X352 Technical Reports









Contents

LO – ALO Handover notes

William Mills, Lisa Crowder & Tim Bronk

IODP Expedition 350: Izu Bonin Mariana Rear Arc

Objective:
The objectives of the expedition:

• recover a high-fidelity record of magmatic evolution during subduction initiation;
• test the hypothesis that FAB tholeiites lie beneath boninites;
• record the chemical gradients within these units and across their transitions;
• understand how mantle melting processes evolve during subduction initiation;
• test the hypothesis that fore-arc lithosphere created during subduction initiation is the birthplace of supra-subduction zone ophiolites;

Leaving from Yokohama, Japan, we completed a 2 day transit to our drilling location southeast of Japan in the Western Pacific. There we cored 1684.6 meters and recovered 561.21 meters at four sites and seven holes.
Labs and Technical Services: Overall there were few hardware or software issues to deal with during the expedition. The DTech demagnetize amplifier and controller developed a number of issues but the staff, working with the science party, were able to overcome for the most part. The JR6 spinner had the normal maintenance issues but has a habit of breaking internal wires.
The continuing saga of 0 TFF images on the SHIL appears to be over. After finding and changing an obscure error setting in the LabView IMAQ libraries, we began to receive "Out-of-Memory" errors that hadn't seen before. Moving the code to a 64-bit version of LabView completely eliminated the issue.
Facilities: Work has finally resumed on the installation of the AC units in the bridge deck offices. Hopefully, by the end of the next tie-up the units will be operational.
Staff: Seth Frank sailed as a Temp Tech in the XRAY Lab. We sailed with two less technicians (Kristin Bronk & Thomas Gorgas) and Zenon Mateo covered the Physical Properties Lab. Lisa Crowder has had additional training in the thin-section lab.

Operational Dates:

START

• Port: Yokohama, Japan (Honmoku Berth #3)
• Arrived: 30 July 2014 @ 1042
• Departed: 4 August 2014 @ 0753

END

• Port: Keelung, Taipei
• Estimated Arrival: 28 September 2014 @ 1500

General Port CALL information

• 30^th July:
  • The oncoming crew moved onboard and completed their cross-over;
  • The Co-chief Scientists and Staff Scientist boarded at the same time to being planning;
  • Loaded Liquid He, and local food ;
• 31^st July:
  • ODL Crew Change completed;
  • Science Party arrived in the afternoon and completed their safety a brief introduction to the ship;
  • Completed elevator stress test successfully;
  • Discharged Microbiology samples via World Courier;
  • Off loaded cores;
  • Completed testing of backup re-entry camera;
  • TAMU EHSD audit;
  • Ocean Leadership audit started;
• 1^st August:
  • Began vessel refueling;
  • Discharged all of the IODP surface freight;
  • Technical staff assist catering with loading food;
  • Ocean Leadership audit continues;
  • Laser and radiation safety course conducted by TAMU EHSD staff;
  • Cryogenic Magnetometer liquid helium refill completed
• 2^nd August:
  • Completed fueling operations;
  • Ocean Leadership audit completed;
  • Begin loading drill pipe and casing;
• 3^rd August:
  • Discharged outbound air freight;
  • Began securing for sea;
• 4^rd August:
  • Last line released at 1100h;

Transit activities

• Expedition 352 started with a 2 day transit from Yokohama to our drilling area in the Western Pacific southeast of Japan. Because of Japanese fishery restrictions, only bathymetric data was collected and the magnetometer was not deployed.
• During the transit, tracks and lab instruments were calibrated and brought into working order.
• Completed Expedition safety inspections.

AMS/Inventory

• Routine Physical counts were done for high-usage items in preparation for the next few high-recovery expeditions.
• Compiled a single list of ECCN and Schedule B numbers in the Logistics/Export Control Folder. All items in shipments to the US need ECCN and Schedule B numbers. We should add numbers as needed.

Shipment

• X352 Cores and Residues will be shipped to KCC from Subic Bay as F353P_CORE.
• Surface Freight will be shipped from Subic Bay as F353P_SURF.
• Air Freight (F352_RAF) and Foreign Air Freight (F352FA) are prepared to ship from Keelung.
• One World Courier Shipment, refrigerated, Germany, 1 piece, F352WC_Jonas

AREA-BY-AREA SUMMARY

Bridge Deck

• The LO office, as well as both OPS offices, have been prepped for an additional air cooler to be mounted in the overhead space.

Core Deck

Core Entry:

• New Laser engraver safety interlock system was installed.

Splitting Room:

• A jig was made for the Mini-corer drill press to hold pieces in place for coring. The jig is very versatile to accommodate different shaped of rocks.
• Noticed a number of blades were mounted the wrong way on the rock saws. MK Diamond does put a rotation direction on the blades.

Core Description Lab:

• Fixed the issues with empty TIFF files on the SHIL.
• A new VCD-S print process was developed for the SHIL images.
• Whole round imaging updates requested by the previous crew where made.

Microscope Lab:

• SEM filament finally burned out and was replaced.

Downhole Lab:

• Garrick and Clay held electronic classes with the teams building two vacuum tube clocks.

CryoMag:

• DTech amplifier and control logic had numerous issues. Scientists and staff where able to work around most. A new system is on order.
• Liquid nitrogen demagnetization was carried out on approximately 20 specimens.
• JR6 was a workhorse this trip but required a lot of TLC by staff.
• Resolved a communication conflict between the Flexit and APCT3 applications.
• Refilled the Cryogenic magnetometer in portcall.

Physical properties Lab:

• New NGR line collimator standard was used to determine sensor response.

Fo'c'sle Deck

Chemistry Lab:

• Titanium squeezer #3 was leaking during squeezing, probably due to heavy, uneven wear on the inner titanium plate. The squeezer will be sent back to shore for repair.

LOWER TWEEN DECK

• It's all good.

Poop Deck

Underway Geophysics:

• Rust removed from level wind and re-greased.

CORE Description

Margaret Hastedt

Summary

Expedition 352 had a total of twelve core describers and a single paleontologist aboard. The DESC templates encompassed macro- and microscopic lithologic descriptions, and calcareous nannofossils.
The main core description templates were inherited from Exp. 351 with relatively minor changes - name and column ordering and value list choices primarily which were nearly all on the extrusive_hypabyssal and intrusive_mantle tabs. This layout was again based on the more traditional component/abundance schemes in use prior to Exp. 350. The Sediment tab saw some consolidation primarily in clast columns (the sedimentologists decided not to differentiate between lithic and vitric clasts and thus reduced the number of categories). They also elected to use paper forms for smear slides and wanted the field order mirrored in the smear_slide tab for easy transcription. The 351 structure tab was replaced with the 344 version at the request of the structural geologists.

Other activities:

• Time was set aside to fix some duplicate column definitions in the 352_microscopic template. Many of these were found in hidden columns but were repaired on the off chance they are unhidden in future. A brief write up on duplicate definition detection with Excel macro code was included in the DESClogik admin help pages on our DESC Google site. Short DESC-download training classes were given to the geochemists so that they could browse descriptions with respect to their chemostratigraphic efforts. Also, Zenon was re-familiarized with DESC v.2. Thanks for all his help this cruise!
• The Marsaglia et al smear slides, atlas and tutorials were offered to the science party very early in the expedition, but saw almost no use as we only had two sedimentologists and both were quite experienced. Maybe next cruise? Note: the physical slides are kept locked up in the SEM drawer in the close-up area of the microscope lab.
• There was no development work on DESClogik this cruise.

