Expedition 336 Technical Reports

EXPEDITION 336 TECHNICAL REPORT.pdf: Link to original PDF

 










CONTENTS

LO – ALO HANDOVER NOTES

WILLIAM MILLS, LISA CROWDER & TIM BRONK

OBJECTIVES:
Investigate the nature of the subseafloor deep biosphere in oceanic crust and overlying sediments. Expedition 336 will initiate these investigations by installing multilevel subseafloor borehole observatories (CORKs) at several sites in a thinly-sedimented basin on the flank of the Mid-Atlantic Ridge called North Pond. In addition, the basaltic crust and overlying sediments were cored and in situ petrophysical data was collected by wireline logging, and hydrologic (packer) experiments.

OPERATIONAL DATES:
START

• Port: Bridgetown, Barbados (Berth 2 South)
• Arrived: 15 September 2011 @0948 hr
• Departed: 17 September 2011 @ 0742

END

• Port: Punta Degado, Azores (Dock #12)
• Estimated Arrived: 16 November 2011

GENERAL INFORMATION
Expedition 336 freight was loaded during the tie-up period in Curacao. The science and technical party boarded in Bridgetown, Barbados.

AREA-BY-AREA SUMMARY (ISSUES NOT COVERED IN THE INDIVIDUAL TECH REPORTS)
BRIDGE DECK
Flying Bridge: Air sampling project for scientist Dale Griffin was installed temporarily above the port-side bridge wing area. Dale is looking a getting funding for a permanent installation.
Planning Room: New faucet installed in coffee counter.
CORE DECK

Catwalk:

• • The chain vise from the core catcher bench was refurbished and reinstalled. We need to make sure that whoever does the core-catcher oils the chain periodically.
  • A new catwalk ruler was made. The one has the inverted measuring mode (right-to-left), similar to the original catwalk ruler

WCMST: The Fast Track was removed to provide bench space for the assembly of the cork thermistor strings. The track will be reassembled before we get into port.

Core Entry

Using the white shelving materials and unistrut, a temporary work bench/ storage rack was made for the osmotic samplers. At the end of the cruise the unistrut and shelving material was disassembled and returned to supply.

Laser Engraver

• • It is working! Thanks to Brad who found and solved the issues with the exhaust ductwork, the Laser is up and running.
  • A special exhaust vent was built into the cabinet that immediately draws all smoke while engraving. There is no wait time to allow the fumes to be evacuated and the door can be open immediately.
  • An exhaust alarm will be ordered in insure that the exhaust system is running.
  • A Sample Master like interface was built into the software to transfer the information from LIMS to the engraver.
  • The core auto-turner still needs some work by Al before it can be used, so for now the sections have to be turned by hand to print the Archive side.

Splitting Room:

• • Waterproof LED lights were added to the tile saws in the core splitting room.
  • A new PVC enclosure was made for the smaller tile saw.
  • The new grey PVC back-splash for the core saw never made it into the X336 shipment. When it arrives it should replace the Plexiglas back-splash and the old Plexi back-splash should be reinstalled under the larger tile saw. A drain will need to be installed into it.
  • Parts (Amphenol waterproof connectors) will be ordered for the tile saws, allowing them to be quick- disconnected for cleaning and maintenance.

CryoMag: The fixed platform (under the desk) supporting the cryo-coller was replaced with a rolling platform tht can be locked under the desk to facilitate maintenance. In addition a cabinet was built around the compressor to suppress sound. Sound proofing material has been ordered to complete the project either during the 340T transit or in Curacao.
Paleo Lab: This lab was taken over by Jeff Wheat and is side kick Sam for preparing and processing the osmo-
sampler.
FO'C'SLE DECK
No issues to report.
UPPER TWEEN AND HOLD DECKS

Pallet Storage and Staging:

• • One of the -86 freezer in the Science Pallet Storage failed prior to the expedition and will be returned for repair.
  • The Fo'c'sle Deck -86 freezer is having problems cooling down and should be returned for repair. We'll discuss this with the oncoming crew.
  • Complete the N2 piping from the gas booster to the tank farm. Installed the pressure sensor to monitor the low pressure side and control the gas booster but we have the wrong type of solenoid, so the project is uncompleted.

• • The materials racks were reorganized and materials high graded.
  • Salt water cooling line installed in Curaco sprung a number of leaks nearly taking out our -86 freezers. The engineers shut the line down and it is scheduled to be replaced during the next expedition.

Core Storage: Dan, Case and Johnny P. finished the materials list for the installation of the new fan coils in the core reefer. Dan plans on starting some of the work during the next expedition.


LOWER TWEEN DECK
Gym: New tread mill needs a conditioning UPS to run without errors.

Lounge and Movie Room:

• • Re-installed projector in movie room and moved the large flat screen into the lounge.
  • Built new rack for AV components. The old wood cabinet is still in the movie room. We either need to modify it and reuse it in another location or break it down for the wood.
  • A condition UPS has been ordered for the projector. We are currently using the SRA's UPS which wil needs to be returned to the Chem lab.

CORE DESCRIPTION

MARGRET HASTEDT

SUMMARY
This expedition was the debut of DESClogik v.2, which was one of two Organization-level major projects during the last tie-up period. A project team comprised of a project leader, 2 developers, at least 4 alpha–testers and a number of beta-testers plus other interested parties contributed a large effort towards taming DESClogik's idiosyncracies/usability issues as well as adding much more functionality and features. Our ultimate success will largely be decided during this and the next expedition.

PROBLEMS ENCOUNTERED:

• • I seriously underestimated the wide gulf between knowing something in theory (DESC features as an Alpha-tester) and knowing it in practice (DESC support). NOT the same! The learning curve is steep and unforgiving at first. My ignorance of shipboard description in Zenon's absence really hampered my ability to show the new version to best advantage. Self-inflicted mistakes in template configuration led to cases of lost data and frustration.
  • Completing the migration of value list management to cloud-based computing early in the expedition was time-consuming on the relatively slow ship's bandwidth. The pace of change moderated after a couple of weeks but was challenging early on.
  • Ditto on the Help pages which are also intended to be available and centrally-managed via the Google Docs site. The MCS's opened up a number of description stations as Internet-capable workstations so that scientists could access the new Help pages, but to be honest I'm not sure many of them did due to workload issues. However, the expanding content on the Help pages is very nice.
  • The introduction of new functionalities led to a number of bugs that were undiscovered during the extensive testing phase. Possibly it might have something to do with the difference between the ship and shore environments, or, how this group of petrologists chose to use the software during description. I believe that hard-rock description is fundamentally much more involved than most sediment description, but that could just be my lack of DESC experience talking.
  • DESClogik still occasionally crashes during use, something I think most of us hoped was addressed in the new version. A number of crash-related emails were sent back and forth to the project team, but some of the shipboard crashes could not be replicated on shore. This sort of apparently random crash behavior gives an unfortunate impression of general instability for which we will probably get nailed again on the cruise evaluations.
  • DESClogik suffered from problems not of its own making as well – depth issues in Sample Master led to two known cases of users being unable to download descriptions against the entire Hole because depth values were far too shallow as reported by the database. Possibly another reflection of drilled-interval havoc but the developers would know better.
  • Lack of sufficiently-old autosaves prevented recovery of some of the lost data very early on. More disappointment. Now addressed.
  • Slow uploads and very slow downloads, especially against the hole in the latter case. Better now that some metadata issues were addressed but it can still be quite a slow process. Ongoing.
  • Piece lookups didn't work until well into when description started. Now fixed.
  • Piece lookup bug activated the tab change asterisk which was confusing until it was fixed; some 'empty' data rows as a result which looked odd at download. Bug fixed.

• • An example of an upload that hung overnight which I didn't learn about until the next morning. Possibly related to depth issues in Sample Master or possibly Autosave?
  • Very late in the cruise (last 3 days) I was uploading some thin section data. I twice saw DESC reporting "Uploading X of 77 records" and then exceeding that number by about 4 records so that in the end it said "Uploading 81 of 77 records." This was after copy/pasting from Excel. That's the first and only time I've seen it do that. Strange.
  • New Read-only columns other than piece lookup don't always work consistently. I'm not sure what I'm doing wrong at this point.

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Things that are really great about the new DESClogik:

• • Template validation on import is a godsend. It immediately alerts you if your value lists (shipside) need refreshing or if there are other errors in column headers etc. Eventually I would like to see it validate for duplicate EC/QC/QV column definitions so that others won't be able to shoot themselves in the foot like I did.
  • Need tooltips back on for regular users – it would help users figure out which true components are qualified without them. I find them extremely handy as an admin user. It would be even better if it was user-selectable whether they displayed or not.
  • The extended retention of Autosave-upon-upload is also extremely useful. These autosaves last the entire 2 months now.
  • Many other features too numerous to list!

GENERAL COMMENTS:
Comments from one petrologist indicated that he at least didn't care for it as a real-time data entry tool. They preferred using spreadsheets and then uploading later. He wanted to be able to do more calculations, averaging etc etc and it's just easier to do what you want and manipulate things in Excel. That's a very valid point because those sorts of calculations have to be predetermined, written into the templates and imported into DESC. You can't just do it 'on the fly'.
All in all, I learned a lot about description and DESClogik and how it fits into the shipboard workflow. I also realize there is a great deal yet to learn about how scientists work. Description is a complicated beast, so I welcome additional training and historical perspectives from experienced project personnel and 'frequent floaters.'

MAGNETICS LAB

MARGRET HASTEDT

SUMMARY
This cruise was highly unusual in that there were no paleomagnetists aboard, nor any real interest in paleomag data. This allowed some time for experimentation and reorganization during slow periods in the Core lab.

GENERAL INFORMATION

• • Shipped old Schonstedt thermal demagger spares
  • SRM refill and training scheduled for Azores
  • Tim Bronk (ALO) waged war on the noisy cryo compressor (see ALO report for details)
  • With info from ASC Scientific, wrote up poop sheet on degaussing the Mu-metal shielding for the TD-48. Doc will be in Cumulus. Shields degaussed on 11/1/2011; ship's heading was 080 and declination at this site is 16W. Did big Mu-metal storage can for good measure.
  • Installed latest version of Rema6W (v.6.1.3) for JR-6A spinner

PROBLEMS ENCOUNTERED

1. JR-6A spinner magnetometer repair: Replaced the bent brass actuator (Fig. 1) , but it still suffered from 'sticking actuator' problems. This was not related to the bent shaft as it happened whether or not the actuator was even installed. The symptoms were evidenced by partial motion of the brass actuator either towards the sample (working position) or the retracted (rest) position, followed immediately by an error indication (#E5 or #E9) when commanding motions with the JR6TEST utility program. An email from Agico with instructions led Garrick to discover that the ground on one of the actuator's opto-switches had fatigued and broken at the switch under its protective RTV coating. This gave rise to false 5V signals from the switch without being triggered by a physical flag. When the JR-6A saw 5V readings from both opto- switches at the same time it would throw an error and stop. Only one opto switch per motion direction should activate at a time.
2. Note: be sure to do a quick alignment check any time you experience a jammed actuator – this often happens when a sample loosens/slips during a spin. The act of attempting a spin while jammed usually results in a misaligned actuator (of the type you check with the large flat disc).

Fig. 1: Brass actuator for automatic sample rotator on JR-6A spinner magnetometer. Note the bend and corrosion present on the lower, used actuator.

1. JR-6A overflow during measurement errors: Agico replied to an email and suggested two things to check first: a) make sure that the spinner's power supply is as far from the pickup unit as possible (manual says 1 meter); b) make sure the shield cap is sitting properly during measurement.

1. Agico also sent a modified version of the JR6TEST DOS utility that will record commands and responses to/from the instrument. Using this utility will allow us to "catch it in the act" so that we can send the file back to Agico for further analysis. I put a copy up in the TAS/dml/software/labsystems folder in the Pmag Support Equipment/Agico spinner/DOS software folder. Look for the diagnostic DOS version.

1. So far, just moving the pickup unit further away from the power supply AND the computer monitor has helped greatly. Monitoring continues.

1. SRM discrete program had a bug in its motion control sequence during sample demagnetization. The tray demag sequence was fine though. It turns out that an extra motion step had been left into the sequence for the Y-axis demag and as a result the tray was not moving during degaussing. I suspect that there was a quick copy/paste when modifying some code and the XQ#STAGING step was left in for the Y-axis. It's really only required for the X-axis and doesn't hurt for the Z-axis (they both demag starting from the same position and in the same direction), but is a no-no for Y. No idea when it happened though. We'll see what the developers say. This bug may go back to the beginnings of this version of the code but it's hard to believe nobody caught it before now. On the other hand, I strongly suspect from my own measurements that it's very hard to see in the data.

DISCUSSION AND MISCELLANEOUS
SRM degausser controller vs. the ARM issue: the cryomag's degausser controller and capacitor banks were sent off during the tie-up period to Applied Physics Systems for modification based on their recommendation at the 2010 Victoria service call. The RMA documents state that the repair consisted of installing a modified PC board and rewiring the output connectors to accommodate low noise output. Accompanying small modifications were made to the gray capacitor bank. This is a modification that the APS technician recommends for all 2G degaussers.
A coil AF-field output check was performed using the DTech calibration coil:
COILrequested meas.operating PRODUCEDfield (mT) Voltage freq.FIELD (Oe)mT
Z 10 0.193152.40 98.39 9.8
20 0.384152.40195.35 19.5
30 0.587152.40298.62 29.9
40 0.763152.40388.16 38.8
50 0.962152.40489.39 48.9
60 1.154152.40587.07 58.7
70 1.354152.40688.81 68.9
80 1.530152.40778.35 77.8
90 1.730152.40880.09 88.0
100 1.937152.40985.40 98.5
X10 0.191144.70102.34 10.2
20 0.378144.70202.53 20.3
30 0.574144.70307.55 30.8
40 0.743144.70398.10 39.8
50 0.938144.70502.58 50.3
60 1.122144.70601.16 60.1
70 1.315144.70704.57 70.5
80 1.481144.70793.51 79.4
Y10 0.188145.05100.43 10.0
20 0.371145.05198.09 19.8
30 0.568145.05303.60 30.4
40 0.734145.05392.32 39.2
50 0.928145.05496.02 49.6
60 1.110145.05593.30 59.3
70 1.300145.05694.85 69.5
80 1.465145.05783.05 78.3


The coils' output is now slightly closer to the commanded value now than it was 2 years ago during X324. Our hope of course was that this modification would somehow solve the complaints of ARMs imparted by the inline degausser, an issue that dates back to the first cruises after the magnetometer was installed on the JR in 1996. I was skeptical about optimism because I think the main issue all along has been DC field leakage through the joins in the Mu-metal shielding of the SRM. Depending on heading field leakage can approach a substantial portion of the Earth's magnetic field at the actual joins (Fig. 2).

