Difference between revisions of "Getting Started"

Revision as of 18:23, 27 September 2016

Welcome to UF Research Computing! This page is intended to help new and uninitiated users understand and use UFRC resources. Be sure to check out our training schedule if you'd like help getting started in person!

Account creation

To create an account with UF Research Computing, you need to read UFRC Account Policy. After you have reviewed the policy, submit an account request.

Logging in

Note that for any given command, <your_username> should be replaced with your GatorLink username.

For example, if your are referencing the command ssh <your_username>@hpg2.rc.ufl.edu and your Gatorlink username is smith, you would use the command:

ssh smith@hpg2.rc.ufl.edu

Windows

Expand this section to view instructions for logging in with Windows.

Since Microsoft Windows does not come with a built-in SSH client, you must download a client from the web.

UFRC recommends using PuTTY or MobaXterm.

PuTTY

Download PuTTY to your local machine and start the program
Configure PuTTY using the configuration instructions for UFRC .
Select the connection you created in the previous step and click "Open"
At the login prompt, enter your username (this should be the same as your GatorLink username)
Enter your password when prompted. You are now connected and ready to work!

MobaXterm

Download MobaXterm to your local machine and start the program.
Click "Start local terminal"
Open a terminal and run ssh <your_username>@hpg2.rc.ufl.edu
Enter your password when prompted. You are now connected and ready to work!

Linux / Unix

Expand this section to view instructions for logging in with Linux/Unix.

Open a terminal and run

ssh <your_username>@hpg2.rc.ufl.edu

Enter your password when the prompt appears. You are now connected and ready to work!

OS X

Expand this section to view instructions for logging in with OS X.

For OS X users, connection instructions are very similar to those for Linux users.

Terminal, the terminal emulation application for OS X, is located in the folder Applications/Utilities.

Start the Terminal application and run

ssh <your_username>@hpg2.rc.ufl.edu

Enter your password when the prompt appears. You are now connected and ready to work!

Transferring your files

The simplest method for file transfer is through the use of graphical file transfer client. UFRC recommends:

FileZilla (Windows, OS X)
WinSCP (Windows)
Cyberduck (OS X)

After you have chosen and downloaded a client, configure the client to connect to sftp.rc.ufl.edu, using your username and password to log in.

SFTP and Rsync file transfers should use the servers dedicated to these transfer types, which are sftp.rc.ufl.edu and rsync.rc.ufl.edu respectively.

Globus is another mechanism for transferring data to and from HiPerGator. See the Globus page for setup and configuration information.

Editing your files

Several methods exist for editing your files on the cluster.

Native Editors

vi - The visual editor (vi) is the traditonal Unix editor; however, it is not necessarily the most intuitive editor. View a tutorial for using vi
emacs - Emacs is a much heavier duty editor, but again has the problem of having commands that are non-intuitive. View a tutorial for using emacs
pico - While pico is not installed on the system, nano is installed, and is a pico work-a-like.
nano - Nano has a good bit of on-screen help to make it easier to use.

External Editors

You can also use your favorite file editor on your local machine, and then transfer the files to the cluster afterwards. A caveat to this is that files created on Windows machines usually contain unprintable characters, which may be misinterpreted by Linux command interpreters (shells). If this happens, there is a utility called dos2unix that you can use to convert the text file from DOS/Windows formatting to Linux formatting.

Using installed software

UFRC uses Environment Modules to provide access to the installed software. Read about the basic usage of environment modules for information on loading software.

Running graphical programs

Please see the GUI Programs page for information on running graphical user interface applications at UFRC.

Scheduling jobs using SLURM

UFRC uses the Simple Linux Utility for Resource Management, or SLURM, to allocate resources and schedule jobs. Users can create SLURM job scripts to submit jobs to the system. These scripts can, and should, be modified in order to control several aspects of the job, like resource allocation, email notifications, or output destination:

See the Annotated SLURM Script for a walk-through of the basic components of a SLURM job script
See the Sample SLURM Scripts for several SLURM job script examples

To submit a job script from one of login nodes via hpg2.rc.ufl.edu, you would use the following command:

$ sbatch <your_job_script>

To check the status of submitted jobs, you would use the following command:

$ squeue -u <your_username>

View SLURM_Commands for more useful SLURM commands.

Getting help

If you are having problems using the UFRC system, please let our staff know by submitting a support request.

