Difference between revisions of "HPC:Login"

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=== Other Pages ===
+
=== Connecting to the PMACS Cluster ===
*[[HPC:Main_Page|HPC Main Page]]
+
Currently, secure shell is the only supported method of connecting to the cluster.  The login machine name is <code>consign.pmacs.upenn.edu</code>  You should probably add "ServerKeepAliveInterval 60" to your SSH client's configuration. After your account is created, you can connect using your PMACS credentials.
*[[HPC:User_Guide|User Guide]]
+
 
*[[HPC:Software|Available Software]]
+
=== SSH Clients ===
 +
==== Windows ====
 +
----
 +
<div class="mw-collapsible mw-collapsed">
 +
The University of Pennyslvania officially recommends [http://www.upenn.edu/computing/product/ <strong>SecureCRT</strong>] as its supported shell client for Windows. However, inexperienced Unix users may find SecureCRT's interface both difficult to navigate and outdated. An alternative software we recommend is [https://mobaxterm.mobatek.net/download.html <strong>MobaXterm</strong>]. MobaXterm comes with a variety of tools such as Keypair generation, FTP, SFTP, tabbed windows, and more.
 +
 
 +
===== MobaXTerm =====
 +
Once you have installed MobaXTerm, you can launch the software and find this screen.
  
=== Connecting to the PMACS Cluster ===
+
[[image:Moba1.PNG|center|750px]]
Currently, secure shell ([http://www.upenn.edu/computing/product/ SSH]) is the only supported method of connecting to the cluster. The login machine name is consign.pmacs.upenn.edu You should probably add "ServerKeepAliveInterval 60" to your SSH client's configuration. After your account is created, you can connect using your PMACS credentials.
+
<br></br>
 +
At the upper left of the window, click "session".
 +
<br></br>
 +
[[image:Moba1.2.png|center|750px]]
 +
<br></br>
 +
This is your sessions window, where you can manage different types of connections (SSH, FTP, SFTP, et cetera).
 +
<br></br>
 +
[[image:Moba2.PNG|center|750px]]
 +
<br></br>
 +
To connect to the cluster, select "SSH".
 +
<br></br>
 +
[[image:Moba2.2.png|center|750px]]
 +
<br></br>
 +
You are now presented with a few options. In the "Remote Host" field you can either enter: <code>mercury.pmacs.upenn.edu</code> if you have <strong>not</strong> logged into the cluster before. Otherwise, the "Remote Host" field can be <code>consign.pmacs.upenn.edu</code> if you intend to submit jobs to the cluster. You should also check the box "Specify Username" and in the "Username field" enter your PMACS ID. Leave the port number 22.
 +
<br></br>
 +
[[image:Moba3.2.png|center|750px]]
 +
<br></br>
 +
For example:
 +
<br></br>
 +
[[image:Moba4.PNG|center|750px]]
 +
<br></br>
 +
Once you have connected to the cluster it will ask you for your password. MobaXterm will remember your settings and save the session for future use under "Recent Sessions" when you open MobaXTerm again. If you would like to avoid having to manually enter your password each time you log in, consider setting up [[HPC:Login#Optional_Section:_Instructions_for_generating_Public-Private_keypairs|<strong>Public/Private</strong>]] key pairs on the cluster .
 +
</div>
  
==== VPN for Off-campus access ====
+
==== Mac OSX ====
The PMACS Cluster is behind a firewall. All users authorized to use the PMACS cluster can use this VPN to establish secure connections to the PMACS cluster when trying to SSH from off-campus. This is a web based VPN that can be accessed [https://juneau.med.upenn.edu/ <strong>here</strong>]. Once a VPN tunnel has been setup, normal SSH connections to the cluster head node: consign.pmacs.upenn.edu can be established.  
+
----
 +
<div class="mw-collapsible mw-collapsed">
 +
Mac OSX already comes with the Terminal application preinstalled which can be used to SSH to the cluster. OSX users do not need install any additional software in order to connect to the cluster. However, more experienced users may find using a third party software such as [https://www.iterm2.com/ <strong>iTerm2</strong>] more to their liking.  
 +
</div>
  
