-

This site is deprecated and will be decommissioned shortly. For current information regarding HPC visit our new site: hpc.njit.edu

Difference between pages "UserAccess" and "ForPSurveyResearchIT"

From NJIT-ARCS HPC Wiki
(Difference between pages)
Jump to: navigation, search
(→‎Windows)
 
(Importing text file)
 
Line 1: Line 1:
−
This page provides information on methods of connecting to NJIT's HPC hosts from Linux, MacOS, and Windows platforms.
+
<div class="noautonum">__TOC__</div>
  
−
==Getting a Login==
+
== ForP.survey.research.it ==
−
Faculty can obtain a login to NJIT's HPC & BD systems by sending an email to ARCS@njit.edu. Students can obtain a login either by taking a class that
+
−
uses one of the sytems or by asking their faculty adviser email ARCS@njit.edu on their behalf.  Your login and password is the same as for any NJIT AFS
+
−
system.
+
  
−
==Secure Shell (SSH)==
+
== 1. Preamble ==
  
−
You must be on the NJIT network (this includes VPN) to ssh directly into the headnode of an HPC cluster.
+
== 2. Demographics ==
  
−
If you are outside of the NJIT network, you cam ssh into afsconnect1.njit.edu or afsconnect2.njit.edu,
+
== 3. Research area ==
−
and from there ssh into the headnode of an HPC cluster.
+
2.1 What is the <strong>general</strong> classification of your research {select all that apply}
 +
<ul>
 +
<li>Bioinformatics </li>
 +
<li>Biophysics </li>
 +
<li>Computational PDE </li>
 +
<li>Computational biophysics </li>
 +
<li>Computational chemistry </li>
 +
<li>Computational fluid dynamics </li>
 +
<li>Computational physics and chemistry </li>
 +
<li>Condensed matter physics </li>
 +
<li>Data Science</li>
 +
<li>Electromagnetism, Wave propagation </li>
 +
<li>Granular science </li>
 +
<li>Image forensics </li>
 +
<li>Materials research </li>
 +
<li>Monte Carlo </li>
 +
<li>Neural networks, genetic algorithms </li>
 +
<li>Software verification, static analysis </li>
 +
<li>Statistical analysis </li>
 +
<li>Steganalysis and image forensics </li>
 +
<li>Transportation data analysis </li>
 +
<li>Other {text box} </li>
 +
</ul>
 +
2.2 Please provide a <strong>brief, specific</strong> description(s) of your research {text box}
  
−
===Linux and MacOS===
+
== IT Needs ==
 +
=== 3. Computational ===
 +
3.1 Does your research require significant computation : Y/N
 +
<ul>
 +
<li>If Y, continue with this section</li>
 +
<li>If N, go to Comments</li>
 +
</ul>
 +
3.2 Which of the following computational hardware do you use, and what is their importance
 +
<ul>
 +
<li>3.2.1 <em>High performance computing (HPC)</em></li>
 +
<ul>
 +
<li>My research currently uses HPC : Y/N</li>
 +
<li>If Y :
 +
<ul>
 +
<li>The importance of HPC to my research is : High, medium, low</li>
 +
</ul>
 +
</li>
 +
</ul>
 +
<li>3.2.2 <em>Lab workstations</em></li>
 +
<ul>
 +
<li>My research currently uses lab workstations : Y/N</li>
 +
<li>If Y :
 +
<ul>
 +
<li>Type of lab workstations used</li>
 +
<ul>
 +
<li>CPU-only</li>
 +
<li>GPU</li>
 +
</ul>
 +
</li>
 +
</ul>
 +
<ul>
 +
<li>The importance of lab workstations to my research is : High, medium, low</li>
 +
<li>My lab workstations are managed by : </li>
 +
<ul>
 +
<li>Academic and Research Computing Systems (ARCS}</li>
 +
<li>IST other than ARCS</li>
 +
<li>Internally by a research group member</li>
 +
<li>Other</li>
 +
<li>Not managed</li>
 +
<ul>
 +
<li>I would like to have my lab workstation(s) managed by IST : Y/N</li>
 +
</ul>
 +
</ul>
 +
<li>What operating system does your group <strong>predominantly</strong> use for your workstations :
 +
  Linux (CentOS, Red Hat, Ubuntu, etc.), MacOS, Windows</li>
 +
<li>If your group <strong>could exclusively</strong> use one operating system for your workstations, which would it be :
 +
  Linux (CentOS, Red Hat, Ubuntu, etc.), MacOS, Windows, One OS is not an optiom</li>
 +
</ul>
 +
</ul>
 +
<li><em>3.2.3 Virtual Desktop Infrastructure (VDI)</em></li>
 +
<ul>
 +
<li>Would you consider an IST-managed VDI environment (with and
 +
without GPU) utilizing bring-your-own-device (BYOD), instead of Linux/MacOS/Windows workstations : Y/N/Maybe</li>
 +
 +
<li>If Y or Maybe :</li>
 +
<ul>
 +
<li>If you would use, or might use, CPU-only VDI</li>
 +
<ul>
 +
<li>What would be the expected daily use of a CPU-only VDI in hours per day : &lt;2, 2-6, 7-12, &gt;12</li>
 +
<li>What is the maximum annual cost you are willing to pay for VDIs (CPU only) : &lt;$100, $100-500,
 +
$501-1000, &gt;$1000</li>
 +
</ul>
  
