AUTEC User’s Guide

 

Justin Vandenbroucke

justinv@hep.stanford.edu

Stanford University

October 2002

 

Introduction

This document gives a brief overview of important information for collaborators (especially new ones) in the AUTEC acoustic neutrino detection study.  Hopefully the organization of code, data, and notes is good enough that it will not need to be changed and I’ll be able to easily answer questions down the line.

 

Web site

The study has a web site at http://hep.stanford.edu/neutrino/SAUND/.  Of particular interest to collaborators is the “internal” section, which has several useful documents sketching the progress of the study.

 

Contacts

Jack Cecil                               cecil@wpb.nuwc.navy.mil 

Our main Navy contact at AUTEC who helped make our use of it possible.  Knows a lot about the big picture of the array and is happy to help us use it well.  Located most often  in West Palm Beach, FL (not at AUTEC itself).

Dan Belasco                          belasco@wpb.nuwc.navy.mil

Our main contact at AUTEC Site 3, where our data acquisition system is.  Dan runs our system (turns it off when they are running a test and back on afterward); installs new data acquisition software when we give it to him; and transfers data to an external hard drive to be shipped to us.  He knows a good deal about computers (would be able to make minor upgrades to the system such as adding memory) and about the AUTEC electronics (hydrophones + amplifiers).  Phone contact with Site 3 is very difficult, but Dan responds to email daily.

Nikolai Lehtinen                   nleht@phys.hawaii.edu

Worked on the project as a post-doc during 2000 and 2001.  Researched and simulated the expected signal in preparation for the experimental study.  Designed the basics of the acquisition system (digital matched filter).  Did a good deal of analysis between when we started taking data in July 2001 and when he left in December 2001.  Knows the physics very well.

Yue Zhao                               newtonii@stanford.edu

Worked on analysis during the summer of 2002.  Analyzed the reflections of signals off the sea floor.  The analysis is useful for constraining the source location (to a cone) and verifying that we understand the acoustics well (transmission and reflection coefficients can be approximated).

Justin Vandenbroucke        justinv@hep.stanford.edu

Worked on the project as an undergrad and then as a temporary employee  from December 2000 to October 2002.  Wrote most of the online data acquisition software, starting from a core that Nikolai wrote.  Installed it at Site 3 and calibrated it with a light bulb drop in July 2001.  Upgraded the system in December 2001.  Analyzed data from July 2001 through October 2002 and made upgrades to the acquisition system that were transferred to Dan Belasco electronically.

 

Computers

Most of the AUTEC work was done  initially on two PC’s (on hep26.stanford.edu by Justin and on hep14.stanford.edu by Nikolai and Yue).  Some was also done on hep.stanford.edu, a UNIX system, as well as on the Stanford leland computing system.  In September 2002 almost all data, analysis tools, and notes were moved to erinyes.stanford.edu, a Linux cluster of 10 CPU’s.  All AUTEC work on erinyes is located  in /Data/AUTEC/.

 

Data

We currently have data from July 2001 to September 2002.  For all of Run I (from installation in July 2001 to upgrade in December 2001), data were copied onto CD’s at Site 3 and shipped to Stanford.  At that point we switched to copying the data to a 60 GB hard drive and shipping the drive back and forth (with a round-trip time of 1-2 months).  The data from the CD’s have been copied to erinyes and the CD’s have been thrown out. Compressed backups of all data (one zip file per daily folder of data) are maintained on hep, in /gratta7/AUTEC/AUTEC_data/, and on hep26, on the D drive.