'''Note 1''' There may be other VPNs managed by PMACS/UPHS. Please ensure that while connecting to the PMACS cluster, you are using this VPN only.
+
=== VPN for Off-campus access ===
 +
Pulse Secure VPN replaces the 'Forticlinet VPN' based remote access, and now all Off-campus connections must be using 'Pulse Secure VPN' to connect to the PMACS environment (Both HPC and LPC clusters), which is secured behind the firewall.  'Forticlient VPN' must be uninstalled, if used before.<br>
 +
  Pulse Secure VPN is different than 'University VPN' and must be turned off while installing/using the 'Pulse Secure VPN'.
  
'''Note 2''' The VPN link above may present you with a self-signed certificate ("Untrusted connection") message. It is good practice to always verify that you are connecting to the right server. The SHA1 fingerprint for the certificate is:
+
==== Pre-requisites ====
<pre> 38:CF:5F:DC:08:08:CD:74:86:50:A2:C2:B5:78:99:8F:66:51:48:76 </pre>
+
Pulse Secure VPN client requires the user must have 'pennkey' created and also enrolled into the DUO 2 factor authentication.
  
'''Note 3''' The web-based VPN is known to work with browsers like Firefox, Internet Explorer (IE) and Safari. There are known issues with using Chrome.
+
Duo enrollment link is below;<br>
 +
::https://twostep.apps.upenn.edu/twoFactor/twoFactorUi/app/UiMain.optinWizard
  
'''Note 4''' Note 3. above is outdated. Subsequent to a recent update to our firewall, the web-based based VPN plugin may no longer work. See updated VPN information below.
+
Duo enrollment status verification link is below;<br>
 +
::https://twostep.apps.upenn.edu/twoFactor/twoFactorUi/app/UiMain.duoPush
  
 +
'Pulse Secure VPN' can be downloaded from the PMACS website.<br>
 +
::https://remote.pmacs.upenn.edu/ 
  
===== VPN Client for Mac OS X (outdated information) =====
+
Pulse Secure VPN client install instructions are given in the below section.
There is a known issue that prevents laptops/desktops running Mac OS X Yosemite from being able to download the VPN client from our firewall appliance. The direct link to the client application is [https://hpcwiki.genomics.upenn.edu/vpn/FortiClientInstaller-Mac.dmg<strong>here</strong>]
 
  
====== Mac OS X El Capitan (outdated information) ======
+
====Instructions to VPN into PMACS====
There is a known issue with Mac OS X El Capitan (10.11) that prevents SSH/SCP/SFTP/rsync connections to the PMACS HPC cluster after the VPN session has been established. The fix is to use the "internal" IP addresses of the head node, consign.pmacs.upenn.edu, and/or the file transfer node, mercury.pmacs.upenn.edu, '''after setting up the web-based VPN tunnel'''. The internal IP addresses of both these systems are:
+
Please use the below instructions(pdf format), to set up your VPN client on either a MAC or a PC.
  
* consign.pmacs.upenn.edu: 172.16.103.23
+
'''MAC OS'''<br>
* mercury.pmacs.upenn.edu: 172.16.103.24
+
[[File:pulse-secure-vpn-mac-os-automated-install-and-configuration.pdf|thumb|left|Pulse Secure Automated Setup on MAC - preferred]]<nowiki>
 +
  -    Preferrred method</nowiki> <br>
  
===== VPN Client for GNU/Linux =====
+
[[File:pulse-secure-vpn-mac-os-manual-install-and-configuration.pdf|thumb|left|Pulse Secure Manual Setup on MAC]] <br>
Download client from [https://hpcwiki.genomics.upenn.edu/vpn/FortiClientInstaller-GNULinux.tar.gz <strong>here</strong>]
 
  
Please also see the section '''[[HPC:Login#More_VPN_INFO|below]]''' for more information on how to run the VPN client on GNU/Linux systems.
+
'''Windows''' <br>
  