DESClogik Issues

Errors were few and pretty benign, other than the usual slowness. Here is a recap:

• Early on we saw some piece number lookups that appeared to be duplicated, but those were a result of edits done in Sample Master rather than problems in DESC proper.
• DESC does not appear to respect unhides on columns if the column was originally hidden in the config sheet at import. Solution: change the flag to visible in the config file and reimport it. Oddly enough, originally-visible columns will remain hidden if any permitted user hides them in DESC. This was something of a problem generating thin section reports because the alteration scientist kept hiding columns on later sites that had been used in the report definition.
• Haunted by a ghost core: having a ghost core at the bottom of U1439C created issues with downloads against the hole in DESClogik. Per Algie: "DESClogik finds the top-depth of the first core selected and the bottom-depth of the last core selected and then downloads and displays all data between those two depths.  U1439C-46G is the last core in hole C and it has a bottom-depth of 532.995; core 44 has a top-depth of 534.55 and core 45 has a top depth of 542.23, therefore DESClogik truncates those cores any time it finds core 46 in its list of selected cores; this includes either selecting hole U1439C or selecting any range of cores that includes U1439C-46."  This hole had other ghost cores but they were always followed by deeper regular cores so it was never an issue before.
• Old bug: the DESC sample selector and other parts of the UI start looking really funky when people change the default text size to a larger one (in the Screen Resolution control panel, "Make text and other items larger or smaller" submenu). Keep it at 'smaller' (100%) to avoid this issue.
• When the sedimentologists began transcribing their paper smear slide data to DESC, they started out using lowercase letters for their abundance codes. This was accepted by DESC without any red boxes as a challenge (lowercase abundance codes are not in the sublists). Ideally the validation would be case-sensitive here. I downloaded and repaired the problem entries in Excel and then copy/paste/re-uploaded. They started using the Caps Lock on their end.
• The alteration scientist reported a very odd issue where a single cell in her template would not upload properly. It would appear to upload just fine, then disappear at download. I could not replicate the problem on a different DESClogik workstation. It may have something to do with her changing the mouse button actions in Windows to mirror the right-button/left-button behavior, since she switched mouse hands at some point. I suspect she may have done this during her DESC session while on the cell at issue. Needs confirmation…
• Never-before-seen funny DESC bug: a scientist got the following pop-up warning in DESC while idling fiddling with the mouse pad during a science discussion. It said "Boom on sample text box changed event". (I'm fingering Tim Blaisdell as the author.) While she fiddled, the Current Sample bottom offset had gone from 82 cm to "82+" and caused the error. She probably hit the plus key on the numeric keypad by accident. After acknowledging the message with the OK button her upload proceeded without incident.
• Not having Num Lock enabled on your keypad makes for decidedly unusual behavior when hitting number keys for DESC entry. The cells start jumping all over the place!

DESC feature request:

Active-cell row and column header highlighting would be very beneficial to users of large, busy templates on big monitors.

Thin Section Report

The thin section report builder and writer performed well this cruise. It took a bit over a week for the petrology-based report format to finalize. It is hard to envision what a report will really look like until there is data to populate it, but the scientists were game. By the third iteration it was essentially finalized. The small number of sediment thin sections we had this cruise were described in the smear slide tab in DESC as there was zero interest in a separate thin section report for them.
Most of the time the DESC technician populates the image links into DESClogik for the main thin section tab (the tab that is the foundation for the number of reports that will be generated). A user guide was created and sent to the office for review as well as circulated among the Exp. 352 core describers. I think only one scientist bothered generating new reports but it's a start at least. The report still needs work on a few outstanding items, particularly how it handles borders and page breaks among other things. Also, Java needs updating on a number of workstations in the Core lab as the TS report writer complains about it at launch. It does work with older Java installs though. Bumped issue to jr_developer.
TS Report Writer note: if the TS Writer is up and running and you have selected a (exported) spreadsheet for it, you cannot re-export from DESC to that spreadsheet. DESC will complain that the file is still open in Excel (which it isn't, but evidently the writer puts some sort of a file lock on it).

SEM

The SEM saw a good bit of use this cruise. The nannofossil paleontologist and the alteration petrologist were the main users. The alteration petrologist received permission to carbon-sputter a single thin section but after that had to content herself with unsputtered ones.
The SEM filament finally burned out (fig. 1) and was replaced at mid-cruise. It had another spacer inserted after complaints about maxed out contrast, which seemed to solve the issue. Files were collected and reorganized per our naming convention and put on Uservol and DATA1 throughout the cruise.

Fig. 1: close-up of broken SEM filament

MAGNETICS LAB

BETH NOVAK
Many pmag cubes
Dtech frozen in the lab
Science standing still!
Excessive fields found!
Bad Amp, Replace Startech Board
Dtech functioning
Spinner not spinning
P1 is running error
Try second spinner
New spinner error
Manipulator is stuck!
Call the ET quick
Dismantle Spinner
Broken wire identified
Saved by the ET
Instrument frozen!
MCS loans a laptop
Instruments working!
Cubes all processed now
Perfect grains of magnetite
Happy Scientists
Beth Novak
Scientists: Claire Carvallo, Will Sager

Summary

The paleomagnetics lab was used extensively this cruise to measure APC, XCB and RCB archive half sections and discrete samples. The sediments consisted of mud and a small amount of volcaniclastic sediment and the basement material consisted of boninite and basalt. Thermal and AF demagnetization was carried out on several hundred shipboard discrete samples. The SRM was used to measure section halves of sediment cores and discrete pieces of hard rock from the archive sections. The Flexit tools were deployed at Sites U1439 and U1440. The spinner magnetometer was used heavily and the Bartington loop was used to measure basement specimens. Liquid nitrogen demagnetization was carried out on approximately 20 specimens.

Issues

1. Multiple issues were noted with the Dtech AF demagnetizer system.
2. Dtech froze during demagnetization cycles. Restarting the PC did not solve the problem.
   • Error given indicated a possible excessive field. Hall probe measurements indicated high fields during demagnetization, especially when both channels were on. We opted to run channel A at -6db and channel B at 0db. The excessive demagnetization error was no longer seen.
   • Note: When the excessive field error was seen during demagnetization, the hall probe measurements indicated peak field was not reached. Demagnetization is halted before excessive field is applied.
3. Dtech software pausing mid-way through demagnetization, no error message given. Appeared to be a communication issue and the Startech Serial Board was replaced on the PC.
4. Dtech control unit powering off/losing power during use. Unknown cause. Waiting on reply from Agico.
5. Amplifier sending a signal to Dtech while power unit was on (appeared off because indicator lights were off), but PC was off. Coils were hot and amplifier was overheating from the prolonged signal. Turning off Dtech when not in use has helped to prevent the issue.
6. Scientists noted an ARM from the Dtech for specimens weaker than 500 mA/m. The scientists opted to use the Dtech for strongly magnetized samples only.
7. When running the Dtech off of a laptop, rather than the center PC in the paleomagnetics lab, the freezing errors with the software were no longer seen.

1. JR6 Spinner 2 presented with a P1 is running error during measurements. When calibration was attempted a value of 999 was displayed. In order to allow the scientists to continue measuring specimens, the JR6 Spinner 1 was deployed. Spinner 1 gave an overflow error during holder correction measurements. The display would indicate a successful holder correction measurement, even though no values were collected. The Rema6w software was installed on a laptop and the JR6 errors were no longer seen on either spinner. It is unclear at this time if these problems were associated with a communication error between the PC and the instruments, but working from a separate laptop seemed to resolve the issue.

1. JR6 Spinner 1 brass actuator froze during measurement. Garrick identified a broken actuator motor wire. Once the wire was repaired, the actuator functioned properly.

1. The Flexit Transit PC Adapter in the downhole lab indicated that the battery was low, even after the battery was replaced. Further investigation revealed that the APCT3 tool and the Flexit were trying to communicate on the same com port. This problem was resolved by using the USB to RS-232 plug in adapter for the Flex it rather than com port 1.

Other

• A Helium fill was completed during the port call in Yokohama prior to Exp 352.
• Broken wires associated with the actuators have been a recurring problem in the spinners.
• We should consider replacing the current actuator wires with silicon wires, which are more flexible.
• Work on the Labview code for correcting cores reversed in the SRM continued. Testing of the code will continue on shore. The program should be ready for technician use prior to Exp 343.

Cryomag readings

h1. CORE and Paleo Prep LAB
UNKOWN AUTHOR

Paleo Lab

The lab was primarily used for the handheld XRF.
Hood C6 is still running too fast per EHSD. I will speak with Roy regarding changing the pulley size to reduce the fan speed.

Core Lab

Core Splitter

Lisa C. is working on a "care and feeding" manual for the core splitter.

Laser engraver

Laser engraver interlock system was upgraded. It now has the following features:

• When the door when closed is always locked.
• When the Laser is off, the door release button is lit. Pressing this button will unlock the door. You must hold the button down while opening the door.
• As before the Laser will not come on if the door is open. The Laser is also disabled if there not sufficient air-flow on the vent.
• When the Laser is in operation the door is locked and the door release button is disabled and not lit.
• Once engraving is completed the door will remain locked for 4 seconds to vent the chamber. After that time the door release button will be enabled and lit.

Laser door interlock upgrade

Objectives:

1. Extend the time delay between the end of laser operation "Marking" and opening of the Laser door by using a programmable system.
2. Add a visual external indication of laser operations and status.

Operation theory:

1. Relay 1: Error Light – A Voltage from connection 37 of the Laser panel would pull in the NO pin of relay1 to a closed state and in turn power the external "Error Light" in the event of an error.

1. Relay2: Ready Light – A Voltage from connection 33 of the Laser panel would pull in the NO pin of relay2 to a close state and in turn power the external "Ready Light" when the Laser system is "Ready".

1. Relay3: Marking Light – A Voltage from connection 29 of the Laser panel would pull in the NO pin of relay3 to a closed state and in turn power the external "Marking Light" when the Laser is "Marking".

