Jeff Mangum's GBT Remote Observing Instructions Page

TIP Last Update: JeffMangum - 18 May 2011

GBT Remote Observing on Mac OSX 10.4.6

See http://www.gb.nrao.edu/gbt/remoteobserving.shtml for all of the goary details. The following are my Mac-specific instructions.


Step-By-Step Command Sequence

Since the descriptions below contain explanations which, though important, can sometimes get in one's way when trying to make a remote observing connection, I list below just the steps and commands necessary to effect a remote observing session. This assumes that you have already enabled your account for vncserver access.

  1. From terminal 1:
    1. ssh -Y stargate.gb.nrao.edu
    2. ssh titania.gbt.nrao.edu
    3. vncserver -geometry 1280x1024
    4. Server responds New 'titania:2 (jmangum)' desktop is titania:2, so X=2
  2. From terminal 2:
    1. Assume port 5901 is not being used, so that Y=1
    2. ssh -N -C -L 5901:titania.gbt.nrao.edu:5902 YOURLOGIN@stargate.gb.nrao.edu
  3. Start Chicken of the VNC
    1. Go to Connection, Open Connection
    2. Enter Host = localhost, Display = Y, your password, check Remember Password, and check Allow other clients to connect. The "Y" in the display parameter above is the "Y" in the port number chosen above.
    3. Hit the Connect button.
  4. Once logged in and connected, start cleo and astrid:
    • astrid
      1. Open a terminal window on the GBT machine (usually titania).
      2. Type the command astrid&. Astrid will start.
      3. Since the pointing and focus fitting routines are anal-retentive by default, it is best to set the heuristics to be relaxed. This is done in astrid as follows: Tools/Options/Heuristics/Relaxed.
    • cleo
      1. In the terminal window opened to start astrid, type the command cleo. A cleo application menu thingy (called "Cleo Launcher") will open.
      2. Go to Launch/Cleo Container. A "Cleo Container" application will open.
      3. Within the "Cleo Container" go to Launch/status, Launch/Utilities and Tools/Scheduler and Skyview, and Launch/Utilities and Tools/Talk and Draw to open tabs within the Cleo Container for these three functions.
      4. 2011-05-18 Update: cleo status fails often, and when it does run it uses a lot of resources. A better option is gbtstatus from any terminal window (best to open a new terminal to run this as you have to resize the window).
  5. When your observing run is complete, log out from the GBT computer (titania) and be sure to kill your vncserver connection with the command vncserver -kill :N in terminal numbe 1 above, where "N" is your vncserver session number (2 in this example).


What You Need

  • A VNC server application. I use Chicken of the VNC.
  • An ssh server.
  • Not to forget the "-Y" switch on ssh when using ssh from a Mac.