===== Updated VPN related information =====
+
[[File:pulse-secure-vpn-windows-automated-install-and-configuration.pdf|thumb|left|Pulse Secure Automated Setup on Windows - preferred]]<nowiki>
If the above approach to downloading and installing the web-based PMACS VPN does not work, the alternate approach is to install the stand-alone VPN console.  
+
  -    Preferrred method</nowiki>  <br>
  
First download the appropriate installer for
+
[[File:pulse-secure-vpn-windows-manual-install-and-configuration.pdf|thumb|left|Pulse Secure Manual Setup on Windows]] <br>
 
[https://upenn.box.com/s/o7yl6jh35o6j3xuu8q6bj6mixt4x4xwh Mac OSX]
 
  
OR
+
When logging into Pulse Secure VPN you will be asked for a secondary password, which is DUO secure code, depending on how you have set up DUO this will mean typing "push", "phone", "text", or entering a secure code.
  
[https://upenn.box.com/s/zknl5nlneve6upn5nyyngkpe7w20n0rv Windows]
+
Push: a DUO popup will appear on the phone setup with DUO that will ask for your Approval (recommended)<br>
 +
Phone: a call will be sent to the number specified and you will be asked to press a key to approve.<br>
 +
Text: a text message will be sent to the number specified and you will be asked to reply to approve.<br>
  
Once the appropriate installer has been downloaded and installed, a reboot may be required to reboot. Subsequently, the stand-alone client console
+
=== Important Host/Server Names ===
must be used, without needing to use a web browser (as described on our wiki).
+
* <code>consign.pmacs.upenn.edu</code> : head node/login server ; Do '''NOT''' run jobs on consign
 +
* <code>mercury.pmacs.upenn.edu</code> : file transfer server and the server where home directories are initailized on [[HPC:Login#Initialize_your_home_area|<strong>First Login</strong>]]; Do '''NOT''' run jobs on mercury either
 +
* <code>juneau.med.upenn.edu</code> : VPN used to connect to the cluster. Use your PMACS ID and password to login into the VPN.
 +
** But first see [[HPC:Login#VPN_for_Off-campus_access|<strong>note</strong>]] about the VPN (above).
  
 
=== First Login ===
 
=== First Login ===
 
==== Important Host/Server Names ====
 
* <strong>consign.pmacs.upenn.edu</strong> : head node/login server ; Do '''NOT''' run jobs on consign
 
* <strong>mercury.pmacs.upenn.edu</strong> : file transfer server and the server where home directories are initailized on [[HPC:Login#Initialize_your_home_area|First Login]]; Do '''NOT''' run jobs on mercury either
 
* [https://juneau.med.upenn.edu/ <strong>PMACS VPN For Off-Campus Access</strong>]
 
** But first see [[HPC:Login#VPN_.28for_off-campus_access.29|<strong>note</strong>]] above about the VPN.
 
  
 
==== Temporary Password Change ====
 
==== Temporary Password Change ====
All PMACS accounts are provisioned with a temporary password. Before you can log into the PMACS cluster for the first time, you will need to change this temporary password. Change of the temporary password and enrollment into the PMACS password reset system can be done [https://reset.pmacs.upenn.edu here]
+
All PMACS accounts are provisioned with a temporary password. Before you can log into the PMACS cluster for the first time, you will need to change this temporary password. Change of the temporary password and enrollment into the PMACS password reset system can be done [https://reset.pmacs.upenn.edu <strong>here</strong>]
 
 
==== Enrollment into the PMACS Password Reset system ====
 
All PMACS account passwords are set to '''expire every 180 days.''' To avoid your password from expiring and possibly preventing access to the PMACS cluster, all cluster users are encouraged to enroll into the reset system.
 
The password reset application can be access [https://reset.pmacs.upenn.edu here]. Once enrolled, this system will also allow you to recover forgotten PMACS passwords and reset known/expired PMACS passwords.
 
