GUI Programs

From UFRC
Revision as of 19:11, 21 October 2016 by Jakers (talk | contribs) (→‎Problems)
Jump to navigation Jump to search

You can run GUI Programs on HiPerGator, but running such applications on a remote server within a supercomputer and displaying them on your local client computer is not as easy as simply running them locally. We try to make the process as smooth as possible. However, we welcome and will listen to feedback. The most difficult part is making sure a remotely running program can be displayed on your local computer as if it were running there and making the interface sufficiently responsive, so you could do your work. We accomplish this task with Xpra software - an open-source multi-platform persistent remote display server and client for forwarding applications and desktop screens. You can read the original basic usage documentation and the full Xpra manual if necessary.

Install Xpra Software on the Client Computer

Since Xpra is required on both ends of the connection you will have to have it installed on your local computer. Xpra client installation depends on the operating system running on your local machine and may require assistance of a system administrator if you do not have the authority to install new software. Once Xpra is installed on your client computer feel free to skip this step. Installation instructions are specific to the operating system running on your local computer:

Windows
MacOS X
Linux.

Start a GUI session on HiPerGator

Single command, no job script

There are two classes of applications that can be started with just one command from the gui environment module and do not require you to provide a job script.

Preset applications

To list applications presets load the gui module and run launch_gui_session -l 

module load gui
launch_gui_session -l

To launch a pre-approved application:

  • Load the gui module if not already loaded
module load gui
  • Launch the application
launch_<application>_gui

For example: 

launch_mzmine_gui

or 

launch_rstudio_gui

See a full example on the RSTudio Help Page. For MATLAB options, please see the MATLAB Help Page.

Simple applications

If you want to run a simple application in which either the environment module name matches the name of the program you want to run or you've already loaded the environment module and know the name of the executable then the process is about as simple as launching a preset application

Load the application environment module if its name is different from the executable name 

<module load application/version>

Launch the executable in a GUI session 

module load gui
launch_gui_session -e <application>

For example 

launch_gui_session -e molden

or 

module load gaussian gui
launch_gui_session gv

Provided Job Script

If you need to pass custom arguments to the application, load pre-requisite environment modules and so on you can provide a simple script (linux format text file) with the required commands as an argument to launch_gui_session.

Make sure to prepend the command that starts the program with xpra_start. For example, a following job script named my_molden.sh will use the molden/5.0 environment module and start molden with a particular model file: 

module load molden/5.0
xpra_start 'molden /ufrc/data/tests/molden/boc-iso-1t.gjf'

Now, to launch molden with the above script run 

launch_gui_session -e molden -f my_molden.sh

Manual launch

Of course, if you prefer to talk directly to SLURM you can write a full job script complete with resource requirements, job name, output file, etc in the #SBATCH section you can submit the script to SLURM manually.

Make sure you use the gui partition 

#SBATCH --partition=gui

and wrap your command with xpra_start as shown above.

You can use a job script for one of the application presets found in the '$HPC_GUI_JOB' directory once the 'gui' environment module is loaded as the base of your own job script.

List GUI Sessions

If you performed a manual launch or used the '-w' argument to the automated launcher command you'll have to manually check on your gui job. Check the job status with 'squeue -u $USER'. When the job starts you have to list the available xpra sessions using xpra_list_sessions command in the gui module. This command will refresh the Xpra session list and provide a convenient list of live Xpra sessions as well as client commands that can be copied and pasted into a terminal on the client machine.

Example
$ module load gui
$ xpra_list_sessions

Output: 

Refreshing the session list for jdoe to remove stale sessions

List of active Xpra sessions for jdoe:

Session: i111a-s222.rc.ufl.edu:3713
    Job ID: 123456, Name: RStudio
    Client command:
         xpra attach ssh:jdoe@i111a-s222.rc.ufl.edu:3713
        or (downloaded script):
         ./xpra attach ssh:jdoe@i111a-s222.rc.ufl.edu:3713

See the respective application pages for details and sample job scripts.

Connect From a Client Computer

Click [expand] on the right side of a section to open that section.

Connecting from outside of UF campus via VPN

The servers in SLURM gui partition are accessible only within the UF campus network. If you are working off campus, you will need to use the VPN to connect to the UF campus network using AnyConnect VPN or similar software. Please see: https://vpn.ufl.edu for additional information.

