Login through your browser: with OnDemand
- SSH Login to HPC
- Start Processing
- Run a Job: Batch Script Basics and Common Terms
- Run Interactive Jobs from Command Line (salloc)
- Slurm Workload Manager
- The Module System: LMOD
- Data Moving and Access