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Account Setup

If you are interested in obtaining more information about using the services at OSC for your research needs, please contact UMaine’s ARCSIM group at um.arcsim@maine.edu.

If you have been contacted by your research advisor, or project coordinator about joining an existing project on OSC, please use the information provided below to get started.

1. Please go to https://my.osc.edu/ and click on the blue 'Sign Up' button to create a new account.

2. Complete the New User Registration form with your information, but DO NOT check the box for PI-eligible.

IF you have been invited to a current project by email, enter the project ID and access number in the box labeled 'Project Access' in the lower right of the registration screen to be added to the given project.

3. Then watch for the account confirmation email and click on the link in that email to confirm your identity.

4. Once you have done that, go back to the portal and login again to confirm account setup. (It might take 24 hours for our system to accept the new account. If it doesn’t work the first time, don’t panic!)

5. Email ARCSIM at um.arcsim@umaine.edu with your account information and he will attach your account to the project allocation.

If you need assistance with HPC account setup, storage allocations, or login access please fill out the Advanced Research Computing services request form.

Once your user account is attached to the correct project, you should be able to follow the user guide (see below) for the system you are on.

Any questions regarding getting things working can be directed to OSC via the "Consulting">”Submit a Ticket” link on the user portal detailed in the help section below.

Help Desk

If you need to access support from OSC, you can do so through the following options. OSC staff members are typically available Monday through Friday, 9AM to 5PM Eastern:

1. By email at oschelp@osc.edu

2. During virtual office hours by signing up for a scheduled slot on the calendar.

3. By phone at Toll Free: (800)686-6472

4. Creating a consulting ticket by completing the form shown here.

User Guides

Please read through the user guide associated with the specific cluster you are using to run your jobs. The primary resource used by UMaine-eDNA is the Owens supercomputer.

New User Training

Owens User Guide

Pitzer User Guide

GPU User Guide

To get an introduction to High-Performance Computing, please read the HPC Basics page.

If you want to learn more about using the command line, we have some useful resources on UNIX Basics.

For detailed instructions on how to perform some important tasks on our systems, check out our HOWTO articles.

Connecting to OSC

The ‘ssh’ command is the standard way to connect to the Owens cluster. SSH is available within Linux and from the terminal app in the MAC OS. If you are using Windows, you will need an SSH client, such as PuTTY, Bitvise, OpenSSH. Initiate a login session as follows to connect to any available node on Owens:

ssh username@owens.osc.edu

To connect with X11 support (usually required for applications with graphical user interfaces):
ssh -X username@owens.osc.edu

You will then be prompted to enter your OSC password.

Directories

There are currently four main directories that you will need to know:

1. Home directory: This directory has a quota of 500GB of storage. This directory is backed up regularly, and not purged. Additionally, home directories are shared across nodes and called by their environmental variable or username:

   $HOME or ~username

2. Project Directory: This directories quota storage is set for each individual project.

   fs/project/projectID

3. Scratch Directory: This directory has no storage quota. This directory is a temporary storage space. Files that have not been accessed in 180 days are subject to purge. Deliberately modifying file access time (using any method, tool, or program) for the purpose of circumventing purge policies are prohibited.

4. Compute: This directory has storage quota of 1TB on Owens. This directory is a temporary storage space and purged when a job is complete.

File Permissions

Files within your primary directory should be private and not viewable to others unless modified by you, the user. These file permission settings are important to understand and implement when working within project directories with shared folder permissions. There are three different permission actions that can be set with a file and three different types of users:

Action	User
Read ( r )	Owner ( u )
Write ( w )	Group member ( g )
Execute ( x )	Everyone else ( o )

NOTE: Each type of user can have one, or all of the permissions listed. Be sure to consider both the file permissions and the directory permissions.

If you want to make a file writable, you need to know who should be allowed to write the file. If you want ‘anyone or everyone’, then you can simply assign the ‘ x ‘ permission to all three types of users using the chmod command, which is the standard command for making changes to permissions of files. First you specify which users you want to modify, then use the plus (+) or minus (-) to add or take away permissions.

1. For example, if you want a file to be only executable by you, the user, input the command as follows: chmod u+x testfile.sh

2. Similarly, if you want the file to be executable by everyone, you would instead use the following command to give executable permissions to all ‘a’ (owner, group, others): chmod a+x testfile.sh

3. To modify the permissions of a folder and all files within it to allow all group members to read, write, and execute contents, use the following command: chmod -R g+rwX testfolder

   In order to view the file permissions for everything within a particular directory, you can check the current permissions by running the following command: ls -ltr The prompt will return information regarding permissions, number of files contained within a directory, and group assigned to a given folder as follows:

The ten permission flags are given in the highlighted box above. The first flag is designated with a ‘d’ to indicate a directory or ‘ - ‘ to indicate a file. The remaining nine flags, in groups of three, indicate:

All combinations of permissions are as follows:

Permission	rwx
read, write and execute	rwx
read and write	rw-
read and execute	r-x
read only	r--
write and execute	-wx
write only	-w-
execute only	--x
none	---

Additional things to note regarding directory permissions:

1. Users who have write permission for a directory can delete files in the directory, without having write permission for those files.

2. Subdirectories can have less restrictive permissions than their parent directories. However, if you change directory permissions recursively ($-R), you are changing the permissions for all files and subdirectories in that directory tree.

3. You can give a user read permission for a file, but the user won’t have access to it without also having permission to traverse the directory tree that contains the file.