Difference between revisions of "Getting Started"

Revision as of 21:37, 26 September 2016

Welcome to UF Research Computing! This page is intended to help new or uninitiated users understand and user HiPerGator. Be sure to check out 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 UFRC Account Policy and then 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

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.

If the above methods seem unfamiliar or intimidating, you probably want to use a graphical file transfer client. UF Research Computing recommends:

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

After downloading, configure the client to connect to sftp.rc.ufl.edu, using your username and password to log in.

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 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 dos2unix that you can use to convert the text file from DOS/Windows formatting to Linux formatting.

Using installed software

We use 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.

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:

$ sbatch <your_job_script>

To check the status of running 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 the UFRC Staff know by submitting a support request.

@@ Line 2: / Line 2: @@
    |__TOC__
    |}
-==Getting an account==
+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!
+==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].
-==Login==
+==Logging in==
-NOTE: If you are using UF's Visitor Wireless, you will not be able to login to our systems using SSH. You will need to arrange for access using some other network.
+Note that for any given command, <code><your_username></code> should be replaced with your GatorLink username.
-===Linux / Unix===
-Open a terminal and run
- ssh <YOUR_USERNAME>@hpg2.rc.ufl.edu
-where <code><YOUR_USERNAME></code> is your Research Computing username, which was sent to you when you got your Research Computing account.
-The command <code>ssh <YOUR_USERNAME>@hpg2.rc.ufl.edu</code> is what you would type in at a command prompt on your system.  After this, it asks you for a password, which you type in. After that, you are logged in and ready to work.  As a concrete example, if your Research Computing username is "smith", you would use the command <code>ssh smith@hpg2.rc.ufl.edu</code> to log into the Research Computing.
+For example, if your are referencing the command <code>ssh <your_username>@hpg2.rc.ufl.edu</code> and your Gatorlink username is '''smith''', you would use the command:
+<pre style="width:80%;">ssh smith@hpg2.rc.ufl.edu</pre>
 ===Windows===
-Microsoft Windows does not come with a built-in SSH client. You have to download a client from the web. We recommend the following software:
+<div class="mw-collapsible mw-collapsed" style="width:70%; padding: 5px; border: 2px groove black;">
-* SSH client - [http://www.chiark.greenend.org.uk/~sgtatham/putty Putty]
+''Expand this section to view instructions for logging in with Windows.''
-** [[PuTTY|configuration instructions for UFRC]]
+<div class="mw-collapsible-content" style="padding: 5px;">
-* SSH client - [http://mobaxterm.mobatek.net/ MobaXterm]
+Since Microsoft Windows does not come with a built-in SSH client, you must download a client from the web.
-* Graphical file transfer clients:
-** '''Note for file transfers: Clients should be configured to connect to ''sftp.rc.ufl.edu''. File transfers connecting to the normal login nodes will not work'''
+UFRC recommends using [http://www.chiark.greenend.org.uk/~sgtatham/putty PuTTY] or [http://mobaxterm.mobatek.net/ MobaXterm].
-** [https://filezilla-project.org/download.php?show_all=1 FileZilla]
-<!-- [http://filezilla-project.org/download.php?type=client FileZilla]. See our [[FileZilla|tutorial on transferring files to UFRC using FileZilla]]. -->
+'''PuTTY'''
-** [http://winscp.net/eng/index.php WinSCP]
+* [http://www.chiark.greenend.org.uk/~sgtatham/putty Download PuTTY] to your local machine and start the program
+* Configure PuTTY using the [[PuTTY|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'''
+* [http://mobaxterm.mobatek.net/ Download MobaXterm] to your local machine and start the program.
+* Click "Start local terminal"
+* Open a terminal and run <code>ssh <your_username>@hpg2.rc.ufl.edu</code>
+* Enter your password when prompted. You are now connected and ready to work!
+</div>
+</div>
+===Linux / Unix===
+<div class="mw-collapsible mw-collapsed" style="width:70%; padding: 5px; border: 2px groove black;">
+''Expand this section to view instructions for logging in with Linux/Unix.''
+<div class="mw-collapsible-content" style="padding: 5px;">
+Open a terminal and run
+ ssh <your_username>@hpg2.rc.ufl.edu
-===MacOS===
+Enter your password when the prompt appears. You are now connected and ready to work!
-For MacOS users, the connection instructions are very similar to those for Linux/Unix users.
+</div>
+</div>
-''Terminal'', the terminal emulation application under MacOS is located in Applications/Utilities.
+===OS X===
+<div class="mw-collapsible mw-collapsed" style="width:70%; padding: 5px; border: 2px groove black;">
+''Expand this section to view instructions for logging in with OS X.''
+<div class="mw-collapsible-content" style="padding: 5px;">
+For OS X users, connection instructions are very similar to those for Linux users.
-Both [http://filezilla-project.org/download.php?type=client FileZilla] and [http://cyberduck.ch/ Cyberduck] are available for MacOS if you prefer a graphical interface for transferring files.
+'''Terminal''', the terminal emulation application for OS X, is located in the folder Applications/Utilities.
-==Running Graphical Programs==
+Start the Terminal application and run
-See the [[GUI_Programs|Gui Programs]] page for information on running graphical user interface applications at UFRC.
+ ssh <your_username>@hpg2.rc.ufl.edu
-==Getting Help==