  
 
==== Initialize your home area ====
 
==== Initialize your home area ====
* With the newly changed password log into the file transfer host: '''mercury.pmacs.upenn.edu'''
+
* With the newly changed password log into the file transfer host: <code>mercury.pmacs.upenn.edu</code>
 
<pre>
 
<pre>
   ssh <your_user_name>@mercury.pmacs.upenn.edu
+
   $ ssh <your_user_name>@mercury.pmacs.upenn.edu
 
</pre>
 
</pre>
  
Remember to replace <your_user_name> above with your PennKey username
+
Remember to replace <your_user_name> above with your PMACS ID. Note that your PMACS ID is identical to your Pennkey username.
  
 
* Upon login, you will see a message similar to
 
* Upon login, you will see a message similar to
Line 76: Line 106:
 
</pre>
 
</pre>
  
* You are now ready to start using the PMACS HPC cluster :
+
* You are now ready to start using the PMACS HPC cluster. Open a new terminal session :
 
<pre>  
 
<pre>  
   ssh <your_user_name>@consign.pmacs.upenn.edu
+
   $ ssh <your_user_name>@consign.pmacs.upenn.edu
 
</pre>
 
</pre>
Remember to replace <your_user_name> above with your PennKey username.
+
Remember to replace <your_user_name> above with your PMACS ID.
  
Once your home area has been initialized, you are ready to use the PMACS cluster. Do '''NOT''' attempt to run jobs on mercury.pmacs.upenn.edu or submit jobs from mercury.pmacs.upenn.edu. Please look at the '''[[HPC:User_Guide|PMACS HPC Users Guide]]''' for information on how to run jobs on the PMACS cluster.
+
Once your home area has been initialized, you are ready to begin using the PMACS cluster. Do '''NOT''' attempt to run jobs on <code>mercury.pmacs.upenn.edu</code> or submit jobs from <code>mercury.pmacs.upenn.edu</code>. Please look at the '''[[HPC:User_Guide|PMACS HPC Users Guide]]''' for more information on how to run jobs on the PMACS cluster.
  
 +
=== File transfer to and from the HPC ===
  
=== File transfer to/from the PMACS HPC Cluster ===
 
 
Transferring data to/from the PMACS HPC cluster is done with program that supports the SSH v2 protocol. Programs like SCP, sFTP, rsync, WinSCP, Filezilla etc. are all supported.
 
Transferring data to/from the PMACS HPC cluster is done with program that supports the SSH v2 protocol. Programs like SCP, sFTP, rsync, WinSCP, Filezilla etc. are all supported.
  
All file transfer operations to/from the PMACS HPC cluster must be done via the '''dedicated file transfer server: mercury.pmacs.upenn.edu'''
+
All file transfer operations to/from the PMACS HPC cluster must be done via the '''dedicated file transfer server: <code>mercury.pmacs.upenn.edu</code>'''
  
 
==== File transfer using command line tools ====
 
==== File transfer using command line tools ====
 +
 +
----
 +
<div class="mw-collapsible mw-collapsed">
 +
 
Poplar command line programs for file transfer include SCP, sFTP, rsync, PSCP etc.  
 
Poplar command line programs for file transfer include SCP, sFTP, rsync, PSCP etc.  
  
The following examples show how to transfer data (in this case, a file named "test") from a laptop/desktop computer to the PMACS HPC using the rsync program via the file transfer server: '''mercury.pmacs.upenn.edu'''
+
The following examples show how to transfer data (in this case, a file named "test") from a laptop/desktop computer to the PMACS HPC using the rsync program via the file transfer server: <code>mercury.pmacs.upenn.edu</code>
  
 
Be sure to replace '''"PMACSUSER"''' in the command below with your PMACS userid
 
Be sure to replace '''"PMACSUSER"''' in the command below with your PMACS userid
Line 100: Line 134:
 
% rsync -av test PMACSUSER@mercury.pmacs.upenn.edu:~/
 
% rsync -av test PMACSUSER@mercury.pmacs.upenn.edu:~/
 
</pre>
 
</pre>
 +
 +
</div>
  
 
==== File transfer using graphical tools ====
 
==== File transfer using graphical tools ====
  
Poplar command line programs for file transfer include WinSCP, FileZilla etc.
+
----
 +
<div class="mw-collapsible mw-collapsed">
  
The images below show the use of FileZilla for file transfer to the PMACS HPC via  the file transfer server: '''mercury.pmacs.upenn.edu'''
+
Popular command line programs for file transfer include WinSCP, FileZilla, MobaXTerm, etc.
  
