Getting Started on MedicineBow
1. Get an ARCC HPC account
If you haven't done this already, please see Getting an ARCC Account
Assumptions
This quickstart makes the assumption that a PI has already requested a project, it has been created, and user accounts have been added. It also assumes Duo mobile has been configured on anyone's phone who is trying to login. ARCC's current flagship HPC system is called MedicineBow. This quickstart only covers MedicineBow, it may be helpful for other systems, but just know that there may be differences.
2. Log into the MedicineBow Web Portal
ARCC uses Open OnDemand to provide the gateway to MedicineBow. Please use a web browser and navigate to https://medicinebow.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 Medicinebow 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 module help for more information.
Generalized steps for specifying all apps to load
**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. ARCC will be providing an additional allocation of 250GB in every MedicineBow /project directory under /project/
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 MedicineBow.
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 MedicineBow OnDemand dashboard or click on files in the drop down menu.
- You should then see your home directory on MedicineBow, 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
h. 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.
MedicineBow and Data-Alcova are accessible and under the GCSv5.4 endpoint name Medbow.
- MedicineBow 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:
!Standard OnDemand Desktop Screen
Want to learn more?
- Links to ARCCs HPC Training: Access our in-depth training pages on for using our cluster resources by navigating through the Digital Tool Tutorials
- Link to Frequently Asked Questions (FAQs)
- Access more information on Open OnDemand here!
- Please see the Intro to Cluster Access tutorials to learn how to remotely access the clusters