Fig. 2: Fluxgate (axial) field profile SRM degauss region with ship's heading as listed. The site declination was 16°

1. As expected, the Mu-metal shields are far more effective when approaching 90 degrees to the ambient field.

'Anticipating' the direction of an ARM on susceptible samples:

A working theory is that the only DC field of concern is the axial (Z) field in the degaussing portion of the SRM. It is the lion's share of the total leaked-field intensity and also the axis that seems to exhibit the most ARMs. The field directly under the Z-coil is generally only a few nT (table inserts in Figs 3-6) but I suspect samples may be picking up the ARMs in the falloff region of the AF field as the sample moves away from the coil, where the field intensity is much higher. Only very detailed rock magnetic testing could confirm this suspicion though.
There are several factors involved that affect leaked-field direction and intensity:

1. 1. Ship's heading (effectiveness of Mu-metal shielding; direction of SRM axial field)
   2. Site location/hemisphere (magnetic field intensity, inclination and declination)
   3. Orientation of sample in SRM during degaussing
   4. Sea state (amount of 3-D SRM motion in Earth's magnetic field)

A number of fluxgate field profiles were performed at mid-cruise during a lull in coring and description activity. The XYZ fields were entered into a spreadsheet and the fluxgate's signs/axes changed appropriately to match the SRM/IODP coordinates. Then the declination and inclination of the internal SRM field was calculated as if it had come from measuring moments of a core in the SRM, in order to give a quick feel for the field directions in a well- known framework. It makes it easy to anticipate how the axial field might change the sample's inclination if it
picks up an ARM (if it were run in the standard Top-Away orientation). An icon in the center of the SRM in the figures displays the typical loading orientation of sections in the magnetometer.
Exp. 336 sites (average): 22.75° N, 46.07° W
NOAA magnetic field calc. values: Dec. -16° 2' W, Inc. 38° 40', total field 36846 nT


Fig.3: Ship's heading nearly aligned with Earth's field. Anticipated ARMs would be progressively steeper positive inclinations, probably quickly in susceptible samples.



























































Fig. 4: ship's heading nearly perpendicular to Earth's field. The vagaries of the measured fields in this heading show a mixed bag of potentially normal or reversed mild ARMs depending on where the sample acquires it. My guess would be slowly steepening normal inclinations.













Fig. 5: ship's heading slightly oblique but turning against Earth's field. SRM Mu-metal shielded well on this occasion (lowest total fields measured). Anticipated ARMs may start biasing towards shallower inclinations for normal polarity samples.


Fig. 6: Ship's heading nearly opposite to Earth's field. Anticipated ARMs would be quickly shallowing inclinations of normal-polarity samples.
Conclusion: We need to do many more SRM field profiles whenever the opportunity arises at sea, and build a larger database of examples such as those in the above figures. Measurements of discrete samples for sequential demags in both the Top-Away and Top-Towards orientations, measured in either the SRM or the Agico spinner would help quantify any ARM acquisition. The goal would be to narrow down exactly where the ARM is acquired – directly under the coil or closer to the shield breaks during demagnetization. I have some discrete sample data for 3 cubes borrowed during Exp. 336 but am not including it in this report. I need an experienced paleomagnetist to look at it first to see if it's even meaningful . The altered basalts were extremely soft magnetically (MDF reached at less than 10 mT!) and may have been poor candidates for testing ARMs.
Recommendation: replace our ancient (bought in 1990!) Hall probe with a new Walker Scientific MD-4D. Needs both axial and transverse probes and an extension cable for them that can reach 3 meters. Analog or digital output capability would be a huge plus. An MG-4D might be a fairly cheap option if we can get the extension cable for it. An alternative would be the high-end MG-10D for precise field mapping of the AF field while the coils are energized but I don't know if that would be worth the $3000 + probes. In any case, it would be instructive to profile the degauss region of the SRM while each coil is demagnetizing to get a more complete picture of ARM acquisition. The portable version would also be very useful for field sniffing in the catwalk and rig floor areas.

PHYSICAL PROPERTY LAB

MAXIM VASILYEV & MARGARET HASTEDT:



NGR

1. 1. 1. NaI detectors position study for NGR was done, using a specially created collimation core for that purpose plus an Acuity 1000 laser and Cs-137 calibration source. Total counts from NaI #1-8 was fitted separately with Gaussian distribution. Detector centers were found to be shifted in the range of 0 to 16 mm. All shifts are in the direction toward the right end of the system (toward the entry to the NGR Logger). That information (together with the NaI detectors efficiency study) should be used into the data reduction program to interpolate the edge correction table.
      2. NaI detectors efficiency study was also done. Spread of efficiencies of NaI detectors #2-6 within 1%, NaI

#7 ~ 1.5% lower than average, NaI #8 ~2.2% and NaI#1 ~4.5% higher.

1. 1. 1. Calibration with K and Th standards for elemental analysis was performed. Mechanical problems with calibrating NaI#8 could be overcome with using special calibration titanium boat without forward wall and replacing current core stopper with one of different construction. Titanium for this new boat was ordered and already received on shore.
      2. K absolute concentrations for both basement holes and one sediment hole were measured. Very good agreement with all K data from ICP and in many places (but not all) with downhole logging data.
      3. Correlation study did not show any visible dependence between the K values and effective densities measured by GRA, even for small (below 1) effective density values. Still the improved method with 2 different linear regions for GRA calibration was proposed, that should improve accuracy of absolute concentration analysis for small effective densities (small pieces of rocks or not filled completely with sediment regions of core sections).
      4. After the changes done with the Whole Round Multisensor Logger NGR see noise from it. It was not seen during the first part of expedition, after a several days of noise reduction at WRMSL done by IT personnel, but came back at second part of expedition. Noise can be seen at the NaI scaler. Counts jump from 500 – 800 per 10 seconds, (normal for sediment core measurements) to 3000 – 4000 or even as high as 15000 sometimes during the movement of core sections on WRMSL. Right now increase in the coincidences between Plastic and NaI scintillators is not seen, but can became evident in case of any further increase of noise rate from WRMSL, which will compromise NGR data. Additional measures for decreasing noises from WRMSL up to the usual level should be taken.
      5. Galil control error ("Error communicating with the Galil controller", code -2) from NGR Core Analyzer software occurred several times this expedition.
      6. From time to time "Run the Experiment" button in the "Scan" window will not work from the first time (while it already have white color and supposed to work after the next press on it). One or two more presses on it always helped to start NGR measuring cycle.
      7. Annoying metal sound from NSK ball screw actuator mainly during the boat "heading home" phase. Actuator was opened, it was found that it is a lot of grease inside and it is uniformly distributed. No actions taken so far.
      8. In NGR Core Analyzer software it can be suggested to change in the right part of the screen under the "Total Counts" "Ch1", "Ch2", ... "Ch8" on to the "Det.1", "Det2", ..."Det.8". Otherwise users may get a little bit confused due to the pretense of (Energy) Channels for each individual detector.

WRMSL

1. At WRMSL PWL system did not centered 100% exactly comparatively to the core section on the rails. As a result, when it closes for measurement, it will first push core section from one side and then from another. In case if core catcher or very short core section is measured, it will rotate a little bit at that moment and from time to time will be pushed into the beginning of the next support rail, where it can get stuck and cause the Galil error, which will require to abort measurement for the whole WRMSL and start all over. Better centered PWL could resolve that problem.
2. Sometimes, when sediment core section which was constructed from 2 separate pieces with empty linear between them, PWL will not able to acquire any signal, when measuring the empty liner. That will also result in Galil error and require to abort and start measurements of core section again. Software modification in PWL could solve that problem.

THERMCON
T-con worked without any problems with rock samples, new pack and on ship unfiltered power supply (white socket). Attempts to measure sediment cores was not successful, most probably due to the high water content in the cores.

GANTRY
Split sections PWL measurements suffered from the fact that the name of the actual instrument to be used and the name of the axes to be measured are the same. It created confusion and data sometimes went in the wrong order into the LIMS. It will be desirable to name instruments (or calipers) differently from just X, Y, Z in the LabView software.

SHMSL
Ocean Optics halogen bulb changed out 9/20/11. Bill and Garrick spent quite a bit of time working on wiring in preparation for introducing the 3D volume-sensing laser/camera.

WRMSL
Helped ETs troubleshoot noise problems with PWL. They traced the problem to grounding issues and servo motor interference on the PWL coax cable between the Rx transducer and the pulser. (See ET report)

PWL
Extensive troubleshooting of PWL components to diagnose calibration inconsistency problem: After the noise issue was solved we had to examine the source code for the PWL. It turns out that the width parameter on the internal peak detection VI had been set too narrowly and failed to make good consistent picks on the somewhat noisy waveforms. Increasing the width from 6 to 24 made a huge difference in consistency. The end result for acrylic measures about 2% too high but at least it's a very consistent 2%, unlike the pronounced doglegs and low values we got early in the cruise.
One other note on PWL: occasionally we experienced timeout errors from the PWL Driver. In almost every case this was when measuring empty liner spacers or on end caps. The consequence is usually having to rerun the section or sections depending on when it happened, since PWL is the last measurement in the sequence. It would be really great if the next iteration of the software will have a gentler way of handling this error (restart measuring from current position/retry this timed-out measurement) rather than the all-or-nothing penalty right now.
The new calibration standards for GRA and PWL were used this cruise for the first time. They work well, but be sure to keep an eye on the GRA standard to ensure that it does not rotate when calibrating. There is a line on the end of the standard next to the pusher to keep it properly aligned. Hold it with your hand during calibration until we devise a more permanent anti-rotation solution.

SHIL
The imager started dropping lines on 10/9/11 which was traced to a nearly-disconnected linear encoder head. The nut had fallen off the attachment screw to the gantry and its screw also backed out of the head. We replaced the missing nut with Nylok nut to prevent a recurrence.
The SHIL was tested with the re-integrated dropped-line checking algorithm. It works well, but we did catch a bug where it was not clearing the error screen and you would see each new error appended to all the previous ones. If you want to test this functionality, gently stall (retard) the gantry while it's imaging if you'd like to the warning pop up at the end of the run. Don't push too hard or you will hang the program!

THERMCON
There were problems reported with the Teka during the transit from Curacao. The instrument's UPS had been plugged back into ship's regulated power when the unit was temporarily relocated to the Splicer corner for X336. Although the UPS is supposed to be a new power-conditioning type it does not solve the bad behavior of the Teka under regulated power. You MUST use unregulated power with the Teka regardless of the presence of a UPS if you expect to get any kind of results from the unit until a final solution is achieved.
Unfortunately, the relatively poor quality of ship's power killed the original new UPS so we switched to the spare unit. NOTE: to help preserve the UPS, it has been switched back to regulated power for the transit to the Azores.
A new version of the Teka software (v.5.0.0 Build 7) was installed at the beginning of the cruise. This version arrived with the redesigned HLQ puck #11023 along with a revised manual. The new puck design with softer potting epoxy worked flawlessly all cruise. Teka has essentially rewritten chapters 7 (TKGraph) and 9 (troubleshooting) in the revised manual.

GANTRY
We began using version 2 of the velocity gantry software this cruise. It generally worked well but we found a bug fairly late in the cruise where the caliper assigns all velocities to the X-axis regardless of what you choose on the screen. On one other occasion the laser quit reading distances properly for some unknown reason. Past a certain distance down a section it would simply reflect the sensor offset (171 cm) in the distance indicator instead of the true distance. A reboot solved that problem.
MAD
This cruise was the debut of MADmax, the new version of the Pycnometer and balance control software. It is easier to use than the old MAD software and prevents many of the misassignment problems for weights and
volumes. However, it is still possible to mess things up especially when you are in a hurry. You will pay a steep price if you try to rush the Pycnometer! When it is measuring, DO NOT attempt to assign new samples to the list or do any other action that will refresh the sample list. It will crash and you will lose the pyc runs. You can still weigh things if they are already entered into the sample list though. Also, don't click too fast when starting the pyc cells running… it's safer to start one cell, wait a few seconds, and then start the next etc. etc. Do the same patient routine when accepting volumes at the end of the runs.

DOWNHOLE MEASUREMENT TOOLS LABORATORY (DHML) REPORT

GARRICK VAN RENSBURG & RANDY GJESVOLD

APCT

• Found the APCT's DC Power Supply faulty. Replaced the fuse.
• Attempted to run the APCT-3 after corking operations and the data logger now thinks it is a cork. The time interval for samples was locked onto 65 min. MCS's investigated. No solution found. Started re setting all of the run parameters until it finally allowed the time to be changed. Our normal run parameters were then reentered and set into the tools. We really do need to make this computer a Downhole only computer. It needs to Run the APCT-3, Set, WSTP Only. This is a re occurring problem. This would be a good application of an IPAD.
• Ran the APCT-3 in Hole 1382B Cores 3, 4 and 5.

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EQUIPMENT STATUS

• 3-Complete Cuting shoes. They have been cleaned and a light lubricant applied to prevent rust.
• 5-APCT-3 Electronics Packages:
  • 1858005C- mV-3008 Counts-43336 *Marked no cal file.

o 1858007C- mV-2974 Counts-942575

• • 1858008C- mV-3221 Counts-108824 *Battery Changed Nov 2011.

o 1858009C- mV-2990 Counts-1031883

• • 1858019C- mV-3209 Counts-14076 *Battery Changed Nov 2011. Has intermittent failure. Found broken wire and 2 cold soldier joints. Problems remain. Sending back to IODP.

• 5-Battery Packs for APCT-3.

o S/N: 1011 Model # 1858-5-00-01D Voltage: 3.114 VDC o S/N: 1062 Model # 1858-5-00-01C Voltage: 3.147 VDC o S/N: 1887 Model # 1858-5-00-01D Voltage: 3.302 VDC o S/N: 1893 Model # 1858-5-00-01D Voltage: 3.297 VDC o S/N: 1944 Model # 1858-5-00-01D Voltage: 3.292 VDC

• 2-SET Tools. Sent back to IODP for upgrades.

• 1-SET-P Tool. Tool #2.

• 8-Battery Packs for SET and SET-P Tool.
  • S/N: HM 001 Model # AMBE150022CPDL1 Oct 19, 2007 o S/N: HM 002 Model # AMBE150022CPDL1 Oct 19, 2007 o S/N: HM 003 Model # AMBE150022CPDL1 Oct 19, 2007 o S/N: HM 004 Model # AMBE150022CPDL1 Nov 26, 2008 o S/N: HM 005 Model # AMBE150022CPDL1 Nov 26, 2008 o S/N: HM 007 Model # AMBE150022CPDL1 Nov 26, 2008 o S/N: HM 008 Model # AMBE150022CPDL1 Nov 26, 2008 o S/N: HM 010 Model # AMBE150022CPDL1 Nov 26, 2008

• 2-Battery Packs for WSTP.