+Enter your password when the prompt appears. You are now connected and ready to work!
-If you are having problems connecting to the UFRC system, please let the UFRC Staff know by submitting a [http://support.rc.ufl.edu Support Request].
+</div>
+</div>
-==Interactive work under Linux==
+==Transferring your files==
-Once you are logged in to a Research Computing server, you will find yourself at a Linux command line prompt. That may be daunting at first. However, you only need to know a small subset of Linux commands to accomplish most tasks. There are many Linux "Getting Started" guides online and in print.  Below are just a few possibilities.  Many more are easily found via a Google search.
+SFTP and Rsync file transfers should use the servers dedicated to these transfer types, which are <code>sftp.rc.ufl.edu</code> and <code>rsync.rc.ufl.edu</code> respectively.
-* [http://www.tldp.org/LDP/intro-linux/html/ Introduction to Linux]
+If the above methods seem unfamiliar or intimidating, you probably want to use a graphical file transfer client. UF Research Computing recommends:
-* [http://www.linux.org/tutorial/view/beginners-level-course Linux for Beginners]
+* [https://filezilla-project.org/download.php?show_all=1 FileZilla] (Windows & OS X)
-* [[Getting_Started_on_Linux]]
+* [http://winscp.net/eng/index.php WinSCP] (Windows)
-* [https://www.lynda.com/Linux-tutorials/Learn-Linux-Command-Line-Basics/435539-2.html Linux Command Line Basics - Lynda.com]
+* [http://cyberduck.ch/ Cyberduck] (OS X)
-** Users with a Gatorlink account can sign into Lynda.com by clicking "Log In," then "Sign in with your organization"
-==A Few Basic Commands==
+After downloading, configure the client to connect to <code>sftp.rc.ufl.edu</code>, using your username and password to log in.
-While it is advantageous to have a working knowledge of the most common Linux commands, it is not a requirement.  For the uninitiated, the following information may be useful as well as a good "Introduction to Using Linux" book.
-{| border=1
+Globus is another mechanism for transferring data to and from HiPerGator. [[Globus|See the Globus page]] for setup and configuration information.
-|-
-! Command !! Description
-|-
-| ls || List files in the current directory
-|-
-| cd || Change directory
-|-
-| more || View a file's contents
-|-
-| mkdir <dir> || Create a directory
-|-
-| cp file1 file2 || Copy a file
-|-
-| mv file1 file2 || Move (i.e. rename) a file
-|-
-| rm file || Delete a file
-|-
-| rmdir dir || Delete an ''empty'' directory
-|}
-==Editing==
+==Editing your files==
-Editing files on the cluster can be done through a couple of different methods...
+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.  That being the case, if you are unfamiliar with it, the following tutorial may be useful.
+* '''vi''' - The visual editor (vi) is the traditonal Unix editor; however, it is not necessarily the most intuitive editor. [http://www.eng.hawaii.edu/Tutor/vi.html View a tutorial for using vi]
-** [http://www.eng.hawaii.edu/Tutor/vi.html VI Tutorial]
+* '''emacs''' - Emacs is a much heavier duty editor, but again has the problem of having commands that are non-intuitive. [http://www2.lib.uchicago.edu/~keith//tcl-course/emacs-tutorial.html View a tutorial for using emacs]
-** Another resource for vi is [[vi | right here]].
+* '''pico''' - While pico is not installed on the system, nano is installed, and is a pico work-a-like.
-** There is also a vi tutorial, '''vimtutor'''. Once logged in, simply type "<code>vimtutor</code>" at the command line to start the tutorial.
-* '''emacs''' - Emacs is a much heavier duty editor, but again has the problem of having commands that are non-intuitive. Again, we have provided a link to a tutorial for this editor.
-** [http://www2.lib.uchicago.edu/~keith//tcl-course/emacs-tutorial.html Emacs Tutorial]
-* '''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 editor on your local machine and then transfer the files over to the Research Computing afterwards. One caveat to this is that with 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 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.
-==Using Installed Software==
+==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.
-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.
+==Running graphical programs==
+Please see the [[GUI_Programs|Gui Programs]] page for information on running graphical user interface applications at UFRC.
-==Running Jobs==
+==Running jobs using SLURM==
+See [[Sample_SLURM_Scripts]] for a simple SLURM job script example.
-See [[Sample_SLURM_Scripts]] for a simple 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:
-||
-To submit this job from one of login nodes via hpg2.rc.ufl.edu, you would use the following command:
 <pre>
-$ sbatch <your job script>
+$ sbatch <your_job_script>
 </pre>
 To check the status of running jobs, you would use the following command:
 <pre>
-$ squeue [-u <username>]
+$ squeue [-u <your_username>]
 </pre>
-|}
-====DRMAA====
-It's possible to submit jobs by using the scheduler API via the DRMAA library. A python example that uses our installed Python DRMAA library can be found in [[Example_pbs-drmaa_python_script]].
-====Notes on Batch Scripts====
-* The script can handle only one set of directives. '''Do not submit a script that has more than one set of directives''' included in it.
-* For more info on '''advanced directives''' see [[PBS_Directives]].
-* Please see our [[Batch Script Explanation | annotated submission script]].
-===Job Status===
-You can view the job status of your jobs and your group's jobs via the [http://rc.ufl.edu/jobstatus/ PBS Job Status] page as described in [[PBS_Job_Status|PBS Job Status Documentation]]
-===Developmental Nodes===
+View [[SLURM_Commands]] for more useful SLURM commands.
-See [[Test_Nodes]] to read about the available interactive servers.
+==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].