−
====Linux====
+
<li>If you would use, or might use, GPU VDI</li>
 +
<ul>
 +
<li>What would be the expected daily use of a GPU VDI in hours per day : &lt;2, 2-6, 7-12, &gt;12</li>
 +
<li>What is the maximum annual cost you are willing to pay for GPU VDIs : &lt;$500, $500-1000,
 +
$1001-2000, &gt;$2000</li>
 +
<li>In your estimation, what percentage of your VDI usage will require GPUs : 0%, 1-25%, 26-50%, 51-75%, &gt;75%</li>
 +
</ul>
 +
</ul>
 +
</ul>
 +
<li><em>3.2.4 Laptops</em></li>
 +
<ul>
 +
<li>My research currently uses laptops : Y/N</li>
 +
<li>If Y :
 +
<ul>
 +
<li>The importance of laptops to my research is : High, medium, low</li>
 +
</ul>
 +
</li>
 +
</ul>
  
−
There are different methods to open a terminal window on the various Linux distributions.  Search the web for instructions specific to the distribution
+
</ul>
−
you are using.  Once a terminal window is opened, enter :
+
  
−
<pre code> localhost> ssh -X -Y ucid@HPC_HOST.njit.edu </pre>
+
3.4 Comments on computational needs (text box)
  
−
You will be prompted for your password. Enter your <b>AFS</b> password. You can omit the -X -Y if you are not using a graphic interface.  Substitute "Kong" or "Stheno" for "HPC_HOST".
+
=== 4. Storage ===
 +
<ul>
 +
<li>How much readily available storage capacity do you need, now and over the next 5 years : &lt;1TB, 1-5TB, 6-50TB, 51-100TB, &gt;100TB</li>
 +
<li>How much archival storage capacity do you need, now and over the next 5 years : &lt;1TB, 1-5TB, 6-50TB, 51-100TB, &gt;100TB</li>
 +
<li>Where do you currently store your data : Hard drive on local workstations,  External drives, USB flash drives, External disk,
 +
AFS, Google Drive, Dropbox, (select all that apply) Other</li>
 +
<li>Are your data backed up : Y/N/Don't know</li>
 +
<li>If Y :
 +
<ul>
 +
<li>What is the backup mechanism : NJIT enterprise, local to lab, commercial cloud, other</li>
 +
</ul>
 +
</li>
 +
<li>What is the maximum annual cost you are willing to pay for storage (no backups) per TB : &lt;$10, $10-25, $26-50, &gt;$50</li>
 +
<li>What is the maximum annual cost you are willing to pay for backed-up storage (or backup services) per TB : &lt;$25, $25-50, $51-75, $76-100, &gt;$100</li>
 +
</ul>
 +
Comments on storage needs (text box)
  
−
====MacOS====
+
=== 5. Software ===
 +
List the top three software applications you use in your research
 +
<ul>
 +
<li>Name [ Opensource | Commercial | Own code ]
 +
</ul>
 +
Comments on software (text box)
  
−
Open a Terminal window. Applications -> Utilities -> Terminal
+
=== 6. Technical Assistance ===
 +
To facilitate your research, assistance in certain areas may be beneficial -
 +
e.g., consultation or tutorials.
  