• • S/N: HM 005 Model # BHEC165042CPSL3 Feb 15, 2011
  • S/N: HM 009 Model # BHEC165042CPSL3 June 08, 2007

IMAGING & MICROSCOPES

WILLIAM CRAWFORD

MICROSCOPES
This Expedition was the next in line after a tie up period. Computers and systems were upgraded during that time and the effect of this rippled through the system. The Mbio scope in the Chem lab would not image with the upgraded OS. Mike Cannon re imaged the computer back to the previous state and the system is fine now. It should be noted the metadata capture/micrograph/capture system is not compatible with the newer windows Os. Whether or not the applications were running on the correct OS system, none of the applications which associate metadata with images would function. This was explained due to a change in the data base which affected the programs globally. Algie Morgan soon recognized the problem and modified the programs to work. The programs affected were the Close-up Capture, The Thin Section Capture (picat) and the Micrograph Capture.
On the same topic, the Image Grab program used to bulk down load the line scan images did not function as well. James tutored me on Lims2e and that system of down load works well to harvest the whole round images which were in real production for the first time. Lims2e is limited however to cores and the Imaging Specialist needs to download scans by days. Algie modified the program to accept the global modifications and also has placed a date range rather than a specific date for downloads. Both programmers were very professional and accommodating.
The new LED source for the Mbio scoped worked well and scientists found it simple and easy to use with no complaints from the scientist. The system failed to shut off on one occasion and the power supply was disconnected and the system returned to service. Only one incident and with more re-occurrence.

LINE SCAN CAMERA
WHOLE ROUND IMAGING
As mentioned earlier, this was the first real implementation of the whole round line scan ability given to the shil. The hope of using an auto program to stitch the images proved to be problematic. The programs, both Photoshop and Panorama maker becomes confused by the sameness of the core and in effect creates portions of the image which are not actually there. Creating a clipping mask drag and drop operation in Photoshop solved this. For the most part, other than the smaller rolling stones, the accuracy of the system is good. It is simple enough to drag the images into the appropriate spot and then nudge them into place as needed to match. The Scientist had no problems capturing the images which were photographed wet in all cases. Together we captured and completed 60 whole round images. No path or place for this completed images has been established for Lims.

ALIGNMENT, COLOR AND DENSITY CALIBRATIONS
The Line scan camera system was checked for dynamic range and calibrated for color by Margaret and I about mid cruise and checked again before each new hole. The holder for the end caps for bar code reading was adjusted and works well. A skipped line detector was implemented in the program and it soon uncovered some problems.
Margaret found a loose bracket in connection with the linear reader. Once this was adjusted and secured the dropped lines went away.
STILL AND VIDEO CAPTURE
The Expedition sailed two videographers with one serving as a director. The worked tirelessly capturing day-to-day activities as well as interviews. The program loaned a few pieces of equipment including lights, light stands, fluid head tripod and other items to help them with their efforts. I assisted when asked and advised when asked otherwise the completed their work without assistance. Other than special projects and events my video efforts were subdued as not to interfere with their efforts.
The video and still equipment works well with one exception of the remote audio mics. This system could not be made to work dispute repeated attempts. This could be operator error or a faulty system. We should consider returning the unit for repair.

CLOSE-UP SYSTEM
This system continues to work very well with the exception of glitches in the printed labels when the odd sample is requested to be photographed. This appeared in Exp 335 with the Junk baskets not fitting well with labeling. At times text wrapping can be a problem which requires tweaking. The close up table was used as for the capture of images for Evert Salas (Microbe detection) and for an Atmospheric Scientist, Dale Griffin, to capture density and color differences in particle filters on a day to day bases.
The ability to have an instant capture displayed which allows tweaking of the images for better texture cannot be over emphasized.
Many covet the space the CLOSE-UP system occupies. An official proposal to relocate the CLOSE-U system is currently on the table. Please note that my system requires a computer, a printer, a monitor and system connections as well as camera and lighting to be one unit. All of this must travel together to be complete.

PICAT (THIN SECTION CAPTURE)
A new thin section tech was employed during this cruise. Ryan McKenna proved to be very capable and a delight to work with. He was shown the PICAT system and had very little problems capturing the thin section images. The scientists used the system for their own need and were very happy. No issues with the system were had other than the image capture/metadata mentioned earlier. The video team used the Canon 5D to record video through the system for their purposes.

IMAGING STATUS TO DATE

• Still Images 97gb
• Video Minimal
• Close-up 88
• Mbio samples ( Salas) 50+
• Atmospheric (Griffin) 61
• Thin-section 153
• Micrographs 355
• Whole Round line scan 60

CHEMISTRY LAB TECHNICIANS REPORT

LISA BRANDT, MIKE BERTOLI


ICP-AES
44 Hard rock samples were analyzed on the ICP. On the first start- up of the cruise, we discovered that the plastic connections on the air knife had become corroded and dissolved. Bill M rigged up a new connection with plastic tubing, Swag-lok, and some wire. The connection held up fine for the three runs. The Air Knife + connections have been added to AMS and replacements should be in the shipment.
ALKALINITY
123 pH/alkalinity samples were analyzed; no issues arose.
GC3-NGA
83 gas samples were analyzed, though as scientist samples and not for safety monitoring. GC3 ran flawlessly; no samples were analyzed on the NGA.
IC
A new version of Chromeleon was installed during X336, version 7.1. The IC Chromeleon software was upgraded to version 7.1. This was a very big change. The IC instrument needed to be completely re- created at the Instrument/Server Configuration level. I then fixed the data section so that we can view the old Chromeleon 6 data as well as the new data created under 7.1. Next, I worked on trying to migrate the methods from 6.8 into 7.1. Allegedly, you're supposed to be able to just re-save your methods files into
7.1 and then they will be magically converted into 7.1 and everything will be awesome, but every time I tried this, I got tons of errors and the methods would not work. So I recreated the methods in 7.1 and have gotten all of them working.
The baseline when pumping eluent displayed a lot of waviness, so we performed the pump maintenance procedure as per the manual included with the pump maintenance kit. We also replaced the guard column on the anions side. Retention times have still shifted faster, so the primary column may need to be replaced.
DA
New software was deployed for the DA on this expedition, and so it was tested and the User Guide and Quick Start Guide were re-written to reflect any changes.
SR ANALYZER
The SRA failed to ignite any glow plug, leading us to contact Weatherford tech support. With some assistance from the ETs, we determined that the TI Excalibur chip wasn't functioning properly. Weatherford is shipping a new board so that we can swap out the bad one with the good one; this should fix our ignition issue. The UPS was
borrowed to supply the movie room projector with power, it needs to be returned when the new UPS's arrive at portcall.
COULOMETER
Coulometric analysis was performed on eight sediment samples; the instrument worked well, and we had no problems with it.
CHNS
Nineteen samples were analyzed on the FlashEA1112 during X336, though only for C,N. While trying to tweak the instrument to better recover S the detector became unruly and we decided to withhold further analysis until this was rectified. The CHNS fails its leak check for both the carrier and reference flows, but this problem has been documented since 2009.
NANOPURE WATER SYSTEM
The water system has had two or three instances of spontaneously leaking onto the bench (~200mL); it hasn't done so for the last two weeks.
CARVER PRESSES
The Carver Presses worked well; the leftmost press sounds like the motor isn't running correctly, and the auto feature sometimes doesn't work. The center press still seems to have a leak around the piston casing.

OTHER CHEM LAB ACTIVITIES
The purge chamber on the anaerobic glove box in the cold room was re-plumbed with shipboard N2 in order to conserve lab gas.
GC2/TOC
Neither were used this expedition.

XRD & SAMPLE PREP LABS

KRISTIN HILLIS

SUMMARY
This was my first cruise in the X-ray lab, and things went relatively well. It was a CORK cruise with some down time that allowed some testing and running practice samples through the entire process. All equipment ran well, with the exception of the switch being replaced on the x-press, explained below.
ICP samples: 48 XRD samples: 51

EQUIPMENT
Thankfully, nothing went terribly wrong with any of the equipment. Several days into the rock crushing process, when I went to use the x-press it would not turn on, despite it working 10 minutes prior on another sample. I originally thought I had tripped a breaker, but after the ET's investigated, they found the on/off switch had failed. The smaller switch has now been replaced with a sturdier one.
I ran into a problem when I ignited a powdered squeeze cake sample from the first site. When I pulled the four samples out, the quartz crucibles had become cloudy and needed to be thrown away. This we believe was due to a lot of carbonate in the samples.
I contacted Bruker once in regard to a scientist wanting to use MacDiff to analyze the data post-cruise. Brian informed me the .UXD file we create should work with almost any software.

THIN SECTION LAB

RYAN MCKENNA

SUMMARY
Fifty-eight thin sections—including two for large format slides— were selected from the rocks brought up in the basalt coring. Only 57 were completed. Going back as far as X301, this is greater than the median number of thin sections made (41), but lower than the average (83).
Most samples were basalt but some plutonic rocks like gabbro and peridotite were made into thin sections as well. Additionally, two sediments were selected for thin sectioning. One sediment—a micritic carbonate (TS#42)—was not completed. Six attempts were made on two separate samplings with a last attempt using the Norland optical adhesive and the UV chamber to mount it to the slide. Unfortunately, even with the use of antifreeze instead of water and cutting half way then turning the sample around and resuming cutting, the sediment would not hold together when cut on the Buehler PetroThin system. Either the slide would break mid-section or the sediment would erode off the slide.
One misfortune occurred during filming in the Thin Section lab. Instead of moving the PetroThin's grinding wheel in the direction away from the cutting wheel, it was moved toward it. This caused the grinding wheel to shave off two teflon pins in the vacuum plate holding the slide in place. To remedy this, a piece of plastic welding rod was brought to me by Tim Bronk (ALO). The diameter of the rod is nearly the same as the teflon pins. A number of new pins were cut and the shaved pins replaced. The rest of the pins that were created were placed in a bag and put in the PetroThin drawer. The plastic welding rod was also placed in that drawer.
Other objects replaced in the lab were the reflected light bulb in the OLM and the prefilter cartridge, RO membrane, and the carbon cartridge in the Barnstead Diamond RO.

PROJECTS
The only project I attempted was to see if using the Norland optical adhesive and the UV chamber to mount billets to slides would work as a viable alternative for mounting. This would cut down the time roughly by a factor of 80 (5 min vs. 360-480 min) compared to the pressure- jig system currently in use. A cement billet was mounted using the Norland-UV method. It adhered nicely to the slide and cut well. Furthermore, when compared as a prepared thin section to another cement thin section made with the pressure-jig mounting step, there were no optical impairments or differences in clarity as perceived by Co-Chief Scientist Wolfgang Bach. On a side note, it was brought to my attention by Margaret Hastedt (Phys Props MLS) that the Norland adhesive was past its use-by date. I suggest further testing of this alternative mounting step with new adhesive in the future.

UNDERWAY GEOPHYSICS & FANTAIL REPORT

WILLIAM MILLS (WITH A LOT OF HAND HOLDING FROM KRISTIN HILLIS)

SEISMIC SYSTEM

• No seismic or VSP surveys were performed during the expedition.
• The seismic streamer, stretch section and leader were removed from the port winch and returned to shore for storage. Please use care unloading the streamer, to prevent kinks every other loop was flipped and lowered into the crate so don't just grab the end and start pulling. You will need to lift each loop out of the box and walk-out the twists. The streamer must be transferred to a suitable reel when it arrives in CS. Do not leave it stored in the crate.

MAGNETOMETER

• The magnetometer was transferred to the port winch and the new deck leader was installed from the U/W lab to the port side winch. The old leader was left in place in case we have to run the system from the starboard winch in the future. Because we do not have spare connectors for the slip ring, we are currently plugging the deck leader into the tow cable after we have deployed the magnetometer. So it goes without saying… you need to unplug the cable before you operate the winch. Signs have been made for electrical switch (on bulkhead) and for the winch control lever to let everyone know that the cable is plugged in.
• On a previous expedition the tow fish suffered a shark strike. Since then, cracks have begun to propagate from the teeth marks along the length of the orange "bumper". A new "bumper" has been ordered. The pressure case does not appear to have any problems.

FANTAIL EQUIPMENT

Starboard Winch

• As mentioned earlier the magnetometer is now operated from the starboard winch which allows for faster deployment and retrieval.
• When operating the winch you may see a brown cloud erupt from inside the winch's drum. This is not smoke but just fine rust that has accumulated over the years of in activity.
• Initially the control lever was very stiff and would not return to the neutral position. The lever assembly was taken apart, cleaned and reinstalled. It is better but does not fully return to the neutral position when released, so be careful when operating. Stronger springs have been ordered.
• When I return to CS I'll have a roller for the rail made to protect the cable. This time it will be made from SS so it won't seize up with rust.
• The level wind mechanism sucks! Jurie has experience with the level wind's electronics, so I would like him to take a look at it. As usual, it continues to move starboard regardless of the position of the fleet

angle sensor. If we cannot fix the problem, I would suggest that we disable the fleet angle sensor and just use the manual controller.

• We need to reinstall the fish-eye mirror over the crane and relocate the light under the heliopad so it doesn't blind the camera. Moving the light will help us see the tow-fish when we retrieve it at night.

Port Winch

• No problems to report.

Deck Crane

• No problems to report.

UNDERWAY LAB
BATHY 2010

• No major problems with the system, other than the heading value (provided by WinFrog) would not update. Checked that the NEMA sentence expected by the Bathy 2010 software and made sure that WinFrog was sending it ($GPHDT) ..no joy. Changed both Bathy 2010 and WinFrog to use/send the

$GPVTG and it works! I have no explanation for why.
SEALINK

• No problems

GPS RECEIVERS

• !worddav91c851529972a1d394d7fff01a3d7a68.png|height=152,width=138!The antenna for the GPS receiver (in the Tech Office) was relocated to a permanent mount on the bridge. The receiver was added to WinFrog as a primary position device "Forward Trimble GPS – IN" and the Aft Trimble set to secondary mode.

• "Look Mom.. No GYRO!" With two GPS receivers, WinFrog is now set up to calculate heading from two positions. Just select the "Use for Heading

35Calculations" for both receivers. The Gyro is set as a secondary Heading device and will take over should one of the GPS receivers drop out. (when you click OK it complains that there are no primary Heading devices but seems to use the calculated values as the Primary heading input regardless).
WINFROG

• Update the ship's profile to actually look like the JR. Used shipyard drawings to create the ship's hull outline and added additional details to show the Helicopter landing pad and Bridge. The moon pool is shown as round and with the correct diameter.

• !worddavd17bd936d1c5c2a1342209e098fcfe8f.png|height=149,width=136!All offsets were updated using the Moonpool as the origin (as before). All offsets are measured from this point (in meters) with the forward-starboard offset as positive values and aft-port

offset as negative values.

• On the ship's outline graphic, I included the physical locations of the sonar dome, the forward and aft GPS antennas. Also I have turned on their

graphics indicator (Configure>Vehicles>Configure Vehicle-Devices> select device
>Edit> select Graphics = On) to show the actual position of the antennas as seen by the GPS . Generally the GPS position of the antenna plots on graphical location shown on the ship's outline and ..often it doesn't! Generally, it will be close (few meters) unless there is problem and then it can plot completely off the ship's outline.

• !worddav48bc4d0d2bb37ac74b26077b1aa76563.png|height=178,width=200!I added offsets (laybacks) for all of our possible data collection points (Seismic streamer, Magnetometer, and Sonar Dome). In the case of the Sealink application, you must set the layback correction to "0" because the

position sent by WinFrog is already corrected for the layback.
Also, I have entered two offsets for the magnetometer (port and starboard) so make sure to use the correct offset if you change the magnetometer winch from ..currently set to MAG-PORT (offset from moonpool to winch + tow cable length).