 +
The image below shows the settings to use in FileZilla, for file transfer to the PMACS HPC via the file transfer server: <code>mercury.pmacs.upenn.edu</code>
 
Be sure to replace '''"PMACSUSER"''' in the image below with your PMACS userid
 
Be sure to replace '''"PMACSUSER"''' in the image below with your PMACS userid
  
 +
<strong>Filezilla</strong>
 +
 +
[[image:file_upload_mercury1.png|center|600px]]
 +
 +
<strong>MobaXTerm</strong>
 +
 +
[[image:Moba5.PNG|center|600px]]
 +
 +
MobaXTerm also supports SFTP during an SSH session. If you are connected to <code>mercury.pmacs.upenn.edu</code> via SSH, you can still easily upload and download files to your home directory.
 +
 +
Select SFTP on the left-hand side, as seen by the arrow in the image below.
 +
 +
[[image:Moba6.png|center|600px]]
 +
 +
You can then download selected files or upload files from your computer via the "Upload" and "Download" buttons, as shown in the image below.
  
 +
[[image:Moba6.1.png|center|600px]]
  
[[image:file_upload_mercury1.png|center|600px]]
+
</div>
 +
 
 +
=== Enrollment into the PMACS Password Reset system ===
 +
----
 +
<div class="mw-collapsible mw-collapsed">
 +
All PMACS account passwords are set to '''expire every 180 days.''' To avoid your password from expiring and possibly preventing access to the PMACS cluster, all cluster users are encouraged to enroll into the reset system.
 +
The password reset application can be accessed [https://reset.pmacs.upenn.edu <strong>here</strong>]. Once enrolled, this system will also allow you to recover forgotten PMACS passwords and reset known/expired PMACS passwords.
 +
</div>
  
 
=== Optional Section: Instructions for generating Public-Private keypairs  ===
 
=== Optional Section: Instructions for generating Public-Private keypairs  ===
 +
----
 +
<div class="mw-collapsible mw-collapsed">
 
For added convenience and security, Public-Private Keys may be used for SSH connections to the PMACS cluster.  
 
For added convenience and security, Public-Private Keys may be used for SSH connections to the PMACS cluster.  
 
   
 
   
Line 139: Line 202:
 
|            45+  |
 
|            45+  |
 
+-----------------+</pre>
 
+-----------------+</pre>
On Windows machines you can generate and use PublicKeys with Putty. [http://www.youtube.com/statcomputing Here] is a link to a Youtube channel which has video tutorials for generating and using Public keys.
+
On Windows machines you can generate and use PublicKeys with MobaXTerm.  
 +
Select MobaKeygen from the "tools" menu.
 +
 
 +
[[image:Moba7.png|center|600px]]
 +
 
 +
Generate a new keypair.
 +
 
 +
[[image:Moba7.2.PNG|center|600px]]
 +
 
 +
Congratulations, you have generated a new Public/Private keypair! You may want to save them for future usage. You can also copy and paste the Public key into your .ssh/authorized_keys
 +
 
 +
[[image:Moba7.3.PNG|center|600px]]
  
 
After generating a Public-Private keypair, copy the contents of the .ssh/id_rsa.pub file to a file named .ssh/authorized_keys in your home area on the PMACS cluster.
 