−
At the terminal prompt enter :
+
Select the areas in which you think such assistance would be of use
 +
<ul>
 +
<li>Programming</li>
 +
<ul>
 +
<li>C/C++, Fortran, Python, Shell, PHP</li>
 +
<li>Parallelization of code</li>
 +
<li>Optimization of code</li>
 +
<li>Other</li>
 +
</ul>
 +
<li>Building software from source code</li>
 +
<li>Backing up data</li>
 +
<li>Sharing data, code, documentation</li>
 +
<li>Security</li>
 +
<li>Fundamentals of working in a Linux environment</li>
 +
<li>Other</li>
 +
<li>Don't know</li>
 +
</ul>
  
−
<pre code> localhost> ssh -X -Y ucid@HPC_HOST.njit.edu </pre>
+
Comments on technical assistance needs (text box)
  
−
You will be prompted for your password. Enter your <b>AFS</b> password.  You can omit the -X -Y if you are not using a graphic interface. Substitute "Kong" or "Stheno" for "HPC_HOST".
+
=== 7. Additional Comments ===
 +
Please provide any additional comments relevant to this survey.
  
−
===Windows===
+
=== 8. Follow-up ===
−
 
+
<ul>
−
A free Secure Shell client can be obtained from the [http://mobaxterm.mobatek.net MobaXterm Site]. In addition to SSH, MobaXterm provides an X windows
+
<li>Can IST contact you for a follow-up to this survey : Y/N</li>
−
server, VNC client and other useful utilities. Download, install, and open MobaXterm.
+
<li>If Y :
−
 
+
<ul>
−
[[File:MobaXterm.open.png|800px]]
+
<li>Do you explicitly want to be contacted : Y/N</li>
−
 
+
</ul>
−
At the terminal prompt enter :
+
</li>
−
 
+
</ul>
−
<pre code> localhost> ssh -X -Y ucid@HPC_HOST.njit.edu </pre>  
+
−
 
+
−
[[File:MobaXterm.ssh.initial.png|800px]]
+
−
 
+
−
You will be prompted your your password. Enter your '''UCID''' password.  You can omit the -X -Y if not using a graphical interface on Lochness. Substitute "lochness" or "Stheno" for "HPC_HOST".
+
−
 
+
−
==Virtual Network Computing (VNC)==
+
−
 
+
−
VNC software creates an image of a remote host's desktop on the user's local workstation or laptop, permitting access to the remote host with a graphical
+
−
user interface (GUI).
+
−
 
+
−
Using VNC, it is possible to use a GUI environment from a remote host as if you were at the console of that host. In addition, it is also possible to
+
−
start long-running jobs, and then disconnect without your jobs terminating.
+
−
 
+
−
===Establish a VNC Server Session on an HPC host===
+
−
 
+
−
*Using the SSH client on your local workstation or laptop, log onto an HPC host.
+
−
*Run ''krenew'' with the arguments below to maintain your Kerberos and AFS credentials
+
−
*Establish the VNC environment and set a VNC session password.
+
−
**Enter ''vncserver''.  You will be prompted for a password, and then a session will be started.
+
−
 
+
−
<pre class=code>
+
−
hpc-host-NM ucid>: krenew -t -b -K 60
+
−
hpc-host-NM ucid>: vncserver
+
−
You will require a password to access your desktops.
+
−
Password:
+
−
Verify:
+
−
 
+
−
New 'hpc-host:8 (username)' desktop is hpc-host:8
+
−
 
+
−
Creating default startup script /home/ucid/.vnc/xstartup
+
−
Starting applications specified in /home/ucid/.vnc/xstartup
+
−
Log file is /home/ucid/.vnc/hpc-host:8.log
+
−
</pre>
+
−
 
+
−
*Note and record your assigned VNC Server desktop number.
+
−
*This VNC session will continue to run unless the process is terminated either by the user terminating the process, or by a host reboot or other abnormal
+
−
operation. '''Do not start more than one VNC Server session'''.
+
−
*Note that if the system is rebooted or your VNC session is otherwise terminated you will need to establish a new session. VNC sessions are stateless,
+
−
which means that desktop numbers are not preserved across logins. You will get a new new desktop number at the next login. 
+
−
 
+
−
*Unless you alter the files created by the VNC server, you will not be asked to set a password again.
+
−
 
+
−
=== Connecting to an established VNC Server Session on an HPC host ===
+
−
 
+
−
Independent of the operating system on your workstation or laptop, the best way to connect to an established VNC Server
+
−
session is through an SSH "tunnel". Connecting to an established VNC server session will require both an SSH client and a VNC client.
+
−
 
+
−
====Linux and MacOS====
+
−
 
+
−
Using the SSH client on the local computer create an SSH tunnel between the local computer and the hpc-host. The
+
−
command is
+
−
 