• Renamed I/O device so it is easy to tell what system the device is communicating with, the data type and whether it is an input or an output device.

• Both WinFrog 1 and 2 are now operating on the Win7 OS.

PROBLEMS


During the expedition we experience two separate problems with the WinFrog communication settings:

1. One morning we noticed the ship was at the wrong heading and the wrong location when compared to DP. Somehow all of the communication settings had swapped between COM and TCP options. After rebooting the system, WinFrog came up with the values still swapped but then in a few minutes the WinFrog reset the communication values???? Don't know why and it hasn't happen again.

1. Prior to leaving our last site there was no data output to the Bathy 2010 and Sealink. After several hours of trouble shooting WinFrog 2, we fired up WinFrog 1 and everything was fine. The next day I went into WinFrog 2 deleted all of the devices from the vehicle and reloaded them. This solved the problem. Why it wasn't working before? I have no clue! Kristin mentioned that WinFrog 2 has a history of being flaky.

DATA SUMMARY
Expedition 336 consisted of 3 main transits (including Curacao to Barbados), multiple transits in DP mode, 3 sites (one legacy sites), and 8 holes.
Transits:CURACAO→ BARBADOS BARBADOS → 395A U1384A → AZORES

Sites/Holes:395A U1382 A,B
U1382 A,B,C,D,E U1384A

WinFrog 2 was the primary computer used to collect navigation data. Bathymetry and magnetic were collected on all transits.

ET REPORT

GARRICK VAN RENSBURG & RANDY GJESVOLD

ET Shop

Installed tubing in Nitrogen Line fitting so it would reach into the Downhole Lab. Conducted quarterly electrical safety checks. Phone ceased to function. This was replaced.

Cryomagnetometer:

• • Manufactured leads for the degaussing wand. Repaired shorted ground wire on Dual Speed Spinner Magnetometer JR-6A.
  • Modified the aft most core description table to mount the Ultraviolet laser scanner for the Debbie Tool. Mounted the instrument and computers on the table. Manufactured a cover for the laser.
  • Chasing excessive background noise on the Whole Round Multi Sensor Logger. Went through the Galil book troubleshooting procedure and this confirms that we have indications of a loose ground. Installed a common ground on the motor. Cleaned up wiring on the Galil and repaired Extension Card wiring. Manufactured a long table in the Core Lab for Cork Osmo Sampler assembly.

Section Half Multi Sensor Logger:

• • Light source failed. This was replaced.
  • Changed out Ocean Optics 30mm Integrating Sphere with an Integrating Sphere with a larger opening.
  • Modified the Galil with an extender card and re routed wiring from the sensors.
  • Manufactured a mount for a Lasiris laser and the Multiscan 3D camera. Preparing to add the 3D camera with laser to the SHMSL.

Section Half Image Logger:

• • Modified the laser mount so that the end caps could be scanned more easily.
  • Ran air ducting to the Laser Engraver to remove exhaust gas generated during operations. Replaced several ceiling tiles.

Micrscopes:

• • Light source bulb for stereo microscope failed. This was replaced.

Core Splitting Room:

• • Tightened all of the fittings on the water hoses.
  • Removed the forward most tile saw so an enclosure can be manufactured. This was later re installed and LED lights added.
  • Added LED lights to one of the other saws also.
  • Forward door opener ceased to function. Found a broken wire on one of the sensor pads. This was repaired.
  • Aft most Tile Saw belt became loose. This was tightened.
  • Repaired hands on the clock for GMT time in the aft end of the core lab.

Phys Prop Lab

• • Repaired several leads for the Thermometers and Conductivity meters.

Cryomagnetometer:

• Manufactured a fan cover for the fan that blows the air through the Cryomag. It had disappeared. The fan was snapping peoples fingers.

Chem Lab:

• The ICP Air Knife failed. The ceramic attachment for the airline turned to powder. Assisted the Lab Officer in manufacturing a replacement fitting.

X-Ray Lab:

• Fisher FS14H Ultrasonic Sink ceased to function. Found the wires had vibrated off of the internal relay. Re attached and ran for 20 min. They vibrated off again. They were soldiered on. Oscillator ceased to function. It's non repairable. A new Ultrasonic Sink has been ordered.

Thin Section Lab:

• Hydraulic Rock Crusher ceased to function. Found one leg of the power in the wall power strip had opened. Cycled the power at L-39 30 and that problem cleared. The Hydraulic Rock Crusher still wouldn't function. Found the run switch to be faulty. This was replaced.

Conference Room:

• Moved the projector screen so a full display will show up on it. TV on forward wall failed. Attempted to troublshoot it. The components are all surface mount technology and too small to repair effectively. It was replaced with the TV removed from the reading lounge. Original TV was surplused.

Upper Tween Deck:

• Installed foot safety switch on the new Drill Press. Ban Saw rail worked loose. This was tightened. Installed two unistrut beams above the gas bottle aft rack.

Lower Tween Deck:

• Repaired Coffee Maker. Thermostat had ceased to function and one of the capacitors had failed. Repaired an audio cable for the geeks.

Gym:

• New Treadmill had a program fault error. This was corrected with a power on restart. Problem later returned. Receiving Error 3 (Speed Irregularity) and Error 103 (Input Current OC Trip). Power and frequency have been checked and are OK. Installed a UPS borrowed from the loggers with power conditioner and the problem cleared. You can run about 20 minutes and the treadmill shuts down.
• Shut down Science lounge for a day and installed the UPS on the new treadmill. Runs up to 45 minutes were tested and the UPS and treadmill had no problems. Moved UPS back to Science Lounge.
• Old treadmill belt was adjusted. It was tracking to the left.
• Speed Bag. Found the speed bag sitting on top of its mount with the steel retaining clip broken off. A new one was manufactured and installed.
• Cleaned up wiring.

Science Lounge:

• TV had black picture and no audio. Found the settings on the TV had been altered. These were re set.
• Updated firmware on the Popcorn Media Player and changed the selection of movies available.
• On Oct 13 found the Popcorn Media Player overheated and non functional. It had been left on for several hours and this caused the overheating condition. Wired in a 120V cooling fan from the mains. If the machine is on the fan will be running.
• Installed a screw in the cover for the hard drive (Child Proofed) to keep people from opening it to access the hard drive. It was opened to help cool it down, which in turn scrambled the movies in the hard drive because it must be powered down to be remove.

• Re installed the projector and the big screen.
• Science lounge Projector was set up properly with its UPS to smooth the power out.
• Ran a cable from the TV system through a DVD player which has a tuner so it can be broadcast on the projector in the Science Lounge.
• Moved the Samsung 60"TV to the reading lounge.
• TV from the reading lounge was moved to the Conference Room. Conference Room TV had ceased to function. It was surplused.
• Manufactured an Audio Visual Cabinet from T-Slot and placed in the lounge. Removed wood cabinet and installed all of the AV equipment into the new rack.

Reading Lounge:

• Installed Sansung 60" TV. Cleaned up wiring.

Fantail:

• Conducted paint and preservation on the Starboard Reelwind and the Crane Shive.
• Cleaned guide rails and worm gear on the port reel wind. Applied Dry-Slide lubricant.
• Installed deck cable for the Magnetometer on the port side.

Misc:

• Manufactured cabling for Mike Storms.
• Repaired tripod for videographer.
• Installed a Gray Cargo Box on the port bridge wing and supplied power for the instruments to be mounted there.
• Installed a GPS antenna on top of the bridge for the Winfrog Navigation system. A new cable was run through the MCT in the LO's Office to the port bridge wing and a stud mounted on one of the poles to mount the antenna. Manufactured a camera mount for the ships photographer.
• Repaired bushes on a vacuum air sampler for one of the scientists. It lasted 41 days and burned the wire off of one of the brushes. No replacements were available so a new brush was manufactured. It was been placed back in service. It lasted four days and burned out the other brush. Manufactured a second one. Ran until the end of the expedition.
• Power supply for a particulate sampler failed. Tied in a DC power supply to get the scientist to the end of the trip.

CURATORIAL REPORT

GEMMA BARRETT

SUMMARY

SAMPLES:
A total of 11920 personal samples were taken during Expedition 336. 1121 shipboard and 11165 personal samples were taken. A total of 936 whole rounds were taken. 130 for IW samples, 130 for microbiology, and the remaining as personal samples.

SHIPMENTS:
A total of 62 core boxes will be shipped to the Bremen Repository holding the 80 cores received on Expedition 336. There is an equal number of 31 working and 31 archive boxes. There were 33 APC, 5 XCB and 42 RCB cores. When unpacking cores, please note that many IW samples were returned without being squeezed for pore water since enough water was extracted from the first IW sample. Therefore, many d-tubes have a larger section at the top and a smaller IW section at the bottom of the d-tube which may be overlooked.
Cores from Leg 197 were found in the reefer on the ship before embarking from Curacao and will be sent back to the GCR upon completion of the cruise as requested by the GCR Superintendent, Phil Rumford. The list of these cores can be found in the table below:

A number of frozen, refrigerated and room temperature sample boxes will be shipped following this expedition. The table below shows the approximate number of boxes of samples being shipped frozen with dry ice (F), refrigerated with blue ice (R) and at room temperature. This number may change slightly as final boxing occurs.

HAND CARRYING SAMPLES:
Fengping Wang will be hand carrying whole round samples back to China. She is in possession of a letter explaining the types of samples she is carrying for customs and immigration officials if it should be needed.

RESIDUES:
Residues will be distributed as follows:
Residues Destination
PP Cubes:All to Olivier Rouxel
TSB Olivier Rouxel, Paul LeCampion & BCR
Smear SlidesAll to Young-Soo Park
IW (Squeeze Cakes) Adina Paytan, Victoria Rennie, Olivier Rouxel, Kasumi Sakata and Archive piece to BCR
IW (Liquid): Victoria Rennie and Geoff Wheat
ICP PowdersAll to BCR
XRD (Unignited powders)Olivier Rouxel & Young-Soo Park
MADC All to BCR

THIN SECTIONS:
A total of 57 thin sections were prepared by Ryan McKenna during this expedition and described by petrologists on board. A thin section for TSB#42 was not capable of being rendered due to its unique physical properties. TS#42 represents the only skip in numbering for the thin sections prepared on this cruise. This thin section has been deleted from the LIMS database. A comprehensive list of thin sections is being sent to the BCR Superintendent and USIO Curator.


ACTION ITEMS

BORROWING THIN SECTIONS:
Yumiko Harigane would like to borrow the following thin section from the Bremen Core Repository: U1382A – 8R-4
- TS#18
Shipping Address:
Yumiko Harigane
National Institute of Advanced Industrial Science and Technology (AIST) Geological Survey of Japan
Central 7, 1-1-1 Higashi, Tsukuba 305-8567 Ibaraki
Japan y-harigane@aist.go.jp Tel: (81) 29-849-1060
Olivier Rouxel would like to borrow the following thin sections from the Bremen Core Repository:

Shipping Address:
Olivier Rouxel IFREMER, Centre de Brest 29280 Plouzane
France orouxel@ifremer.fr Tel: (33) 2-98-49-87-08
SOFTWARE

SAMPLEMASTER:
There were extensive issues with SampleMaster on this cruise. Currently, there are problems with the parameter search causing the program to crash frequently and issues with printing on upload. At this time, there are a number of different versions on different computers throughout the labs. Algie Morgan is planning the release of a new version of SampleMaster which he has been working on for a few weeks. I requested that this version not be released until all sediment core had arrived on deck. I will test this new version as extensively as possible and report any problems to the developers to prevent any hold-ups for the crew on Mediterranean Outflow.
An extensive report was requested from shore about SampleMaster's deficiencies on this cruise. The first round of problems encountered before the first version release on the JR on 10/12/2011 included:

1. Performance speed: the program is running exceptionally slow! It may take 30 seconds to a minute for a page to update
2. When deleting samples, you can no longer click on a sample to add it to the Sample Deleter List. You either have to scan the barcode or enter the text id manually
3. The copy/paste function isn't fixed. You can paste information into SampleMaster but often cells with drop down menus have to be re-entered by hand. Copying and pasting information from SampleMaster to Excel is also problematic. Sometimes it works and other times not, depending on what you want to copy and paste
4. The 'last curated length' appears to generate random values for length not associated with either the created or curated lengths. These values have been corrected to the curated lengths for all sections for Hole U1382A. Is this column needed/necessary? From what I've heard from other technical staff, this column was originally generated for something that is not really used anymore on the ship
5. Occasionally, the recovered length in LIMS Reports would list 0m after we had uploaded the created lengths for the sections. When we re-uploaded the data, the recovered length would appear. This happened at least twice that I know of for the 11 cores (on one instance, it had to be uploaded twice before the recovered length appeared).

After 10/12/2011 version release:

Problems #1 & #5 have been fixed. Problem #3 has been resolved and the upload function also appears to be working effectively. Problem #4 still persists but the ALO's and I simply edit this field when entering the curated length to be the same value. Problem #2 still has not been fixed. Samples have to be deleted either by printing off a label to scan or typing in the Text ID for each sample to be deleted.
Problems encountered after first release and before second version release on JR 10/22/2011:

1. Cannot edit any samples taken on catwalk (MBIO whole round samples). Am able to edit any samples taken off of the working half.
2. Sample hierarchy presented in parameter search is not correct. Email sent to Algie is below with screenshot:

After 10/22/2011 version release:

Both of these problems were fixed by the 10/22/2011 release of Sample Master.
REQUEST CODE MANAGER:
During transit, this program was not functioning. The shipboard developers were notified and the program was re- released. After some testing, I found that assigned sample request codes were not being recalled in SampleMaster after they had been assigned a sample request number in Request Code Manager. David Fackler worked on the problem and Request Code Manager is now functional and no further issues were found.


NEW ITEMS

LASER ENGRAVER:
The laser engraver was used on core liners during this expedition. Engraving the liners before binning out hard rock as well as engraving the sections of sediment worked effectively and efficiently. If the laser engraver goes down temporarily, the Dremel tools are still in their original stations for engraving. I will show the oncoming curator how to program sections for etching into the laser engraver at cross over.


SAMPLING AT SITE 395A

CORK, THERMISTOR STRING, STINGER, SINKER BAR & PLATFORM SAMPLING
Samples were collected at various locations on the CORK, ROV platform and of the thermistor string on September 23rd by microbiologists within the science party. The quantities and locations of samples are provided in the table below. Eleven archive microbiology samples will be shipped back to the BCR upon completion of the cruise as requested by the ship-board scientists.
These samples were classified in SampleMaster with the parent being the hole. The depth for the ROV platform was noted as 0m because a negative depth was not recognized upon upload.

The detailed sample list can be seen in its entirety in the Appendix. The locations of microbiology sampling are highlighted in Figure 1.

Figure 1. Diagram of CORK pulled from Hole 395A and sampling locations.




