CRUISE REPORT: SR01b
(Updated MAR 2017)






Highlights


                              Cruise Summary Information

                     Section Designation  SR01b
      Expedition designation (ExpoCodes)  74JC20161110
                                 Aliases  JR16002
                        Chief Scientists  Yvonne Firing / NOC
                                   Dates  2016 NOV 10 - 2016 DEC 03
                                    Ship  RRS James Clark Ross
                           Ports of call  Mare Harbour, Falkland Islands - 
                                          Port Stanley, Falkland Islands

                                                      54° 40.02’
                   Geographic Boundaries  57° 59.06’              54° 34.97’
                                                      61° 02.94’

                                Stations  30
            Floats and drifters deployed  3 Deep APEX floats deployed
          Moorings deployed or recovered  0

                                 Contact Information:
                                   Dr Yvonne Firing
                   National Oceanography Centre • Southampton • UK
              Tel: +44 (0)23 8059 9669 • email: yvonne.firing@noc.ac.uk




















National
Oceanography Centre
NATURAL ENVIRONMENT RESEARCH COUNCIL




                             National Oceanography Centre

                                 Cruise Report No. 41

                         RRS James Clark Ross Cruise JR16002
                                 10 NOV - 03 DEC 2016
                    Hydrographic measurements on GO-SHIP line SR1b

                                 Principal Scientist
                                       Y Firing






                                         2017










National Oceanography Centre, Southampton 
University of Southampton Waterfront Campus 
European Way
Southampton 
Hants SO14 3ZH 
UK

Tel:  +44 (0)23  8059 9669
Email: yvonne.firing@noc.ac.uk












©  National Oceanography Centre, 2017




















































DOCUMENT  DATA SHEET



AUTHOR                                                            PUBLICATION
    FIRING, Y et al                                               DATE      2017
TITLE
    RRS James Clark Ross Cruise JR16002, 10 Nov - 03 Dec 2016. Hydrographic 
    measurements on GO-SHIP line SR1b.
REFERENCE
    Southampton, UK: National Oceanography Centre, Southampton, 43pp.
    (National Oceanography Centre Cruise Report, No. 41)
ABSTRACT
     RRS James Clark Ross cruise JR16002 included work contributing to two National 
     Capability projects.

     Bottom pressure recorder (BPR) landers previously deployed on the northern and 
     southern continental slopes of Drake Passage to monitor ACC transport as part of 
     Antarctic Circumpolar Current Levels from Altimetry and Island Measurement 
     (ACCLAIM) were recovered, wrapping up a 28-year time series. The twenty-second 
     complete occupation of the Drake Passage GO-SHIP section SR1b obtained full-depth 
     temperature, salinity, and lowered ADCP velocity profiles at 30 stations, along 
     with water column samples for oxygen isotope analysis and with underway 
     measurements, with the objectives of investigating and monitoring interannual 
     variability and trends in Antarctic Circumpolar Current structure and property 
     transports and Southern Ocean water mass properties as part of Ocean Regulation 
     of Climate by Heat and Carbon Sequestration and Transports (ORCHESTRA). 
     Deployment of three Deep Apex autonomous profiling floats was also intended to 
     contribute to ORCHESTRA as well as the global Deep Argo programme.






KEYWORDS

ISSUING ORGANISATION    National Oceanography Centre
                        University of Southampton Waterfront Campus
                        European Way
                        Southampton SO14 3ZH    UK
                        Tel: +44(0)23 80596116    Email: nol@noc.soton.ac.uk
     A pdf of this report is available for download at: http://eprints.soton.ac.uk


                         This page intentionally left blank



















































Contents

1  Personnel                                                                         8

2  Itinerary and Cruise Track                                                        8

3  Objectives                                                                        9

4  Narrative                                                                         9

5  Bottom pressure recorder landers                                                 12
   5.1  Lander 1                                                                    13
   5.2  Lander 2                                                                    13
   5.3  Lander 3                                                                    14
   5.4  Lander 4                                                                    14
   5.5  Lander 5                                                                    15

6  Hydrographic Measurements                                                        15
   6.1  CTD operation                                                               16
   6.2  Lowered Acoustic Doppler Current Profiler (LADCP) operation                 17
   6.3  Data Processing                                                             18
        6.3.1  CTD processing for each cast                                         18
        6.3.2  LADCP processing for each cast                                       19
   6.4  Water sample collection and analysis                                        20
        6.4.1  Dissolved oxygen analysis                                            21
        6.4.2  Salinity analysis                                                    22
   6.5  CTD data calibration and results                                            23
   6.6  References                                                                  24

7  Deep APEX autonomous profiling floats                                            25
   7.1  Float S/N 0015 (rudics ID 0046)                                             27
   7.2  Float S/N 0013 (rudics ID 0049)                                             28
   7.3  Float S/N 0012 (rudics ID 0048)                                             29

8  Underway Data Collection and Processing                                          30
   8.1  Configuration of linux workstation 'fola'                                   30
   8.2  SCS data streams                                                            30
   8.3  Underway surface thermosalinograph and salinity calibration                 31
   8.4  Bathymetry                                                                  31
   8.5  Vessel Mounted ADCP                                                         32
        8.5.1  Configuration and K-sync                                             32
        8.5.2  Data quality                                                         33
   8.6  EK60                                                                        33

9  AME Report                                                                       34
   9.1  Instrumentation                                                             34
   9.2  CTD Communications Issues                                                   36
   9.3  Additional notes and recommendations for change / future work               39

10  Acknowledgments                                                                 43

CCHDO Data Processing Notes                                                         44

















List of Figures

    1  JR16002 cruise track                                                          9
    2  Stations 1-10: LADCP zonal (u, blue) and meridional (v, red) velocity 
       profiles and error amplitude (gray dashed) based on LDEO IX inversion 
       using navigation data and bottom tracking.                                   20
    3  Stations 11-20:  LADCP zonal (u,  blue) and meridional (v, red) velocity 
       profiles and error amplitude (gray dashed) based on LDEO IX inversion using 
       navigation data and bottom tracking.                                         21
    4  Stations 21-30:  LADCP zonal (u,  blue) and meridional (v, red) velocity 
       profiles and error amplitude (gray dashed) based on LDEO IX inversion 
       using navigation data (all stations) and bottom tracking (all except 22 
       and 23).                                                                     22
    5  Good Niskin bottles (blue circles) and good samples (red xes) measured 
       (for SBE35 T), analysed (for salinity and O2), or stored (for δ18O; 
       duplicates indicated by yellow dots).                                        23
    6  Histograms of temperature and salinity residuals, and depth profiles of 
       salinity residuals with colour indicating station number (blue to red).      24
    7  Scatter plot of bottle and calibrated CTD oxygen (left, µmol kg-1), and 
       residuals (µmol kg-1) as a function of depth, with colour indicating 
       station number (blue to red).                                                25
    8  Calibrated temperature on SR1b, 18-24 November 2016. The contours and 
       columns of filled circles both come from the 2-dbar profiles (downcast 
       profiles except where other-wise noted in the text).                         26
    9  Calibrated salinity on SR1b, 18-24 November 2016. The contours and 
       columns of filled circles both come from the 2-dbar profiles (downcast 
       profiles except where otherwise noted in the text).                          27
   10  Calibrated dissolved oxygen on SR1b, 18-24 November 2016. The contours 
       and columns of filled circles both come from the 2-dbar profiles 
       (downcast profiles except where otherwise noted in the text).                28
   11  CTD wire termination with arrows indicating deformation of the cable.        38
   13  SME32/SBE35 Y-cable with damage visible.                                     39




List of Tables

   1  SR1b CTD/LADCP stations.                                                      14











1  PERSONNEL

    Scientific & SP Personnel               Ship's Personnel
Yvonne Firing (PSO)  NOC             Ralph Stevens        Master
Anastasiia Domina    U. Liverpool    Timothy Page         Chief Officer
Elaine Fitzcharles   BAS             Iain Mackenzie       2nd Officer
Giuseppe Foti        NOC             Waveney Crookes      3rd Officer
Geoff Hargreaves     NOC             Robert Bellis        3rd Officer
Emlyn Jones          NOC             Thomas Dutton        Deck Cadet
Madeline Miller      Harvard U.      Michael Gloistein    ETO Comms
Eric Sanchez Muñoz   U. Concepción   Neil MacDonald       Chief Engineer
Eleni Tzortzi        U. Hamburg      Gert Behrmann        2nd Engineer
Hugh Venables        BAS             Marc Laughlan        3rd Engineer
                                     Aleksandr Hardy      4th Engineer
William Clark        BAS AME         Craig Thomas         Deck Engineer
Andy England         BAS IT          Stephen Amner        ETO
                                     Richard Turner       Purser
                                     Helen Jones          Doctor
                                     David Peck           Bosun/Sci. Ops
Stacey Adlard        BAS             Albert Martin Bowen  Bosun
Neil Brown           BAS             George Dale          Bosun's Mate
Paul Cousens         BAS             Sheldon Smith        AB
Caroline Elvidge     BAS             Samuel English       AB
Iain Gordon          BAS             Graham Waylett       AB
Ben Hallgath         BAS             Robert Leech         AB
Matthew Jobson       BAS             Francisco Hernandez  AB
Terence Lay          BAS             Glyndor Henry        Motorman
Theresa Murphy       BAS             Gareth Wale          Motorman
Renny Nisbet         BAS             Colin Cockram        Chief Cook
Jack Olney           BAS             Gary Morgan          2nd Cook
James Scott          BAS             Lee Jones            Steward
Douglas Stacey       BAS             Nicholas Greenwood   Steward
Jennifer Symmons     BAS             Graham Raworth       Steward
Alexander Taylor     BAS             Rodney Morton        Steward




2  ITINERARY AND CRUISE TRACK


The cruise track and science operation sites are shown in Figure 2.


