X-Ray Crystallography Facility | 410-413 Kasha Laboratory

Institute of Molecular Biophysics

Florida State University, Tallahassee, FL 32306-4380, USA

(850) 644-6448

tsomasundaram@fsu.edu

http://www.sb.fsu.edu/~soma


X11vnc and Remote Monitoring

Remote monitoring of Data Collection

 

Procedure for remote monitoring and data collection using X11vnc

 

 

Keywords: X11, X11vnc, Vnc, Virtual Network Computing, Remote, SSH, Secure connection, localhost, tunneling, x11tunnel, x-server, MarCCD, data collection, vncviewer, remote monitoring



Table of contents

Introduction. 3

Layout 3

Data Collection System Location (KLB 413).. 3

Remote viewing and monitoring. 4

Procedure for remote monitoring.. 4

Microsoft Windows Environment. 4

Linux Environment. 4

Common Procedure.. 5

Remote Desktop View... 7

Hardware Information. 8

MarCCD 165.. 8

Software Information. 8

X11vnc.. 8

Vncviewer.. 8

Conclusion. 9

ă 2003-2010 Thayumanasamy Somasundaram

414 Kasha Laboratory | Institute of Molecular Biophysics

Florida State University

Tallahassee, FL 32306-4380

E-mail: tsomasundaram@fsu.edu • URL: http://www.sb.fsu.edu/~soma

Phone 850.644.6448 • Fax 850.644.7244

May 27, 2010

Version 1.0

Keywords: X11, X11vnc, Vnc, Virtual Network Computing, Remote, SSH, Secure connection, localhost, tunneling, x11tunnel, x-server, MarCCD, data collection, vncviewer, remote monitoring

 


X11vnc and remote data monitoring and collection

Procedure for remote monitoring and data collection using X11vnc

Document Version: 1.0 (May 27, 2010)

Introduction

In early 2010 X-Ray Crystallography Facility needed to add remote monitoring of data collection from a Linux machine located in KLB 413 (see Layout 1).  The following note describes the procedure for achieving this from another lab location or from user’s home.  A copy of this Note will be posted in XRF web site shortly after receiving suggestions from the users.

Layout

Data Collection System Location (KLB 413)

 

Layout 1  Location of Data Collection System in KLB 413

Data collection from MarCCD165 using the Linux workstation spruce.sb.fsu.edu has been very successful for the last decade. However, several users have expressed that they would like to have an option for keeping an eye on their data collection from their labs rather than visiting the x-ray facility. This request is relevant especially to those whose labs are located across the campus. In addition, occasionally the marCCD x-ray shutter stops responding to data collection GUI and remain closed while the data collection and phi axis rotation progress resulting in the accumulation of empty image frames (no x-ray exposure).

Remote viewing and monitoring

To alleviate these problems Computer Resources and XRF have come up with one solution: use X11vnc via secure shell to monitor the data collection remotely. Using this protocol people who have secure access to IMB computers and secure access to MarCCD data collection machine can remotely monitor the “live” data collection session. If needed, they can modify or correct errors if they detect any problems. Shown below is the way to do the remote monitoring.

Procedure for remote monitoring

Microsoft Windows Environment

If you are planning to use MS Windows operating system to monitor then,

Ensure the following:

§         Run one of the X-window servers for Microsoft Windows, like:

o        XMing or

o        XWin32, etc

§         Run one of the a SSH Clients for Microsoft Windows, like:

o        Putty or

o        SSH, etc

For Putty or SSH

§         Enable X11 Forwarding

§         Make it as part of the default settings

For Windows X-servers

§         Run Xming or XWin32 X-Server in background

Linux Environment

If you are planning to use Linux then,

Many of above requirements are already available to you.

Common Procedure

Make a first secure connection to an IMB Linux machine with username and password (gauss, in this example)

From this Linux machine (gauss, in this example) make a secure connection to spruce by issuing the command shown in the next column

ssh –L 5900:localhost:5900 marccd@spruce.sb.fsu.edu

Once prompted for password, issue ‘marccd’ user password for spruce.sb.fsu.edu

From spruce issue the command, startvnc

Now make a second secure connection to a Linux machine in IMB with username and password

From this Linux machine (gauss, in this example) issue the command vncviewer localhost

Remote Desktop View

Now one will see the exact desktop of spruce as shown below

Now one can control the Desktop remotely as though one is sitting right in front of the console.

After the monitoring and possibly correcting the errors just log-out of both the sessions.

If there is need one can repeat the procedure as many times as needed.

Log out

 

Repeat

Hardware Information

MarCCD 165

MarCCD 165

The Rigaku Osmic marCCD set-up consists of a 12 kW Rigaku RU-H2R Copper rotating anode generator with 0.3 x 3.0 mm2 x-ray filament (cathode), Osmic Purple confocal multi-layer optics purged in helium gas, and an automated marCCD detector with an active area of 165mm diameter with a 0.079 mm resolution. The image can be read in three seconds and has two byte depth thus generating a grey scale image of ~8.4 MB size, a 10x eye piece and a c-mount photographic attachment for digital documentation. A Linux machine controls the data collection.

Figure 1  MarCCD165 with horizontal phi axis with cryo cooler

Software Information

X11vnc

X11vnc is a (server) version of vnc (Virtual Network Computing) that allows a user to see the real X11 display of a remote computer. Note that for a MS Windows environment there is really one display and therefore regular VNC will work. But for multi-user environment like Linux/UNIX there can be as many as X11 display one wants. So using regular VNC will allow the user to open a display on the remote machine and that display is not the one a user sitting at the console will see. However, X11vnc makes this possible.

X11vnc was developed by Karl J. Runge a physicist turned Sun Microsystems Software Engineer.

X11vnc version: x11vnc: 0.9.3 lastmod: 2007-09-30

Vncviewer

Vncviewer is a (client) viewer for any Virutal Networking Computing server. The client version of this software is available for many platforms. The current version of Ubuntu version’s details are given below:

VNC Viewer Free Edition 4.1.1 for X - built Apr 16 2008 13:02:40

Conclusion

As explained in this Note, it is possible for a user who has secure account access to IMB Linux computer systems and secure access to MarCCD computer system to remotely monitor the data collection from their lab or home. If you have any further questions or comments please contact Soma.