HARD ROCKCORE FLOW AND SAMPLING


Sites: U1382A & U1383C
Sites 1382A and 1383C were drilled for hard rock. Due to microbiology sampling, microspheres were used for all hard rock cores and technicians were instructed not to throw away or touch the microsphere bag if it was encountered when processing the core catcher. Once core was on the catwalk, the core would be sectioned and quickly brought into the splitting room. The sections were shaken out onto split core liners sprayed with a 10% ethanol solution. At this time the lead microbiologist on shift would consult with the lead petrologists on shift and decide on the whole round microbiology samples to be taken. The samples were measured and documented by
the curator / ALO. A picture was taken of each whole round with a label. The whole rounds were handled with baked foil and rushed to the microbiology lab for smashing and put into bags to go in the -86 freezer. Microbiology whole rounds would be entered into SampleMaster to allow the chemistry technicians to begin printing labels for the samples even though the depths are later changed when the hard rock is curated and binned. This allowed samples to be labeled before being put in freezers. The microbiologists are aware that the curated depths are different from the ones printed on their sample labels and preferred to have labels earlier for bagging rather than later to avoid confusion in the freezers.
We frequently had petrologists handling hard rock whole rounds before they had been curated even after frequent warnings not to. The Curator and ALO would make sure at least one technician was in the splitting room monitoring the core while core liner etching and SampleMaster entry took place. Cores were then curated and run through the tracks and 3D imager before being split and followed the normal hard rock core flow.
Each evening at 22:00, the petrology and physical properties scientists would gather to decide on the shipboard sampling for geochemistry (XRD, ICP & CHNS), thin sections and PP cubes for the cores that had been fully processed since the previous day. This allowed the curator to enter all entries into SampleMaster, prepare bags with labels and start cutting the samples before finishing their shift. The samples would then get passed onto the x-ray technician at the beginning of their shift at 00:00 and the thin sections technician. The system worked well and a similar system will be suggested on similar hard rock recovery expeditions.
At the end of U1383C, portions of 8R-2 and 8R-3 were returned by the microbiologists after the site summary had been completed. These pieces were originally intended to be returned (~2 weeks previously) by the microbiologists but forgotten about. These sections had to be re-imaged through the tracks and edited in the database which presented a setback in the day's activities for the core lab technician, curator and ALO. This was explained to the microbiologists and future samples were returned within ~1 day.


SEDIMENT CORE FLOW AND SAMPLING
Sites: U1383D/E, U1382B, U1384A
The lead microbiologist for sediment and I coordinated closely to complete a comprehensive and easily understood plan for catwalk sampling. This included a diagram for each section with the scientist's request code, freezer to be stored in and whole round length. Different plans were created depending on if it was a mud line core, middle core or near basement core. This was created before core arrived using the estimated depth of sediment but was easily modified as core came up. A SampleMaster template was also created following this plan and updated as modifications were made to the overall catwalk sampling plan. This proved effective and easy to use for myself and the ALO's with very few errors made in SampleMaster and none on the catwalk. Due to the large number of samples being taken for microbiology from each core, the microbiology sampling plan was scaled down after the first hole to remove non-essential sampling and smaller samples where possible.
Sediment was laid out on the catwalk and measured in 150cm sections. The microbiologists and geochemists were most interested in the deeper sections of the core so sections were measured from the bottom of the core to ensure that the last section in each core was a full 150cm section for sampling. After each section was measured and labeled, the lines for cutting IW and microbiology samples were drawn starting that the bottom. Before any whole round was cut, first the section was capped at the top to prevent sediment migrating up the core liner, changing the initial recovered length. A team of microbiologists used coolers on the catwalk to store their samples while cutting took place. Syringes were taken by one scientist for a few different people at the top of each section. After all WR cutting was complete, the remaining sections were moved into the core lab for laser engraving, labeling and wheeled down to the reefer for oxygen profile measurements. Cores would spend between 4-6 hours
in the reefer and technicians in the core lab would be called to retrieve them. After equilibrating to temperature and acetoning end caps, the sections would then be run through all tracks and then split. The physical properties scientist would collect electronic resistivity data at 10cm intervals down the core with a probe. MADC samples would then be taken and scientists would be paged to place their flags for sampling if they did not have a standard sampling plan. Cores were only split during the daytime when the physical properties scientist was on shift and able to do probe measurements.


CURATION NOTES

CHNS
The CHNS is not registering a sulfur peak in its data collection and was not run during the end of the expedition. The oncoming curator should be regularly informed about whether CHNS can be run which will affect whether powders should be made by the x-ray technician.

BORROWING THIN SECTIONS DIRECTLY FROM THE JR
The Expedition Project Manager questioned why scientists couldn't borrow thin sections directly from the JR as long as they were well documented by the sea-going curatorial representative. This discussion was continued between the EPM and the USIO Curator and other related parties. No change in policy has been made and thin sections continue to be sent to their respective repository before being sent out to the science party.

PUBLICATIONS REPORT

ALYSSA STEPHENS

SUMMARY
Expedition 336 has proven to be a productive and variable expedition. The main focus of my work was to generate Visual Core Descriptions for hard rock and sediment, and to proof, format, and track all volume materials (including text, figures, and tables). There are Visual Core Descriptions for six sites: U1382A U1382B, U1383C, U1383D, U1383E, and U1384A. Some of these sites contain both hard rock and sediment. The volume materials collected cover three sites: U395A, U1382A, U1383C, and a fourth which covers all added sediment holes.
As we added four holes of sediment late into the schedule, I anticipate the following for VCDs and volume materials. VCDs will be completed in a timely manner. Volume materials, though some of the scientists may be a little slow, will be turned in during the final few days with a bit of prodding (by Staff Scientist and me). I anticipate some minor adjustments and/or new material to be added following the expedition, as the turnover time for (this last site's) volume materials is low.
Since we did not anticipate (nor receive) high core recovery, I was able to learn more about JR operations and assist in different capacities around the ship. I assisted with CORKing activities each time they were scheduled. Additionally, I was also able to help with the coring process – from assisting the Curator with labeling and splitting core, to helping sedimentologists gather samples.
As a first time Yeoperson, I encountered challenges (both anticipated and unanticipated), learning curves, and adjustments. However, I was fortunate to sail with a very helpful and patient group of people. Members of the technical staff went out of their way to assist me with any issues I encountered related to life and work onboard.
Minor issues with software/programs have occurred; however, these were all addressed in a timely manner and did not disrupt my workflow to any huge extent.

EQUIPMENT & SOFTWARE PERFORMANCE SUMMARY
We are using a (relatively) new version of Strater, so though I had some experience with this on shore before coming out to ship, there were still a few adjustments. An upgrade performed a few weeks into the expedition corrected a couple of minor issues that were impacting VCDs and templates.

DATABASE, ENTRIES, AND DATA UPLOAD OR DOWNLOAD RELATED
Lims2Excel proved to be quite problematic during the first weeks of the expedition. Namely, we had issues with the way depth exported from both SampleMaster and DESCLogik. As all of my data is plotted against depth, this was unacceptable. Fortunately, we were not coring at that point, so I discovered these issues while practicing with test data. The L2E programmer fixed numerous bugs with their respective programs, and by the time we had our first core on deck, a majority of the kinks had been worked out. His support was invaluable.
There were some issues with DESCLogik as far as data entry. During the first round of core descriptions, the scientists had some trouble with the program freezing, with the template setup, and with some of the options and ways of working in the program. This affected my workflow as they were unable to (for a time) enter data into DESC, and so I was not receiving data for my VCDs in a timely manner. The DESC administrator worked these issues out as quickly as possible, and we were back on schedule shortly. (Her support also has been invaluable.) These issues did not arise again after the first round of core description.

VOLUME MATERIALS
This portion of my tasks was exceptionally smooth. Scientists were made aware of the volume submission process (including formats, labeling and naming conventions, etc.) - which I credit with being a huge factor in the smoothness. I also kept a tracking sheet (for both my and their benefit) and informed them of time limits so as to keep them focused on the goal of submission. Additionally, I had the help of an excellent Staff Scientist who kept after the scientists for materials.

GENERAL DUTIES PERFORMED

• • Provided administrative support. This includes: assisting the scientists with various tasks, getting supplies, helping with travel issues.
  • Provided graphics and publications support throughout the expedition. This includes proofing, formatting, editing and tracking all volume materials. Also, providing assistance with drawing of figures.
  • Distributed and completed necessary expedition paperwork. This includes: wireless device list, communication policy, photo release, manuscript and copyright forms, special release form for IODP re: the movie being produced.
  • Collaborated with the Staff Scientist to create server directories for the scientists, as well as creating the Publication directory for transfer of volume material to shore.
  • Worked with DESCLogik administrator to create accurate data reports for use with VCDs, thin sections, and smear slides.
  • Worked with L2E programmer to test for bugs, and to identify problems so that future users of L2E will not experience these.
  • Worked with science party: in my creation of VCDs to ensure that the data they wish to be represented was, and that it was scientifically accurate and aesthetically pleasing.
  • Provided support for methods figures and core recovery summary figures
  • Modified initial shore-created Strater templates and Methods figure during the expedition to display specific patterns, symbols, and plots. Continued to update these as needed.
  • Uploaded weekly web photos. This project included selecting ~20 of the ~50 submitted photos each week, writing captions and identifying persons in the photo, editing in PhotoShop, editing HTML pages with captions, uploading to the website, and proofing all.
  • Assisted and coordinated social events, including: birthdays, expedition t-shirt contest, kite contest, and parties.

ADDITIONAL DUTIES

• • Assisted the Education Officer by filming all videoconferences.
  • Assisted the ET with various small electrical and related tasks.

• • Assisted the Imaging Specialist with PhotoShop and Excel related issues. (Creating masks, writing scripts, and creating spreadsheets)
  • Communicated with shore staff regularly to provide updates and seek expertise.
  • Restocked Publication supply cabinet as needed, and provide science party with supplies per request.

SUGGESTIONS

• • Additional time training with DESCLogik and L2E. I was fortunate enough to have weeks at the beginning of the leg to run test data before we received core. However, a true shipboard experience (maybe a week long or so) training module on shore would be something worth looking in to for a new Yeop. This way the Yeop may not only work with the programs, but with the people in charge of them. We had an excellent set of templates in place in DESC, and again, I had the benefit of time before core. But if a Yeop expects core right away, it would do them good to have their Strater template already mapped out regarding which column in DESC maps to which column in Strater.

• • Post volume material format, labeling, and naming conventions material all over the ship. Though most of the scientists retained and implemented the lessons taught, not all did. It was a bit of a time waster to go through and rename (and relabeled within) the files, and to additionally go through the report and rename every instance of said file.

DEVELOPER'S REPORT

ALGIE MORGAN AND JAMES ZHAO

OVERVIEW
This document highlights changes in laboratory data acquisition and collection systems, and changes in the development work environment. Notable issues and changes are presented in-line. Issues not addressed and features requested are collated in Addendum C: Issues and Features. Bracketed attributions are provided to aid in routing questions that do and will arise.
Curation and Core Handling

SAMPLEMASTER
Production remains at release 2.2.1.0. As of this writing version 2.2.1.1 is nearly ready for deployment. Developers will coordinate with the Curator (Gemma Barrett) to deploy 2.2.1.1 so that we do not interfere with core flow during the last days of the expedition when sediment coring is occurring.
Notable revisions in 2.2.1.0:

• • Fixed bug in cut and paste feature, this feature has not worked in the past several versions.
  • Revised Core Entry sheet to correct problems with hiding columns incorrectly. User can now select to lock Piston, Rotary, or All columns in place so that data entry does not cause them to hide.
  • Remove all routines that parse parent data from label-id, all data is now filled in from data retrieved from LIMS.
  • Fixed bug where edits to samples not descended from a core failed without giving error; edits now work properly
  • Fixed bug in Parameter search: if you performed a parameter search after first performing a hierarchy search the Sample Table tab would show Exp/Site/Hole/Core/Core-Type/Section/Section-Half information for the previously selected parent; now Sample Table always shows correct information from parameter search, it does not hold information over from parent.
  • Re-factored significant blocks of code to improve readability, added comments to aid in understanding the logic of the methods.
  • Several other minor bug fixes.

Notable revisions in 2.2.1.1 (pending deployment):

• • Fixed "Import from Excel File". This feature was broken in the last several versions but now works normally.
  • Fixed bug on Core entry sheet: bit-information was not uploading properly.
  • Fixed bug in Section label "Print on Upload" feature that caused labels to print out of order.
  • Re-factored additional blocks of the source to rationalize the code and to comply with C# and general programming best practices. Continued to document the code through additional comments where appropriate

Known Issues not yet resolved:

• • Crashes when you use Tools | Admin | Delete-Sample Menu: if you try to populate the list of samples to delete by navigating to a sample on the View tab, then highlight the sample you want to delete and click the "Add Samples to Delete" button, a check-box appears in the SampleDeleter window that has no text- id. If you click the "Delete Samples" button in the SampleDeleter screen SampleMaster crashes and you have to restart it.
  • When "Print Labels on Upload" is checked samples with any value in Comments field do not print, they upload successfully, but no label is printed for them. All other sample labels print normally.

LASER ENGRAVER (LAZER KATJIE)
The laser engraver was successfully deployed and used on Expedition 336. All of the development and operations instructions were provided by Bill Mills.
Notes:

• • In the previous test version, Lazer Katjie tech used the Web Tabular print services to send data to the computer controlling the engraver and Lazer Katjie had to be running to capture data. This toss and catch method resulted in a lot of dropped balls. To correct this situation, a "Sample Master" like interface was added using web service calls to populate the data controls.
  • The code is part of a LabView project with an executable build and installer.
  • To do before the ship docks is to archive the code in SVN.
  • Occasionally the 404 error is thrown by the web service call. Unsure why but the data download is not affected.

-mills

GEOLOGY
DESCLOGIK
There was no development of DescLogik on ship, but significant changes were deployed from shore. All modifications to DescLogik on Expedition 336 were made by Chris Bennight and Tim Blaisdell, and then deployed by checking out tagged release versions and building and deploying from shipboard build box. The current version is at 3.23.4.56.
Notable revisions in DescLogik:

• • Fixed issue where auto-population would not properly occur in certain circumstances.

• • Fixed issue where logging services was getting sent the results of each calculation.
  • Removed "move data to new sample" option
  • Removed "group with other row" option
  • Fixed bug with Piece lookup on templates.
  • Fixed bug where application crashed when user scrolled through a template then clicked on any of the locked columns.
  • Added a color legend window.
  • Fixed various issues causing excessive calculations due to metadata columns.
  • Fixed issue where metadata column was triggering a changed by indicator erroneously.
  • Fixed issue where all piece column didn't work against current ship dataset.
  • Fixed issue that templates cannot be overwritten.
  • Added feature that prevents the overwriting/editing of flags with the default_config value in the database set to true.
  • Fixed issue where login process conflicts to sample master login
  • Fixed issue where error sheet returned by template import validation failure will no longer replace the text in cells, but will instead place the error message in a note associated with the cell allowing the user to modify and reupload the same sheet.
  • Fixed issue where custom list on different parameters with the same name would all merge together
  • Fixed issue where importing tab names from an excel definition can cause errors when the tab name differs only in case from a default tab name

¿
[The above is a partial list; only the most significant changes are listed. For a full list of all changes made during Expedition 336 refers to Tortoise SVN log for the DescLogik project.]100

BARREL SHEET PRODUCTION (VCD)
<span style="color: #243f60">L2E (LIMS2EXCEL):</span>
FEATURE enables LIMS2Excel splice download function.
BUG displays the wrong depth value at the beginning of the expedition.

