University-Wide Remote X Application Server

This document is specific to the University-wide Remote X Application Server. There is a similar, but separate, document specific to the Rutgers-Camden campus’ Remote X Application Server.

Getting Started with the Remote X Application Server

The Remote X Application server enables any Rutgers student, faculty, or staff to remotely access software on this University-wide cloud service. This is accomplished via Virtual Network Computing, a graphical desktop sharing system used to remotely control another computer. The VNC environment resembles the experience of using a desktop Linux system.

Before accessing the apps.rutgers.edu Cloud service, go to https://netid.rutgers.edu/ and click service activation in the left margin. Once you select the Apps Cloud service and complete the NetID service activation script, it will set up your account on the Apps server and your account is immediately available for use. There’s no delay as with some other service activations.

To access the server you need to visit https://apps.rutgers.edu using a browser that supports HTML5. Most browsers support HTML5 including the following browsers which have been tested:

Internet Explorer 9 and higher
Mozilla Firefox 21.0 and higher
Safari 5.1.9 and higher
Google Chrome 16.0 and higher

Accessing the Application Server from a Desktop System or Mobile Device

Go to https://apps.rutgers.edu/ from your desktop or iOS/Android device. The keyboard support for mobile devices is limited to the software keyboard on those devices, so some special characters may not be available.
Once you navigate to the above URL, press the Connect button. Then enter your NetID at login on the black window (shown below) and press Enter. You will then be prompted to enter your password, and after you are done press Enter. Nothing will be printed on the screen as you type your password.
Shortly after authentication, you will see the Linux desktop (shown below), you can then launch a number of common applications from the Main Menu. Notice that the bottom edge of the desktop displays the icons used to launch applications and you may need to scroll thru or resize your browser window.

Adjusting Applet Resolution

Users who need a larger desktop and have better resolution on their screen may adjust the resolution when they are prompted to log into a new session. Append the preferred resolution to the NetID. Examples:

For 1280×1024 resolution: netid:geom=1280×1024 — where netid is the user’s actual NetID
For 1680×1050 resolution: netid:geom=1680×1050 — where netid is the user’s actual NetID

For this to take effect, you must be starting a new session, and this setting will persist until you use the logout option. The smaller default size takes up fewer resources on the server and avoids forcing users with small displays to constantly scroll around to see their entire desktop.

Common Applications

Most of the Scientific/Math applications can be found in the main menu, under the Education area. Under the main menu, you’ll also find the Internet, Office and Programming areas that contain most of the other applications. Common applications include:

For those students interested in purchasing a copy of Maple, SPSS, Matlab, SAS, etc. for use on their own personal computer systems, please visit https://software.rutgers.edu. Students can download Mathematica from https://software.rutgers.edu since the site license was extended to include:

Math & Science

Desktop

Programming

Getting Started with Apps HPC Resources

Apps’ High-Performance Computing (HPC) service now makes HPC capability available for instruction and some basic research. The Apps cloud service is made up of 2 Debian Linux systems with one prioritized for basic desktop support using time sharing while the second system is prioritized to run longer running programs and HPC jobs with no desktop support. Essentially, one logs into apps.rutgers.edu, edits programs, runs programs, views results, and now one can submit longer running & HPC jobs from Apps to run on apps.hpc.rutgers.edu. Hence, another set of commands are used from an Apps Terminal session to submit jobs to apps.hpc.rutgers.edu.

For some perspective, apps.hpc imitates the HPCC initiative by using the “slurm” scheduler, and its associated commands (srun, sinfo, squeue, sbatch, etc.). The slurm commands are documented on the http://hpcc.rutgers.edu/technical-information/job-submission web site (alternatively, a quick startup guide for slurm can be found at https://computing.llnl.gov/linux/slurm/quickstart.html) or via the unix man pages (i.e. “man srun” from a Terminal session). Note that apps.hpc has 32 cores and 750gig of memory.