 

Data shipments

Here is the procedure we have been following for data transfer:

The external hard drive for transferring data is shipped back and forth between Site 3 and Stanford via Jack Cecil in West Palm Beach.  When new shipments of data arrive on the external hard drive, the data are copied to erinyes.  This can be done with WinSCP and typically takes overnight.  A zip file is also made for each daily folder of data, and these zip files are copied to both hep and hep26.  The data are verified by reading all fields of all files and then Dan is notified that he can delete them from the Site 3 PC (he leaves copies there until this notification in case there is a problem).  The hard drive is then shipped to Jack Cecil:

 

Jack Cecil

Naval Undersea Warfare Center

Detachment AUTEC

801 Clematis St.

West Palm Beach, FL 33401

561-832-8566

 

Both Jack and Dan Belasco are notified via email to expect the hard drive.  Dan will then hold the hard drive until notified to ship it.  The PC at Site 3 can hold 40 GB of data.  If it fills up be can start compressing it, but this is time consuming.  Expect ~ 2 weeks in each direction for transit between Stanford and Site 3.

 

Log files and concluding notes

As of this summer I got more organized and started online log files in which I made entries detailing progress on the project.  Each entry includes the names of relevant Matlab programs, so this is probably the best way to learn about existing analysis code.  Some entries contain very useful information that would be time-consuming to duplicate, but unfortunately you have to wade through many entries to find it.  Hopefully briefly skimming the logs would be enough to have an idea of what’s there.  Yue made similar notes that are separted into different documents by subject.  Both Yue’s and Justin’s notes are available in the “internal” section of the web site.  Useful images (including plots) can be copied directly from these pages in .jpg format.

 

Online software

All past and current versions of the Labview online (data acquisition) software are archived on erinyes in /Data/AUTEC/AUTEC_programs_archive/.  Initially both current and old versions of each subprogram were kept in the same directory, but this became cumbersome.  Now each version of the code has a folder to itself (AUTEC_programs_yyyy.mm.dd/) and is independent of all other versions.

 

Online software upgrades

Significant upgrades can be made on hep26.  They can be debugged to a large degree using the simulated setup on hep26.  hep26 is an exact duplicate of system at Site 3 with the single exception of having a faster hard drive.  It has the same data acquistion card and BNC interface.  The BNC interface is plugged into a signal generator that can generate three independent signals (which are then duplicated among 7 digitized channels).  To upgrade the code, my procedure has been: duplicate the most recent folder;  rename it according to the date; make changes to the new version.  I then make the folder and its contents read-only, compress the folder, and put it on a web site.  I then email the URL to Dan Belasco who can download it and install it.  It should have the format AUTEC_programs_yyyy.mm.dd.zip.  That way he keeps all old versions and can revert to one if necessary.  It’s worthwhile to have Dan email ~5 minutes of data to you so you can verify it further than is possible with the hep26 setup.

 

Offline (analysis) software

Data can be analyzed on erinyes using hep26 as an X terminal.  There are two X servers on hep26: XSecure Pro (a trial version which quits after a couple hours but is fast), and Exceed (a trial version good for ~40 days which doesn’t quit but is quite slow with the Matlab editor for some reason).  All online software is on erinyes in /Data/AUTEC/AUTEC_analysis.  This folder has several subfolders, including m_files, mat_files, and text_files.  m_files contains Matlab programs.  Matlab can be run from an ssh connection to erinyes (with Exceed or Xsecure running) by typing “matlab –nodesktop” (the nodesktop option makes it run faster).  There are many independent Matlab programs that perform various analysis tasks and there are several utilities that are used by many programs, as you will discover by reading several analysis programs.

Recent Matlab programs are better documented than older ones.  The m_files folder contains many programs, some of which are obsolete.  Some but not all of these have been moved to m_files/obsolete/.  Matlab programs typically write the output of their analysis to .mat files in the mat_files folder.  A program called program_name.m typically analyzes an hour of data and writes it to a file program_name.yyyy.mm.dd.hh.mat in the folder mat_files/name/.  Another program would then be used to plot the outuput in these .mat files.  Most plots can be produced within a minute or so with a .m program that reads .mat files generated by a different program that may have taken many hours to run.

The m_files directory contains many independent pieces of analysis code.  Most are reasonably named, but it’s generally difficult to find a particular one for a particular task.  The best way to find them is likely to look through Yue and my notes as described above.  These give the names of relevenat .m programs.