+
−
ssh -L <<i>local-port</i>>:localhost:<<i>remote-port</i>>  <i>ucid</i>@hpc-host.njit.edu
+
−
 
+
−
The local port should be set to 5900 and the remote port is 5900 + (the desktop number assigned when the VNC session was established.)
+
−
 
+
−
<pre code>
+
−
localhost> ssh -L 5900:localhost:5901 ucid@hpc-host.
+
−
</pre>  
+
−
 
+
−
=====Linux=====
+
−
 
+
−
After the SSH tunnel is created, open a terminal and enter ''vncviewer localhost''. A window will appear and you will be prompted for a password. Enter
+
−
the password created when the VNC session was established.
+
−
 
+
−
<pre code>localhost> vncviewer localhost
+
−
</pre>
+
−
 
+
−
[[File:VNC_Authentication_VncAuth_.png]]
+
−
 
+
−
You are now connected to your VNC session.
+
−
 
+
−
=====MacOS=====
+
−
 
+
−
There are several VNC clients available for Mac. This example will use
+
−
[http://sourceforge.net/apps/mediawiki/tigervnc/index.php?title=Welcome_to_TigerVNC TigerVNC].
+
−
[http://sourceforge.net/projects/tigervnc/files/ Download] and install TigerVNC according to the instructions.
+
−
 
+
−
After the SSH tunnel is created, open TigerVNC.
+
−
 
+
−
Application -> TigerVNC Viewer 1.3.0
+
−
 
+
−
Enter "localhost" for the VNC viewer.
+
−
 
+
−
[[File:VNC Viewer Connection Details.png]]
+
−
 
+
−
Click "Connect". A new window will appear prompting for a password. Enter the password created when the VNC
+
−
session was established. Click 'OK.'
+
−
 
+
−
[[File:VNC_authentication.png]]
+
−
 
+
−
You are now connected to your VNC session.
+
−
 
+
−
====Windows====
+
−
 
+
−
[http://mobaxterm.mobatek.net MobXterm] can be used as both an SSH and VNC client.
+
−
 
+
−
Select 'New Session.'
+
−
[[File:MobaXterm.clk.nw.sess.png|100px]]
+
−
 
+
−
Choose "VNC" and click "OK"
+
−
 
+
−
[[File:MobaXterm.choose.vnc.png|100px]]
+
−
 
+
−
Enter the hostname that the VNC server is established on. The Port number is : 5900 + (the desktop number obtained when the VNC session was established).
+
−
Select "Connect through SSH gateway (jump host)". Enter the hostname that the VNC server is established on for the "Gateway SSH server", 22 for the
+
−
"Port", and your UCID for "User". Click "OK".
+
−
 
+
−
[[File:MobaXterm.vnc.sess.setup.1.png|100px]]
+
−
 
+
−
The first password prompt will be for the SSH tunnel. Enter your AFS password.
+
−
 
+
−
[[File:MobaXterm.vnc.sess.pwd.1.png|100px]]
+
−
 
+
−
The second password will be for "vncuser on localhost". Enter the password created when the VNC session was established.
+
−
 
+
−
[[File:MobaXterm.vnc.sess.pwd.2.png|100px]]
+
−
 
+
−
You are now connected to you VNC session.
+
−
 
+
−
[[File:MobaXterm.vnc.session.png|100px]]
+
−
 
+
−
==Ending a VNC Server session==
+
−
 
+
−
*Using ssh from your local workstation or laptop, log on to the HPC host where the vncserver is running.
+
−
 
+
−
*Enter ''vncserver -kill <desktop number>'' Where ''<desktop number>'' is the desktop number assigned when the VNC Server Session was established.
+
−
 
+
−
<pre class=Code>
+
−
hpc-host-NM ucid>: vncserver -kill :8
+
−
Killing Xvnc process ID 31460
+
−
</pre>
+
−
 
+
−
[[Category:HPC and BD Wiki Users]]
+

Revision as of 16:14, 10 January 2023

ForP.survey.research.it

1. Preamble

2. Demographics

3. Research area

2.1 What is the general classification of your research {select all that apply}

  • Bioinformatics
  • Biophysics
  • Computational PDE
  • Computational biophysics
  • Computational chemistry
  • Computational fluid dynamics
  • Computational physics and chemistry
  • Condensed matter physics
  • Data Science
  • Electromagnetism, Wave propagation
  • Granular science
  • Image forensics
  • Materials research
  • Monte Carlo
  • Neural networks, genetic algorithms
  • Software verification, static analysis
  • Statistical analysis
  • Steganalysis and image forensics
  • Transportation data analysis
  • Other {text box}