Step-By-Step Instructions

  1. If this is your first time running VNC on the GB computing system, you need to set your VNC password as follows:
    1. Log into the NRAO computer: ssh -Y stargate.gb.nrao.edu
    2. In the terminal window on the remote (NRAO) computer, type at the Linux prompt: vncpasswd
    3. Enter your chosen VNC server password. Remember, this password should be different from your NRAO Linux account password as it will be shared with support staff when you require assistance.
  2. Start the VNC server on the GBT computer:
    1. Log into the NRAO computer (you can use the same login session as you started above if you wish): ssh -Y stargate.gb.nrao.edu
    2. Once you are logged into the NRAO computer, and regardless of your remote computer:
      1. In the terminal window on the remote (NRAO) computer, type at the Linux prompt: ssh titania.gbt.nrao.edu
      2. At the Linux prompt on titania, type: vncserver. If you have a big monitor connected, you can use something like vncserver -geometry 1280x1024.
      3. Once you have typed vncserver, the system will reply (e.g.) New 'titania:2 (USERNAME)' desktop is titania:2 In this case, your VNC session number is 2. Remember this number since you will need it later. In the instructions below, the VNC session number is designated as X.
      4. Leave this connection open to the server. Later, it will be used to kill processes on titania associated with the VNC session.
  3. Open up an SSH tunnel from your local computer to the GBT computer. Do this by starting another terminal on your local computer and typing (the "Y" is a free local port on your machine, while the "X" in the port number is your VNC server session number from above): ssh -N -C -L 590Y:titania.gbt.nrao.edu:590X YOURLOGIN@stargate.gb.nrao.edu. For the "Y" in the above, consider the following:
    • If you are running the Apple Remote Desktop Manager (installed in October 2007 on many Macs in CV by CIS), you cannot use "0", as this remote desktop application uses port 5900.
    • A good start is to try "1", but higher numbers may be necessary.
    • If you have trouble finding a free port use netstat -a | grep 59 to list all ports in use.
  4. Start the VNC viewer on your local computer. Do this by:
    1. Starting Chicken of the VNC.
    2. Go to Connection, Open Connection
    3. Enter Host = localhost, Display = Y, your password, check Remember Password, and check Allow other clients to connect. The "Y" in the display parameter above is the "Y" in the port number chosen above.
    4. Hit the Connect button.
  5. The VNC Viewer window to titania will now appear. In this window you can start astrid, start cleo, open xterms, etc. almost as if you were sitting in front of a titania screen.


Shutting Down Your VNC Server

From one of your titania login sessions, and regardless of your remote computer:

  • In the terminal window on the remote (NRAO) computer, type at the Linux prompt: vncserver -kill :N, where N is the VNC server number.


Starting astrid and cleo

  • astrid
    1. Open a terminal window on the GBT machine (usually titania).
    2. Type the command astrid&. Astrid will start.
    3. Since the pointing and focus fitting routines are anal-retentive by default, it is best to set the heuristics to be relaxed. This is done in astrid as follows: Tools/Options/Heuristics/Relaxed.
  • cleo
    1. In the terminal window opened to start astrid, type the command cleo&. A cleo application menu thingy (called "Cleo Launcher") will open.
    2. Go to Launch/Cleo Container. A "Cleo Container" application will open.
    3. Within the "Cleo Container" go to Launch/status, Launch/Utilities and Tools/Scheduler and Skyview, and Launch/Utilities and Tools/Talk and Draw to open tabs within the Cleo Container for these three functions.


A Caution About Spectrometer Input Power Levels

ALERT! 2007/10/18: The following is no longer necessary. Now iftarget is set automatically and should not be set in the spectrometer setup file.

Currently, one must set the iftarget parameter in your spectrometer setup file in order to properly balance the input levels into the spectrometer. You should set iftarget in the range 0.5 to 0.1. To see that this works during your observations you should, in cleo:

  1. Look at the spectrometer field in the devices tab
  2. The numbers should be about 1.4 when you are using the 50 MHz or 12.5 MHz bands;
or if using 800 or 200 MHz, they should be about 0.8

It is anticipated that, in the very near future, users will not have to set iftarget, and that the M&C system will set the proper input level appropriately.

-- JeffMangum - 15 Feb 2007

A Note About Receiver Configuration Warnings in Astrid

I regularly see the following warning when setting-up the GBT receivers:

Checking telescope
[18:45:36] Warning: Configuration complete but inconsistencies were found
between the M&C system and the configuration tool. Verify the configuration
[18:45:36] (manager,    parameter,   expected value,  actual value )
[18:45:36] ('Rcvr4_6', 'tuning_frequency', '4786.9215', '4786.921')
<<<<<<<<<<<

According to Melinda Mello, this warning notifies the user that the values read back from the telescope are different than the values that the config tool sent to the telescope. Sometimes this can indicate a serious issue, but many times it results from a rounding difference. The expected value and the actual value of the Manager parameter is provided to the user so that they can make the determination (or contact a support scientist) as to whether there is a serious issue with the system. Within all of my observations the warning indicates either a rounding error between what the config tool sent to the Receiver Manager and what it reports back in the tuning frequency or a data type conversion difference in the LO manager. These warnings indicating minor rounding differences and are innocuous.