<span style="color: #243f60">CORRELATOR</span> <span style="color: #243f60">DOWNLOAD</span>
FEATURE displays a short cut menu so that scientists can select data set easily. Also adds friendly messages on the user interface.

<span style="color: #243f60">STRATER:</span>
No changes this expedition

<span style="color: #243f60">CLOSEUP,</span> <span style="color: #243f60">MICROPHOTO,</span> <span style="color: #243f60">THINSECTION</span> <span style="color: #243f60">CAPTURE</span>
ImageCapture: We experienced numerous problems with ImageCapture. There was one small problem with the new x_project field not being recorded properly - it was hard-coded to put 'XXX' in the x_project field. Then there were numerous rounds of label-format fixes to the small and large photog labels to print properly. We also experienced difficulty getting it to build with the Atalasoft library; were forced to uninstall an older version and
install new version using 'dev" account on build box. NOTE: this requires that all builds for this project must be performed under the dev account, otherwise the license is not recognized and the application will not function properly.

<span style="color: #243f60">RADVAN</span>
Cahn Balance: Not used; no change for this expedition.

GEOPHYSICS
<span style="color: #243f60">WHOLE</span> <span style="color: #243f60">CORE</span> <span style="color: #243f60">SYSTEMS</span>
Whole-round logger (WRMSL) and Special task logger (STMSL): [To be completed by Morgan]. Natural gamma (NGR): No change for this expedition.
<span style="color: #243f60">SPLIT</span> <span style="color: #243f60">CORE</span> <span style="color: #243f60">SYSTEMS</span>
Line-scan imager (IL): Deployed version 2.2.0.2 of IL on the imaging host. This version adds the "dropped line scans" check that prompts the operator if the number of dropped lines exceeds a certain threshold; currently this limit is set to 3.
To Be Completed: visiting scientist Tania Lado Insua reported:

1. The warning screen that displays when dropped lines exceed maximum does not clear previous messages; i.e., the errors that appear in that warning box are cumulative over previous runs. The application must be closed and reopened to clear previous dropped-line messages.
2. Maggie requested that we also write the dropped lines information into a file and put it in the file with the archived images. Currently there is not convenient way to get this information; the warning screen does not allow copying or cutting text from it.

Sonic velocity (GANTRY): Deployed version 2.0.0.2 of Gantry track software to fix a bug in the formatting of the files; it was putting the instrument in the first line of the file, modified it to put the analysis (PWAVE_C, PWAVE_B) to conform to formats of other track data files in Core Lab.
To Be Completed: visiting scientist Tania Lado Insua pointed out that this track recording the axis incorrectly on the P-wave caliper; it enters "velocity_x" in the data file regardless of which axis they choose when making the measurement.

REFLECTANCE AND SUSCEPTIBILITY (SHMSL):

[MILLS].

Discrete sample systems

Thermal conductivity (TCON): No changes for this period. Moisture and density (MAD): No change on this expedition
MADMax: On 3 November we attempted to deploy a new version Blaisdell committed but after deploying it we could not save measurements from the pycnometer. We made several attempts to find and correct the problem
but were not able to correct the problem, so we rolled back to the version we were running when we departed Barbados. This application is functional, but there are several known issues that need to be corrected as early as possible:

• • Scanning a barcode to enter a sample into the main sheet while a pycnometer measurement is in progress causes the application to freeze when the pycnometer measurement completes and the operator attempts to save the volume measurement. (Reported by Tania Lado Insua on Exp. 336)

• • When measuring with more than one pycnometer cell simultaneously, when the measurements complete and are waiting to be "accepted" or "canceled"; if the user attempts to accept or cancel multiple measurements too rapidly it will cause the application to freeze; the operator must click to accept or cancel one of the pycnometer measurements, wait for the value to register on the main screen, then click to accept or cancel the next measurement, etc. (Reported by Blaisdell while testing application in Curacao Tie-up).

PALEOMAGNETICS
Point susceptibility: Not used this expedition. [This is applied on some expeditions as a stand-alone quality check.] Kappa Bridge KLY-4S: Not used this expedition; no change in this instrument.
GPS sighting: Not used this expedition.
Superconducting magnetometer (SRM section): Not used this expedition; see Core Tech report for minor modifications made in track software [Hastedt].
Superconducting magnetometer (SRM discrete): Not used this expedition; see Core Tech report for minor modifications made in track software [Hastedt].
Fluxgate Field Survey: Not used this expedition.

UNDERWAY
Navigation, bathymetry feed. The backup server on which this data feed runs was updated to Windows 7 x32. OS and software upgrade was handled by MCS's and Mills.
For a period of approximately 36 hours between 5 November and 6 November the JavaNavigationLoader was not operational. We were operating this application on the Developer Build box. After we discovered that it was not active we tried to restart it and found that it would not read the IP transmission from the WinFrog system. Mills, Zhao, and Morgan all analyzed this problem, with significant help from MCS Cannon and Core Tech Hillis. At approximately midnight on 6 November we retried the JavaNavigationLoader and found that it once again functioned normally. At this time we have no explanation of why it stopped working and then restarted working; no changes were made to the source code, its configuration files or the WinFrog system in Underway. [See Section called "Pending Development Projects" later in this report for proposed long-term solution to navigation data upload.]
Magnetometer: Not used this expedition.
GEOCHEMISTRY
Alkalinity. No change for this expedition. ChemWorklistGenerator. No change for this expedition. Coulometer. No change for this expedition.
ICPAnalyzer. No change for this expedition. X-ray fluorescence. No change for this expedition.
OPERATIONS
Core/VIT winch counter video overlay: We experienced quite a lot of difficult with the system used to poll the coreline / VIT meters in the Subsea shop and send those values to the Xbob device so it can be displayed on the Rig Floor channel on the VBrick system After considerable troubleshooting by the Ops engineer, the MCS's and the software developers we tracked the bulk of problem to serial port contention on Krakatoa caused by Ops and MCS's attempting to use Hyperterminal as a diagnostic tool while the system is in operation. As we worked through the problems it became clear that the use of the name of Xbob or XBobber for the software application that reads the data from the Veeder meter and transmits it to the Xbob video overlay device caused a considerable amount of confusion. So, while I was making other changes to perform logging to LIMS.LOGS table I renamed that application. Using the advice of the operations superintendent and engineer I renamed the application "VeederDepth". The appropriate changes have been made in the software project file and the SVN repository.
RigWatch: No change for this expedition.

OTHER
<span style="color: #243f60">REPORTING</span> <span style="color: #243f60">SYSTEMS</span>

WebTabular reports:

• • Deployed a new version of WTR that includes the following modifications:
  • Significantly faster response for Science Data reports.
  • Depth-scale names now appear at the top of their respective depth columns instead of as a separate column.
  • Fixed bug in file-download; files no longer have extraneous "test" text in left-hand column.

LIMS Reports:

Feature displays alternative depth drop down list box. The default value is CSF-B. Now, LIMS Report shows both CSF-A and alternative depths.
Feature displays splice drop down list box so that the user can select the splice option to download the splice data.
Feature the project and expedition list are cached so that they can appear on the LIMS Report rapidly.
LIMSPeak: No change this expedition.
Gas bottle monitoring: No change this expedition.

<span style="color: #243f60">WEB</span> <span style="color: #243f60">SERVICES</span>
IODPUtils: [To be completed by Morgan].
lims-webservices-java (jar): We deployed version 3.1.1.6 of this utilities jar file; it contains the following changes:

• • Fixed bugs in getters and setters for sect_offset and sect_offset_bot properties.
  • Fixed bugs in getters and setters for x_offset properties.
  • Fixed bug in getters for getBot_offset() pseudo-property.
  • Add x_sect_offset and x_sect_offset_bot to list of Sample.reportableFields.
  • Add getters and setters for x_sect_offset and x_sect_offset_bot properties in org.iodp.usio.lims.object.Sample class.
  • Added new properties: x_core, x_core_type and x_section, and x_sect_half.
  • Added new getter and setter methods for x_core, x_core_type and x_section and x_sect_half properties.
  • Added x_core, x_core_type and x_section, x_sect_half to list of reportable fields.

These changes were primarily to clean up a proliferation of "offset" values and to fix some bugs that were causing offset values to be displayed incorrectly in WTR.
java-utils (jar): Current version deployed to ship: 1.4.1.1; it contains the following the modifications:

• • Added new toBoolean method to StringUtilities class. This method accepts commonly used string representation of boolean values and converts them to their equivalent java.boolean equivalent.

1. ET web-services wrapper (Lims.dll): No change this expedition. Resteasy-asman: No change this expedition. resteasy-desclogik-services:

There was no development of resteasy-desclogik-services on ship, but significant changes were deployed from shore. All modifications to resteasy-desclogik-services on Expedition 336 were made by Chris Bennight and Tim Blaisdell, and then deployed by checking out tagged release versions, and building and deploying from shipboard build box. The current version is at 1.6.8.6.

• • Fixed issue where read-only column service matches on depth ranges which are < or > as opposed to <= or

>=.

• • Added function that queries desc data for a template (for all tabs on template).
  • Added feature that deleting list now requires an extra confirmation step.
  • Added feature that displaying messages from the server (success or error) UI dialogs will now persist until the user clicks (anywhere on the screen) instead of fading out after 7 seconds.
  • Fixed issue with value list parsing when values have the same value and same header and same value list name - but different value lists (size_name/size_name_max was the precipitating issue).

resteasy-image-tiling No change this expedition.
resteasy-lims-webservices: Current version running on ship: 4.4.5.4. The major changes in this version include:

• • Bug fix: extraneous text "file" removed from first column of file.
  • Two new services deployed and ready for use by other applications

• • Several smaller bug fixes.
  • Adds capability to download Sample 'x_...' fields directly from LIMS instead of trying to parse them from a label-id field.
  • Adds several new utilities to aid in extracting and checking data for validity.
  • Corrects webservice bug that prevented uploading of cores and sections into LIMS when no comment entered on Core.

resteasy-monitor No changes this expedition. resteasy-reports
FEATURE modifies all the report queries to get CSF-A depth from x_sample_depth table, as top_depth and bottom_depth are deprecated.
FEATURE adds alternative depth scale parameters to all the reports so that LIMS Report can be used to view alternative depth.
FEATURE adds slice Id parameters to track reports and image reports so that these reports can be used to view splice data.
FEATURE generates a new web service function to return the alternative depth. FEATURE generates a new web service function to return the splice Id.
FEATURE generates a new web service function in order to return the project and expedition list.
Resteasy-affinesplice-webservices No change this expedition
ops: We wrote a new service called insertNavData that inserts navigation data into the ops database. This was done at the request of Mills in preparation for writing an application that will be under the control of the Underway tech (or a replacement designated by the Lab Officer). [See section called "Pending Development Projects" later in this report]
WTR [To be completed by Morgan]

LABORATORY SYSTEM SERVICES
MegaUploadaTron: No changes made this expedition. Zebra Printers: [To be completed by Morgan].
LIMS
SET_SAMPLE_LABEL_FIELDS: Modified to handle samples that do not follow the normal HOLE - SITE - CORE -
SECTION - SECTION-HALF hierarchy.
Component Name Changes: I changed the COMPONENT.NAME value from "comment" to "comments" for the following analyses:

• • GRA
  • MS
  • NGR
  • ORIENT
  • PWAVE_B
  • PWAVE_L
  • VANE_SHEAR

MISCELLANEOUS
Depth Updates: No change this period [shipboard environment only]. Database Overview: No change this period [shipboard environment only].
JProbe: Utility for to allow monitoring and troubleshooting web apps and webservices. This utility was deployed primarily as an aid to find potential memory leaks in dboverview.
NGRAverage: Special purpose application written for Maxim to allow him to extract GRA data from LIMS and perform analyses to calculate K concentrations. This application was written in Python by a contract developer. At the beginning of the expedition he reported that it would not connect to LIMSODV, but it worked on shore. Zhao got it working by modifying the connection parameters in the program.

DEVELOPER RESOURCES

Desktops

Desktop box: No changes this expedition. Macintosh: No changes this expedition. Environment: No changes this expedition.

Servers

Load balancing: No changes this expedition. BUILD box: No changes this expedition.
Old BUILD box: We got a notice from MCS's that they are supposed to deactivate the old developer build box and take it back to shore. Fackler and I audited the computer to find out what was on it. When we were satisfied that we had everything that we needed we notified the MCS's that they could deactivate it at their discretion.
Digital master library: This local cache of instrument host and development system drivers and control software now has a permanent home:
JR \\jr1\vol1\tas\dml
HQ \\odpads\tas\dml
Test servers: None available at this time.
Krakatoa: This has been moved to complete control by MCS's and Ops personnel. Dev account has been removed. Ops has requested that all remote access to the server be restricted to the computer in the Ops office on the Bridge deck.

SVN
Deprecate JR Tree: We continued the process of moving all of our source code into a single repository maintained on shore. So far the following projects have been switched to shore:

• • java/depth-calculator

• • java/lims.java (lims-webservices-java)
  • java/L2E
  • java/resteasy
  • java/resteasy-affinesplice
  • java/resteasy-lims-webservices
  • java/resteasy-printing-webservices
  • java/utils
  • java/WTR
  • NET/SampleMaster
  • LabVIEW/gantry

PL/SQL Version Control: As part of the effort to begin versioning all of our PL/SQL procedures, functions, views, and triggers we created a project branch /hq/db/lims/plsql. We then checked all of the PL/SQL code into that project. Going forward we will be able to tag versions as we make changes to any of these artifacts.


SOP / DOCUMENTATION
Build Box: we wrote a document detailing the purpose of the developer build box which includes a detailed list of all software installed on the build box, and detailed procedures to be used to deploy all software on the JR. This document is stored on the developer website: https://sites.google.com/site/iodpdeveloperwork/procedures; see the document titled "JR_Build_Box.docx." Our intent is that this document be used to ensure that we begin to deploy software in a controlled manner and that we have documentation about what changes each software version includes and clearly defined procedures for how to rollback if we need to. This document should be modified frequently as procedures are modified.
Change Management: We continued to refine the process of change management and deploying new software in a controlled manner. We developed a template for emailing notifications to interested parties prior to the deployment of any application or webservice; see https://sites.google.com/site/iodpdeveloperwork/procedures/ChangeManagementRequest-JR.docx. There is also a document outlining the procedures to be followed to deploy software: see https://sites.google.com/site/iodpdeveloperwork/procedures/ChangeNotificationProcess.docx.