2.2 Please provide a brief, specific description(s) of your research {text box}

IT Needs

3. Computational

3.1 Does your research require significant computation : Y/N

  • If Y, continue with this section
  • If N, go to Comments

3.2 Which of the following computational hardware do you use, and what is their importance

  • 3.2.1 High performance computing (HPC)
    • My research currently uses HPC : Y/N
    • If Y :
      • The importance of HPC to my research is : High, medium, low
  • 3.2.2 Lab workstations
    • My research currently uses lab workstations : Y/N
    • If Y :
      • Type of lab workstations used
        • CPU-only
        • GPU
      • The importance of lab workstations to my research is : High, medium, low
      • My lab workstations are managed by :
        • Academic and Research Computing Systems (ARCS}
        • IST other than ARCS
        • Internally by a research group member
        • Other
        • Not managed
          • I would like to have my lab workstation(s) managed by IST : Y/N
      • What operating system does your group predominantly use for your workstations : Linux (CentOS, Red Hat, Ubuntu, etc.), MacOS, Windows
      • If your group could exclusively use one operating system for your workstations, which would it be : Linux (CentOS, Red Hat, Ubuntu, etc.), MacOS, Windows, One OS is not an optiom
  • 3.2.3 Virtual Desktop Infrastructure (VDI)
    • Would you consider an IST-managed VDI environment (with and without GPU) utilizing bring-your-own-device (BYOD), instead of Linux/MacOS/Windows workstations : Y/N/Maybe
    • If Y or Maybe :
      • If you would use, or might use, CPU-only VDI
        • What would be the expected daily use of a CPU-only VDI in hours per day : <2, 2-6, 7-12, >12
        • What is the maximum annual cost you are willing to pay for VDIs (CPU only) : <$100, $100-500, $501-1000, >$1000
      • If you would use, or might use, GPU VDI
        • What would be the expected daily use of a GPU VDI in hours per day : <2, 2-6, 7-12, >12
        • What is the maximum annual cost you are willing to pay for GPU VDIs : <$500, $500-1000, $1001-2000, >$2000
        • In your estimation, what percentage of your VDI usage will require GPUs : 0%, 1-25%, 26-50%, 51-75%, >75%
  • 3.2.4 Laptops
    • My research currently uses laptops : Y/N
    • If Y :
      • The importance of laptops to my research is : High, medium, low

3.4 Comments on computational needs (text box)

4. Storage

  • How much readily available storage capacity do you need, now and over the next 5 years : <1TB, 1-5TB, 6-50TB, 51-100TB, >100TB
  • How much archival storage capacity do you need, now and over the next 5 years : <1TB, 1-5TB, 6-50TB, 51-100TB, >100TB
  • Where do you currently store your data : Hard drive on local workstations, External drives, USB flash drives, External disk, AFS, Google Drive, Dropbox, (select all that apply) Other
  • Are your data backed up : Y/N/Don't know
  • If Y :
    • What is the backup mechanism : NJIT enterprise, local to lab, commercial cloud, other
  • What is the maximum annual cost you are willing to pay for storage (no backups) per TB : <$10, $10-25, $26-50, >$50
  • What is the maximum annual cost you are willing to pay for backed-up storage (or backup services) per TB : <$25, $25-50, $51-75, $76-100, >$100

Comments on storage needs (text box)

5. Software

List the top three software applications you use in your research

  • Name [ Opensource | Commercial | Own code ]

Comments on software (text box)

6. Technical Assistance

To facilitate your research, assistance in certain areas may be beneficial - e.g., consultation or tutorials.

Select the areas in which you think such assistance would be of use

  • Programming
    • C/C++, Fortran, Python, Shell, PHP
    • Parallelization of code
    • Optimization of code
    • Other
  • Building software from source code
  • Backing up data
  • Sharing data, code, documentation
  • Security
  • Fundamentals of working in a Linux environment
  • Other
  • Don't know

Comments on technical assistance needs (text box)

7. Additional Comments

Please provide any additional comments relevant to this survey.

8. Follow-up

  • Can IST contact you for a follow-up to this survey : Y/N
  • If Y :
    • Do you explicitly want to be contacted : Y/N
Retrieved from "https://wiki.hpc.arcs.njit.edu/index.php?title=UserAccess&oldid=759"