Connecting from Linux

In the simplest case paste the client command presented by the launcher or from the xpra_list_sessions output into a terminal.

Manual syntax
$USERNAME is your UF GatorLink username, $SERVERNAME is the GUI server address, and $PORT is the X11 port.
xpra attach ssh:$USERNAME@$SERVERNAME:$PORT

Example: testuser@jr-physics:~$ xpra attach ssh:testuser@i21a-s3.rc.ufl.edu:143 --desktop-scaling=on --dpi=96

Note
if you close the application window using the close button in the top right (or left) corner, this will exit your application and terminate your SLURM gui session. Use 'Ctrl+c' key combination in the terminal windows where you ran the xpra attach command to disconnect the session if you plan to reconnect later.

Connecting from MacOS X

Simply execute the xpra shell script you downloaded during client software installation. If not installed, change into the Xpra installation directory before running Xpra executable. 

cd /Applications/Xpra.app/Contents/MacOS

Use the client command provided by 'xpra_list_sessions' to connect while adding any local options you need to improve the viewing experience like

Desktop scaling
--desktop-scaling=on
Resolution, dpi (dots per inch)
--dpi=96

Example: 

./Xpra attach ssh:test-user@i21a-s3.rc.ufl.edu:143 --desktop-scaling=on --dpi=96

or with the wrapper script in place 

xpra attach ssh:test-user@i21a-s3.rc.ufl.edu:143 --desktop-scaling=on --dpi=96

Once the GUI application windows is displayed on your local computer if you close the window using the close button both the application and SLURM gui session will close. If you want to simply detach the session and come back later click on the terminal window where you ran the client command and use the 'Ctrl+c' key combination to detach the session.

Connecting from Microsoft Windows

Note: this is done ON YOUR PERSONAL COMPUTER since you will be connecting from it to HiPerGator.

Navigate to the install location of xpra (normally C:\Program Files (x86)\Xpra\) .

In MobaXterm
cd "/drives/c/Program\ Files\ \(x86\)/Xpra/"

Alternatively, call the xpra shell script you downloaded during client software installation.

Example
./xpra attach ssh:test-user@i21a-s3.rc.ufl.edu:143 --desktop-scaling=on --dpi=96

or with the wrapper script in place 

xpra attach ssh:test-user@i21a-s3.rc.ufl.edu:143 --desktop-scaling=on --dpi=96

Once the GUI application windows is displayed on your local computer if you close the window using the close button both the application and SLURM gui session will close. If you want to simply detach the session and come back later click on the terminal window where you ran the client command and use the 'Ctrl+c' key combination to detach the session.

Application Scaling

Xpra applications can encounter scaling issues for may reasons given the complexity of different connections. If your GUI application's fonts look small, large, or distorted, here are a couple of options that might be helpful.

Desktop Scaling

You can enable desktop scaling on your client by adding a parameter to your local client command. This command is "desktop-scaling=" and can be set to: on, off, auto, or a fixed value.

Example

Start a MATLAB GUI session: 

$launch_matlab_gui

From the output copy the client command to your local machine and add the desktop scaling parameter: 

$xpra attach ssh:$USER@i21a-s3.rc.ufl.edu:11764 --desktop-scaling=on

DPI

In order to help with font scaling issues, you can pass this parameter to your local installation by adding the dpi= option to your connection command. This forces a particular DPI to be used if it is supported by both server and client.

Example

Start a MATLAB GUI session: 

$launch_matlab_gui

From the output copy the client command to your local machine and add the desktop scaling parameter: 

$xpra attach ssh:$USER@i21a-s3.rc.ufl.edu:11764 --dpi=96

Problems

No active Xpra sessions found

If you run into an issue where you get an error such as this when initiating the Xpra session: 

Waiting for the job to start as '-n' (nowait) argument was not specified.

The xcrysden job '2517510' has started. Listing all active xpra sessions.

Refreshing the session list for jiangjun413 to remove stale sessions

No active Xpra sessions found for 'jiangjun413'

Check to be sure that you are not loading in a different version of python. This will break Xpra as above.

Retrieved from "https://help.rc.ufl.edu/mediawiki/index.php?title=GUI_Programs&oldid=15350"