Difference between revisions of "Getting Started"

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{|align=right
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[[Category:Essentials]]
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  |__TOC__
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Welcome to UF Research Computing! This page is intended to help new clients getting started on HiPerGator use.
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  |}
 
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==Getting an account==
 
−
To get an account at the UF HPC Center, you need to read the UF HPC Center [http://www.hpc.ufl.edu/index.php?body=policies Policies] and then put a request in at our request page. That page is [http://www.hpc.ufl.edu/index.php?body=authuser located here].
 
  
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==Logging In==
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Note that new users are highly encouraged to take the [[New_user_training|New User Training]] course to familiarize themselves with using a supercomputer for research, save time, and avoid many beginner mistakes.
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To login to the cluster, you need an SSH client of some sort. If you are using a linux or unix based system, there is most likely one already available to you in a shell, and you can get to your account very quickly.
 
  
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If you are having problems connecting to your account, please let the HPC Staff know by submitting a [http://bugzilla.hpc.ufl.edu Bugzilla Request].
 
−
===Linux / Unix===
 
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The login host at the HPC Center is <code>submit.hpc.ufl.edu</code>.  Here is how you would go about logging in via a linux or unix account:
 
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{|
 
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|
 
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<pre>
 
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ssh -Y <YOUR_USERNAME>@submit.hpc.ufl.edu
 
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</pre>
 
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|}
 
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where <code><YOUR_USERNAME></code> is your HPC Center username, which was sent to you when you got your HPC Center account.
 
  
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The command <code>ssh -Y <YOUR_USERNAME>@submit.hpc.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 HPC Center username is "smith", you would use the command <code>ssh smith@submit.hpc.ufl.edu</code> to log into the HPC Center.
+
=From Zero to HiPerGator=
 +
===Initial Consult===
 +
If a face-to-face discussion about the group's needs is needed you can [https://outlook.office365.com/owa/calendar/UFITResearchComputingSupport@uflorida.onmicrosoft.com/bookings/ schedule an appointment] to [https://www.rc.ufl.edu/get-support/walk-in-support/ meet with one of the UF Research Computing Facilitators] face-to-face or virtually, or [https://support.rc.ufl.edu/ submit a support request to start the conversation].
  
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The <code>-Y</code> flag is used to indicate that X11 should be tunneled to your local machine.
 
  
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===Windows===
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For the initial interview we recommend prospective users to be ready to answer questions such as:
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For Microsoft Windows, things are a bit trickier. Windows does not come with a built-in SSH client, and this makes things difficult. What you have to do is download a client from the Internet and install it, then use that client. We recommend the following:
 
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* For a shell client, [http://www.chiark.greenend.org.uk/~sgtatham/putty Putty]
 
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** [[PuTTY]] configuration instructions (HPC)
 
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* For a file transfer client, [http://winscp.net/eng/index.php WinSCP]
 
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Both of the above clients have documentation at their websites. Once you are logged in and have a prompt that resembles that in the Unix / Linux section above, you can continue with this tutorial.
 
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====X Windows Connectivity====
 
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For those users that want to also have X-Windows connectivity on their Windows PC's, there are options. The most recent one we have found is a software suite called [http://www.straightrunning.com/XmingNotes/ Xming] that has a free version available at [http://sourceforge.net/projects/xming/files/Xming/6.9.0.31/Xming-6-9-0-31-setup.exe/download SourceForge]
 
  
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===Macintosh===
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* Does the data fall under FERPA, HIPAA, or another restricted classification?
−
For Macintosh users that are running OS X (those who are not running OS X are in a whole different category of user) the instructions are very similar to those of Linux.
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* Explain in simple words what your research is about.
 +
* What file types will be processed initially?
 +
** Input files, average size of individual files, total amount of data in Gb/Tb, etc.
 +
* What software or pipeline is needed to process the files?
 +
Define success for you:
 +
* What is the expected output?
 +
** Expected results, output file types and individual file size, amount of data produced after processing in Gb/Tb.
 +
* Do you have any estimations on compute needs?
 +
* Are you or will you be working with external collaborators?
  