Figure 1: JR16002 cruise track









3  OBJECTIVES


RRS James Clark Ross cruise JR16002 was a combination of logistics and two science projects: 

  • Continuous Ocean Monitoring Methods: Drake Passage
    A Hibbert, NOC
    Aim: To recover five bottom pressure recorder (BPR) landers from the continental 
    slopes on either side of the passage, contributing to the long time-series of 
    Antarctic Circumpolar Current transport through Drake Passage; to maintain tide 
    gauges at Stanley, Vernadsky, and Rothera.

    Funded by NERC National Capability ACCLAIM.

  • Hydrographic measurements in Drake Passage 
    Y Firing, NOC
    Aim:  To make high-quality repeat hydrographic measurements on GO-SHIP line SR1b, 
    continuing a near-annual time series begun in 1993, to obtain complementary 
    station and underway currents   and underway meteorology data, and to deploy deep 
    profiling floats, in order to monitor Southern Ocean watermasses and 
    circulation pathways and Antarctic Circumpolar Current volume and property 
    transport.

    Funded by NERC National Capability LTS-M ORCHESTRA




4  NARRATIVE


The JCR’s planned departure from the Falkland Islands on 8 November was delayed by fueling 
schedules, but we left Mare Harbour on 10 November, headed for Signy. Underway data 
collection was started when we reached open water. A test CTD/LADCP cast to 1000 m was 
conducted on the way to Signy, mid-day on the 12th, in order to test equipment, systems, and 
instruments (all of which performed nominally); it was also useful for showing the 
hydrography volunteers how to conduct casts, water sampling, and data processing. Some 
weather was encountered during the crossing to the South Orkneys.
   
We reached Signy on the 13th, and the initial station party went ashore in a Humber, 
determining that (fortunately) the bay and dock were clear of ice, and ice/snow cover at the 
station was also lower than average. Over the next two and a half days, with the assistance 
of work parties from the science and other SPPs, the snow and ice was cleared away, station 
supplies were brought ashore from the cargo tender and carried to their destinations, and the 
station made ready for occupation and operation. On the 15th, some personnel were taken to 
neighboring Gourlay Point to assist in setting up for penguin colony monitoring   by moving 
nest-marking bricks to the colonies, as well as see the nesting Adelies and Gentoos up close. 
With the station in good condition (in particular, with operating generator and radio), the 
JCR departed Signy in the late afternoon of the 15th and headed back northwest toward 
Burdwood Bank to start the hydrography and BPR work.
   
As we were approaching Burdwood Bank and the start of the SR1b section, it was discovered 
that there had been more serious damage than previously realised to the CTD winch wire on the 
preceding cruise. BAS AME headquarters instructed the ship to switch from this wire to a 
secondary drum, which turned out to require a day of work on the part of the engineers and 
AME tech to get it to a working state. In the interim, since we could not begin the CTD 
section, we proceeded to the BPRs on the northern continental slope, visiting all three 
through the day on the 18th, although only two were successfully recovered (Section 5).
   
We then returned to the 200-m isobath and started SR1b CTDs on the evening of the 18th, 
proceeding quickly through the stations over the next days.  The weather was exceptionally 
good during this part of the cruise, such that we had no weather delays on the entire 
section. The plan for the floats was to deploy all three south of the Polar Front, to keep 
them from being swept quickly out of the area.  It appeared we had crossed the Polar Front at 
station 14, but currents were still strong at stations 14 and 15, so the first float was 
deployed at station 16, in the early hours of the 21st, and the second at station 19, later 
the same day.
   
On station 22, communications with the CTD failed while it was ascending at about 500 m. They 
returned at about 250 m, and the CTD was recovered to deck normally. Given the issues earlier 
in the cruise, as well as more energetic seas in the preceding hours, the initial hypothesis 
was that the problem was in the CTD winch wire. This was reterminated twice, as described in 
Section 9, until the termination tests passed, adding a short delay before starting station 
23.
   
On station 23, CTD communications failed again, this time when the upcast had just started, 
at about 3430 m; they returned around 2300 m, and were briefly lost again around 2100 m. The 
upcast proceeded from there, and once the CTD was recovered the Sea Unit was swapped out for 
a spare, along with the dissolved oxygen sensor (which had briefly appeared to give erroneous 
readings after the comms failure). For both stations 22 and 23, no bottles were able to be 
fired during the communications dropouts, and scans were not incremented, but otherwise the 
records appeared nominal, and as the downcasts were complete we did not attempt to redo the 
stations. The last float was deployed following station 23, on the evening of the 22nd, and 
we continued with the CTD section.
   
Stations 24 and 25 ran normally. On station 26, CTD communications were lost in the middle of 
the downcast, and did not resume; therefore, the CTD was recovered for additional testing. 
The CTD winch wire again appeared slightly deformed, so was reterminated in a series of 
stages (Section 9). Tests were   run with various configurations of the wire, Sea unit, and 
CTD sensors, which eventually led to checking the SBE32/SBE35 Y-cable beneath the CTD, and 
finding it to be damaged. Once this cable was replaced, the communications problems did not 
recur.
   
During this process, we visited the two southern Drake Passage BPRs, which were conveniently 
nearby at this point, and successfully recovered one of the two. Since the previous cast had 
been incomplete, we returned to station 26 and conducted a second cast, this one and the rest 
of the stations were successful. Station 30 was completed very early on the 24th, marking 
just under 5 days from the start of the section.
   
The second float deployed had leaked on the 23rd, and we considered returning to recover it 
after completing SR1b, given the current and forecast weather conditions, and the desire not 
to delay the Rothera call further, we decided to head for Rothera and attempt a recovery on 
the return.
   
After steaming through the Bransfield Strait, we headed out to the continental slope to skirt 
around the ice on the way to Adelaide Island.  Although the ice had appeared to be thinning 
and we had hoped a storm during our transit would blow it offshore, the island was still 
surrounded by porridge ice.  We made it to within 55 (as-the-crow-flies) nautical miles of 
Rothera, but were turned back by increasing ice pressure on both the morning of the 27th and 
the morning of the 28th. After consultation with Cambridge, the decision was made to return 
to Stanley, fly people and limited supplies into Rothera via the DASH, and attempt the rest 
of the base relief at a later date.
   
The leaking float was by this time drifting rapidly eastward, but fortunately we were given 
the authorisation to detour to recover it, and reached it on 1 December.  The sea state was 
not ideal but the float was eventually spotted, lost, and spotted again with the help of an 
updated GPS fix. A heroic recovery followed, and, having determined the water had not leaked 
into the battery and turned it into a bomb, we secured the float and proceeded back to Port 
Stanley.
   
Underway data collection was stopped when we reached the continental shelf on the evening of 
2 December, and we docked at Port Stanley on the morning of the 3rd.




5  BOTTOM PRESSURE RECORDER LANDERS
   Geoff Hargreaves

   
Personnel from National Oceanography Centre (Liverpool) were present on cruise JR16002 to 
attempt the recovery of five bottom pressure recorder (BPR) landers that had been deployed in 
the Drake Passage during the previous twenty-four months, as part of an ongoing National 
Capability research programme. This programme has now finished so the equipment that is 
already in place has to be recovered.
   
There were five landers deployed across Drake Passage, three in the northern section near 
Burdwood Bank and two in the southern section near Elephant Island. The recovery of the BPRs 
was be undertaken during the hydrography transect as the deployment positions are on the SR1b 
CTD line. The hydrography section began in the northern part of Drake Passage and as such, 
the three northern BPRs were to be recovered first. There were two BPRs to recover from the 
1100m contour line on the slope of Burdwood Bank and one from 2000m depth.
   
Three landers, deployed in January 2015, were recovered, while the two deployed in January 
2016 failed to rise from the seabed, although communications were successful and all release 
units (two on each lander) were responsive. Details follow, with the landers designated 1 - 5 
in the order in which they were visited on JR16002.


5.1  Lander 1
   
The first BPR position the ship went to was 54°58.800 S, 57°58.031 W; this BPR was deployed 
in January 2015. The acoustic deck unit was connected to the ship's hull transducer and the 
EA600 echo sounder and swath bathymetry were deactivated making acoustic conditions perfect 
and quiet. Communication with both of the acoustic release units on the lander was clear and 
trouble free. The release command was transmitted to both acoustic units and both responded 
by indicating the command had been received and activated.
   
The release system on the landers is a burn wire-based system that requires a voltage to be 
applied to a piece of Inconel wire loop and a current then passes through the water to a 
cathode.  The Inconel wire gradually dissolves and once completed, the release module (which 
is held together by a pin passing through the Inconel loop) separates and the release gate 
can open, dropping the ballast weight that secures the lander to the seabed.  The frame, 
which is now positively buoyant, ascends to the surface where it can be recovered. Five 
minutes after transmitting the release commands the lander had released from the seabed; it 
ascended at 0.5 m s-1 to the surface where it was recovered.


5.2  Lander 2
   
The ship then repositioned to the next lander position at 54°58.817 S, 57°59.309 W; this 
lander was deployed in January 2016. Once again acoustic conditions were excellent and both 
acoustic units on the lander were activated and sent the command to activate the release.  
The acoustic release units on the lander behave as transponders, in that they reply on a 
certain frequency when they detect a signal on a different frequency.  Each unit responds to 
different frequencies and this allows the operator on the ship to communicate with more than 
one device. In normal operation, one ping is transmitted when it detects the correct 
frequency signal. Once the release command is received, four pings are transmitted.
   
Both of the acoustic release units on the lander were responding with four pings after having 
received the release command. Since the acoustic conditions were very good, this could be 
heard through the headphones of the acoustic deck unit and also observed on the display. 
After an hour on station, pinging to the acoustic units on the seabed, there was still no 
sign of the lander releasing and coming back to the surface. All of the signs were that the 
acoustic releases were working normally but the lander hadn't separated from the ballast 
weight.  The recovery attempt was halted and the ship proceeded to the next site.