User home directories are visible on both apps.rutgers.edu and apps.hpc.rutgers.edu Once your program is saved in your home directory along with your data, start up the terminal program on your desktop, and submit your programs to apps.hpc. You can use srun to submit longer running jobs as well as run parallelized code that uses C++, Matlab, Mathematica, R, Stata, Open MPI, and other packages.

Note that to raise apps.rutgers.edu to a higher level of service, we needed a second system in case Apps had a hardware failure. So if Apps has a hardware failure, then apps.hpc will be temporarily changed from the HPC server into the desktop server, apps.rutgers.edu, until the problem is resolved. Hardware failure on apps.rutgers.edu should be very unlikely, and therefore we have expect apps.hpc.rutgers.edu to remain available more than 99% of the time.

User Quota

User quotas are 150 megabytes by default. You can use the Terminal application and type “quota -v” to review your quota usage. For additional temporary space, please send your requests to apps-admin@camden.rutgers.edu It should be noted that temporary space will not be backed up, while normal home directories will be.

Printing

If you try to print from an application on the server, you will find only one printer available in the print dialog box. The Print-To-PDF pseudo-printer prints to a PDF file. The first time you print something, a “PDF” directory will be created in your account. Any time you print something, a PDF file will get created in that directory.

You can then refer to the “Transfering Files” section below to transfer the PDFs to your local machine and then print the PDFs out on your local printer.

Some applications don’t name their created PDFs well. For instance if you print from Mathematica, the PDF file will always be called “_KDE_Print_system.pdf”, so if you print multiple worksheets from Mathematica they will always be given that name. Other applications give more descriptive names to the PDF files.

Transferring Files

To transfer files between your local system and the apps.rutgers.edu server, you should use the SFTP protocol. The SSH File Transfer Protocol (SFTP) is a network protocol for transfering, accessing and managing files on remote file systems. There are SFTP command line clients available for Windows, Linux and Mac systems (as noted below). Alternatively, the WebDrive software (available from software.rutgers.edu for free) allows you to drag files between your computer’s desktop and a folder on apps.rutgers.edu.

After installing and launching WebDrive, select New Site. Select Connect by Server Type (SFTP, WebDAV, FTP, etc.) and click Next. (If you see an SFTP choice, move to the next step). In the Server type field, choose SFTP (ssh) and click Next. In the “Domain Name / IP Address” field, enter apps.rutgers.edu and click Next (leave other fields as is). Leave Client Hostkey at No Host Key and click Next. (If you are asked, move to the next step.) In the username field enter your NetID, and in the password field enter your NetID password, then click Next. Enter Rutgers Apps (or another name) in the site name field. You can leave the drive letter at the default (usually E: or F) and click Next. Click Finish to save this Site info.

The new site will now appear in the site list whenever you open WebDrive. Simply select it and click on Connect to open it. You can move your files to the WebDrive desktop which is going to be your desktop on rutgers apps.” Authored by Apps users. (updated 3/3/14)

SFTP for Windows

If you don’t already have an SFTP client installed on your system, then go to the Rutgers Software Portal and download the “Secure Shell and FTP Client“.
Open your SFTP client and for server, enter: apps.rutgers.edu
Enter your Rutgers NetID and password to connect to the server, then simply use the client to transfer files back and forth between your local computer and the server.

SFTP for Linux and Mac

Open the Terminal application on your system to get a shell/command-line prompt.
Then run the following command to connect to the server:
```
sftp <netid>@apps.rutgers.edu
```
Replace <netid> with your Rutgers NetID.
Once connected to the server you can use the put command to upload files to the server, and the get command to download files from the server. The ls command shows you remote directory contents while the lls command shows you local directory contents. The cd and lcd commands allow you to change the remote and local (respectively) current directories.

Java

The following file transfer information pertains to using Java to access apps.rutgers.edu cloud service.

If you prefer to use Java to access Apps, there is a link at the end of the text on the login page that will use Java to make the connection.