After generating a Public-Private keypair, copy the contents of the .ssh/id_rsa.pub file to a file named .ssh/authorized_keys in your home area on the PMACS cluster.
 +
 +
 +
'''INSTRUCTIONS BELOW, TO COPY PUBLIC KEYS, INDICATE USING THE HEAD NODE. YOU CAN ALSO USE OUR DEDICATED FILE TRANSFER NODE: mercury.pmacs.upenn.edu '''
  
 
<pre>
 
<pre>
Line 153: Line 230:
 
<pre>[$USER@consign ~]$ chmod 600 .ssh/authorized_keys </pre>
 
<pre>[$USER@consign ~]$ chmod 600 .ssh/authorized_keys </pre>
  
=== More VPN INFO ===
 
Below are screenshots that describe how to use the PMACS VPN on GNU/Linux systems:
 
  
 +
'''INSTRUCTIONS ABOVE, TO COPY PUBLIC KEYS, INDICATE USING THE HEAD NODE. YOU CAN ALSO USE OUR DEDICATED FILE TRANSFER NODE: mercury.pmacs.upenn.edu '''
 +
</div>
 +
 +
=== More VPN Info===
 +
----
 +
<div class="mw-collapsible mw-collapsed">
 +
The screenshot below describes how to use the HPC VPN on MacOS systems:
 +
 +
[[image:PMACS_VPN_OSX_setup.png|center|500px]]
 +
 +
 +
Below are screenshots that describe how to use the HPC VPN on GNU/Linux systems:
  
 
[[image:Forticlient1-1.png|center|500px]]
 
[[image:Forticlient1-1.png|center|500px]]
  
 
+
If presented with a warning message indicating that the SSLVPN certificate is invalid, click "Continue" as it can be safely ignored.
  
 
[[image:Forticlient2.png|center|500px]]
 
[[image:Forticlient2.png|center|500px]]
 
  
  
 
[[image:Forticlient3.png|center|500px]]
 
[[image:Forticlient3.png|center|500px]]
  
 +
</div>
  
 
+
=== Other Pages ===
[[image:Forticlient4-1.png|center|500px]]
+
----
 +
<div class="mw-collapsible mw-collapsed">
 +
*[[HPC:Main_Page|HPC Main Page]]
 +
*[[HPC:User_Guide|User Guide]]
 +
*[[HPC:Software|Available Software]]
 +
</div>

Latest revision as of 21:07, 30 November 2022

Connecting to the PMACS Cluster

Currently, secure shell is the only supported method of connecting to the cluster. The login machine name is consign.pmacs.upenn.edu You should probably add "ServerKeepAliveInterval 60" to your SSH client's configuration. After your account is created, you can connect using your PMACS credentials.

SSH Clients

Windows


The University of Pennyslvania officially recommends SecureCRT as its supported shell client for Windows. However, inexperienced Unix users may find SecureCRT's interface both difficult to navigate and outdated. An alternative software we recommend is MobaXterm. MobaXterm comes with a variety of tools such as Keypair generation, FTP, SFTP, tabbed windows, and more.

MobaXTerm

Once you have installed MobaXTerm, you can launch the software and find this screen.

Moba1.PNG



At the upper left of the window, click "session".

Moba1.2.png



This is your sessions window, where you can manage different types of connections (SSH, FTP, SFTP, et cetera).

Moba2.PNG



To connect to the cluster, select "SSH".

Moba2.2.png



You are now presented with a few options. In the "Remote Host" field you can either enter: mercury.pmacs.upenn.edu if you have not logged into the cluster before. Otherwise, the "Remote Host" field can be consign.pmacs.upenn.edu if you intend to submit jobs to the cluster. You should also check the box "Specify Username" and in the "Username field" enter your PMACS ID. Leave the port number 22.

Moba3.2.png



For example:

Moba4.PNG



Once you have connected to the cluster it will ask you for your password. MobaXterm will remember your settings and save the session for future use under "Recent Sessions" when you open MobaXTerm again. If you would like to avoid having to manually enter your password each time you log in, consider setting up Public/Private key pairs on the cluster .

Mac OSX


Mac OSX already comes with the Terminal application preinstalled which can be used to SSH to the cluster. OSX users do not need install any additional software in order to connect to the cluster. However, more experienced users may find using a third party software such as iTerm2 more to their liking.

VPN for Off-campus access

Pulse Secure VPN replaces the 'Forticlinet VPN' based remote access, and now all Off-campus connections must be using 'Pulse Secure VPN' to connect to the PMACS environment (Both HPC and LPC clusters), which is secured behind the firewall. 'Forticlient VPN' must be uninstalled, if used before.