5.3  Lander 3
   
The third lander visited was located at -55.03909 S, -5794898 W at a depth of 2000 m. The 
lander deployed at this location in January 2015 was a different design from the previous two 
and required the use of an over side transducer or dunker unit, rather than the hull 
transducer.  This acoustic system transmits a coded signal to the sea unit. Communication was 
established and the release sequence initiated. This involved transmitting a sequence of 
commands to the sea unit, culminating in the release command. This unit uses a motor driven 
release mechanism.  It was necessary to interrogate the unit again to determine if the 
release operation had been successful, which it had. This lander ascended at about 1 m s° to 
the surface and once spotted on the surface was quickly recovered.


5.4 Lander 4
   
At the southern end of the Drake Passage there were two BPRs to recover, both at a depth of 
1000 m. The BPR at 60°50.9842 S, 54°41.9039 W, deployed in January 2015, was attempted first. 
Both acoustic releases were communicating well and the first unit was sent the release 
command and responded to indicate it had received the command. The second unit was sent the 
release command and it appeared to indicate it had received the command. The ship moved a few 
hundred metres away from the deployment position whilst the acoustics were monitored for sign 
of the lander releasing from the seabed.  One acoustic was responding with four pings and the 
other was responding with a single ping. The release command was sent several times to the 
second unit to try and activate the release mode but without success. After nearly an hour on 
station, the lander still had not released and the ship was repositioned to be directly above 
the BPR. The release command was transmitted again to both sea units and both units responded 
positively to indicate that it had been received.  Eight minutes later and the lander 
released from the seabed, ascended to the surface at about 1 m s? and was recovered onto the 
ship.


5.5  Lander 5
   
The ship then positioned itself at the site of the final BPR, deployed in January 2016, at 
60°51.1070 S, 54°43.7376 W. Once again, the release commands were transmitted to both release 
units and both replied to indicate they had received the command. The units were periodically 
interrogated to determine if the lander had released from the seabed but this did not happen. 
After an hour of trying to recover the lander, the ship left the site and headed north to 
continue with the CTD stations. About six hours after leaving the BPR site, the ship was back 
again to undertake the CTD cast at that position.  This allowed the acoustic sea units to be 
checked and both were found to be responding, indicating that the frame was still on the 
seabed.



6  HYDROGRAPHIC  MEASUREMENTS
   Yvonne Firing, Madeline Miller, Eric Sánchez Muñoz


The 30 CTD/LADCP casts on SR1b are summarised in Table 1.


Table 1: SR1b CTD/LADCP stations.

stn   bottom date,  start  end   latitude  longitude   max CTD  Niskins  float
       time (UTC)   time   time     (S)       (W)       press
                                                        (dbar)
---  -------------  -----  ----  ---------  ---------  -------  -------  -----
001  16/11/18 2302  2255   2309  54 40.02’  57 58.95’    157       4
002  16/11/19 0123  0108   0144  54 55.31’  57 59.01’    711       6
003  16/11/19 0253  0234   0318  54 58.58’  57 58.96’    981       6
004  16/11/19 0437  0406   0516  55 00.40’  57 59.00’   1675       8
005  16/11/19 0647  0608   0733  55 04.19’  57 58.97’   2239       8
006  16/11/19 0910  0821   1006  55 07.28’  57 58.99’   2777       8
007  16/11/19 1148  1053   1250  55 10.21’  57 59.01’   3159      10
008  16/11/19 1444  1334   1610  55 12.86’  57 59.00’   4068      12
009  16/11/19 1935  1824   2102  55 31.01’  57 59.06’   4284      12
010  16/11/20 0049  2323   0226  55 50.04’  57 49.20’   4832      12
011  16/11/20 0556  0456   0705  56 09.02’  57 37.30’   3438      10
012  16/11/20 1038  0931   1156  56 28.13’  57 23.47’   3859      12
013  16/11/20 1502  1408   1605  56 47.00’  57 13.86’   3242      10
014  16/11/20 1927  1821   2044  57 06.82’  57 00.65’   3791      12
015  16/11/20 2345  2242   0100  57 25.28’  56 49.81’   3727      12
016  16/11/21 0438  0337   0603  57 44.19’  56 38.70’   3585      24     0015
017  16/11/21 1000  0848   1140  58 03.04’  56 26.85’   4010      12
018  16/11/21 1532  1426   1651  58 22.24’  56 14.87’   3951      12
019  16/11/21 2027  1924   2157  58 40.98’  56 03.26’   3809      24     0013
020  16/11/22 0238  0115   0358  59 00.20’  55 51.50’   3836      12
021  16/11/22 0827  0719   0945  59 20.03’  55 39.07’   3818      12
022  16/11/22 1409  1307   1516  59 39.79’  55 26.75’   3737       9
023  16/11/22 2142  2034   2233  59 59.43’  55 14.05’   3552      18     0012
024  16/11/23 0307  0208   0416  60 19.92’  55 02.06’   3488      10
025  16/11/23 0750  0657   0855  60 40.05’  54 49.52’   3148      12
026  16/11/23 2011  1927   2112  60 47.98’  54 44.52’   2618      15
027  16/11/23 2252  2222   2334  60 50.00’  54 43.26’   1750      12
028  16/11/24 0043  0026   0110  60 51.04’  54 42.55’    958       8
029  16/11/24 0242  0231   0300  60 58.96’  54 37.65’    579       7
030  16/11/24 0415  0407   0426  61 02.94’  54 34.97’    348       4



One stainless steel CTD system was prepared with a 24-way carousel. Details of the 
instrumentation are given in Section 9. Operation was normal on the 30 stations conducted 
during the cruise, with the following exceptions.

  • During station 20, the bow thruster failed when the rosette was descending around 
    600 m, leading to the CTD being recalled; however, as the reset was successful by 
    the time the CTD had reached about 150 m, the downcast was recommenced.  Not 
    returning the CTD all the way to the surface meant that the downcast depth profile 
    for station 20 was discontinuous.
  
  • On station 22, communications between the underwater package and the deck unit 
    failed between 505 and 250 m on the upcast.

  • On station 23, they failed on the upcast between approximately 3428 m (shortly 
    after starting up from the bottom) and 2300 m, and again briefly around 2100 m.

  • On the first cast at station 26, a CTD fault on the downcast at 1630 m (in 2540 
    msw) led to recovery of the CTD; this station was revisited and a successful full-
    depth cast conducted following BPR operations and repairs to the CTD cables.

The CTD communications failures are discussed in Section 9, and their handling in data 
processing in Section 6.3.1.



6.1  CTD operation

Data were acquired with SeaSave V 7.22.3.
   
After each cast, two batch scripts were run: BASsvp, which prepares a sound velocity profile 
and a CTD listing for transmission to the UK Met Office; and JR16002  sbeproc, which, in 
three steps, exports as text file (.cnv), applies time alignment of oxygen data (5s for 
sbeox0Mm/Kg and sbeox0V, but note that the hysteresis correction is applied later in Mexec 
processing, NOT here), and applies a cell thermal mass correction for conductivity (alpha = 
0.03. tau = 7.0000 on both primary and secondary).  The resulting files have 
suffix_align_ctm. The batch scripts also copied the raw and processed data onto the network 
drive, legdata.
   
SBE35 temperature data were uploaded using SeaTerm after finishing a cast. SBE35 temperature 
data can be logged when a Niskin bottle is fired. If the SBE35 is set to 8 samples, it 
requires approximately 13 seconds to make a measurement, calculated as 8 * 1.1 seconds plus 
an overhead; the procedure followed for bottle firing was therefore to wait 30 s for 
equilibration, fire a bottle, and wait 15 s to ensure the SBE35 measurement had been taken.  
Data are stored internally and must be downloaded at the CTD deck unit as a separate process 
from the CTD data transfer. The SBE35 data are then transferred as a collection of ASCII 
files.



6.2  Lowered Acoustic Doppler Current Profiler (LADCP) operation
   
The 300-kHz Workhorse LADCP was installed in a downward-looking configuration on the CTD 
rosette (see Section 9). The instrument was configured (right) to sample 25 x 8-m bins, with 
data collected in beam co-ordinates and rotated to earth co-ordinates during processing.
   
The LADCP was connected to a charger and by a serial cable to the CTD computer in the UIC for 
programming prior to each station and data download after each station, using BBTalk. Pre-
deployment tests were performed at least once daily, generally once per 12-hour watch.
   
Data downloaded after each station were copied to the network data drive in ladcp/JR16002, 
with names of the form JR16002 NNN.000, along with deployment logs, JR16002 NNN.txt.

LADCP  command file:
CR1
RN 
JR16002 
WM15
TC2 
LP1
TB 00:00:02.80
TP 00:00.00
TE 00:00:01.30 
LN25
LS0800 
LF0 
LW1 
LV400 
SM1 
SA011 
SB0 
SW5500 
SI0
EZ0011101 
EX00100 
CF11101 
CK
CS


6.3  Data Processing

6.3.1  CTD processing for each cast
   
The CTD data processing followed the methods used on previous SR1b and other NOC MPOC 
cruises, using the Mexec software suite ("A User Guide for Mexec, v3.0", available from the 
NOC Marine Physics and Ocean Climate group).  The version used in this case, 
mexec_processing_scripts_v3, streamlines the setting of cruise-specific options but does not 
change the processing steps from previous versions. The Mexec processing follows the initial 
SeaBird conversions and corrections described above. The necessary directories and links were 
set up at the beginning of the cruise using conf script jr16002 (found in the home directory 
on fola, see Section 8). After each cast, ctd linkscript was used to copy files to fola and 
set up additional symbolic links to filenames following mstar convention.
   
For each cast the initial processing was done by running ctd_all_part1, mdcs_03g, and 
ctd_all_part2. The scripts called by these wrapper scripts, and the corrections, averaging, 
and calculations completed and files generated by each, are detailed in the Mexec user guide 
(v3.0) and in cruise reports for JR306 and JR15003. mdcs_03g requires hand-selection of cast 
start and end times (generally based on pressure and oxygen fields; see JR15003 report).
   
Processed data could then be examined using mctd_checkplots to view sensor and up-down cast 
differences as well as compare nearby profiles, with particular attention paid to any drift 
in deep temperature or salinity (expected to be relatively stable) over time. The 24-Hz data 
were checked for spikes in either of the temperature or conductivity sensors using 
mctd_rawshow and, if necessary, edited using mctd_rawedit. In this case, a few spikes in 
either primary or secondary conductivity or both were removed from stations 1, 2, 3, 5, 8, 
10, 12, 13, 14, 15, 20, and 27.
   