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One thing that may be tough for a Macintosh user is finding a way in which to get to a command prompt in the first place so that they can use the linux-style commands. In order to get a command prompt, you need to start a terminal session. The terminal program on a Macintosh is located in Applications/Accessories. When a user starts this program, they start a terminal session whose prompt is located at that user's home directory.
+
===HiPerGator Accounts===
 +
====Sponsor Username and Group Creation====
 +
The group's sponsor has to be the first person to [https://www.rc.ufl.edu/access/account-request/ request a HiPerGator account] indicating that they are a new sponsor. In the process we will create their sponsored group.
  
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From there, you should be able to follow the [[Getting_Started#Linux_.2F_Unix | linux]] based instructions listed above.
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====User Account Creation====
 +
Group members will be able to [https://www.rc.ufl.edu/access/account-request/ submit HiPerGator account requests] indicating their PI as the sponsor. Once approved, their HPG Linux accounts will be created.
  
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If there is anyone out there that knows of a GUI application for Mac that makes the use of SCP easier, please let me know and I will include it here.
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====Joining a Group====
 +
Once their HPG username is created users must [https://support.rc.ufl.edu submit a request] to be added to a sponsor's group. Once the sponsor or an assigned manager replies to the request with approval, the user is added to the requested group. Accounts can only be added to groups with active resource allocations (see below for details).
  
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==Looking Around==
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[https://support.rc.ufl.edu Request to be added to a group]:
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We expect the users of the HPC Center cluster to already have a working knowledge of the linux operating system, so we are not going to go into detail here on using the operating system. Below are some links to webpages that describe a lot of this, however:
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* Include the following in the Summary line: "Add [username] to [groupname] group".
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* [http://www.tutorialized.com/tutorial/Basic-Linux-Shell-commands/21596 Basic Linux Shell Commands]
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* Include the reason in the request's description.
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===Basic Commands===
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* If possible, add your sponsor's email to the ticket's CC list.
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{| border=1
 
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|-
 
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! Command !! Description
 
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|-
 
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| ls || List files in the current directory
 
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|-
 
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| cd || Change directory
 
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|-
 
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| more || View a file
 
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|-
 
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| mkdir <dir> || Make a directory
 
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|-
 
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| cp file1 file2 || Copy a file
 
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|-
 
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| mv file1 file2 || Move/Rename a file
 
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|-
 
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| rm file || Remove a file
 
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|-
 
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| rmdir dir || Remove an ''empty'' directory
 
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|}
 
  
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===File System===
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===Trial Allocation===
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We have a structured file system that is important to know about. Please read about it here: [[HPC File System]]
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We recommend that the group's sponsor [https://gravity.rc.ufl.edu/access/request-trial-allocation/ request a '''free''' trial allocation] for storage and computational resources to get the group started on HiPerGator. Group members can then use HiPerGator for the 3 month duration of the trial allocation to figure out what resources and applications they really need.
  
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==Editing==
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===Purchasing Resources===
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Editing files on the cluster can be done through a couple of different methods...
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After or while the group uses a trial allocation to determine the computational and storage resources it needs the group's sponsor can submit a purchase request for [https://gravity.rc.ufl.edu/access/purchase-request/hpg-hardware/ hardware (5-years)] or [https://gravity.rc.ufl.edu/access/purchase-request/hpg-service/ services (3-months to longer)] to invest into the resources to cover the group's HiPerGator use.
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===In-System Editors===
 
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* '''vi''' - vi is the basic editor for a number of people. Using the editor is not necessarily intuitive, so we have provided a link to a tutorial.
 
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** [http://www.eng.hawaii.edu/Tutor/vi.html VI Tutorial]
 
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** There is also a VI tutorial on the system that you can use, called '''vimtutor'''. Once logged in, simply type the following on the command line and it will take you on a tutorial for VI:
 
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<pre>
 
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$ vimtutor
 
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</pre>
 
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** Another small resource for vi is right here in our [[vi | wiki]]
 
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* '''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.
 
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** [http://www2.lib.uchicago.edu/~keith//tcl-course/emacs-tutorial.html Emacs Tutorial]
 
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* '''pico''' - While pico is not installed on the system, [[nano]] is installed, and is a clone of pico.
 