1. Relay4: Time Delay Activation Relay – Relay4 Pin1 is activated by the "Marking" state.

1. A Voltage from connection 29 of the Laser panel would pull in the NO pin of relay4 to a closed state connecting a 24V dc supply to the Time Delay Relay. When Relay4 changes state indicating that "Marking" is completed the TD Relay would energize the TD Relay output after a set time. This is to allow more time for gasses to be removed from the laser chamber. Now the illuminated push button is energized. To open the Laser Door you need to push the illuminated button and pull on the door handle.

1. Relay5: Relay5 Pin1 is activated by "Marking" state, connection 29 of the Laser panel.
2. Relay5 Pin7 is connected to E-Stop B through one of Bills Phiget boards; this is an added function to stop the track via software. The NC pin is grounded. When Marking is active and connection 29 is energized, the relay changes state, now relay5 Pin7 is connected to relay6 Pin12 (NO). Pin12 is in turn connected to Pin10 (NC) of Relay6.

1. Relay6: Relay6 Pin1 is activated by the Airflow Switch.

1. Pin7 is connected to number 22 of the Laser Door interlock, 24Volt is present when the door is closed. So, if the Airflow state is low the voltage from Relay5 will pull E-Stop B high if the user tries to run the laser. If the airflow is operational the relay would switch pin7 to pin12 and the E-Stop B would stay low.

1. Relay7: Relay Pin1 is activated by the Airflow Switch.

1. Realy7 Pin7 is connected to number 12 of the Laser Door interlock, 24Volt is present when the door is closed. In the event the door closed and the Airflow switch is open the voltage from the Laser Door interlock would pull the "Trigger inhibit" high. If the airflow is operational the relay would switch and pin7 would be connected to pin12 and the Trigger inhibit would stay low.

PHYSICAL PROPERTY LAB

ZENON MATEO

SUmmary

Expedition 352 continued on the success of the preceding ones without any major issues on the loggers and tracks for measuring the physical property of core materials. The combination of sediment and igneous rock cores fully utilized the capacity and flexibility of these analytical systems. Several exercises were conducted to further evaluate instrument performance.

SYSTEMS

Whole Round Multi Sensor Logger (WRMSL):

• The WRMSL worked very well during the entire expedition. Measurements at 2.5 cm interval were performed on the sediment cores and at 0.5 cm for the igneous cores. After the acquisition, the MS and GRA profile of the igneous cores were automatically filtered using the piece log to extract only the data from pieces that are more than 10 cm long.

Issues and suggestions

• If the pump for the PWC in the WRMSL is to be turned off for a while, the rubber tubing in the peristaltic wheel collapses or welds and not allowing water to flow. Pull out this wheel and manually open the tube. Water may also be manually injected from the intake using a squirt bottle. Several replacement segments of this rubber tubing were cut and stored in the Velocity drawer under the STMSL. Also make sure that two outlets for water to flow out are almost level; if not, momentarily plug the working outlet until water starts flowing on the other outlet.
• The water used for the PWC component currently needs to be replenished and emptied almost every day. But this water does not get in contact and therefore not contaminate the actual sample. To prevent any possible flooding and damage on nearby instruments in cases these containers are not emptied, it is proposed that the water used can be re-circulated into just one carboy and the water can just be replaced less frequently (e.g. once a week)

Natural Gamma Ray Logger (NGRL):

• Similarly, the NGR collected data without any major problems, with sediment cores measured at 300s per position and igneous cores at 1200s per position.
• Two background measurements and energy calibrations were performed at the beginning and middle of the expedition. Though the initial background measurement was only done for 6 hours due time constraints, a second set was performed for 12-hour. Rescanning of several representative sections using both 6 and 12-hour calibration sets of files revealed that the total count only varied by less than 1%. Six-hour background collection time can therefore be allowed if (1) transit time and distance between sites is short (cf. Expedition 350); and, (2) the drilling site is at low latitudes. Energy calibration involved only adjusting the "bias box" in order to fine tune the channel and set the energy of the Cs and Co photo peaks.
• Exploratory exercise was conducted using the collimator in order to determine the homogeneity of the NaI detectors, among other objectives. A list of the initial results is given below/attached file, not to be taken for actual calculations but simply to serve as a guide for designing any further activities using the collimator.

Issues

• Uploading error caused when the TextID was missing in the summary and data excel files and the LabelID was in the wrong column. Manual entry of TextID and correction on column assignment solved the problem.
• A previously noted high-frequency sound emanating from the electronics cabinet was still observed and should be followed up for the next tie-up period in Subic. An assessment of the rear cooling fans is suggested by Mr. Gorgas and the electronic technicians.

Thermal Conductivity (Therm-Con):

• Thermal conductivity measurement was done on sediment cores using the needle probe and on every igneous core with suitable pieces using the puck/half-space probe. Sediment cores produced only a few reliable data but those from the discrete pieces yielded very good results.
• The measurement resolution was high enough that the downhole thermal conductivity profile matches well with other physic-chemical parameters and lithologic interpretations.
• In using the half-space puck, it was observed that in a sequence, there appears to be an increase in the values, which stabilizes around the 3^rd reading. Given this and the time available afforded by the rate of coring, 5 measurements were often made instead of the usual 3.

Improvement recommendations:

• Revisit the use of the mini-puck which would be useful for XCB biscuits and RCB pieces to ensure continuous downhole coverage of this parameter. The initial deployment of this half-space puck revealed inaccuracies in the measurements and was therefore sent back to TAMU.
• Probe heating parameters should also be included in the comments field so that it can be used to evaluate results after data acquisition.
• De-bugging and workflow-integration of application (Algie Morgan) to automatically rename and re-format the TeKa output file for better data evaluation using TkGraph.
• In two occasions, an error message in German appeared during the drift calculation stage, apparently referring to an issue with a semicolon. With only one button available, clicking this brings the application back to normal mode.
• Towards the end of the expedition, there were several instances when the probe (#H11027) condition did not pass the initial system testing, indicating a defective probe or poor connection. In all cases, the cable connections on both ends are detached and air-sprayed to remove any possible dirt and then re-attached. In the succeeding expeditions, this probe should be monitored if it is really getting defective.
• Several instances when the uploader could not find a file from the *.dat list of thermal conductivity replicates. This happens because TK04 sometimes append an extra pair of digits in the list of filenames in the *.dat file. Simply open this file, delete these extra characters to match the actual *.erg and *.dwl files in the folder.

Moisture and Density (MADMAX)

• As always, this analytical system consistently produced very precise results. With each batch of pycnometer measurements, one cell was calibrated and the results were uploaded to to LIMS and entered into a master spreadsheet on the MadMax PC desktop.

Issues

• Pycnometer standards not updating replicates due to updated sequence of result numbers in database (cf. Developer's report)
• Cell 1 gave 5 to 7 cm³ overestimates for actual samples, but not for sphere standards. No possible reason can be identified. A change of O-ring and cell recalibration got rid of the problem.
• Difference in temperature setting for pycnometer water bath and actual value in configuration file. An exercise was done to determine the effect on previous measurements and the results are shown below.

1. CONFIG FILE FLUID TEMPERATURE=28; WATER BATH=26.2

^#10.2 cm³ sphere standards * - see table below graph

2. CONFIG FILE FLUID TEMPERATURE=26; WATER BATH=26.2

3. CONFIG FILE FLUID TEMPERATURE=26; WATER BATH=28

4. CONFIG FILE FLUID TEMPERATURE=28; WATER BATH=28

1. 1. 1. 1. Except for cell 6, there is a tendency for lower volume estimates when config file temperature setting is different from actual water bath temperature.
         2. except for cells 2 and 6, closest to the average value is when the temeprature system is maintained at 26^oC, alluding to stability afforded bya system closer to room conditions. Alternatively, it could have also been the most common temperature setting during the averaged period since X349
         3. Maximum deviation from overall mean is 0.025 cm³, compared to the average standard deviation of all cells at 0.074 cm³.

NOTE however that the overall average since X349 is unconstrained (i.e., includes possible changes in the size of aluminum insert, or a change of pycnometer cell)
Mean since X349

Additional analysis from David Houpt:
The temperature set in the config file, and the temperature at which the cells are being maintained, so long as they are close to room temperature +/- 15 deg. C, is irrelevant to the measurement as helium's ideal gas character is pretty much the same from ca. 10 to 40 deg. C. In other words, stable temperature throughout the measurement is far more important than what the temperature is, provided you're in or close to the range of 10-40 deg. C. Even stability can be somewhat forgiving, because (in the range of temperatures we are working) P is proportional to T in Kelvins.  As K is nearly 300 (as the example will show), that means ca. 1/3 of one percent is the error of a 1 degree shift.