On station 20, an issue with the winch around 600 m led to the downcast being aborted; the 
issue resolved itself around 150 m and the downcast was resumed from there. While simple 
depth-bin averaging of the downcast T, S, O time series did not produce large discontinuities 
at either end of the repeated depth range, it did result in an unusually wiggly section 
around the lower end. The 2-dbar average version of record for this station therefore comes 
from the upcast.
   
CTD communications failures (Section 9.2) on stations 22 and 23 produced not only missing 
data but also extremely large spikes, followed in some cases by oscillating bad values, in 
all or most parameters for a range of scans around the complete comms dropouts.  Because some 
of the bad values were so far out of range, it was difficult to use the mctd_rawedit 
graphical interface to remove all the bad data. Therefore, code was added to mctd_rawedit and 
to its cruise-specific options to set all variables measured by the CTD to NaN for the ranges 
of scans where one or more parameters were bad, as determined by examination of the raw file.  
This code was modeled on similar code to edit the 24hz file in mctd_03.  Note that because 
the cause of the communications failure was in the underwater unit, scans were not 
incremented during the dropouts, so that the pressure record is discontinuous. A precise 
record of the dropout lengths is not available.
   
For casts where the raw data were edited using mctd_rawedit, smallscript_postedit was run to 
regenerate the derived files.


6.3.2  LADCP processing for each cast
   
Data for each station were processed on fola using the LDEO-IX software package, developed at 
Lamont-Doherty Earth Observatory (LDEO). The software uses an inverse method to calculate 
velocity profiles, optionally including LADCP bottom tracking and/or VMADCP upper ocean 
velocities as constraints.  At-sea processing was performed using only ship navigation 
(ladcp/ix/DL_GPS) or navigation and bottom tracking (ladcp/ix/DL BT).
   
Directories, links, and parameter files for LADCP processing were set up at the beginning of 
the cruise using conf script jr16002, and by running lad_linkscript_ix after each cast.  Once 
a 1-hz ctd file has been generated (by ctd_all_part1), list ctd 1hz(nnn) can be run to export 
time, lat, lon, press, temp, psal into ascii to be used by the LDEO processing; 
ladctd_linkscript_ix makes links to these files. While the LADCP processing can be run 
without the CTD data, position from the CTD 1-hz file is used to compute the magnetic 
deviation.

Matlab script ixpath sets up the necessary paths for LDEO-IX LADCP processing, which should 
be run from ladcp/ix/data/. The different versions of set_cast_params*.m are called by 
different versions of process_cast*.m to run IX processing of the LADCP data with different 
constraints:
  • process_cast_v5.m calls set_cast_params_v5.m to include only navigation data
  • process_cast_v4.m calls set_cast_params_v4.m to include navigation and bottom 
    tracking data

For stations 22 and 23, where CTD communications failures led to discontinuous pressure time 
series, processing version 4 produces erroneous profiles.  The LADCP profiles in Drake 
Passage produced by the LDEO-IX inverse using navigation and bottom tracking (or, for 
stations 22 and 23, navigation only), are shown in Figures 2 to 4. The erroneous surface 
layer segment (and large error bounds) visible at   station 26 results from a small gap in 
the LADCP data; a more complete profile might be recoverable by modified processing.



6.4  Water sample collection and analysis

Water samples were drawn from the Niskin bottles in the following order: dissolved oxygen 
sample and any duplicates; oxygen isotope sample and any duplicates; salinity sample.  The 
distributions of water samples, along with SBE35 temperature calibration points, are shown in 
Figure 5. Niskin firing depths were chosen based on the downcast profiles in an attempt to 
cover the pressure, temperature, salinity, and oxygen ranges, while taking samples both in 
regions of low variability (for calibration), and at extrema (including the bottom layer, the 
surface mixed layer, and subsurface temperature, salinity, and oxygen extrema, where these 
features appeared).
   
In general samples for all quantities were drawn from all good Niskins (and an SBE35 sample 
was collected whenever a Niskin fired), except that extra samples were drawn for oxygen on 
the last few casts after the oxygen sensor was switched out (Section 9.2).  Outliers were 
flagged as 3 (questionable) where a large difference between CTD and calibration value 
appeared attributable to a property gradient, and as 4 (bad) where errors in sampling or 
analysis were noted (for the most part, errors in sample drawing for O2, and incomplete 
sealing of stoppers for salinity). Flagged SBE35 samples might indicate that the Niskin was 
closed too quickly for a good, equilibrated reading. Oxygen isotope samples were taken in 
plastic bottles, with duplicates in glass bottles taken at the deepest and shallowest Niskin 
on most casts.   On a few later casts a triplicate oxygen isotope sample (in a plastic 
bottle) was taken as well.

6.4.1  Dissolved oxygen analysis
   
Sampling and analysis procedures closely followed the GO-SHIP manual procedures for dissolved 
oxygen (Langdon, 2010).
   
After collection, a Milli-Q water seal was applied to the neck of the sample flasks and 
samples. 30 minutes after sample collection was completed, the flasks were shaken again, 
using the vigorous wrist- snapping inversion motion to ensure that the reaction was complete. 
Samples were generally in the lab for a minimum of 1 hour before titration. When ready to 
titrate, the water seal was dried with a Kimwipe and the stopper of the flask carefully 
unsealed by gently twisting back and forth.  A 1 mL aliquot of H2SO4 from the bottle-top 
dispenser was added to the flask, immediately followed by a clean magnetic stir bar. The 
flask was placed on the stir plate and the electrode and burette were carefully inserted to 
place the tips in the lower-middle depth of the sample flask. The initial volume of Na2S2O3 
for each sample was 0.3 mL, after which the titration proceeded using the pre-set program on 
the Metrohm automatic titration system, with amperometric determination of the titration 
endpoint.

Duplicates
   
For each cast, at least one Niskin bottle was sampled in duplicate and analyzed for oxygen 
concentration. During the casts that corresponded to float release, at least two Niskin 
bottles were sampled in duplicate.

Blanks and standards
   
A set of blanks and standards was analyzed at least once every 24 hours (more frequently at 
the beginning of the analyses) during the cruise sampling and analysis period to monitor the 
evolution of the concentration of the batch of Na2S2O3 (this did not need to be refilled). 
One set of blanks was three flasks prepared as described by Langdon (2010), Section 7.1.  
After the first titration endpoint was reached in each flask (with the volume of Na2S2O3 
added to reach the endpoint recorded as V1), a second 1 mL aliquot of KIO3 was added to the 
same flask and the titration was repeated and recorded as V2.  The initial volume addition of 
Na2S2O3 at the beginning of the titration was set to 0 mL for the blanks.

One set of standards was five successive flasks with 10 mL iodate standard (0.01 N/1.667 mM 
KIO3 from OSIL) prepared as described in Langdon (2010), Section 7.2.  The initial volume 
addition of Na2S2O3 during the titration was 0.3 mL for the standards.

Calculations and conversions
   
The conversion from titre volume to moles of oxygen to oxygen concentration was computed 
following Langdon (2010) and references therein. Density based on the sample bottle draw 
temperature and calibrated CTD salinity was used to convert from µmol L-1 to µmol kg-1 as 
part of Mexec processing. 

At least one duplicate was taken at each station (two for 24-bottle casts). The duplicate for 
the first station showed a large disagreement, so that both values were flagged as bad. 
Otherwise, the duplicate rms difference was 1.6 µmol L-1 (compare with sample oxygen 
concentrations ranging from 170 to 360 µmol L-1).


6.4.2  Salinity analysis
   
Between 4 and 24 water samples for salinity analysis were drawn for each CTD cast (one per 
Niskin bottle fired). The distribution of bottle sample locations in Drake Passage is shown 
in Figure 8 and 9. Samples were taken in 200ml glass sample bottles, which were rinsed three 
times before filling to the shoulder, and sealed with a clean dry disposable plastic stopper 
after drying the neck of the bottle. Clean (freshwater rinsed) and dry caps were added to 
secure the stoppers. Once filled, crates of samples were stored in the Bio Lab for a minimum 
of 8 hours before analysis to allow equilibration to the laboratory temperature.
   
Salinity sample analysis was performed, by various watchstanders, on the BAS Guildline 8400B 
Salinometer, Serial No. 68533, in the Bio Lab, using a bath temperature of 24°C and 
attempting to keep the room temperature around 21.5°C. Standard procedures were followed: A 
sample of IAPSO Standard Seawater, batch P158 (K15 = 0.99970) was run before and after each 
set of up to 24 samples for salinometer calibration. We flushed the volume with expired P155 
or previously opened bottles of P158 before starting new sets of runs to bring it closer to 
the standard salinity, and with milli-Q for intervals between runs.
   
Bottle sample conductivity readings were read from the autosal and logged by hand. Three 
readings were taken for each sample and standard.  In some cases, the first reading was 
obviously different from the second two, and was discarded as having been insufficiently 
flushed.  A few other outlier readings were also discarded, but otherwise the three readings 
were averaged.
   
Before comparison with the CTD data, the sample readings are adjusted for the salinometer 
offset, or the difference between the standard reading and its label value, by linearly 
interpolating between the offsets derived from the initial and (where completed) final 
standard analysis for each set of samples.

These offsets ranged from 0.7x10-4 to 2.7x10-4 (median 1x10-4), generally decreasing through 
the cruise; values larger than 2x10-4 corresponded to underway samples. Drifts within a 
sample set were up to ±0.6 x 10-4, with a median absolute value of < 0.1 x 10-4.



6.5  CTD data calibration and results
   
A variety of extra steps is available after other processing has been carried out, as 
described in "A User Guide for Mexec, v3.0", to add navigation and sample data to the files. 
On JR16002 we ran these steps together once all casts were completed and all salinity and 
oxygen calibration data had been obtained.
   