PENDING DEVELOPMENT PROJECTS

NAVIGATION DATA
Because of ongoing issues with retrieving navigation data from the WinFrog system and loading it into the Ops database Mills reported that he can easily write an application that pulls the navigation data from the WinFrog system and make a RESTEasy service call to load this data into the database. In preparation for this we have already added a service to ops-webservices called insertNavData that performs the same function as the current JavaNavigationLoader. Mills has not written his LabVIEW application to call this service, so it is not being used at this time. (See section on webservices for more information)

NGR – K CONCENTRATIONS
After uploading GRA and NGR data to LIMS Maxim manually calculates K concentration values, and then requests that we upload them. This is a time-consuming and tedious process that must be handled by writing "manual" resteasy-lims-webservices/re?service=logResult requests. We need to find a way to automate this, or at least write a special purpose uploader that will perform this function.



DATA STATISTICS
See Addendum D: Sample, Test, Result Statistical Methods for the respective query methods (#).

#
DATA ACQUIRED
Breakdowns of samples analyzed, tests conducted, results collected: organized by analytical tests. See Addendum B: Data Acquired Method for query method.

ADDENDUM A: DESCLOGIK DATA DASHBOARD
Observed column indicates number of result records present for that tab and template. Does not reflect actual rows you will see in DESCLogik—better used as a gross indication of presence/absence of data. Status (S) column separates notes and separates canceled (X) content from "live" (E) production content.

Method. Query used to extract the above content.
set timing on linesize 160 pagesize 50000 column "User" format a10
column "Exp" format a8 column "Hole" format a6 column "Stat" format 999999 column "S" format a1
column "Template'n'Tab" format a70 select
count(distinct r.test_number) "Stat"
, s.x_expedition "Exp"
, s.x_site||s.x_hole "Hole"
, r.entered_by "User"
, r.status "S"
, regexp_substr(r.entry,'^[|]') ||': ' ||regexp_substr(r.entry,'[^|]$') "Template'n'Tab" from
sample s inner join result r on s.sample_number = r.sample_number where 1=1
and s.sample_number in (select sample_number from sample where x_expedition in ('335', '335(312) ')) and r.analysis='DESC' and r.name='templateID' and r.entry like '335%'
group by s.x_expedition, s.x_site, s.x_hole, r.entered_by, r.status
, regexp_substr(r.entry,'^[|]') ||': ' ||regexp_substr(r.entry,'[^|]$') order by 2, 3, 5, 6, 4;













ADDENDUM B: DATA ACQUIRED
Sample Column Query
select analysis, count(distinct sample_number) from test where sample_number in (select sample_number from sample where x_expedition in ('335', '335(312)') and instr('ICPAR', status) > 0) and instr('ICPAR', status) > 0 group by analysis order by analysis;

Test Column Query

select analysis, count from test where sample_number in (select sample_number from sample where x_expedition in ('335', '335(312)') and instr('ICPAR', status) > 0) and instr('ICPAR', status) > 0 group by analysis order by analysis;

Result Column Query

select analysis, count from result where sample_number in (select sample_number from sample where x_expedition in ('335', '335(312)') and instr('ICPAR', status) > 0) and instr('EMAR', status) > 0 group by analysis order by analysis;

ADDENDUM C: ISSUES AND FEATURES
Items in green have been addressed. Others are outstanding. To be forwarded to the appropriate Lab Working Groups. Bracket indicators "[x###]" identify carry-overs from previous expeditions and reports.

<span style="color: #243f60">SECTION</span> <span style="color: #243f60">HALF</span> <span style="color: #243f60">IMAGER</span>
BUG [x334] Imager will randomly drop line scans in interval between 100 and 120.
FEATURE [x334] Recovering from image scan errors [wrong name assigned] is difficult: name embedded in the full and consumer image must be fixed, relational data and metadata in LIMS must be fixed, file names on the ASMAN catalog must also be fixed. Would like a tool to automate the process. The image may be re-scanned only in some circumstances—on a sediment expedition color alteration in air is often rapid—in those cases it is desirable to preserve the first scan.

<span style="color: #243f60">SRM</span> <span style="color: #243f60">SECTION</span>
FEATURE [x330] Desirable to have a "skip list" for hard rock expeditions. Reduces post-data-upload processing. Increases up-front run setup. Skip list used to skip measurements at piece edges, rubble bins, rollers, and material known to produce undesirable results.

<span style="color: #243f60">MEGAUPLOADATRON</span>
BUG [x330] When the application is first started and "Set Upload Directory" is used to set a new watch directory, the application must be fully shut-down and restarted before it will populate the upload list with files in the selected directory.
BUG [x330] Identical to the above, but for the 'Set Log Directory".
FEATURE Application does not allow specification of the "Archive" directory. Is presently hard-coded relative to the selected input directory (aka watched dropbox). Would be useful to give the technicians that flexibility.
FEATURE Display the watched and managed directories on the front panel status bar.
BUG [x334, x335] If an external process has a lock on a file, the uploader can move it, but leaves a zero-length file in the watched directory. The desire is to prevent the zero-length file [detect lock conditions before moving] or delete the file after moving [still detect lock conditions, but clean up in safe-to-move cases where a target file of the same name but possibly different timestamp exists that is non-zero in content]. Report occurrences of the lock condition to the central logging facility.
BUG When a raw file is generated that lacks a sample identifier, MUT goes through the motions of uploading it, then gives an error. That error is not meaningful to an end-user. Change it.
<span style="color: #243f60">SAMPLEMASTER</span>
BUG [x334, x335] Occasionally when printing labels from the View tab the application will crash and must be restarted. Afterwards reprinting the labels print successfully. Precise reproducibility case not yet identified.
BUG SampleMaster does not clear orange background after samples are uploaded successfully. Orange background can only be cleared by restarting SampleMaster or selecting the affected rows and using "Delete entire row..." feature.
BUG [x330, x334, x335] When autoprint on upload is enabled, program often fails to print the first label. Occurs during section and sample-table entry. Fault is known to be in SampleMaster [tracing HTTP traffic indicates label is already missing in the stream submitted to the printer services]. Issue in SampleMaster is related to keeping track of how many valid rows of data are in the spreadsheet. An off-by-one problem of some sort: zero-indexed vs. 1- indexed spreadsheet rows; possible failure in updating row-count when deleting row(s) or clearing the form.
BUG Use of the right-click "Delete entire row..." feature is frequently associated with the above two errors.
BUG When the legacy flag is set on samples, SampleMaster acts as if it is uploading the samples, then fails without a meaningful message. The legacy flag is used to intentionally prevent data edits on selected material.
SampleMaster should display a message to this effect to the end-user.
BUG Entering pieces. As piece lengths are spaced out, the red validation highlighting comes on for the bottom interval of about half of the records. Appears that an incorrect validation rule is being applied. Results in having to click twice to force an upload.
<span style="color: #00b050"><strong>FEATURE</strong></span> <span style="color: #00b050">Piece length</span> <span style="color: #00b050">defaults to bin</span> <span style="color: #00b050">length</span> <span style="color: #00b050">if piece</span> <span style="color: #00b050">length not specified.</span> <span style="color: #00b050">Test what</span> <span style="color: #00b050">happens if no</span> <span style="color: #00b050">bin length</span> <span style="color: #00b050">is</span> <span style="color: #00b050">specified.</span> <span style="color: #00b050">First</span> <span style="color: #00b050">release</span> <span style="color: #00b050"><ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="543f9c48-a9ca-44ec-8918-17661b99e2dd"><ac:plain-text-body><![CDATA[2.2.0.12 [Blaisdell].

\\ *BUG* Copy down does not honor above row setting of Y/N for auto-splitting. \\ *BUG* Auto-splitting Y/N is not honored. Always splits. Technically is a function of the logSample web-service. *BUG* Hierarchy search now shows part of a horizontal scrollbar that has not been displayed previously. *BUG* Edit mode: tabs lack drop-down lists like the data entry tabs carry for Test lists and Tool types. Driller see similar for Flapper selection on Cores. \[Curator, Drillers\]. \\ *BUG* Edit mode tabs: cut and paste not available in this mode. *BUG* Editing pieces does not properly update the x_sect_offset field. *BUG* SampleMaster no meaningful message returned when samples will not upload: when legacy field set. \\ *FEATURE* SampleMaster Enable hierarchy browser to display other samples--stick to hierarchy rather than type. Partition routine types (HOLE, CORE, SECT, HALF) to top of list, but still show others (based on ancestry) below the canonical ancestors. \\ *FEATURE* Default sort order makes it difficult to find samples. Useful to be able to apply other sorting criteria based on user column selections \[Broyles x335\]. Protype implemented \[Blaisdell\]. \\ *BUG* Possible code regression over earlier builds. "Slow" to upload samples compared to 2.1.1.6 release. Watching traffic in HTTP proxy/debug tool (Fiddler) shows that: Given a list of samples edited, ALL get uploaded, even if only one field changed. Very inefficient. Recalculation of depths occurs at the end, but is presently occurring for the Hole instead of a list of specific samples where offset, curated length, or advancement changed. Logic needs to tighten up in SampleMaster to improve: Inserts, update handling for dirty records Efficient application of depth recomputation \\ Temporarily removed

automatic depth recomputation step [Blaisdell].

Stop-gap ony. \\ *BUG* SampleMaster depends on parsing of Label_id field to assign hole, core, section, section half parentage. Not very robust given sample with ancestry outside the traditional core, section hierarchy. Also is tied to underlying resteasy-lims-webservices...getLimsData call bugs. \\ *BUG* Overloaded UI. When browsing for samples to edit, should only show edit, view tabs that have samples to look at. If tab is empty, hide it. Conversely show it again when mode or content changes. \\ *BUG* Sample cataloged against immediate ancestor hole, cannot subsequently be edited because label ID parsing in SampleMaster is incorrect for these sample leading to inability to identify actual sample parentage \[Broyles x335\]. \\ *BUG* Piece entry. Cells turn red inappropriately--e.g. when bin bottom is beyond length of material? Correct the validation behavior. \[Peng x335\]. \\ *FEATURE* File upload for LOI spreadsheets. \\ *FEATURE* File upload for XRF spreadsheets and files. Processing is not yet routine. *FEATURE* File upload for Kappa Bridge data. *FEATURE* File upload for JR-6A spinner files. \\ *FEATURE* Replace independent downhole tools data parser and file loaders (SET, SETP, APCT3, WSTP) with dedicated module within MUT framework. \\ *FEATURE* Replace independent core orientation tool (FlexIT) data loader with dedicated module within the MUT framework. \\ *FEATURE* Replace navigation bathymetry magnetometer data feed with direct MUT upload of selected NMEA content from the local WinFrog *.RAW files. Greatly simplifies the tool chain. Reduces technician workload at end of expedition (as files will be cataloged to ASMAN as uploaded. Improves technician control of system as loader module is then contained on WinFrog system (one less password and server system to navigate). \\ *FEATURE* Incorporate Thermcon uploader process into the MUT framework. Reporting \\ *BUG* WebTabular \[reported by Steve Midgley on 8 April 2011, as this report was being created\] not reporting RCB hole on the "Drilling Summary (Core Tech Sheet" report. Also, after RCB hole information is entered in SampleMaster the "master" totals at the end of the report no longer display. \\ *FEATURE* Analysis and components lists indexed on the Apache web-server (linked via the Web Tabular Science Data report page) are static and tend to be out of date. Would be useful to automate refresh of these reference pages via an Oracle job or an operating system cron job. Web-tabular \\ *BUG* Return of standards data is inconsistent or fails outright. Selecting exp=QAQC, analysis=GRA, QAQC=true returns no data. Exp=QAQC, analysis=PYC, QAQC=true returns lots of data. Why? Info: Fiddler shows web-service error. Debugging. \\ \\ *BUG* WTR Return of standards data is inconsistent or fails outright. PWAVE_C QAQC results will not display. Web services appears to be generating an exception. Trace and fix. Info: variant of GRA item first logged. \\ *BUG* Precise behavior of QAQC and QAQC reporting is not clear from the report. Examine in code and add definitions to the display. Info: QAQC queries by group_name. Expedition querying is orthogonal to this so returns nothing. \\ *BUG* Specifying filter by selected user name returns results regardless of those names. Not used or not applied against the appropriate columns? \\ *FEATURE* Image report: (1) single report for all possible kinds of images; (2) use the thumbnails where we have them so people can see the content with the data record. \[Crawford\]. The distinction between "thin section image" vs "micrograph of a thin section" vs "closeup of a thin section" is non-sensical hair-splitting from the reporting and data retrieval stand-point. "I took a picture. Where is it?" Searching one place is easier than searching 3 or more. \[Same issue applies to LIMS Reports imaging queries.\] Alternatives in the form of Pivot reports prototyped

[Bennight].

\\ \\ MOISTURE AND DENSITY *FEATURE* Pycnometer—sort sample list in container number order; currently the order is completely random. \\ *BUG* Pycnometer: Sample-list is not honoring "canceled" results, if there are canceled results the container- number/text-id will show up in the sample list multiple times. \\ *BUG* \[x330\] Duplicate MAD_MASS analyses are being generated: same sample_number, same test_number, different result_numbers. Been happening for 3 expeditions now. Balance change? Log test change? Unknown. Checking. Should use existing test record created by SampleMaster at sample cataloging time. We are obtaining duplicate container entries and mass_dry entries on MAD_MASS records: one comes from SampleMaster, the other from? Balance or web-service or invocation combo. \\ *FEATURE* \[x334\] MAD analyzer: it would be nice to have a software tool that allows users to scan LIMS and detect common problems in the MAD_MASS, PYC, and MAD analyses. On expeditions with heavy MAD analysis such a tool could be used to proactively find and correct problems. \\ PYCNOMETER DIAGNOSTICS \\ *FEATURE* remove settings panel--not needed for diagnostics control. *FEATURE* cell buttons should only set context, not trigger action. *FEATURE* operator should have full control of the cell inputs and outputs to test behavior of electronics connected to PCI 6224 A/D I/O card. \\ MADMAX \\ *FEATURE* Subsume above considerations into line-items for MadMax. Resteasy Error Reporting \\ \\ \\ \\ *BUG* Occurrences of phoning home to millstone.iodp.tamu.edu have been observed. Clean up configuration to use production services in local environment. \\ JANUS2LIMS \\ *FEATURE* Enable Janus2Lims to selectively migrate sample categories, e.g. only thinsections, only headspace. \\ *BUG* crashes when run on x64 (laptop). Due to Oracle dependency management. If Oracle installed locally, assembly search path and load order precedences can result in the wrong version of Oracle being invoked, instead of the copy deployed with Janus2Lims. \\ *BUG* does not cause depths to compute (verify) \\ *BUG* generates its own legacy style depth scale (12761) \\ *BUG* swaps curated and liner length (variance between historical sediment vs. hard rock field usage?) *BUG* should use curated length (x_length) to compute x_offset, not liner lengths (x_orig_len) *FEATURE* Support import of specific sample types. E.g. Thin Sections only. \\ SHMSL \\ *BUG* \[x335\] Point susceptibility control data check file is not referenced properly in the MSPOINT raw data file. File placed on disk under the "control data" heading rather than "calibration data" heading. Content is presently not loaded or available in LIMS. \\ BUG

[x335]

Skip list does not work on SHMSL. Using skip list results in a file being saved with XXXX in the name. Or no file at all. Fixed

[Mills].