• 10 deg. C is 283 K, so a shift of one degree during the measurement has a 1/283 effect, or 0.35%.
  • 40 deg. C is 313 K, so a shift of one degree during the measurement has a 1/313 effect, or 0.32%.  It's slightly advantageous to maintain a warmer-than-room-temperature state for simple arithmatical reasons, and it's also easier to maintain a setpoint above room temperature than equal or below, so I have been recommending a set point around 35 to 40 deg. C.

On to masses and temperature fluctuations. It has been proposed that the expansion of helium as a consequence of this experiment might cause a temperature fluctuation (Joule-Thompson effect).  This is true, however: Less than 100 mL of helium at 19 psi over atmosphere is in the system (volume of main chamber), or 2.4 atmospheres of helium at 40 deg. C.  Using the ideal gas law, we derive that: 2.4 atm x 100 mL x 1 L / 1000 mL x 1 m^3 / 1000 L = moles of helium x 8.20574 x 10^-5 m^3 atm K^-1 mol^-1 x 313 K reducing that for moles of He, we get 0.00973 moles He, which has a mass of 0.00973 x 4.0026 g/mole = 0.039 g = 39 mg. Conversely, the aluminum block is approximately 1 kg, or 1,000,000 mg. Even a 10.0 degree change in helium temperature (and it's a fractional degree expanding 100 mL at 19 psi to 175 mL at 10.9 psi) would result in a very small change in net temperature in the chamber + helium.  The heat capacity of gaseous He is 5.193 J/(g x K), and Al is 0.897 J/(g x K). 5.193 J/(g x K) * 313 K * 0.039 g = 63.4 J 5.193 J/(g x K) * 323 K * 0.039 g = 65.4 J added joules for a 10 degree change in helium temperature = 2.0 J 0.897 J/(g x K) * 313 K * 1000 g = 280761 J +2 J from helium change = 280763 J 280763 J / 1000 g / 0.897 J/(g x K) = 313.00223 K As the temperature change from helium expansion is << 10 deg. C (in fact, it's near zero because He at these pressures doesn't cool or heat on expansion), you can see it can be completely ignored in the experiment.

Gantry (V_p)

• For the objectives of this expedition, only the P-wave caliper was used to collect velocity measurement on PMAG cubes. This coordination and sharing of samples allowed for more efficient utilization of cored materials and should be endorsed as a good practice for succeeding expeditions.

Issues

• At the beginning of the expeditions, the actuator for the Y-Bayonet fork transducers was reported to be non-functional. However, a quick test showed no signs of problems. Nonetheless, the bayonet transducers were not used for the samples collected.

System Evaluation

In Expedition 345 (Hess Deep), an exercise was conducted on the acrylic standard demonstrating that for immediately successive measurements, there appears to be a logarithmic increase in the estimated velocity that seem to stabilize from around the 3^rd measurement. This was repeated during this exercise, but using one actual cube of unsaturated igneous rock. Three series were performed: (1) successive runs with water was placed in between the transducer and the unsaturated cube and , (2) successive runs without putting water between the transducer and the unsaturated cube; and, (3) non-successive, single runs with variable time interval and no water placed between the transducer and the unsaturated cube.
Given the above conditions, the results are illustrated in the graphs below for the x-, y- and z-axis. These corroborate the findings from Expedition 345 that there is indeed a logarithmic increase in velocity estimates. In the graphs below, there appears to be a higher curvature and intercept and slightly smaller r² when water is present in between the sample and transducer. In a set of 10 measurements, the range is about 3.5 % of the mean value. Though the curvature is less and the r² is higher for the set-up with no water in between transducer and sample, this is not really the logical set-up for which we need to estimate the velocity.
From these results and those from the Expedition 345 exercise, several ideas can be considered. (1) Multiple measurements need to be taken. At least three replicates but only take the last or highest value. (2) Take five measurements and average the last 4 replicates. (3) Collect 10 measurements and take the average.

Section Half Image Logger (SHIL)

• This logger collected both section-half and whole-round images. However, the problem with the creation of "zero kilobyte TIFF" files continued until the beginning of the expedition. The developmental work implemented to solve this issue is described in the developer's technical report.
• A stand-alone Labview module was also created for printable forms for manual descriptive annotation of section-half photos.

Section Half Multi Sensor Logger (SHMSL)

• This track system was successfully used in both the sediment and hard rock cores. The pieces of igneous rocks were individually propped up and stabilized with plastic for better contact with the integrating sphere and MS probe.

Issues

• There were two instances when all the axes lost homing reference that none of the options in the application were able to reset the motion, only a soft abort and computer restart.

NGR collimator exercise

Zenon Mateo and Margaret Hastedt
In recent years, several parameters and variables were identified to fine-tune the NGR logger and completely take advantage of its capability. This exercise is conducted to address a few objectives that are collected from several expedition scientists and IODP staff:

1. Profile each NaI crystal detector in terms of the response to a given source (Cs-137) and determine the homogeneity.
2. Explore the need for a detector-specific, high resolution edge correction table (Blum)
3. Determine a solution for correcting the edge effect of each section measured (e.g. cut out the top and bottom 5 cm of the data -Houpt)
4. Establish the position of the motion control system (home position) to the NGR chamber and detector series.
5. Carry out more experiments to determine the "effective detector positions" instead of the constant 20.00 cm spacing currently assumed (Blum).
6. Define the amount of gamma ray signal overflow or scatter from one detector to adjacent detectors. Assess the potential for creating a function to deconvolve actual signals within the physical boundary of each detector (Mills, Gorgas).

PART 1: Defining parameters and variables for the exercise

Before proceeding with the actual exercise and perform a full array scan, there is a need to better understand the behavior of the system in terms of the geometric characteristic of the collimator, the procedure followed by the software, the timing and even the orientation of the source. These variables need to be constrained in order to better isolate the actual signal and response of the NaI crystal detectors and properly assess the edge effect and homogeneity of the crystals.

Methodology

For this part of the exercise, and to have more efficient use of time, we only focused on Detector 1. The NGR Position Tester v. 1.0.0.0 was used to drive the NGR boat using the following parameters:

Five runs were made using the plane collimator with the shorter end towards the chamber. The square plates on either end were adjusted to stabilize the cylinder inside the boat. On top of the collimator is a Cs-137 source disk with an activity of 0.9219 uCi or 34,110 disintegrations/second as of April 1, 2007. A sixth run was made but with 3 pieces of lead bars taped over the source. This is to test how much the NaI crystals detect gamma rays scattered outside of the perimeter of the crystal. For comparison, a run was also made using the original point collimator.

Results and Discussion

Figure 1: Plot of total gamma ray count for various runs across NGR detector 1. Six runs used the planar collimator and, for comparison, one run used the point collimator.

Comparison between the point and the plane collimators

The plane collimator is expected to project a larger and laterally extended beam into the NaI crystal, resulting in higher total count of gamma rays compared to the point collimator (Fig. 1 and 2). More importantly, the distribution curve for the point collimator is a normal, rounded peak Gaussian curve, whereas the plane collimator has a characteristic plateau and steep sides. Similar curves are generated by other systems when signal oversaturation is reached. However, this can be ruled out because distribution curves with lower total count also display a similar geometry (e.g. curve Plane-2-Pb). This implies that the plane collimator performs better in profiling and in characterizing the detector response because it can integrate a larger slice of the NaI crystal and it results in a more realistic curve that can be better analyzed (see next section).
A particular system behavior that needs to be accounted for is also revealed in these five successive runs across the same detector #1. There is a progressive increase in the total count that is very evident across the NaI crystal (Fig. 1). This cannot be accounted for by residual signals because gamma particles have nanosecond lifespan and that the NGR system (NaI crystals and electronics) do not retain residual signals of these events (Houpt, pers. comm.). A software re-start was also made once in between the entire acquisition period and the time in between runs varied from about 0.5 to 7 hours. In between short interval runs, the source remained at the home position and for runs with long interval in between, the source was kept away inside the safe box. Another set of runs was performed at 10 second instead of the initial 180 second counting time per position. With all other parameters maintained, the resulting curves did not show the progressive increase in peak signal.
NaI crystalmetal casingmetal casingDETECTOR
Figure 2: Detail of the plot of the seven runs over detector 1. The upper five curves used the plane collimator; in the middle, the dashed gray line is the result of three lead bars placed on top of the source disk; and the lowermost, dash-dot gray line is the total count using the point collimator. The thick and thin gray vertical bars respectively represent the measured position of the detector #1 casing and NaI crystal.