Temperature, salinity, and oxygen were calibrated on JR16002, using samples taken at 
locations shown in Figure 5.  We first evaluated the comparison between CTD temperatures and 
the 315 good SBE35 readings, and applied temperature offsets increasing over the course of 
the cruise from -1.3 to+1.6 m°C (sensor 1) and from -0.3 to +2.6 m°C (sensor 2).
   
We then evaluated the comparison between CTD salinities and 280 good bottle salinities. The 
comparison was done in conductivity space, by converting bottle salinities to conductivity at 
the calibrated CTD temperatures. CTD conductivity adjustments with station number dependence 
and piecewise linear pressure dependence were chosen to minimise the median and standard 
deviation of the bottle conductivity to CTD conductivity ratio, and are approximately 
equivalent to salinity offsets ranging from -2.65 x 10-3 to 1.33 x 10-3 (sensor 1) or -4.33 x 
10-3 to -1.12 x 10-3. Post-calibration comparisons between CTD and SBE35/bottle 
temperature/salinity are shown in Figure 6.
   
Finally, we used the calibrated salinity to compute density and convert oxygen concentrations 
to µmol kg-1 for comparison with CTD oxygen. 260 good bottle oxygen values from stations 1 
through 23 were compared to the first CTD oxygen sensor, used up through station 23, and 62 
good bottle oxygen values from stations 24 through 30 were compared to the second CTD oxygen 
sensor, used from station 24 on. We least-squares fit a calibration function, Oo(a1 +a2N)+a3 
+a4P , where Oo is the uncalibrated CTD oxygen, N is the station number (1 to 30), and P is 
pressure, to the bottle data from stations 1-23, producing Ocal(N≤23) = Oo(1.04 - 4 x 10-4N)+ 
3.1 + 12 x 10-4P . Because we had relatively few samples available to calibrate the second 
sensor, and their depth range in particular was limited (as the last stations were over the 
continental slope), for stations 24-27 we did not include pressure dependence, resulting in 
Ocal(N ≥ 24) = Oo(1.33 - 10.4 x 10-3N) + 15.1. Post-calibration comparisons between CTD 
oxygen and bottle oxygen are shown in Figure 7.
   
Sections of calibrated temperature (Figure 8), salinity (Figure 9), and oxygen (Figure 10) 
show a number of features, including the northerly position of the Polar Front and cold, 
dense, young shelf water not only at the top of the Antarctic continental slope but also in 
blobs found offshore at the base of the slope between 200 and 800 m depth.



6.6  References

Langdon, C., 2010. Determination of Dissolved Oxygen in Seawater by Winkler 
    Titration Using the Amperometric Technique. In The GO-SHIP Repeat Hydrography 
    Manual: A Collection of Expert Reports and Guidelines. Hood, E.M., C.L. Sabine, 
    and B.M. Sloyan, eds.  IOCCP Report Number 14, ICPO Publication Series Number
    134. Available online at: http://go-ship.org/HydroMan.html.




7  DEEP APEX AUTONOMOUS PROFILING  FLOATS
   Yvonne Firing

Three Deep APEX (Teledyne Webb Research) 6000-m depth-rated autonomous profiling floats were 
deployed in southern Drake Passage on SR1b, intended to contribute to monitoring deep water 
properties and pathways for ORCHESTRA, as well as to the global Deep Argo program. All three 
floats leaked within days to weeks of deployment and had to be recovered. Common aspects of 
the operations are summarised here, with more specifics for each float in the subsections 
below.

   The initial mission.cfg loaded to the floats was:
ActivateRecoveryMode off 
AscentRate 0.12
AscentTimeout 608
AscentTimerInterval 300
BuoyancyNudge 70
DeepDescentCount 2000
DeepDescentPressure 3500
DeepDescentTimeout 5
DeepDescentTimerInterval 60 
DeepProfileFirst on 
DownTime 3809
EmergencyTimerInterval 3600
IceBreakupDays 14
IceCriticalT -1.78
IceDetectionP 50.00
IceEvasionP 20.00
IceMonths 0000
IdleTimerInterval 3600
InitialBuoyancyNudge 300 
LeakDetect on 
LogVerbosity 5
MActivationCount 2000
MActivationPressure 25.00
MinBuoyancyCount 800
MinVacuum 7
ParkBuoyancyNudge 10
ParkDeadBand 50
ParkDescentCount 2000
ParkDescentTimeout 911
ParkDescentTimerInterval 3600
ParkPressure 3500
ParkTimerInterval 3600
PnPCycleLen 1 
PreludeSelfTest on 
PreludeTime 120
SurfacePressure 5.00
TelemetryRetryInterval 900
UpTime 728
   
This mission DeepDescentCount and ParkDe- scentCount had to be revised when they proved to be 
much too high to allow the floats to dive to the target pressure of 3500 dbar (see below). 
They were changed to 1250 before deployment of the 3rd float (0012), and for the other two 
floats when they downloaded  updated .cfg  files  from the server upon resurfacing following 
their initial missions.
   
The sample.cfg, intended to record CTD and oxygen measurements while in park phase, at the 
hourly ParkTimerInterval  setting,  in  addition  to the profiles, was:
<PARK>
SAMPLE CTD 6500 5 0.0 DBAR
SAMPLE OPT 6500 0 0.0 DBAR
<ASCENT>
SAMPLE OPT 6500 300 20.0 DBAR
SAMPLE OPT 300 100 10.0 DBAR
SAMPLE OPT 100 0 5.0 DBAR
<SURFACE>
SAMPLE OPT 6500 0 0.0 DBAR
<ASCENT>
PROFILE CTD 6500 0 2.0 1.00 #Regime:1
   
Before the cruise started, all three floats were tested on the ship using sys_self_test.  For 
each, the top of the crate was removed and the deck box cable plugged into the float comms 
port and by a serial-usb connector or serial-ethernet connector  to a macbook pro running 
miniterm.py. The line feed must initially be set to CR, by typing Ctrl-T Ctrl-L twice, for 
some input to be recognised correctly.  The float is then woken by pressing the deck box 
reset button, and is put into console mode by typing m console. sys_emerg_clr  can be run in 
case the float has gone into emergency mode, but will put in idle state, so it must be 
followed by m console. su  root  allows  verbosity to be set by typing dbg_verbosity 5 (this 
appears to be necessary only once unless the float is completely reset). With dbg verbosity 
set to 5, sys_self_test was run. This includes a variety of platform (voltage, vacuum, and 
engine) tests, sensor tests, and satellite communications tests comprising both transmit and 
receive attempts through both RUDICS and dialup. All the floats had some trouble seeing the 
sky and/or establishing sufficient communications in their securing location in the forward 
section of the aft deck (near the superstructure), so were moved as far aft as possible to 
retry the comms tests. The floats were moved around in their crates either with a pallet jack 
or (for short distances) by walking the crates.
   
The floats were then secured on the aft deck for the transit to Signy, Signy call, recrossing 
to Burdwood Bank, and the northern part of the station. They were stored with their lids on 
except when performing additional tests (described below), which could take a number of 
hours.
   
Before deployment (4 to 12 hours prior), the conductivity sensors were flushed using a weak 
solution   of triton cleaner (supplied by SeaBird for the ship CTD and available from the AME 
department), following as closely as possible the procedure outlined by TWR. The T-C Duct 
top, Anti-Foulant Device, and T-C Duct base were removed, exposing the top of the 
conductivity cell. It was not possible to attach tygon tubing to the conductivity cell port 
(although the same tubing fit over the rosette CTD port), so the cleaning solution was 
dripped into the cell using a syringe until the cell was filled.  This did produce a small 
amount of spillage down the sides of the CTD, which was rinsed.  It was allowed to sit for 1 
hour and then the exhaust tube on the pump outlet was removed to allow the cleaning solution 
to drain. MilliQ water was then flushed through in the same way (without the soaking time).
   
Each deployment followed a CTD cast. One side of the crate was removed, then the remaining 3 
together (by removing the base screws). A strop through the lifting bail, secured over a 
wooden fid, was used with the Effer crane to lift each float over the starboard rail, 
lowering it into the water while the ship was slowly underway, and releasing by pulling out 
the fid.



7.1  Float S/N 0015 (rudics ID 0046)
   
0015 passed its initial tests (on 9 November) except for the communications test. It failed 
the Iridium receive test, and then became stuck in a loop of "Modem not responding to ‘AT’ 
command.  Power cycling modem." and "Iridium modem not enabled." TWR attempted to 
troubleshoot by having additional commands run. Running modem test on its own produced the 
same result a number of times over several days, while modem_show followed by modem_chat and 
manually inputing the AT command ran without error.  After a few days, modem_test stopped 
producing the error (and ran successfully multiple times), and TWR concluded it had solved 
itself and the float could be deployed.
  
During the CTD cast at station 16, m_deploy was run, producing successful sensor and buoyancy 
tests and successfully transfering configuration files from the server.  It transitioned into 
parkdescent mode well before the cast finished, but due to a misunderstanding of the 
acceptable order of operations and different timeouts, was reset (using the deckbox) to run m 
deploy again. It initially went into emergency mode, presumably (see below) due to the air 
bladder not quite reaching target pressure due to the low temperature, but on a second try 
passed the tests except the communications tests. Since it had previously downloaded the up-
to-date configuration files from the server, the float was put into idle mode to deflate its 
bladders and be deployed for pressure activation. It was deployed at 0640 UTC (0340 local) on 
21 November and observed to sink.
   
The float initially dove only 1500 m (see above). After mission updates it successfully dived 
deeper, but on mission 7 it descended substantially deeper than expected (3946 m), likely hit 
the bottom, and subsequently leaked while in park phase.  It then went into emergency mode 
and surfaced.  As the humidity levels subsequently recovered, indicating the desicant had 
absorbed the moisture, TWR decided to attempt a short mission, which aborted due to further 
leaking at 850 dbar.  0015 was recovered by the US Antarctic Program ARSV Laurence M. Gould 
on the morning of 17 December, to be returned to TWR for diagnosis and repair or replacement.