\\ \\ BUILD BOX *FEATURE* Centralize maven repository support. Recommend the tool Nexus over previously examined tool Archiva. \\ *FEATURE* Centralize .NET assembly, external OEM, DLL support. Recommend the tool NuGet. Already in use for DescLogik. \\ *FEATURE* Chat server for the development group. If it catches on, expect it will replace JR_Programmers email group. \\ VIDEO OVERLAY TRANS(X)MITTER (AKA XBOB) \\ *FEATURE* Remove email notification. Sufficient to print a meaningful message to the video overlay display. \\ *FEATURE* Revise the serial communication to auto-recover from serial link failure. No operator intervention should be required to re-establish communication unless total failure of a component occurs. \\ DATABASE \\ *FEATURE* Tagging tests by project. Web-service revisions: (1) populate changed_by field appropriately from submitted user/pass; (2) add support and default behavior for x_project in sample and test. \\ *FEATURE* Automated synchronization for DESCINFO schema configurations. Thoughts towards LIMS configurations too. Asynchronicity required. Robustness in the face of unreliable connectivity absolutely required. Paves the way for real-time trickling of sample, test, result. Functionality provided by Oracle archive logging and the Oracle streams package. See Oracle whitepaper "Asynchronous Change Data Capture Cookbook". \\ WEB SERVICES \\ *FEATURE* Load balancing Provide Lims.NET support for base path in load balance servers--e.g. web.ship.iodp.tamu.edu:80/ws should get carried through by SampleMaster and DESCLogik when invoking a connection via load balancing. \\ *BUG* Resteasy-lims-webservices getLimsData will not return selected fields: e.g. x_hole, x_core, x_core_type, x_section, x_sect_half. Service was written before these fields were added as a convenience. The convenience applied is sample parent lookup; attribution of offset relative to section half for many types of samples. \\ BUG Image tiling services. Does not generate tiles if the core or section is null. Yet another casualty of hanging junk baskets off of holes. Fixed

[Bennight].

\\

[ADVANCED]

BULK PRINTER \\ *BUG* Fails to substitute many fields in the sample labels generated: x_core_type, x_core. Leads to labels printing with the ugly substitution variables on them. \\ *FEATURE* Can print anything by typing into Exp, Site, Hole, Core field; but populating Sample Identity field results in substitution variables being displayed on the label rather than the provided text. \\ *BUG* Printing 1 or 2 replicates of a label works. But 6 replicates fails silently. Why? \\ LIMS REPORTS \\ *FEATURE* Replace "Download file?" with radio-button set: Display below (default) | Display in new tab | Download file. \\ *FEATURE* Revise layout to make more efficient use of screen real-estate. Combine Select Report Tree and Select Sample Range. Make Select Report Tree scrollable and when selection made fill in selection in slide-box header. Select Sample Range should never fully obscure Selected report. Remove "Select Depth Scale". Move "Advanced Filter Options" where "Select Sample Range" used to be. Default display it. The "About this Report", "Example Report" and actual content then all move to the far left and pull up in visibility. Report title line and header should display filter parameters applied for report verification. \\ \\ IMAGE CAPTURE (CLOSEUP, THIN SECTION, MICROGRAPHS) \\ FEATURE Extend the sample lookup capability. Need to be able to search by sample type. Used test-list in this case to tag a junk basket sample. Release 1.0.9.5 added sample type search capability

[Fackler,

Bennight]. \\ *BUG* Label IDs are mangled with different business logic than in SampleMaster or other label printing programs, leading to filenames that do not closely resemble sample label content. \\ *BUG* Long labels do not wrap appropriately. Different wrapping behavior required for material with only hole ancestry vs. core and section ancestry included. Adapt the business logic for x335 corner cases. \\ *FEATURE* Change default directory where captured images are dropped. Keep ending up in TEMP directory rather than archiving in the configured image directory or preferrably defacto default "c:\data" directory.. Revise defaults so this occurs under c:\Data like other stations. \\ *FEATURE* Add better support for John Beck workflow, where images are treated as external selections (Import) rather than acquired and placed direct from TWAIN acquisition. \\ *BUG* Atalasoft TWAIN driver receives errors when communicating with the Spot acquisition driver under Windows 7 x32. Communication in progress with vendor. Need to complete debug cycle with vendor programming staff. \\ THERMCON LOADER \\ *BUG* Opening access yaps about security issues when attempting to convert old access files generated by the thermcon software. \\ *BUG* Interface not providing enough guidance about what it is doing. Have encountered cases of sample directory three levels deep where placement of data for a different sample was at each level. \\ TPFIT DATA LOADER \\ *FEATURE* Fold into MUT data load framework. *FEATURE* Add support to load the WTF file if present. *FEATURE* All files of the same base name should be moved to the archive directory together. Several files are left hanging. \\ *FEATURE* Enable operator to identify which tool was used if not clear from data file name: SET, SETP, APCT3, and one other one. \\ *BUG* Verify. Are we loading temperature data as at the bottom of the previous \[specified\] core? Is the supplied drillers depth for the measurement being converted to CSF-A? \\ \\ \\ \\ \\ \\ \\ \\ \\ \\ \\ \\ \\ \\ WRMSL & STMSL \[With respect to subversion codebase +https://build/svn/jr/LabVIEW/msl/trunk+ which is applied to both systems.\] \\ *BUG* End-of-travel switch has no effect when triggered. Works find on STMSL. \\ *BUG* Running a sample followed by running a standard-as-part-of-the-sequence results in motion but no measurement for the standard or remaining portion of the previous sample. \\ *FEATURE* Revise the PWL Get data from array class to conduct a check for driver errors as the other equivalent methods do. Improves robustness in case of errors at the sensor driver level. \\ *FEATURE* When a Bartington driver serial read error occurs, it can result in a zero measurement. Revise to return NaN for this no (failed) observation case. \\ *BUG* End-of-travel switch is only checked once. If the dialog is Ok'd without actually releasing the switch (clearing material), the program goes into error handling and shuts down. \\ *BUG* Check for laser obstruction during "Find Laser" operation only checks once. If the operator clears the dialog box without clearing the obstruction, the puck racks out at the forward limit. \\ *FEATURE* Improve user experience for configuration file management from within the code. *FEATURE* Ability to skip measuring over a list of intervals or an entire range is still desirable. *FEATURE* Clarify the function of the pusher vs. material under study. Improve the interface wording to reflect this distinction. \\ ADDENDUM D: SAMPLE, TEST, RESULT STATISTICAL METHODS \\ SAMPLE METHOD REFERENCE]]>

1. select count "Routine Samples" from sample;
2. select count "Exp Samples" from sample where x_expedition in ('335', '335(312)') and standard='F' and instr('ICPAR', status) > 0;
3. select count "Std Ref Materials" from sample where x_expedition='QAQC' and standard='T' and instr('ICPAR', status) > 0 and sample_name not like 'CONT%';
4. select count "Exp Canceled Samples" from sample where x_expedition in ('335', '335(312)') and standard='F' and instr('X', status) > 0;
5. select count "Samples Filfilling Requests" from sample where x_expedition in ('335', '335(312)') and (x_req_code is not null or x_requestor is not null) and instr('ICPA', status) > 0;
6. select count "Routine Shipboard Samples" from sample where x_expedition in ('335', '335(312)') and (x_req_code is null and x_requestor is null) and instr('ICPA', status) > 0;
7. select sample_type, count from sample where x_expedition in ('335', '335(312)') and instr('ICPA', status) > 0 and sample_type in ('HOLE', 'CORE', 'SECT', 'SHLF', 'PC', 'TS', 'SS') group by sample_type;

TEST METHOD REFERENCE

1. select count "Total Tests" from test;
2. select count "Exp Tests Conducted" from test where sample_number in (select sample_number from sample where x_expedition in ('335', '335(312)') and instr('ICPAR', status) > 0) and instr('ICPAR', status) > 0;
3. select count "Exp Tests Canceled" from test where sample_number in (select sample_number from sample where x_expedition in ('335', '335(312)') and instr('ICPAR', status) > 0) and instr('X', status) > 0;
4. select count "Ext QAQC" from test where sample_number in (select sample_number from sample where standard='T' and instr('ICPAR', status) > 0) and instr('ICPAR', status) > 0 and date_received > to_date('2011-04-13 00:00:00', 'yyyy-mm-dd hh24:mi:ss') and date_received < to_date('2011-06-08 23:59:59', 'yyyy-mm-dd hh24:mi:ss');

RESULT METHOD REFERENCE
select count "Total Results" from result;

1. select count "Exp Results" from result where sample_number in (select sample_number from sample where x_expedition in ('335', '335(312)') and instr('ICPAR', status) > 0) and instr('EMAR', status) > 0;
2. select count "Exp Results Cancled" from result where sample_number in (select sample_number from sample where x_expedition in ('335', '335(312)') and instr('ICPAR', status) > 0) and instr('X', status) > 0;
3. select count "QAQC Results" from result where sample_number in (select sample_number from sample where standard='T' and instr('ICPAR', status) > 0) and instr('EMAR', status) > 0 and entered_on > to_date('2011-04-13 00:00:00', 'yyyy-mm-dd hh24:mi:ss') and entered_on < to_date('2011-06-08 23:59:59', 'yyyy-mm-dd hh24:mi:ss');

SYSTEM MANAGER'S REPORT

ANDREW TREFETHN AND MIKE CANNON



SUMMARY:
During Expedition 336 the IT infrastructure performed as intended with minimal adverse impact to operations. Some resources such as GroupWise Web Access and file access would stop occasionally and would require restarting the service. The Cumulus service on Etna continues to consume disk space at the rate of about 6% per day until disk full alarm threshold is reached. A restart of the service frees disk space, frequency is about 10 days. We had some hardware failure in our tape library but this caused no interruptions to service.

SERVERS (MICROSOFT):

• • The Microsoft servers performed well during this expedition with no major issues to report.
  • Decommissioned the old developer build server (ear) and sent it back to College Station.
  • Finalized installation of Pinatubo, the new developer build server. It is now fully functional.
  • Krakatoa locked up once during the expedition and required a reboot. After rebooting users were able to log in normally.

SERVERS (NOVELL):

• • The Novell servers performed well during this expedition with no major issues to report.
  • We fully implemented Samba (SMB) file services for this expedition and it worked as expected, operating across multiple platforms, Windows, Mac, etc. This allowed scientists to access volume one and two without installing the Novell client on their personal computers.

SERVERS (SOLARIS):

• • The Sun servers performed well during this expedition.
  • Continued service calls with Modula4 concerning Cumulus not releasing allocated disk space. Volume space fills at a rate that the Cumulus service requires stop/start functions performed on it every 10 days. As of this writing the ticket is still pending and under investigation by the vendor. Canto, the manufacturer of Cumulus has committed to a software revision addressing this issue.

EVA4000 STORAGE:

• • No problems were encountered with the EVA, it performed as it should.

NETWORK:

• • No major problems were encountered with the network. No major changes were made.

PRINTERS:

• • No major problems were encountered with any of the printers or print services.

PC/WORKSTATIONS:

• • Replaced a defunct hard drive in PC51559.
  • PC51569 continued to lock up and reboot. It was replaced with PC51570
  • PC51163 (Dionex), PC51552 (Laser), PC51645 (Winfrog1) and the Panasonic Toughbook were migrated from Windows XP to Windows 7.
  • PC90762 in the drill shack had an issue where it would turn completely grey after 20 minutes of idle time and required the driller to touch the screen to display RigWatch again. We installed software to prevent the computer from going into the grey screen mode.
  • The Bathy system operating system became corrupted during the beginning of the expedition. We ultimately re-imaged the computer with a good image and the system booted normally.

APPLE MAC WORKSTATIONS:

• • We received a replacement power supply unit for MAC51942 but it was an incorrect part. We shipped the PSU back to College Station. The proper unit was ordered and will arrive at the next port call.

SATELLITE/INTERNET/PHONES:

• • The VSAT system performed well after the tune up during the previous tie up. The only outages we experienced were from solar interference. The antennas were able to reacquire the satellite on their own without any intervention from the MCS.

OTHER EQUIPMENT:

• • A tape drive failed in the library. A ticket was started with HP and a replacement will be sent out to the next port call.
  • The therm-con system's UPS failed. The spare UPS was put in place and the defunct unit is being shipped back to College Station for repair and replacement.
  • Installed a new Startech serial to LAN converter for the tracer pump in the mud pump room, configured and tested functionality.

SPECIAL PROJECTS:

• • Added two UPS protected outlets to the far wall in the MCS office.
  • Worked on Veeder Depth and Xbob extensively with Algie Morgan to track down intermittent issues with the core line depth display. After changes in hardware settings and modifications to the software it appears to be much more stable now.
  • Updated Cumulus with the latest release of technical documents
  • Video distribution proposal creation.
  • Worked with SCIOPS and engineering to create specifications for the SCIOPS Data Ship and Shore Synchronization Initiative.

CORE DECK ACCOMODATION

MIDGLEY
0600-1800*KLAUS*
0600-1800*EDWARDS*
TBD*BACH*
TBD
FO'C'SLE DECK ACCOMODATION






MILLS, BILL
0900-2300*BECKER*
TBD*WHEAT*
TBD*ANDERSON*
TBD*STORMS*
1800-0600*FURMAN*
0600-1800
BERTOLI
1200-0000*RHINEHART*
0000-1200
GRIGAR
1200-0000*BRONK*
0000-1200
CROWDER
1200-0000
MAIN DECK ACCOMODATION






JORGENSEN
TBD GRIFFIN TBD*WANG*
TBD MAGNUSSON TBD*PETTEIGREW*
TBD*SAKATA*
TBD
LADA INSUA
TBD*GARRIK*
1200-0000
GJESVOLD
0000-1200*BERTOLI*
1200-0000
VASILYEVA
0000-1200*MORGAN*
0000-1200
ZHAO
1200-0000*STEPHENS*
1200-0000
HILLIS
0000-1200*ORCUTT*
TBD*TREFETHEN*
0000-1200
CANNON
1200-0000*HADDAD*
TBD HIRAYAMA TBD*CRAWFORD*
0600-1800
MC KENNAM
1800-0600*BRANT*
0000-1200
BARRETT
1200-0000*HASTEDT*
1200-0000
UPPER 'TWEEN DECK ACCOMODATION



MILLS, HEATH
TBD ROUXEL TBD*SALAS*
TBD MEISSNER TBD*RENNIE*
TBD*LE CAMPION*
TBD NAKAMURA TBD*HULME*
TBD PARK TBD*BACKERT*
TBD RUSSELL TBD*ETLLINGER*
TBD BROWN TBD

CORE BOX INVENTORY SHEETS

CORE BOX INVENTORY SHEETS

CORE BOX INVENTORY SHEETS

CORE BOX INVENTORY SHEETS