Effects of the plane collimator design and construction

Both point and plane collimators are designed to have a circular source disk sitting on top. Without any lead shielding on top, this allows non-collimated gamma rays to have a generally upward semi-spherical scattering, whereas a more directed (collimated) downward beam is projected into the NaI detector. However, the non-collimated gamma rays can also potentially reach the crystal. To test this hypothesis, a run was made with three bars of lead taped over the source on top. A decrease in the total count is noted, confirming that non-collimated gamma rays also register in the detectors.
A slight inward incline of the plateau or crest is also consistently shown by all of the total count distribution curves (Fig. 2). Initially, we thought that this could be due to the increasing containment of gamma rays as the source moves farther into the center of the chamber. However, a separate run was made with the collimator cylinder rotated 180 degrees (i.e., the top end previously closest to home position is now the bottom). The resulting curve showed a reversed inclination compared to those in Fig. 2. This may indicate that the plane between the two pieces of lead is not perpendicular to the long axis of the cylinder. A forward bias, possibly due to successive beam overlapping, therefore causes this crest inclination. This slant in the plane collimator also causes the asymmetry of the distribution curves seen in Fig. 1. A quick caliper measurement of the forward Pb cylinder in the collimator indicates a very minute difference of as much as 0.15 mm of the top and bottom regions of the plane. These can be solved by iterative adjustment of the aluminum plates on one end of the collimator. A less-time consuming and more permanent solution is to re-machine these two ends of the lead cylinders in order to make the collimation plane perpendicular to the cylinder long axis. Alternatively, the titanium boat, the inner Teflon railing or the inner NGR tube itself may not be completely parallel to the axis of the chamber.


Figure 3: Detail of the crest of the total count distribution curves in Fig. 1.

Detector characterization using the plane collimator

The ultimate goal of this exercise is to determine the homogeneity of the NaI crystals and if this is reflected in the responsiveness to gamma ray events. And if there is heterogeneity in the crystal detectors, what possible correction can be applied.
To approach these questions, the mean of the five total count distribution curves was calculated and plotted in Figure 3 (black line), together with the first derivative or slope. The resulting slope curve shows peaks and dips that coincide well with the empirically measured boundary of the metal casing and the actual NaI crystals. For comparison, the distribution and slope plot for the point collimator hardly defines these important physical boundaries.
Furthermore, the first derivative curve also defines an approximately 7.5 cm mid-section of the NaI crystal to have a consistent response to the Cs-137 source (Fig. 3). For defining detector-specific edge correction, this initial result indicates the utility of a plane collimator.



Figure 4: Summary of the total count distribution curve of gamma rays from a plane collimator. Note that the given position of the detector casing and NaI crystal are measured independently, but shows good coincidence with the calculated slope of the total distribution curve.

Spectral signature

In all the runs, the Cs-137 peak is stable and only varied by about 1.2 marks around 218. This spectral shift in the Cs-137 photopeak is also noted when both Cs and Co are simultaneously used during the energy calibration, but at a lower magnitude of about -5 marks.
These Cs-137 photopeaks also display a progressive increase of 495 counts through the successive runs using the plane collimator, similar to the trend shown by the total count (Fig. 1 and 5). With the point collimator, this Cs-137 photopeak is very subdued, lower in count than the Compton backscatter peak around channel 72, which is similar in count to those run using the plane collimator. This reflects the low amount of Cs-137 gamma rays passing through the hole. Such statement is supported by the plot of the run using the plane collimator but with lead bars on top of the source. This resulted in a Cs-137 peak similar to the other plane collimator runs because of the similar slit size. However, the Compton backscatter peak is reduced by as much as 37% due to the shielding effect of the lead bars.


Figure 5: Spectral signal of various runs.

Additional Questions

1. Is it also possible that the estimated thickness of the crystal sector with uniform response (i.e., flat slope of the total count profile) can also be a function of the thickness of the collimated gamma ray beam projected into the crystal? A thinner collimation plane would theoretically provide a more detailed profile of the crystal, and therefore a smaller segment on either ends where edge effect would be evident (e.g., the curved segment of the total count and slope curves on either side of the detector).
2. If the width of the collimation plane does affect the profiling resolution, is it then possible to construct a detector-specific edge correction?
3. Similarly, does decreasing scanning interval (e.g., every millimeter instead of 0.5 cm) also produce a sharper corner for the total count plot?
4. Does this curvature property also vary with the strength of the source used in profiling the crystal, such that a weaker source will produce a more rounded Gaussian curve? Especially considering that most of the core materials measured are orders of magnitude weaker than the Cs-137 source being used in this exercise.
5. Is the progressive increase in the total count across the NaI crystal due to the long counting time relative to the intensity of the source used? If this progressive increase is not observed at shorter counting time, does it imply a maximum span for counting gamma ray events vis-à-vis the source intensity? Does this shift have significance in the actual measurement of core materials? Is there an undocumented instrument drift for the NGR?

Notes

1. First measurement is taken at the point where the actuator moves the top of the boat to the desired starting position. Source would then be at a position less than the offset placed (e.g. Start position = 10 cm; Offset of center of source = 6.4; First measurement at 10-6.4=3.6 cm)
2. Second measurement: top of boat = 16.4 cm from home position; Source position = 10 cm. Only the succeeding measurements will be taken at the specified increment (e.g., 0.5 cm).
3. Home position of the top of the boat is 0.5 cm on the yellow tape, which has a zero position 0.8 cm from the face of the front door.
4. In the fourth and fifth runs, the source disk was rotated 90 and 180 degrees in order to determine if the source orientation has an effect in the result (cf. NGR User Manual by Vasilyev).

DOWNHOLE MEASUREMENT LAB

ZENO MATEO, RANDY GJESVOLD and GArrick Van Rensburg

APCT-3

During the expedition, there appears to have been some questions raised on the accuracy or reliability of the collected APCT-3 temperature data using tool #22. In particular, it was thought to be about 2 degrees higher than tool #7. An exercise was then conducted to evaluate the temperature readings from the APCT-3 compared to an available Fisher Scientific digi-thermo. Note that the data presented below is from an uncontrolled set-up using regular ice and cold water inside an ice chest or small refrigerator.
Based on the results of this bench-testing, the temperature measured by tools #7 and #22 have a good correlation with a slope of 1.08 and an r² of 0.95 for a temperature range of 1 to 13^oC (Graph A below). However, the intercept of this linear trendline indicates an offset of about 2.2^oC between the two APCT-3 tools. Compared to the Fisher Scientific digi-thermometer, the data from APCT-3 tool #22 was more comparable with trendlines close to unity and smaller offset compared to tool #7 (Graphs B and C).
The above results were later validated by the shore-based engineers who indicated that tool #22 was just recently calibrated in May 2014 and the rest were at a much earlier date and will therefore need to be sent back for more proper calibration.
The most recent calibration files for these tools were also installed in the Downhole Laboratory PC 52698. These *.wtc files were simply copied into
C:/Program Files/Antares/WinTemp/CalibrationFiles/
WinTemp 4.0.0.0 will then use these specifically named calibration files and apply them when an actual instrument readout (data download) is performed.

IMAGING & MICROSCOPES

TIN FULTON

Summary

Expedition 352 has been a low recovery, but successful expedition. The main focus of my work was to proof the line scan images for all the core recovered, photograph all close-up requests and thin sections, produce or edit the weekly photos and write the captions, produce the group photos, t-shirt stencil production and co-ordinate the ironing party, assist the scientists with microscope set-up and issues and provide assistance on the catwalk with the core retrieval.
No major issues with software/programs occurred. Any minor issues occurred early on; these were all addressed in a timely manner and did not disrupt my workflow to any extent.

Equipment & Software Performance Summary

I used Photoshop to edit/produce images for the cruise. Image Grabber to download the line scan images and Excel to sort the data for whole round sample check. These all worked fine as expected.

General Duties Performed

• Generated the "mug photos"
• Downloaded and proofed all of the line scan core images.
• Downloaded and stitched the whole round core images.
• Photographed the close-up requests and thin sections.
• Photographed and edited the weekly photo submissions and produced the captions.
• Produced all of the group photos.
• Printed the T-shirt stencils and coordinated the ironing party.
• Assisted with the core retrieval on the cat walk.

Additional duties

• None this cruise as the work load was moderately heavy.

Issues

• Epson Inkjet printer has clogged nozzles. This is not a problem yet, however, it may be at some point in the future. I had to run a couple of nozzle cleanings before printing for productions.
• Thin section camera (PICAT) light source had to be serviced once by ET. Simple fix – bulb replacement.