7.2  Float S/N 0013 (rudics ID 0049)
   
0013 passed its initial tests (on 9 November); although it threw up the "Modem not responding 
to ‘AT’ command.  Power cycling modem."  error once, the power cycle appeared to work as it 
continued without further error (not counting partial transmission failures, resolved by 
moving the float away from the superstructure).
   
During the CTD cast at station 19, m deploy was run and all tests passed, except the dialup 
test (which was judged to be due to the float position near the superstructure).  Having 
passed the tests, it started to deflate the bladders, and was deployed following the CTD cast 
at 2213 UTC on 21 November. Although it did not sink right away, it subsequently sank and 
completed an initial cycle to 1500 m (due to the incorrect DescentCount settings).
   
During its second cycle, 0013 detected a leak, entered emergency mode, and returned to the 
surface shortly before the end of the SR1b CTD section.  It was recovered, by detouring on 
the return from Rothera to Stanley, at 1407 UTC on 1 December.  Due to the rough sea state 
the initial attempts to hook the lifting bail with a boathook were unsuccessful, so it was 
grappled through one of the hardhat handholds and recovered by hand. Upon recovery it had a 
visible amount of water in the glass sphere, but this water did not appear to have contacted 
the electronics or battery, as the float was still communicative.  It was repacked in its 
wooden crate and consigned to FIPASS at the end of the cruise for return to TWR.



7.3  Float S/N 0012 (rudics ID 0048)
   
0012 was initially intended to be deployed second, but failed tests in m deploy and went into 
emergency mode. This was diagnosed by TWR as being due to the air bladder not quite reaching 
the expected pressure in cold temperatures (its initial test, like that of float 15, occurred 
in the early hours of the morning). As sys_self_test showed all other tests passing, TWR 
suggested switching off the PreludeSelfTest setting. After doing this, and updating the 
DeepDescentCount (see above), m_deploy was run during the CTD cast at station 23.  Although 
all tests passed, the float did not transition out of prelude to parkdescent state after 120 
minutes, but rather remained in prelude state, with the reply to m state including the 
message that ╥PRELUDE state timeout has occurred╙, and the bladders remaining fully inflated. 
midle was not effective in getting it out of prelude state, but sys_emerg_clr was able to put 
it into idle mode and start deflation of the bladders. The float was deployed (in 
idle/pressure activation mode) when the bladders had partially deflated, at 2314 UTC on 22 
November. It did not sink right away but successfully dove to 3644 dbar in its first cycle.
   

0012 also leaked after 7 missions, and was recovered by the Gould on the evening of 16 
December, to be returned to TWR.





8  UNDERWAY DATA COLLECTION AND  PROCESSING
   Yvonne Firing


8.1  Configuration of linux workstation ‘fola’
   
The NOC MPOC OCP group brought a linux workstation (fola), which was the primary platform for 
data analysis during the cruise.  The jcr cruise data directory was made available by 
mounting on fola.  That directory includes SCS data streams, data from other sources such as 
CTD, LADCP, VMADCP, and the legwork directory.  The network data directory was mounted on 
fola so that /mnt/data/cruise/jcr was the parent directory of the individual cruise data 
directories identified by date. Cruise jr16002 was current 20161106.
   
The script conf_script_jr16002 set up the data and processing directories, symbolic links, 
and templates required for data syncing and processing in Mexec and otherwise, including 
links to the legdata directory and its legwork subdirectory.
   
Workstation fola was backed up on a daily basis during the active part of the cruise.  The 
JR16002 part of the legwork directory was copied over to fola at the end of the cruise. A 
complete dump of cruise data and software was copied using rsync from fola to one of two 
Transcend portable hard drives. These drives were used to carry data back to NOC at the end 
of the cruise, including a final identical backup of fola on two drives.



8.2  SCS data streams
   
A selection of underway data streams on the JCR are made available on the ship network 
through the SCS system. The SCS data streams (ashtech [nav/ash], ea600 [sim], anemometer 
[met/surfmet], oceanlogger [ocl], gyro [nav/gyros], seatex-gll [nav/seapos], em122 [em122], 
seatex-hdt [nav/seahead]) were processed on fola during the cruise.  The gyrocompass, 
underway fluorometer, and TIR sensors were not functioning for all or much of JR16002. The 
emlog, gravity, usbl, tsshrp and furuno navigation data were collected but not processed.
   
Preliminary stream parsing was started at the beginning of the cruise by running conf script 
TPL followed by sedexec_startall. Most SCS data were processed in 24-hour segments, using m 
daily proc, which processes and averages each day’s data (including vector averaging for 
wind), producing averaged, appended files for the SCS streams. Winch data were processed by 
CTD station as part of standard CTD processing (ctd all part2.m). Additional processing for 
bathymetry and oceanlogger thermosalinograph data is described below. At the end of the 
cruise data parsing on fola was stopped by sedexec_startall.
   
More details on SCS data on the JCR, and on processing steps for underway data, are given in 
the cruise reports for JR306 and JR15003.



8.3  Underway surface thermosalinograph and salinity calibration
   
TSG data read in as part of the daily processing were set to absent when the pumps were off, 
or where flowrate indicated unreliable supply.  At the end of the cruise the full record was 
cleaned by running mtsg_medav_clean_cal to perform initial processing; mtsg_findbad to 
interactively find bad times, and mtsg_medav_clean_cal again to remove them in 
ocl/ocl_jr16002_01_medav_clean.nc.
   
A total of 59 underway samples were analysed for oceanlogger salinity calibration. Samples 
were drawn from the underway supply in the Prep Lab as often as every 4 hours during science 
time in ice-free areas, following the same procedure as for Niskin bottle samples, and the 
time noted in a logsheet to the nearest minute. They were analysed following the procedure 
described for CTD salinity samples. Nine were flagged as outliers (in all but two cases, at 
times of strong salinity gradients); the median offset of +0.005 psu based on the remaining 
50 samples was added to the oceanlogger time series using mtsg_apply_salcal, producing 
ocl/ocl_jr16002_01_medav_clean_cal.nc.



8.4  Bathymetry
   
Two bathymetry streams are available via SCS: the ea600 single-beam echo sounder, and the 
centre beam of the em122 multibeam (swath) system. The EA600 data were frequently bad because 
the automatic bottom detector failed to detect the correct return. To maximise use of other 
acoustic instruments (see below), the EM122 swath echosounder was turned off for much of the 
SR1b section (for later CTD stations, it was only turned on briefly when coming on station to 
get a good depth fix), and was not logged there nor in other areas where swath bathymetry had 
been collected previously.
   
Following the daily processing, msim_plot and mem120_plot were called to select and flag bad 
data from the EA600 and the EM122 centrebeam. This flagging is interactive, based partially 
on comparison between the EA600 and EM122, when both were available, as well as with historic 
bathymetry data. After editing, mday_02(‘M_SIM’,’sim’,day) and mday_02(‘M_EM122’,’em122’,day) 
are run to add each  day to the appended files. The full swath data are reported but not 
cleaned or otherwise quality-controlled aboard the ship.



8.5  Vessel Mounted ADCP
   
A vessel-mounted 75-kHz Teledyne RD Instruments (RDI) OceanSurveyor Acoustic Doppler Current 
Profiler (ADCP), with 30° beamangle, a transducer depth of 5 m, and a heading alignment of 
60.08°, was run throughout the cruise to measure horizontal velocity. The range of the 
instrument is up to 800 m, depending on scatterers, sea state, and the ship’s motion.  The 
instrument was run through the RDI VMDAS system, collecting single-ping ENR data and 10-
minute average LTA data, as well as parsing position and heading data from the seatex and 
(when available) the synchro gyrocompass.


8.5.1  Configuration and K-sync

Configuration parameters were input using a set of files corresponding to either watertrack 
or bottom track mode and to either independent triggering or triggering by the Simrad K-sync.  
The instrument was set to sample up to 800-m depth, except for one interval during which it 
was mistakenly set to look only to 500 m. When in water depths shallower than 800 m for some 
period of time, sampling was (re)started in bottom track mode, in which each second ping is a 
bottom-tracking ping, used to calibrate the heading alignment. In deeper water, watertrack 
mode was used to maximise the number of pings.
   
When sampling with the EK60 or the EM122 (or both), the Simrad K-sync was used to coordinate 
pinging. When the EM122 was in use the following K-sync settings were required to obtain a 
reasonable number of ADCP pings:

    1. Uncheck "echosounder is master" in the swath settings

    2. Set the ADCP to be triggered every 3.4 s (the setting here must be ≥ the ping 
       separation it would require on its own, or it will miss pinging on alternate 
       triggers)

    3. Use three or more trigger groups, with only one including the EM122; this way, 
       the long wait the EM122 forces in deep water only occurs every few ADCP pings, 
       and only decreases the number of ADCP pings by ~20%

When only VMADCP and EK60 were on, the ADCP was set to ping every 3.4 s, with the EK60 
pinging at twice the rate.


8.5.2  Data quality
   
During some periods of higher sea state, the data quality was noticeably affected by bubbles. 
The reduction in quality depends not only on the sea state but also on the ship’s heading 
relative to the seas, and is generally less serious when on-station as the ship tends to 
maintain a position that minimises motion. Occasional spikes in amplitude in the middle of 
the VMADCP depth range might have been due to the EK60.
   
The principal obstacle to obtaining high-quality VMADCP data on this cruise was the lack of 
high-quality, high-frequency synchro gyro heading data. The LTA files were processed using 
the UH CODAS software (available from http://currents.soest.hawaii.edu), but more extensive 
processing and editing of ENR data is required and will be performed ashore.



8.6  EK60
   
The Simrad EK60 is a multifrequency echosounder designed to detect different species of 
zooplankton or fish.  Acoustic backscatter data at 38, 70,120, and 200 kHz were collected 
opportunistically for most of the cruise, with the EK60 triggered twice per VMADCP ping. 
These data have not been processed in any way.