@@ Line 2: / Line 2: @@
    |__TOC__
    |}
-Welcome to UF Research Computing! This page is intended to help new or uninitiated users understand and user HiPerGator. Be sure to check out [https://wiki.rc.ufl.edu/doc/Training our training schedule] if you'd like help getting started in person!
+Welcome to UF Research Computing! This page is intended to help new and uninitiated users understand and use UFRC resources. Be sure to check out [https://wiki.rc.ufl.edu/doc/Training our training schedule] if you'd like help getting started in person!
 ==Account creation==
-To get an account at the UF Research Computing, you need to read [https://www.rc.ufl.edu/about/policies/account/ UFRC Account Policy] and then [https://www.rc.ufl.edu/help/account-request/ submit an account request].
+To create an account with UF Research Computing, you need to read [https://www.rc.ufl.edu/about/policies/account/ UFRC Account Policy]. After you have reviewed the policy, [https://www.rc.ufl.edu/help/account-request/ submit an account request].
 ==Logging in==
@@ Line 62: / Line 62: @@
 ==Transferring your files==
-The simplest method for file transfer is through the use of graphical file transfer client. UF Research Computing recommends:
+The simplest method for file transfer is through the use of graphical file transfer client. UFRC recommends:
-* [https://filezilla-project.org/download.php?show_all=1 FileZilla] (Windows & OS X)
+* [https://filezilla-project.org/download.php?show_all=1 FileZilla] (Windows, OS X)
 * [http://winscp.net/eng/index.php WinSCP] (Windows)
 * [http://cyberduck.ch/ Cyberduck] (OS X)
@@ Line 82: / Line 82: @@
 ===External Editors===
-You can also use your favorite editor on your local machine, and then transfer the files to the cluster afterwards. One caveat to this is that files created on Windows machines usually contain unprintable characters, which may be misinterpreted by Linux command interpreters (shells). If this happens, there is a utility called <code>dos2unix</code> that you can use to convert the text file from DOS/Windows formatting to Linux formatting.
+You can also use your favorite file editor on your local machine, and then transfer the files to the cluster afterwards. A caveat to this is that files created on Windows machines usually contain unprintable characters, which may be misinterpreted by Linux command interpreters (shells). If this happens, there is a utility called <code>dos2unix</code> that you can use to convert the text file from DOS/Windows formatting to Linux formatting.
 ==Using installed software==
-We use [[Modules|Environment Modules]] to provide access to the installed software. Read about the [[Modules_Basic_Usage|basic usage of environment modules]] for information on loading software.
+UFRC uses [[Modules|Environment Modules]] to provide access to the installed software. Read about the [[Modules_Basic_Usage|basic usage of environment modules]] for information on loading software.
 ==Running graphical programs==
-Please see the [[GUI_Programs|Gui Programs]] page for information on running graphical user interface applications at UFRC.
+Please see the [[GUI_Programs|GUI Programs]] page for information on running graphical user interface applications at UFRC.
+==Scheduling jobs using SLURM==
+UFRC uses the Simple Linux Utility for Resource Management, or '''SLURM''', to allocate resources and schedule jobs. Users can create SLURM job scripts to submit jobs to the system. These scripts can, and should, be modified in order to control several aspects of the job, like resource allocation, email notifications, or output destination:
+* See the [[Annotated_SLURM_Script|Annotated SLURM Script]] for a walk-through of the basic components of a SLURM job script
+* See the [[Sample_SLURM_Scripts|Sample SLURM Scripts]] for several SLURM job script examples
-==Running jobs using SLURM==
-See [[Sample_SLURM_Scripts]] for a simple SLURM job script example.
 To submit a job script from one of login nodes via hpg2.rc.ufl.edu, you would use the following command:
@@ Line 97: / Line 101: @@
 $ sbatch <your_job_script>
 </pre>
-To check the status of running jobs, you would use the following command:
+To check the status of submitted jobs, you would use the following command:
 <pre>
-$ squeue [-u <your_username>]
+$ squeue -u <your_username>
 </pre>
 View [[SLURM_Commands]] for more useful SLURM commands.
 ==Getting help==
-If you are having problems using the UFRC system, please let the UFRC Staff know by submitting a [http://support.rc.ufl.edu support request].
+If you are having problems using the UFRC system, please let our staff know by submitting a [http://support.rc.ufl.edu support request].