Image Files Produced

• 591 Close-ups Images
• 232 Thin-section Images
• 580 Line Scan Images
• 167 Whole Round Composite Images
• 33.26 GB Still Images

CHEMISTRY LAB TECHNICIANS REPORT

Lisa Brandt & Rachael Gray
Ampulator
No ampoules were sealed.
The ampulator abides—
Waiting to be used.
Balances
Samples were weighed out.
No problems were reported.
Balance was achieved.
Carver Presses
Water poured from seams.
A squeezer will be sent home.
Can it be repaired?
Cary Spectrophotometer
The Cary worked well
To analyze ammonia
And phosphate also
CHNS
Carbon was present
Hydrogen was detected
Data uploaded
Coulometer
CaCO3
Was measured and uploaded
No issues were found
Freeze-drier
In the freeze-drier
Cold vacuum, like outer space
Samples become dry.
Gas Lines/manifold
Gases flow like wind
But more highly pressurized
From the upper tween.
GC3/NGA1
All headspace samples
Measured upon GC3
Not the NGA.
Hydrogen generators
Reservoir is full
Of purest cleanest water.
Like ponds in winter.
IC
Anions measured
And cations quantified.
Porewater: who cares?
ICP
Scientists do not
Like Analyzer software
Good luck, programmers!
We ran so many
ICP samples we need
More germanium
Salinity
Test salinity.
Learn seawater is salty.
A revelation.
SRA
Did not use this one.
It sat, neglected, on bench.
SRA is sad.
Pipettors
The pipettors all
Worked fine, dispensing volumes
With great precision.
Alkalinity
Used the old software.
No issues were reported.
With this instrument.
Chloride
New titrator here.
But new cables are not here.
Cables in Subic?
TOC
TOC broken.
We packed it up in a box.
To visit Texas.
Water system
The water system
Worked fine but will be replaced
When the ship ties up.
Misc
XRF was used.
Mortar and pestle broken.
We need new timers.

Sample Summary

System Status

AmpUlator

The ampoule sealer was not used.

Balances

No issues to report for the balances.

Carver Presses

No issues to report for the presses. Titanium squeezer #3 was leaking during squeezing, probably due to heavy, uneven wear on the inner titanium plate. The squeezer will be sent back to shore for repair.

Cary Spectrophotometer

The Cary was used to analyze ammonium and phosphate concentrations, with no issues to report.

CHNS

Carbon and nitrogen were measured on sediments on the CHNS, and carbon and hydrogen were measured on hard rocks. There were no issues with the unit.
A new standard, CNS Soil Reference Material (3.496% carbon, 0.365% nitrogen, 0.063% sulfur), was received and issued TextID PWDR5968501; however, we had difficulty getting good calibration curves with this standard. A combination of rock standards and sulfanilamide were used to analyze for carbon and hydrogen. Since the scientists performed significant "offline" calibrations and corrections of the data, Spreadsheet Uploader was used to add the final data to LIMS.

Coulometer

The coulometer was used to analyze for calcium carbonate, no issues to report.

Freeze-drier

The freeze-drier was used, no issues to report.

Gas Lines/manifold

No issues to report.

GC3/NGA1

All headspace samples were analyzed on the GC3. The NGA was calibrated, but not used.

Hydrogen generators

No issues to report.

IC

The IC was used for porewater analysis, no issues to report.

ICP

ICP was used heavily to analyze sediment and hard rock samples (no porewaters). A technique proposed by geochemist Jeff Ryan, involving the addition of LiBO¬2 to the final nitric acid dilution solution (7.5 g/L), was used to enhance the ICP analysis.
The geochemists discovered a bug in the ICP Analyzer software. Basically, when you run a standard more than once during a sequence, instead of treating each replicate of a standard separately, for drift calculations the software is averaging all the replicates together. We worked around this by entering duplicates of standards into the database. If you run one standard as JP-1, and then another as JP-1_1, the software will drift correct them separately. These duplicate standards were added to the LIMS database and then the standards tab of ICP Analyzer so that the software would work correctly.
The geochemists also proposed a list of changes and improvements to the ICP Analyzer software. They are mostly concerned with the speed of the software and would prefer it to take less time when performing the displays and calculations. Summed up from Algie, the concerns are:
1) The application should give some feedback when it is performing long-running background progresses; e.g., it should prominently display some kind of progress bar.
2) It will be helpful if the application can cache data it downloads from the database so it can be used in subsequent analyses; downloading the data from the database is fairly time-consuming so caching the data should help speed later analyses considerably.
3) The scientists on Expedition 352 felt that it is not necessary to include all of the graphs in the spreadsheet that is produced. This just bloats the size of the file and makes it difficult to work with. They prefer making the data available so that they can produce their own graphs as they need them.
The scientists did use ICP analyzer to perform their concentration calculations, but we were unable to use ICP Analyzer to upload the data into LIMS. We ended up using Spreadsheet Uploader to upload the data. This is because they decided to average the concentrations for an element over multiple wavelengths that gave a good calibration, instead of picking a single wavelength. Wavelength is a required data component that needs to be present for the data to be parsed out into LIMS Reports, so all data was uploaded with the wavelength component being 0 NANOMETER.
One other issue that came up, that I can foresee being a complaint from the scientists, is that we ran out of the Germanium single element ICP standard solution. Yttrium solution is usually added to the 10% HNO₃ acid dilution solution at a final concentration of 10 ppm, to be used as an internal standard. The scientists decided that they wanted to analyze the rocks for Yttrium concentration, so Germanium was used instead. We stock the Ge solution in smaller quantities, so we ran out of it. It should be discussed at a LWG meeting if we want to include the option of using a different element, such as Germanium, for a potential spiking solution, and up the stock level as needed.

salinity

The optical refractometer was used, no issues to report.

SRA

The SRA was not used.

Pipettors

No issues reported.

titrations

alkalinity

No issues to report. The "old" alkalinity software was used for all analyses.

Chloride

No issues to report. The new (spare) chloride titrator was received but cannot be set up and tested without the proper USB cables. They have been requisitioned and should arrive in Subic.

TOC

Upon the recommendation of the X351 technicians, the TOC will be packed up and sent back to shore for repairs by OI during the tie-up.

Water system

No issues to report. New Barnstead systems will be installed during the tie-up.

Misc

The XRF was initially set up in the MBIO area but eventually was moved upstairs to the paleo prep area, and was operated by the scientists.
We sent in two requisitions for the chemistry lab. One for a new agate mortar and pestle, since a scientist dropped the pestle and it broke in half. We epoxied the pestle back together, and taped the seam with electrical tape, but ordered a replacement anyways. We also req'd 3 new triple display timers, since ours have gone missing and the one from X-ray is also not working all that well.

Scientists:

• Marguerite Godard, Inorganic Geochemist, University Montpelier II
• Maria Kirchenbaur, Inorganic Geochemist, Universität Köln
• Yibing Li, Inorganic Geochemist, Chinese Academy of Geological Science
• Jeffrey Ryan, Inorganic Geochemist, University of South Florida

XRD & ICP SAMPLE PREP LABS

Seth Frank
Diffraction of souls
Renders obsolete the thought
Of X-Ray screenings
-an original haiku by the one and only Seth Frank

Summary

This expedition saw a mix of materials, from sediment to mudstone to volcanic clastics. All equipment functioned well on the expedition
ICP samples: 147 (83 standards) Total: 230
XRD samples: 123

Methods

The Bruker Diffractometer worked well, no issues with the operation of software or subsequent technologies (Haskris).
The ICP Prep/bead making process this expedition went smoothly.

Equipment and Software

The X-Ray Diffractometer operated with no issues, and no QA/QC was run either, yet all analysis produced from the software indicated that the machine was working perfectly. The freeze dryer in the Thin Section lab was used sparingly, after the chem techs offered to use the one in the Chem lab since they weren't using one of their bulbs. Therefore, I do not recommend a change of the oil in the Thin Section freeze dryer.
The ICP process ran smoothly, with no unforeseen problems. Every now and then some of the standards would have small pieces of bead stuck to the bottom of the Pt crucibles, but water and acid bathing always removed the problem. There were 9 new Pt crucibles brought on board for this expedition, and they all worked much better than the older ones, so deference was given to them for bead making.
Personal recommendation: I do recommend switching out the old Pt crucibles for the newer Pt crucibles, as those worked with significantly less issue when consolidating beads just after they come out of the bead maker.
All other facets of ICP worked with no issue.
Problems/Issues
The only issue worth mentioning is the oven in the X-Ray lab. There is a rust problem that sometimes would drop into the crucibles, making the need for re-cleaning essential. There is also a white substance produced that collects on the door, and pools under the door on the outside of the oven. Nobody seems to know what it is, and the oven works fine, but the substance seems to be a byproduct of something unknown, and it is difficult to clean. Recommend having someone more experienced look into whatever is happening with the oven. No other notable issues.