-- JeffMangum - 2011-05-08

Filling data into SDFITS

The first step in reducing GBT data using GBTIDL is to convert the data to SDFITS format. This is accomplished using a program called sdfits, which runs from the unix prompt, only in Green Bank.

Help is available for the sdfits program as follows:

  • sdfits -help

In addition to the online help, the sdfits program has full documentation including development status, known issues, request list, and usage examples.

The sdfits program offers three levels of calibration, identified by the -mode switch as "raw", "cal", or "avg". Users of GBTIDL will generally want to select no calibration (-mode=raw) and use IDL routines to do the calibration, instead. With -mode=raw, the sdfits file will contain one row of data for each phase of the data collection. That is, sig_calon, sig_caloff, ref_calon, and ref_caloff phases are all stored individually in the SDFITS file.

The sdfits program writes data into the current directory by default, so it is wise to change into a directory in which you can write large files before running sdfits. In Green Bank, you have a quota on your home directory so it is best not to fill large datasets into your home area.

2009/03/19: The current release of SDFITS must be run on a 32-bit machine, and several of the machines in GB, including ssh.gb (prospero) and euclid, are now 64-bit machines. You can run SDFITS on the following machines:
  • fourier
  • bratac

There is an online computer listing which might be helpful.

Typical use of SDFITS looks like this:

  • ssh fourier.gb.nrao.edu
  • cd /home/scratch/username
  • NOTE: Starting 2011-06-01 the -fixbadlags option is now the default. Don't need to set this flag unless you do not want to fix bad lags (so you would use the -nofixbadlags option)
  • To process just one GBT data file: sdfits -mode=raw -backends=acs /home/gbtdata/AGBT01A_001_01
  • To write multiple sessions to one SDFITS file: sdfits -mode=raw -backends=acs -append /home/gbtdata/AGBT01A_001_01 MyData

The resulting SDFITS file, assuming it contains spectrometer (ACS) scans, is called AGBT01A_001_01.raw.acs.fits. If the specified scan range also includes data from the DCR or Spectral Processor, then a separate output file will be created for each backend.

It is easy to work with data from multiple SDFITS files at the same time in GBTIDL. Simply use dirin instead of filein. Since scan numbers may repeate from one observing session to another (even within the same project) it often is simpler to work with one SDFITS file at a time, although GBTIDL does provide ways to work with multiple occurances of the same scan number.


Using GFM to View your Project's FITS Files

It is often useful to look at your project's FITS files, such as your pointing or focus measurements, after your run is over. For example, you can use the peak amplitude values derived from your pointing and focus measurements to determine your flux calibration. To use GFM on one of the GB machines to peruse your data do the following:

  1. ssh -Y euclid.gb.nrao.edu (or fourier will also work)
  2. GFM
  3. select "File -> Open"
  4. select your project directory, then select the "ScanLog.fits" file in the project directory

GFM will eventually fill in some header information for each scan in the left panel. At this point you can peruse the scans in your project:

  • Click a scan in the left panel (e.g. scan 1, the first of a peak) to see the data for that scan.
  • You will see LL polarization by default. To examine RR pol, you need to go to the Tools -> Options -> Data Processing menu. Or, you can go to the "Continuum" tab and look at uncalibrated data there.

If you want to use the pointing and focus scans to derive your flux calibration:

  • Select the polarization that you want to look at from the "Tools / Options / Data Processing" tab
  • Select the first of your pointing scans
  • Select the "Pointing" tab
  • Read the "Hgt" value from the fit on the plot

Do this for all pointing measurements/polarizations.

-- JeffMangum - 2009-03-20
Topic revision: r23 - 2011-06-03, JeffMangum
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