9  AME REPORT
   William Clark, AME support engineer


9.1  Instrumentation


LAB Instruments

Instrument                 S/N Used  Comments
-------------------------  --------  --------
AutoSal                    68533     Lab temp PC freezes occasionally; hard reset gets 
                                     it working. IT investigating.
Scintillation counter      N
Magnetometer STCM 1        N
XBT                        N


ACOUSTIC

Instrument                 S/N Used  Comments
-------------------------  --------  --------
ADCP                       Y
PES                        N
EM120                      Y
TOPAS                      N
EK60                       Y         Tripped breaker when power cycling; user error.
                                     Turn off in UIC before unplugging/replugging.
EK80                       N
SSU                        N
USBL                       Y
10 kHz IOS pinger          N
Benthos 12 kHz pinger      N
  S/N 1316 + bracket
Benthos 12 kHz pinger      N
  S/N 1317 + bracket
MORS 10 kHz transponder    N


OCEANLOGGER

Instrument                 S/N Used  Comments
-------------------------  --------  --------
Barometer1(UIC)            V1450002
Barometer1(UIC)            V1450003
Foremast Sensors
Air humidity & temp1       3898*
Air humidity & temp2       3896*
TIR1 sensor (pyranometer)  2993*     Not working
TIR2 sensor (pyranometer)  2992*     Not working
PAR1 sensor                0127*
PAR2 sensor                0126*
prep lab
Thermosalinograph          4524698
  SBE45                      -0018  
Transmissometer            527DR
Fluorometer (10AU)         1100243
Flow meter                 811950
Seawater temp 1 SBE38      0767
Seawater temp 2 SBE38      0771      Sensor swapped; was 0765 (not configured)
                                     * Serial numbers with an asterisk not personally 
                                       observed


CTD (all kept in cage/ sci hold when not in use)

Instrument                 S/N Used  Comments
-------------------------  --------  --------
Deck unit 1 SBE11plus      0458
Underwater unit            0771      S/N 0541 used for casts 024, 025, 026
  SBE9plus
Temp1 sensor SBE3plus      5623
Temp2 sensor SBE3plus      4874
Cond1 sensor SBE 4C        3491
Cond2 sensor SBE 4C        1912
Pump1 SBE5T                2395
Pump2 SBE5T                1807
Standards Thermometer      0051
  SBE35
Transmissometer C-Star     1505DR
Oxygen sensor SBE43        0242      S/N 0620 used until cast 023.
PAR sensor                 70636     Initial incorrect calibration; data reprocessed.
Fluorometer Aquatracka     12-8513   Altimeter PA200 26993
                             -003
LADCP                      14443
CTD swivel linkage         1961018   Test cast with S/N 196115.
Pylon SBE32                1106
Notes on any other part 
  of CTD e.g. faulty cab-
  les, wire drum slip 
  ring, bottles,swivel, 
  frame, tubing etc.


AME UNSUPPORTED INSTRUMENTS BUT LOGGED

Instrument                 Working?  Comments
-------------------------  --------  --------
EA600                      Y
Anemometer                 Y
Gyro                       Y
DopplerLog                 Y
EMLog                      Y





9.2 CTD Communications Issues

Symptoms

The CTD Deck Unit lost communications with the Sea Unit during the deployment.
   
The Deck Unit Error alarm was active but not constant (random beeping) and communications 
sometimes resumed allowing the cast to be completed. The winch operator observed this was not 
like previous cable issues he had seen, when the alarm is steady.
   
There was no obvious relation to depth; most failures occurred on the up-cast at varying 
depths and time elapsed.

Solution
   
The issue was found to be the Y cable connecting the SBE9plus unit to the SBE35 and SBE32, 
which was damaged in two places allowing water ingress.
   
In case of future communication issues which manifest themselves with the CTD on the deck, a 
recommended debugging step would be to disconnect ALL instruments from the 9plus (leaving 
only the sea cable connected) and attempt communications; if the problem is with a cable or 
instrument, communications should be successful with the faulty part unplugged.  Each sensor 
can then be tried in turn to identify the exact culprit.

Diagnosis and repair
   
After recovery to deck after the first occurrence, an Insulation Resistance (IR) test was 
performed. This gave a result worse than expected (exact value wasn't recorded) so the 
decision was made to reterminate the cable. The initial failure appeared to coincide with the 
ship rolling, casting further doubt on the wire, however later failures did not. This was 
probably a coincidence, if not a faulty recollection. As is standard procedure, the cable was 
IR tested one the termination was complete.  This gave a reading in the region of 22 MΩ. The 
pass mark for this test is 10 MΩ (higher is better); however, memory suggested we usually 
get results much higher than this. A resistance test confirmed no short circuit.
   
Due to this lower than expected result, another re-termination is performed immediately (i.e. 
CTD not deployed in between.) This again gave an IR test result in the region of 22 MΩ. A 
resistance test confirmed no short circuit.
   
To further narrow the fault location, the communications cable was disconnected in the 
Traction Winch room (as the next disconnect point above the termination) and the cable tested 
from the UIC to the Traction Winch room. The test result is >4000 MΩ (beyond tester range) 
suggesting no fault.
   
The test was then performed from the Traction Winch room down, through the sea cable. This 
again gave a result in the region of 22 MΩ, confirming the issue to be at some point on the 
sea cable. The slip rings were checked and cleaned with the Deck Engineer; the IR test was 
performed again with no change to the result.
   
As the termination tests passed, albeit not as well as expected, the decision was made to 
deploy the CTD and observe the results.
   
The CTD reached the bottom (3800 m) without issue; however, the issue reoccurred not long 
after beginning the up-cast. Once again, communications were restored during the cast, with a 
further drop out and restoration of communications later. The Dissolved Oxygen sensor (SBE43 
S/N 0620) was observed to give erroneous readings.
   
One recovered to deck, the cable was immediately IR tested. The measurement was initially 
erratic, measuring between 5 MΩ and 45 MΩ, eventually setting around the 20 to 22 MΩ point.  
This was considered a pass, as the erroneous sensor data suggested this was not necessarily a 
cable fault.
   
At this point the 9plus Sea Unit was replaced. This is underwater part with which the deck 
unit communicates and it was thought a fault with this might produce the observed errors-
erratic communications and an invalid sensor reading.  Also replaced was the dissolved oxygen 
sensor, in case the fault was in fact with this-testing later proved the sensor to be fine 
(CTD cast JR16002 999).

No changes were made to the cable or termination at this point. The CTD was deployed to 
approximately 3500 m with no issues.

The CTD was again deployed again to approximately 3500 m, with no issues.
   
The CTD was deployed to a target depth of 2500 m, with communications lost at approximately 
2100 m on the down-cast. Error alarm intermittent again, but communications did not resume. 
CTD recovered   to deck and cable immediately IR tested. Readings approximately 5 MΩ.
   
Careful inspection of the termination revealed slight cable deformation through the cable 
grips (Figures 11 and 9.2).


Figure 11: CTD wire termination with arrows indicating deformation of the cable.


The decision was made to methodically trim the cable back through the termination (Figure 
9.2), performing IR test between every grip point.  The cable was cut with a grinder, 
allowing a clean cut which measured open-circuit.
Test results:
  • Pigtail removed: 0.5 MΩ
  • Cut past grip 3, CTD side: 0.3 MΩ
  • Cut past grip 2, CTD side: 0.3 MΩ
  • Cut past grip 1, CTD side: 0.01 MΩ
  • Cut past grip 1, ship side: 0.3 MΩ
  • Cut past grip 2, ship side: 0.5 to >4000 MΩ (Unstable)
  • Cut past grip 3, ship side: 0.2 MΩ
  • Extra 2 m cable removed: >4000 MΩ   Figure 11. Termination diagram.
This suggested there may have been some damage in this section. As the bulldog grips are 
tightened to specific torque settings and had been used for a large number of terminations 
this year alone, they were replaced with new units supplied by the Deck Engineer.  The cable 
was again re-terminated and the IR test result was good (1000 MΩ), but the CTD communications 
tests failed (9plus S/N 0541). A number of tests were conducted in sequence:
  • Short circuit cable test passes (R ~ 100 Ω.)
  • Open circuit cable test passes (R > 4000 Ω.)
  • Buzz-test comparison with old pigtail confirms correct conductor wiring.
    - Cable/termination has now passed every test.
  • Plugged cable into second 9plus beside CTD-communications succeed (9plus S/N 
    0771).
    - Suspect faulty 9plus, but suspicious as to why this might be.
  • Swapped 9plus units on CTD, communications fail (9plus S/N 0771).
    - Suspect faulty sensor.
  • Unplugged Oxygen, Altimeter, PAR, Transmissometer and Fluorometer; communication 
    fails.
  • Unplugged SBE32/SBE35 Y-cable-communication passes.
    - Suspect faulty SBE32 and/or SBE35.
  • Reconnected all except SBE32/SBE35-communication passes.
  • Unplugged SBE32 and SBE35 independently, communication fails each time.
    - Suspect faulty cable.
  • Replace SBE35/SBE32 cable-communications pass.
Removal of old SBE32/SBE35 Y-cable revealed damage to outer with inner cable insulation 
visible (Figure 13).


Figure 13: SME32/SBE35 Y-cable with damage visible.


Aftermath
   
After replacing the SBE9plus/SBE35/SBE32 cable, the CTD has performed as normal. The testing 
above leaves me with the following thoughts/suggestions:

  • SBE 9plus (S/N 0541)-Used during testing, probably OK.
  • SBE 45 (S/N 0620)-Removed during testing, later tested to be OK.
  • What are good values for the IR test? In this case the termination may have been a 
    red herring, but where has the 10 MΩ value come from if we typically measure 
    orders of magnitude more?
  • All cables on CTD have since been removed and checked for damage; none give cause 
    for concern.



9.3 Additional notes and recommendations for change / future work

CTD
   
On instruction from Cambridge, the CTD cable was swapped with the spare drum and the spare 
swivel installed. This process was complicated by the fact the spare system had not been 
properly tested and so was not in a fully working state.