THIN SECTION LAB

EMILY FISHER

Summary

On the ocean blue
Two hundred and thirty two
Samples taken now
Breccia Basalt Rock
Sections thinned 30 microns
Boninite and FAB
Mixed with black glasses
Surfaces impregnated
Made smooth and made flat

Equipment

Equipment all good
Routine maintenance complete
No problems noted

UNDERWAY GEOPHYSICS & FANTAIL REPORT

William Mills

Magnetics

Per the Deputy Director instructions, the towed magnetometer was not deployed on the IBM expeditions.

BathyMetrics

The Bathymetric system ran without incident. Data was collected on the transits to and from our drilling area, and at each site water depth determination.

Fantail Equipment

Deck Crane

Cleaned and greased the crane. Powered up the crane and ran it thru a full functional test. Parts for the electrical connector at the base of the crane where ordered.

Winch

The slide on the level wind had heavy rust. Dri Slide is a good lubricant but not a good protectant. The rust was removed and heavy grease applied to prevent future rusting. To prevent grit from sticking to grease, the slides where wrapped in plastic.
This protection should hold up until we put the winch back into service and then we can go back to using Dri-Slide.

GI-Guns

Not used.

Underway Software

You are probably aware of the Site Fix, JRNavigator and maybe even the HDG program used in the paleomag lab. There is another program called EPC that is used to control and annotate the EPC thermal printers, and another program called BEACON used on Hess Deep to plot the position of the VIT. All of these programs depend on a direct connection with the WinFrog application for their navigation data. WinFrog only supports a one-to-one connection with a single Device (see WinFrog literature). This can be problematic when we switch WinFrog to another computer breaking all of the connections or when there are multiple clients competing for the same port number.
For a while I have been working on a solution to create a single server to connect WinFrog (and other networked data source) that would serve multiple clients without the above issues. I have finally succeeded with an application called JRData Server (currently running on WinFrog 2) that uses the LabView Shared Variable Engine (SVE). SVE has greatly simplified the whole process on both Server and Client side.
Currently JRData Server is running on WinFrog 2 but can operated from anywhere on the network and the client applications will still locate and connect to it. It is now the source of data for the JRNav Google Earth which will eventually replace JRNavigator, in providing the Google Earth display on the Ship's Information Channel and for providing data for the new IODP Web Site.
The JRNav GE is installed on the Ship's Information PC in the LO's Office. Both applications are meant to be started at the beginning of an expedition and left on. Once JRData is pointed at WinFrog it will run indefinitely and even recover from a network outage on its own. JRNav GE requires a bit more attention as it provides a real time feed of the ship's position to the IODP web site. Who will be assigned to do this has not been decided.
User guides for both applications are available on the PC's hosting the software. Also, there is a more information in the Developer's report.h1. ET REPORT
Garrick Van Rensburg & Randy GjesvolD

Operations Office

Installed a small table top between the desks in the aft end of the office. Manufactured 3 sets of mounts and mounted all 3 computers off of the floor.

Co-Chief Scientists Office

Manufactured 1 set of mounts and mounted the computer up off of the floor.

LO's OfficE

Repaired the ceiling after new lights were installed and the new AC was installed.

DHML

Used as a workshop for various projects. APCT-3 electronics assembly 1858022C returned from IODP. We currently have three APCT-3 electronics assemblies. Conducted battery checks with the following results:

• 1858005C-2.967 VDC
• 1858007C-3.043 VDC
• 1858220C-3.066 VDC

Cleaned and prepped shoes for use. Tool 1858022C was used for the following holes:

• U1449A cores 04, 06, 08 and 10.
• U1440A cores 04, 06, 08 and 11.

This tool just returned to the ship from IODP. It seemed a little off after the first couple of runs so we ran an ice bath test with tool 1858007 for comparison. Tool 1858022C comes up with about 2.3 degrees C higher than 1858007C. Conducted a long string of tests with a calibrated thermometer and determined that tool 1858022C is accurate. Calibration files from the shore were sent out and all of the tools have had new calibration files down loaded. Tools 1858005C and Tool 1858007C will be sent back to IODP for a full calibration.

Rig Instrumentation

Rigged up VIT back up communication system. Searched for the pipe counter several times. It appears to have gone missing.

ET Shop

Completed Laser Safety Training and Radiation Safety Training. Smoothed large scratches in mounting plates and polished them.

Paleo Lab

Light Bulb failed on one of the Kaiser System V light sources. This was replaced. Samsung Monitor failed. Picture was upside down and the colors looked like a Kaleidoscope. Replaced the monitor.

Core Lab

Mounted new door locks and rewired the Laser safety circuits. Manufactured a new control board and installed new LED lights inside the cover. Thermcon UPS began alarming. Found the receptacle breaker tripped. This was re set and the UPS recharged. Added Silicone Lubricant to the slide bars on the SHMSL and the SHIL. Vidmar cabinet on the starboard inboard side of the corelab forward had a drawer sticking. It is missing one of the wheels. Manufactured a rough replacement. Drawer is currently working but a new wheel needs to be ordered. Changed out the Bansbach Easylift (P/N H0N0N-42-200-463/25LBS (112N) hydraulic piston on the SHMSL. Manufactured a new table for the core entry area. The old temporary table has gone missing.

Cryomagnetometer

Assisted in the Helium refill. Continue to have issues with the demagnetizer giving errors. We have three separate issues. 01).The computer keeps dropping the run program. As a temporary work around it is being run from a laptop. 02).The Amplifier is not working correctly. Numerous calibrations have been attempted. The Amplifier was re set to just run on the B side and this has eliminated the errors for a while and then they reappeared. A new amplifier has been ordered. 03).The Demag Unit keeps powering itself off. A UPS was jury rigged as a temporary replacement. The JR-6A Spinner Magnetometer (S/N 09090 ) rod stuck. During investigation found that one of the small green wires to the UP DOWN Motor had fatigued and broken. This was repaired. DETEC UPS model APC 1500 with IODP number N1895 has had batteries B1 and B2 replaced.

NGR:

Cleaned the filters to the NGR.

Microscope Lab

Checked the Microscope Light Source on the forward end of the lab for proper power output. It was calibrated to within ¼ of 1 Volt AC. Checked the backup Light Source Power Supply and it was calibrated to within ½ Volt AC.

Core Splitting Room

Found the Parallel Saw to have one blade mounted backwards. This was corrected. These were both replaced about two weeks later because they had dulled. Replaced blade on the super saw Aug 31 2014. Replaced blade on single large saw Sept 14 2014. Power ON/OFF Switch is suspect.

Liquid N₂ Gen:

Ran from July 29-30, Aug 08-09, Aug 17-18, Aug 25-26,

-80Freezer:

Cleaned out the filter and de frosted. Replaced the alarm battery.

Upper Tween Deck

-80 Freezer was found alarming. Silenced the alarm. During investigation it was found that the second stage cooling is no longer working. The Freezer will be shipped back during the Subic Bay standown for repair. Removed shipping material and brought the new -80 freezer on line. It took a day for the battery to charge and quit alarming.

Gym

Added air to the Speed Bag. Replaced fan on top of the Amplifier. The old one has ceased up. The fan in stock was too small. A larger fan was borrowed from the electricians. New fans are on order. The Speed Bag mount broke. A new one was manufactured. The power switch on one of the Air King wall mount fans failed. It was removed because it had become a safety hazard. A new one is on order.

Lounge

The loveseat kept tearing the wires out of the TV Cable connection so it was moved to the ceiling.

Movie Room

Updated the programming on the Popcorn media player and added a few new movies to it. Cleaned the filters out on the projector and changed the bulb.

FaNtail

Cleaned and greased the crane and conducted a function check. Greased the slides. Cleaned, greased and plastic wrapped the slide bars on the port reel wind in preparation for the stand down.

Underway

Manufactured a storage area on top of the forward Vidmars for bulk storage. Put together a book of information for the fantail crane.

CURATORIAL REPORT

Chad Broyle

SUMMARY

Samples

A total of 5,515 samples were taken for Expedition 352. We took 1,736 shipboard samples and 3,779 personal samples. 568 meters of core material was recovered during this expedition.

Shipments

Core- 5 pallets of 100 core boxes will be shipped from Subic Bay, Philippines to the KCC in Kochi, Japan. The core boxes will be divided into Working and Archive pallets. The electronic Core Box Inventory is being sent via email with this report (Exp352CoreBoxInventory.xlsx). The handwritten Core Box Inventory was scanned as a pdf file and is being sent via email with this document for cross referencing (Exp352CoreBoxInventoryHandwritten.pdf). The pallet information is found in the following file: 352PalletInformation.xlsx. A pallet of Leg 60 and 195 borrowed from the KCC is also included in this shipment.