  Pulse Secure VPN is different than 'University VPN' and must be turned off while installing/using the 'Pulse Secure VPN'.

Pre-requisites

Pulse Secure VPN client requires the user must have 'pennkey' created and also enrolled into the DUO 2 factor authentication.

Duo enrollment link is below;

https://twostep.apps.upenn.edu/twoFactor/twoFactorUi/app/UiMain.optinWizard

Duo enrollment status verification link is below;

https://twostep.apps.upenn.edu/twoFactor/twoFactorUi/app/UiMain.duoPush

'Pulse Secure VPN' can be downloaded from the PMACS website.

https://remote.pmacs.upenn.edu/

Pulse Secure VPN client install instructions are given in the below section.

Instructions to VPN into PMACS

Please use the below instructions(pdf format), to set up your VPN client on either a MAC or a PC.

MAC OS
File:Pulse-secure-vpn-mac-os-automated-install-and-configuration.pdf - Preferrred method

File:Pulse-secure-vpn-mac-os-manual-install-and-configuration.pdf

Windows

File:Pulse-secure-vpn-windows-automated-install-and-configuration.pdf - Preferrred method

File:Pulse-secure-vpn-windows-manual-install-and-configuration.pdf

When logging into Pulse Secure VPN you will be asked for a secondary password, which is DUO secure code, depending on how you have set up DUO this will mean typing "push", "phone", "text", or entering a secure code.

Push: a DUO popup will appear on the phone setup with DUO that will ask for your Approval (recommended)
Phone: a call will be sent to the number specified and you will be asked to press a key to approve.
Text: a text message will be sent to the number specified and you will be asked to reply to approve.

Important Host/Server Names

  • consign.pmacs.upenn.edu : head node/login server ; Do NOT run jobs on consign
  • mercury.pmacs.upenn.edu : file transfer server and the server where home directories are initailized on First Login; Do NOT run jobs on mercury either
  • juneau.med.upenn.edu : VPN used to connect to the cluster. Use your PMACS ID and password to login into the VPN.
    • But first see note about the VPN (above).

First Login

Temporary Password Change

All PMACS accounts are provisioned with a temporary password. Before you can log into the PMACS cluster for the first time, you will need to change this temporary password. Change of the temporary password and enrollment into the PMACS password reset system can be done here

Initialize your home area

  • With the newly changed password log into the file transfer host: mercury.pmacs.upenn.edu
  $ ssh <your_user_name>@mercury.pmacs.upenn.edu

Remember to replace <your_user_name> above with your PMACS ID. Note that your PMACS ID is identical to your Pennkey username.

  • Upon login, you will see a message similar to
 
 Creating home directory for <user_name>
  • You are now ready to start using the PMACS HPC cluster. Open a new terminal session :
 
  $ ssh <your_user_name>@consign.pmacs.upenn.edu

Remember to replace <your_user_name> above with your PMACS ID.

Once your home area has been initialized, you are ready to begin using the PMACS cluster. Do NOT attempt to run jobs on mercury.pmacs.upenn.edu or submit jobs from mercury.pmacs.upenn.edu. Please look at the PMACS HPC Users Guide for more information on how to run jobs on the PMACS cluster.

File transfer to and from the HPC

Transferring data to/from the PMACS HPC cluster is done with program that supports the SSH v2 protocol. Programs like SCP, sFTP, rsync, WinSCP, Filezilla etc. are all supported.

All file transfer operations to/from the PMACS HPC cluster must be done via the dedicated file transfer server: mercury.pmacs.upenn.edu

File transfer using command line tools


Poplar command line programs for file transfer include SCP, sFTP, rsync, PSCP etc.

The following examples show how to transfer data (in this case, a file named "test") from a laptop/desktop computer to the PMACS HPC using the rsync program via the file transfer server: mercury.pmacs.upenn.edu

Be sure to replace "PMACSUSER" in the command below with your PMACS userid

% rsync -av test PMACSUSER@mercury.pmacs.upenn.edu:~/

File transfer using graphical tools


Popular command line programs for file transfer include WinSCP, FileZilla, MobaXTerm, etc.