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* '''nano''' - nano has a good amount of on-screen help to make it easier to use.
 
  
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===External Editors===
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Some groups may have access to shared departmental allocations. In this case, instead of purchasing resources, group members can [https://support.rc.ufl.edu/ request] to be added to the departmental group to gain access to the shared resources.  
−
You can also use your favorite editor on your local machine and then transfer the files over to the HPC Cluster afterwards. One caveat to this is that with files created on Windows machines, very often extra characters get injected into text files which can cause major problems when it comes time to interpret the files. If this happens, there is a utility called <code>dos2unix</code> that you can use to remove the extra characters.
 
  
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==Running Jobs==
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Some examples of departments with shared allocations include the [http://ufgi.ufl.edu/ Genetics Institute], [http://epi.ufl.edu/ Emerging Pathogens Institute], [https://stat.ufl.edu/ Statistics Department], [http://biostat.ufl.edu/ Biostatistics Department], [https://www.eng.ufl.edu/ccmt/ Center for Compressible Multiphase Turbulence (CCMT)], [https://chp.phhp.ufl.edu/research/affiliated-centers/center-for-cognitive-aging-memory-cam/ Cognitive Aging and Memory Clinical Translational Research Program (CAMCTRP)], [https://efrc.ufl.edu/ Center for Molecular Magnetic Quantum Materials], [https://www.phys.ufl.edu/ Physics Department], and [https://plantpath.ifas.ufl.edu/ Plant Pathology Department]. In addition, several research groups working on collaborative projects have shared allocations accessible to members of those projects.
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===General Scheduling===
 
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Jobs from faculty investors in the HPC Center are now favored over jobs from groups who did not invest in the HPC Center.
 
  
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Job scheduling has been a big topic with the HPC committee in the last several months. The HPC Center staff has been directed by the committee to improve the quality of service of job scheduling for jobs coming from investors in the HPC Center.  This means reducing the time spent in the queues and allowing jobs from the investors to capture the full share of the resources that they have paid for.  The HPC committee recently adopted a document which spells out what they want.
+
'''At this point a group is established on HiPerGator and can continue their computational work. See below for more details on the basic use.'''
  
−
Jobs can be submitted on '''submit.hpc.ufl.edu'''.
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=Using HiPerGator=
 +
To use HiPerGator or HiPerGator-AI you must have basic understanding the following concepts:
 +
* Use the various [[HPG Interfaces]] to connect to the system.
 +
* See [[HPG Computation]] for an overview of running analyses on HiPerGator.
 +
* Read [[HPG Scheduling]] for an overview of managing resources in jobs.
 +
* Learn how to manage data on the filesystems in [[Storage]] and how to transfer it in or out in [[HPG Data Management]].
  
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===Torque Scheduler===
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Click on the buttons below to explore.
−
The [http://www.clusterresources.com/pages/products/torque-resource-manager.php Torque Resource Manager] has been installed on the HPC cluster, and is slowly being switched over to from the PBS Pro scheduler as time goes on. The [[Maui]] scheduler is also running in this environment.
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<div style = 'text-align: center;'>
 +
[[Image:Interface.png|frameless|upright=1| link=HPG Interfaces]]
 +
[[Image:Computation.png|frameless|upright=1|link=HPG Computation]]
 +
[[Image:Scheduling.png|frameless|upright=1|link=HPG Scheduling]]
 +
[[Image:Storage.png|frameless|upright=1|link=HPG Data Management]]
 +
</div>
  
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The Torque scheduler is installed on the cluster, and accepts the same commands as the PBS Pro scheduler with a couple of exceptions. Currently we are experimenting with these packages so that we can provide improved scheduling to HPC users. While we are still learning about Torque and [[Maui]], our experiences so far have been good and we are guardedly optimistic that Torque and Maui will end up being the resource manager and scheduler for the HPC Center sometime in the not-too-distant future.
+
=Getting help=
−
 
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If you are having problems using the UFRC system, try our resources at [https://help.rc.ufl.edu/doc/Category:Help Help] or let our staff know by submitting a [http://support.rc.ufl.edu support request].
−
Please note the following.
 