To allow communications via the new cable, the BNC connection in Scientific Wiring junction 
box J.B. F10 (traction winch room) has been swapped from CTD Wire 1 to CTD Wire 2, on BNC 
port 1.  Other wiring remains the same.
   
A recommendation going forward would be, as a matter of course, to swap the drum in use every 
one or two years to keep them tested. This is also suggested for other duplicated equipment, 
as it is extremely inconvenient to be fault-finding during a scientific cruise.
   
Having swapped the swivel, data from the LADCP was used to see how, if at all, the CTD was 
rotating. The CTD appears to rotate freely, predominantly on the down-cast and consistently 
clockwise.  The lack of any issues arising from this rotation suggests all is as it should 
be. (Plots for all casts available on request.)
   
A problem was experienced which caused loss of communication with the CTD while deployed (see 
Section 9.2). This was initially thought to be a problem with the termination of the sea 
cable, although repeated attempts at reterminating did not solve the issue.
   
The problem was traced to a Y-cable on the CTD, connecting the SBE9plus Underwater Unit with 
the SBE32 Rosette and SBE35 Thermometer. Two points of damage were observed (Section 9.2) 
allowing water ingress.  Replacing this cable solved the issue.  All other cables on the CTD 
have since been removed and inspected-while there are minor signs of wear, this seems to be 
consistent with normal use and is not expected to cause another issue. I would suggest all 
the cables be inspected at least once a year, ideally during installation at the start of the 
season.
   
In case of future communication problems, unplugging instruments from the SBE 9plus would be 
a quick and relatively easy test before the more cumbersome task of re-terminating the sea 
cable-although this test requires the problem to manifest itself with the CTD on the deck.

CTD PAR Sensor
   
PAR calibration noticed to be incorrect after CTD cast 014.  Correct calibration found and 
entered before cast 015 and previous casts reprocessed.

CTD Dissolved Oxygen Sensor
   
During cast 023 the Dissolved Oxygen sensor (SBE43) produced erroneous values on the up-cast.  
This was assumed to be related to the ongoing communication issues, however the sensor was 
swapped before the next cast as a precaution.
   
Interestingly, when attempting to review the failure after the CTD work was completed, 
replaying the archived data in Seasave did not show the data anomaly.
   
While the ship was loitering near Rothera a test CTD cast was performed with both SBE43 
sensors attached to the CTD-one per T/C duct.  These gave very similar readings which 
strongly suggest that the removed sensor is good to use, as was suspected. Data archived as 
cast JR16002 999.

CTD Depth Ratings
   
Having changed the CTD to a longer (circa 8000m) sea cable, and knowing some instruments were 
definitely not rated to 8000m, I researched the maximum depth rating for the equipment we 
currently use, tabulated below in depth order:


            Instrument             Model               Max Depth (m)
            ---------------------  ------------------  ------------
            Deck unit              SBE 11plus           N/A
            Fluorometer            Aquatracka Mk III    6,000
            Transmissometer        Wet Labs C-Star      6,000
            LADCP                  Workhorse Sentinel   6,000
            Underwater unit        SBE 9plus            6,800
            Temperature            SBE 3plus            6,800
            Conductivity           SBE 4C               6,800
            PAR                    QCP2350              6,800
            Altimeter              PA200                6,800
            Standards Thermometer  SBE 35               6,800
            Pylon                  SBE 32               6,800
            Dissolved oxygen       SBE 43               7,000
            Pump                   SBE 5T              10,500


I do not know the extent of interest for conducting CTD casts past 6000m, however many of the 
default CTD instruments we use are not rated to the current capacity of the JCR winch system-
this should be kept in mind if deep casts are performed to prevent equipment damage.

CLAM
   
SCS now provides echosounder depth information to CLAM winch screen.  This is formatted using 
a variation on the EA600 data format (format previously hardcoded into CLAM), but provides 
EM122 depth as the winch operators indicated a preference for the more accurate EM122 over 
the more frequently active EA600.
   
However, the SCS system has been set up ready to provide either the EA600 or EM122 data. IT 
can facilitate changing the source.
   
Ideally CLAM would be modified to identify which echosounder is available and preferentially 
choose the EM122, but modifying the software has not proved straightforward.
   
CLAM froze for unknown reason before cast 020 and unfroze for similarly unobvious reason 
while searching for the issue; it was possibly power cycling the electronics box in the 
Traction Winch Room which resolved it. This is not a major problem as it has only happened 
once and the winch can be driven from the winch console screen with the CTD providing depth 
information.

USBL
   
The USBL was used primarily because, having experienced issues during cruise JR15007, I was 
keen to see if it was working better after the Sonardyne repairs/calibration. It additionally 
served as another reference point for CTD depth and position when using an untested CTD 
wire/winch.

The beacon was attached to the CTD for a number of deployments to test; the summary is below:
  • Beacon 1 used (BAS beacons have been given arbitrary numbers for easy 
    identification)
  • No configuration changes were made (to beacon or software) from those set JR15007I 
    do not know the extent of interest for conducting CTD casts past 6000m, however 
    many of the default CTD instruments we use are not rated to the current capacity 
    of the JCR winch system-this should be kept in mind if deep casts are performed to 
    prevent equipment damage.
  • Tracking was good with USBL head flush to hull and fully extended
    - Becomes unreliable at less than 50m depth; presumably due to (known limited) 
      beam angles.
    - Appears to work well with SWATH running.
  • USBL, CTD and CLAM wire depths typically matching to within 10m, often better 
    (some differ- ence to be expected.)
   
From the tests conducted, I am satisfied that the USBL is currently working correctly and 
could be   used for locating items. As the beacons are preconfigured, hopefully it should 
also be straightforward to use.  A USBL cue card has been produced and left near the USBL 
station, written with the target user being an AME engineer (i.e. some knowledge of ship 
assumed)-feedback is encouraged.

Oceanlogger
   
Sea water temperature sensor 2 was not returning a value. After swapping sensor cables around 
for testing, it was suggested this might be because the sensor address is not correctly 
configured-after unsuccessful attempts to change the address, the sensor (S/N 0765) was 
swapped with the spare (S/N 0771) which worked immediately. It seems we were just unlucky 
that the two of the three installed included the unconfigured one.

XBT

Monitor found to be faulty; replaced with spare from stock. No XBTs launched this cruise.







10  ACKNOWLEDGMENTS
   
Many thanks are due to the Master, officers, and crew of the JCR, and to the BAS technical 
staff, in particular for their extra efforts to make sure the science could be completed 
despite technical and logistical challenges, and to recover the float that leaked during the 
cruise. Y. Firing also thanks Geoff Hargreaves and Emlyn Jones for assistance with float 
troubleshooting and deployment, and volunteers Anastasiia Domina, Giuseppe Foti, Madeline 
Miller, Eric Sanchez, Eleni Tzortzi and Hugh Venables for running the hydrographic section; 
with special thanks to Hugh Venables and Elaine Fitzcharles for assisting with the 
hydrography and sample analysis in addition to their original duties on the trip.  We are 
also grateful and indebted to the US Antarctic Program, the officers and crew of the ARSV 
Laurence M. Gould, and April Brown and the other Antarctic Services Contractor technical 
staff aboard and supporting the LMG, for going out of their way to recover two more of the 
floats deployed during JR16002.






























CCHDO Data Processing Notes

•  File Merge SEE
sr1b_74JC20161110_ct1.tar.gz (download) #e73a1
Date: 2017-01-17
Current Status: merged


•  CTD exchange and netcdf formats online SEE 
Date: 2017-01-17
Data Type: CTD
Action: Website Update
Note: 
    2016 74JC20161110 processing - CTD/merge - CTDPRS,CTDTMP,CTDSAL,CTDOXY,CTDFLUOR,CTDXMISS

2017-01-17

SEE


Submission

filename                     submitted by  date       id  
---------------------------- ------------- ---------- -----
sr1b_74JC20161110_ct1.tar.gz Yvonne Firing 2016-12-19 12492

Changes
-------

74JC20161110_ct1.zip
        - added header NUMBER_HEADERS
        - changed header name SECT to SECT_ID
        - renamed ct1.csv files to exchange format
        - added units comments
        - added cruise information as commented header

Conversion
----------

file                    converted from       software               
----------------------- -------------------- -----------------------
74JC20161110_nc_ctd.zip 74JC20161110_ct1.zip hydro 0.8.2-48-g594e1cb


Updated Files Manifest
----------------------

file                    stamp            
----------------------- -----------------
74JC20161110_ct1.zip    20170117CCHSIOSEE
74JC20161110_nc_ctd.zip 20170117CCHSIOSEE

:Updated parameters: CTDPRS,CTDTMP,CTDSAL,CTDOXY,CTDFLUOR,CTDXMISS

opened in JOA with no apparent problems:
     74JC20161110_ct1.zip
     74JC20161110_nc_ctd.zip

opened in ODV with no apparent problems:
     74JC20161110_ct1.zip


					
•  File Online Carolina Berys
74JC20161110.exc.csv (download) #a944a
Date: 2017-01-13
Current Status: unprocessed


•  File Online Carolina Berys
NOC_CR_41.pdf (download) #6365e
Date: 2017-01-13
Current Status: unprocessed


•  File Submission Robert Key
74JC20161110.exc.csv (download) #a944a
Date: 2017-01-12
Current Status: unprocessed
Notes
Robert Key
I received a revised file that contained ctdoxy from Yvonne today. Ran through QC and 
reprinted with minor header edits as well. Replace file sent on 10th with this one.






•  File Submission Yvonne Firing
NOC_CR_41.pdf (download) #6365e
Date: 2017-01-12
Current Status: unprocessed
Notes
cruise report



•  File Online Carolina Berys
sr1b_74JC20161110_ct1.tar.gz (download) #e73a1
Date: 2017-01-04
Current Status: merged



•  File Submission Yvonne Firing
sr1b_74JC20161110_ct1.tar.gz (download) #e73a1
Date: 2016-12-19
Current Status: merged
Notes
74JC20161110, WOCE line SR1b/SR01, 2016/11/10 - 2016/12/03, RRS James Clark Ross (JR16002)