When using this server there will be times when you’ll need to transfer files between your local system and the server. This can be accomplished by clicking on the “File Transfer” button that is located at the top of the application server window. Just remember that “Local Machine” is your computer and “Remote Machine” is the Apps server. In both instances, you are placed in the root directory which you will not be able to write to, and therefore you will need to select your preferred directory for both Local and Remote machine. In the case of the Apps server (Remote Machine), you typically will want to select your home directory which you can identify by using the Terminal Icon and typing the pwd command in the Terminal window. In the case of your local machine, you will need to select a directory that you will use for storing the new file or the directory where your file resides.

Java: Transerring files from the server to your local computer

If you want to save/download your files from the remote server onto the local computer, follow these steps:

Open the “File Transfer” window and select the file from the list of files under “Remote Machine”.
Click the Receive button on the file transfer window. When the message “file successfully received” appears at the bottom of the window, the file has been saved to your local machine.

Java: Transferring files from your local computer to the server

If you want to save/upload your files from your local machine onto the remote system, follow these steps:

Open the “File Transfer” window and select the file from the list of files under “Local Machine”.
Click the Send button on the file transfer window. When the message “file successfully sent” appears at the bottom of the window, the file has been saved onto the server.

JAVA: Troubleshooting

Because there have been a number of security problems related to Java, without timely updates, the default login page for apps.rutgers.edu uses HTML5 which also works for iPads, iPhones, Android, and other mobile devices. A recent (1/20/14) headline: “Java has just been declared to be the source of 91% of malware on users computers.”

If you prefer to use Java to access Apps, there is a link at the end of the text on the apps.rutgers.edu login page that will use Java.

You need a browser that supports Java (at least version 1.6.0 Update 45), to use this service. This service has been tested with:

Internet Explorer 9 (tested 5/1/12)
Firefox 21.0 (tested 5/23/13)
Safari 5.1.9 (tested 5/23/13)
Google Chrome v16.0 (tested 5/1/13)

If you experience trouble, the problem may be related to your Java plug-in. To verify Java functionality and perform a quick Java test, visit javatester.org to see what is recommended (version 1.6.0_45 is working as of 5/23/13).

You can download the most current version of Java at java.com.

If the login process is not working properly, it may be necessary to restart your browser.

Logging Off / Suspending the Session

When you are finished using the Remote X Application Server there are two ways to log off.

Suspend Session: Closing your browser or clicking the “Disconnect” button will keep the remote X session running on the server. Later on you can reconnect to the server and continue working with your saved session. Leaving your session running uses up valuable resources on the server, so logging off is preferable to suspending the session.. If you leave yourself logged in, remember there are times when we need to perform maintenance on this server and we may need to reboot it. Please remember to save all of your work, because if we reboot the server you will lose any unsaved data.

Log Off: From the main menu, choose the “Log Out …” option to log you out of the server and close your session as well as disconnect you from the server. This is the preferred method of disconnecting from the server since it frees up the server’s resources for others to use.

Maintenance Window

The maintenance window for this server is the first Friday of every month from 6-7 am. During this time, the server may be unavailable and may also be rebooted. Please remember to save your work daily, and schedule long jobs so that they will finish before the maintenance window starts.

Idle Sessions

In order to manage this shared resource for all, idle sessions that have not been accessed for more than 3 days will be removed from the system. This is done because idle sessions prevent resources from being used by others. If you are running a job that will take longer or that you are trying to maintain a session over time, you need to login and check the status in order for it to not be seen as an idle session.

Because of some Simultaneous User Limits the Idle Timeout has been reduced to 24 hours for Maple and SPSS.

Students can run Matlab, Mathematica, Stata, SPSS, SAS, and Maple in both the public computer labs as well as on apps.rutgers.edu However, because SPSS and Maple licenses are for a limited number of simultaneous users, their idle timeout has been reduced to 24 hours. Idle timeouts are checked at midnight.

Apps User Community

A mailing list has been created to foster an Apps User Community at Rutgers. To join, you can subscribe by logging in to the Apps User Sakai Site. Postings are made to this site to notify users of new software being made available, to notify users when Apps has been upgraded, and to survey the Apps user community.

Requests for additional software (particularly open source software) can be directed to apps-admin@camden.rutgers.edu.