−
 
 
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* If your job is single-threaded (1 cpu) and does not have heavy I/O requirements, it does not need to run on an infiniband-enabled node.  In that case, you should include the "gige" property in your PBS resource specification as follows
 
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<pre>
 
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#PBS  -l nodes=1:ppn=1
 
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</pre>
 
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* If you need to run an mpi-based application that has not been rebuilt for OpenMPI 1.2.0+Torque, please send us a note and we'll be happy to rebuild  what you need - first come, first serve.
 
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* If you build your own MPI-based application executables, you should use the MPI compiler wrappers (mpif90, mpicc, mpiCC) in /opt/intel/ompi/1.2.0/bin.  These wrappers will automatically pull in the correct libraries.
 
−
* We will continue to tune the maui scheduler to provide fair and efficient scheduling according to the policies established by the HPC Committee and within the capabilities of the maui scheduler.    Keep in mind that these policies include priority and quality-of-service commitments to those faculty who have invested in the resources within the HPC Center.
 
−
 
 
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====Trivial Example====
 
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{|
 
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|-valign="top"
 
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|
 
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<pre>
 
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#! /bin/sh
 
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#PBS -N testjob
 
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#PBS -o testjob.out
 
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#PBS -e testjob.err
 
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#PBS -M <INSERT EMAIL HERE>
 
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#PBS -r n
 
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#PBS -l walltime=00:01:00
 
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#PBS -l nodes=1:ppn=1
 
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#PBS -l pmem=100mb
 
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date
 
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hostname
 
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</pre>
 
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||
 
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To submit this job from [[submit.hpc.ufl.edu]], you would use the following command:
 
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<pre>
 
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$ qsub <your job script>
 
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</pre>
 
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To check the status of running jobs, you would use the following command:
 
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<pre>
 
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$ qstat [-u <username>]
 
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</pre>
 
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or [http://www.hpc.ufl.edu/ HPC] --> Utilization --> [http://www.hpc.ufl.edu/index2.php?body=queue2 Torque Queue Status]
 
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|}
 
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'''More information on PBS scripts can be seen with our [[Sample Scripts]].'''
 
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====Notes on Batch Scripts====
 
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* 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, as this will cause the [[Moab]]/Torque system to reject the script with a ''qsub: Job rejected by all possible destinations'' error. This problem was first seen when a user complained about a script that was being rejected with this error. Upon further inspection of their script, it was found that the script had concatenated versions of itself in the same file.
 
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* For more info on '''advanced directives''' see [[PBS_Directives]]
 
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* For a more detailed explanation of what is going on in a [[Batch Script Explanation | batch script]]
 
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====Troubleshooting Batch Scripts====
 
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* Ensure that you are using the proper MPI execution command for your software. If your software is compiled for MVAPICH, you should be using ''mpiexec''. If it is compiled for OpenMPI, you should be using ''mpirun''.
 
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==Compiling your own==
 
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By default, when you first login to the system you have compilers setup for the Intel OpenMPI compilers. This gives you access to C, C++, F77 and F90 compilers in your path, as well as the mpicc and mpif90 compilers for OpenMPI applications. If you want to change this, you can use a selector program on the cluster called "mpi-selector". The command specification for this is as follows:
 
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<pre>
 
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/usr/bin/mpi-selector options:
 
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Options for MPI implementations:
 
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--register <name>    Register an MPI implementation with the central
 
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                      mpi-selector database.  Requires use of the
 
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                      --source-dir option.
 
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--source-dir <dir>    Used with --register, indicating that <dir> is
 
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                      where mpivars.sh and mpivars.csh can be found.
 
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--unregister <name>  Remove an MPI implementation list from the
 
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                      central mpi-selector database.
 
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Options for system adminsitrators:
 
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--system              When used with the --set and --unset options,
 
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                      act on the system-wide defaults (vs. the
 
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                      per-user defaults).  When used with --query, only
 
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                      show the site-wide default (if there is one).
 