The image below shows the settings to use in FileZilla, for file transfer to the PMACS HPC via the file transfer server: mercury.pmacs.upenn.edu Be sure to replace "PMACSUSER" in the image below with your PMACS userid

Filezilla

File upload mercury1.png

MobaXTerm

Moba5.PNG

MobaXTerm also supports SFTP during an SSH session. If you are connected to mercury.pmacs.upenn.edu via SSH, you can still easily upload and download files to your home directory.

Select SFTP on the left-hand side, as seen by the arrow in the image below.

Moba6.png

You can then download selected files or upload files from your computer via the "Upload" and "Download" buttons, as shown in the image below.

Moba6.1.png

Enrollment into the PMACS Password Reset system


All PMACS account passwords are set to expire every 180 days. To avoid your password from expiring and possibly preventing access to the PMACS cluster, all cluster users are encouraged to enroll into the reset system. The password reset application can be accessed here. Once enrolled, this system will also allow you to recover forgotten PMACS passwords and reset known/expired PMACS passwords.

Optional Section: Instructions for generating Public-Private keypairs


For added convenience and security, Public-Private Keys may be used for SSH connections to the PMACS cluster.

On Mac OS X and GNU/Linux systems, run the following command from within a terminal and follow the on-screen instructions. Please DO NOT copy-paste. Read each command and run the command on your own:

$ ssh-keygen
Generating public/private rsa key pair.
Enter file in which to save the key ($HOME/.ssh/id_rsa):
Enter passphrase (empty for no passphrase):
Enter same passphrase again:
Your identification has been saved in $HOME/.ssh/id_rsa.
Your public key has been saved in $HOME/.ssh/id_rsa.pub.
The key fingerprint is:
xx:xx:xx:xx:xx:xx:xx:xx:xx:xx:xx:xx:xx:xx:xx:xx asrini@
The key's randomart image is:
+--[ RSA 2048]----+
|          .      |
|       kjweo     |
|        x B E x  |
|         * B l + |
|        S +aser .|
|           + +   |
|          . weq  |
|           . x 12|
|            45+  |
+-----------------+

On Windows machines you can generate and use PublicKeys with MobaXTerm. Select MobaKeygen from the "tools" menu.

Moba7.png

Generate a new keypair.

Moba7.2.PNG

Congratulations, you have generated a new Public/Private keypair! You may want to save them for future usage. You can also copy and paste the Public key into your .ssh/authorized_keys

Moba7.3.PNG

After generating a Public-Private keypair, copy the contents of the .ssh/id_rsa.pub file to a file named .ssh/authorized_keys in your home area on the PMACS cluster.


INSTRUCTIONS BELOW, TO COPY PUBLIC KEYS, INDICATE USING THE HEAD NODE. YOU CAN ALSO USE OUR DEDICATED FILE TRANSFER NODE: mercury.pmacs.upenn.edu

[$USER@consign ~]$ if [ ! -d $HOME/.ssh ]; then mkdir -m 700 $HOME/.ssh; fi 

[$USER@consign ~]$ vim .ssh/authorized_keys

One SSH public key per line; save and close the file

Then change the permissions on the file:

[$USER@consign ~]$ chmod 600 .ssh/authorized_keys 


INSTRUCTIONS ABOVE, TO COPY PUBLIC KEYS, INDICATE USING THE HEAD NODE. YOU CAN ALSO USE OUR DEDICATED FILE TRANSFER NODE: mercury.pmacs.upenn.edu

More VPN Info


The screenshot below describes how to use the HPC VPN on MacOS systems:

PMACS VPN OSX setup.png


Below are screenshots that describe how to use the HPC VPN on GNU/Linux systems:

Forticlient1-1.png

If presented with a warning message indicating that the SSLVPN certificate is invalid, click "Continue" as it can be safely ignored.

Forticlient2.png


Forticlient3.png

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