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--user                When used with the --set and --unset options,
 
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                      act on the per-user defaults (vs. the
 
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                      site-wide defaults).  When used with --query, only
 
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                      show the per-user default (if there is one).
 
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Options for users:
 
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--list                Show a list of the currently registered MPI
 
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                      implementations.
 
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--set <name>          Set <name> to be the default MPI selection.
 
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--unset              Remove the default MPI selection.
 
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--query              Shows the current default MPI selection.
 
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--yes                Assume the answer is "yes" to any question.
 
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--no                  Assume the answer is "no" to any question.
 
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--verbose            Be verbose about actions.
 
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--silent              Print nothing (not even warnings or errors;
 
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                      overrides --verbose)
 
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--version            Display the version of /usr/bin/mpi-selector.
 
−
</pre>
 

Latest revision as of 17:56, 19 August 2024

Welcome to UF Research Computing! This page is intended to help new clients getting started on HiPerGator use.

Note that new users are highly encouraged to take the New User Training course to familiarize themselves with using a supercomputer for research, save time, and avoid many beginner mistakes.


From Zero to HiPerGator

Initial Consult

If a face-to-face discussion about the group's needs is needed you can schedule an appointment to meet with one of the UF Research Computing Facilitators face-to-face or virtually, or submit a support request to start the conversation.


For the initial interview we recommend prospective users to be ready to answer questions such as:

  • Does the data fall under FERPA, HIPAA, or another restricted classification?
  • Explain in simple words what your research is about.
  • What file types will be processed initially?
    • Input files, average size of individual files, total amount of data in Gb/Tb, etc.
  • What software or pipeline is needed to process the files?

Define success for you:

  • What is the expected output?
    • Expected results, output file types and individual file size, amount of data produced after processing in Gb/Tb.
  • Do you have any estimations on compute needs?
  • Are you or will you be working with external collaborators?

HiPerGator Accounts

The group's sponsor has to be the first person to request a HiPerGator account indicating that they are a new sponsor. In the process we will create their sponsored group.

User Account Creation

Group members will be able to submit HiPerGator account requests indicating their PI as the sponsor. Once approved, their HPG Linux accounts will be created.

Joining a Group

Once their HPG username is created users must submit a request to be added to a sponsor's group. Once the sponsor or an assigned manager replies to the request with approval, the user is added to the requested group. Accounts can only be added to groups with active resource allocations (see below for details).

Request to be added to a group:

  • Include the following in the Summary line: "Add [username] to [groupname] group".
  • Include the reason in the request's description.
  • If possible, add your sponsor's email to the ticket's CC list.

Trial Allocation

We recommend that the group's sponsor request a free trial allocation for storage and computational resources to get the group started on HiPerGator. Group members can then use HiPerGator for the 3 month duration of the trial allocation to figure out what resources and applications they really need.

Purchasing Resources

After or while the group uses a trial allocation to determine the computational and storage resources it needs the group's sponsor can submit a purchase request for hardware (5-years) or services (3-months to longer) to invest into the resources to cover the group's HiPerGator use.

Some groups may have access to shared departmental allocations. In this case, instead of purchasing resources, group members can request to be added to the departmental group to gain access to the shared resources.

Some examples of departments with shared allocations include the Genetics Institute, Emerging Pathogens Institute, Statistics Department, Biostatistics Department, Center for Compressible Multiphase Turbulence (CCMT), Cognitive Aging and Memory Clinical Translational Research Program (CAMCTRP), Center for Molecular Magnetic Quantum Materials, Physics Department, and Plant Pathology Department. In addition, several research groups working on collaborative projects have shared allocations accessible to members of those projects.

At this point a group is established on HiPerGator and can continue their computational work. See below for more details on the basic use.

Using HiPerGator

To use HiPerGator or HiPerGator-AI you must have basic understanding the following concepts:

Click on the buttons below to explore.

Interface.png Computation.png Scheduling.png Storage.png

Getting help

If you are having problems using the UFRC system, try our resources at Help or let our staff know by submitting a support request.

Retrieved from "https://help.rc.ufl.edu/mediawiki/index.php?title=Getting_Started&oldid=29039"