Frozen and Refrigerated Samples

1 refrigerated shipment (JONA) is being sent via World Courier during the port call in Keelung, Taiwan. This shipment includes 1 refrigerated cooler (JONA samples) to:
Ms. Ann-Sophie Jonas
Department of Organic GeochemistryInstitute of GeosciencesChristian-Albrechts-Universität zu Kiel Ludewig-Meyn-Str. 1024118 KielGermany ann-sophie.jonas@web.deTel: (49) 431 880 2874

Residues

1 pallet of residues will be shipped with the Exp. 352 cores from Subic Bay. The residue distribution is as follows:

Thin Sections

A total of 236 thin sections were prepared by Emily Fisher on Expedition 352. The thin section inventory is being sent via email with this report (Exp352ThinSectionInventory.xlsx). This spreadsheet reflects all of the thin sections that were made. The thin sections will be shipped from Subic Bay with the Exp. 352 cores at the beginning of October, 2014.
Action Item: Thin sections will be sent to the KCC after Exp. 352 at the beginning of October, 2014. John Shervais and Scott Whattam have requested to borrow Exp. 352 thin sections from the KCC. In the case of overlaps, please send to Dr. Shervais first. A list of requested thin sections is being sent with this report (Exp352ThinSectionBorrow.xlsx.). A list of scientist addresses is also being sent with this document.

Smear Slides

The core describers prepared and described 336 Smear Slides. A complete list of smear slides is being sent via email with this document to the KCC. (Exp352SmearSlideInventory.xlsx). Smear slides will be shipped from Subic Bay to the KCC with Exp. 352 core at the beginning of October, 2014.

CURATION & SAMPLING

Pre-site to Site Conversion

Catwalk Sampling

Sediment Cores (U1439, U1440, U1441, U1442)

The following is a summary of standard shipboard samples that were taken during Exp. 352.

Geochemistry

• Interstitial Water (IW): Standard IW whole rounds for pore water analysis were taken on these sites for APC and XCB cores.
• Head Space (HS) Gas: Standard head Space Gas samples were taken for every sediment core on these sites.
  • 1 per Core.
  • 1 plug or chip (5cc).

Paleontology (PAL)

The following plan was implemented for sediment catwalk PAL samples:

• 5 cm Whole Round
• Taken from bottom of Core Catcher (CC)

For U1441 and U1442 only the HS and PAL samples were taken since only RCB drilling was implemented.

Section Half Shipboard Sampling (All Sites)

Working Halves

Sampling shifts for scientists were assigned for sediment sampling. Personal samples were taken for Aaron Avery, Steffen Kutterolf, Hong Yan Li, Alastair Robertson, and Kenji Shimizu. Katerina Petronotis requested all shipboard sediment PMAG cubes for her personal research. Katsu Michibayashi requested all shipboard hard rock PMAG cubes for his personal research.

Carbonate Analysis (CARB)

• 1 per section for sediment cores.

Moisture and Density (MAD)

• 1 per section (sediment), as needed (hard rock)
• 10 cc syringe (sediment), 8 cc cube (hard rock)

Paleomagnetism (PMAG)

• 1 per section (sediment), as needed (hard rock)
• Picked by sampling scientist.
• Japanese style 7cc cube (soft sediment), 8cc cube (hard rock)
• 8cc cut cube shared with Moisture and Density (MAD) analysis most of the time.

Nannofossils (NANNO)

• As needed in sediment
• Toothpick sample

PAL (Additional)

• As needed to refine ages.
• Toothpick sample

Thin Section Billets (TSB)

• As requested by science party

Archive Halves

Smear Slides (SS)

Core Describers took toothpick samples as needed from archive halves for core description.

Sample Parties

All hard rock personal samples for the shipboard scientists were taken on board to accommodate their research. There were a total of 6 sample parties during Exp. 352. We attempted to time the sample parties during bit changes and logging.
We first allowed them to place their personal dot sticker labels on the core material. The Sampling Allocation Committee (SAC) then reviewed their choices, and resolved conflicts. The scientists were then allowed to mark their exact samples with a wax pencil. We arranged for a four hour period where they could all mark their samples together. After this, they submitted their exact sample list to me in an Excel spreadsheet. I compiled the spreadsheets, uploaded the data to the LIMS database (via Sample Master), and printed sample labels. I also printed out log sheets for all of the samples sorted by Core, Section, and Top Offset (cm).

Section Half Core Wrapping

Working & Archive Halves

All soft sediment working halves were wrapped in Glad Wrap per standard operating procedure. We used thick shrink film on working halves and archive halves for all hard rock material. These sections are distinguished by blue dots on the end caps of their corresponding d-tubes.

COMPUTER SOFTWARE & HARDWARE

Microsoft Excel Macros

Maggie Hastedt created four Excel macros to ease the frustration experienced when dealing with large sample lists, and subsequent uploads to the LIMS database via Sample Master. The original intent was to prevent Sample Master from throwing up errors or crashing completely when uploading sample data to LIMS. A preformatted spread sheet that upload correctly from Sample Master was given to the scientists with specific instructions. All of the macros are written for this particular format.
The first macro (SamplePartyVetter.bas) does the following:

1. Ensures Expedition numbers are constant and do not increment (a common fill-down issue in Excel)
2. Site numbers start with capital U, have at least 4 digits, and don't increment either (incrementing can be OK but it should be flagged 'just in case' for accidental fill-down mistakes)
3. Holes must all be upper-case letters from A-Z, no numbers
4. Cores have to be numbers and never negative.
5. Core types must be either H, X, R, F or G, nothing else
6. Sections have to be numbers greater than zero, or "CC"
7. Section half is required to be "W" (figure anything else is a mistake or a very special case so flag it)
8. Parent Curated Length column must be blank (This column is a Sample Master requirement) For large shore based sample party, we should ensure that the scientists fill in this information as they often request samples that are longer than the curated length. The macro will need to be adjusted accordingly
9. Sample type must be upper-case member from a list from LIMS supplied to the scientists by the curator.
10. Tool names must be upper-case members of an appropriate list from LIMS/Sample Master
11. Top offset must be a number 0 or greater, no blank cells allowed
12. Top offset is greater than or equal to bottom offset.
13. Bottom offset must be a number > 0, no blank cells are allowed
14. Columns M, N, P and S should be blank (Sample Master pasting requirement)
15. Volume column: This specifically checks given volume of QRND samples based on a formula the curators use.  If given value is less than a calculation based on sample offsets, it is flagged.  My experience is that QRND (for hard rock) is the most commonly underestimated sample volume. Checks that the Comment field is100 characters or less. The macro does not flag blank cells if they are not causing errors.

The second macro (curat_trimconcat.bas) inserts a concatenated column to create Sample Master friendly label IDs from the individual columns. It also copies the whole spreadsheet and pastes the values into a new, separate worksheet tab.  This is the sheet that is actually copied and pasted into Sample Master for upload to the LIMS.
The third macro (SP_printformatter) automatically formats the master sample spreadsheet into a printable form on 11x17 paper. It also places red lines between Cores, and blue lines between Sections.
The fourth macro (combine_spreadsheets.bas) takes a folder of scientist submitted spreadsheets (*.xlsx files) and combines them into a single spreadsheet.

Sample Master v6.0.0.0

The autofill function for Piece orientation was not working. Algie fixed this and deployed the new version. An old bug resurfaced where the catwalk length is not updated in the Core tab after section entry.

LIMS Editor (LIME)

LIME was an essential component towards making this a successful expedition. It was used extensively during and after shipboard sample parties where thousands of samples were taken.

Sample and Data Request (SaDR)

The poor internet connection on Expedition 352 made it difficult to use the SaDR system. Katerina (staff scientist) and I had scientists submit their sample request revisions to us and we stored copies on our local hard drives and the uservol server. I would like to work with the developer team in the future to see if we can simplify and optimize the system for the slow connection on the JR. Another option is to have the system work via the intranet on the ship for subsequent syncing with the shore database.

PUBLICATIONS REPORT

KEITH DUPUIS
This is the Publications Specialist's summary report for Expedition 352. It is broken down into two main sections: Publications summary and YEOP summary.

Publications Summary

Visual core descriptions (VCDs) were created for 4 holes on Expedition 352. A total of 283 VCDs, or individual barrel sheets, were created. Table 1 lists the number of VCD's per hole by type (e.g. Sediment or Hard rock) and the core labels.
Table 1 Number of Sediment and Hard rock VCD's created for each hole. The core labels (the range) are also listed.

The VCD's were created daily, posted to Uservol on the Ship's Server, and printed to paper. A Methods / Legend was created for the VCD patterns and symbols. A Hole Summary/Recovery plot was produced for each hole. The recovery plot was very popular. It appears in every section of each Site Chapter (except the Intro. and Operations) in some modified form.
The Sediment and Hard Rock VCD templates are shown in Figure 1 below. The layout was chosen by the scientists. They used a graphical list of previous Expedition VCDs to communicate their preferences (similar to the ones in Figure 1.) The VCD layout was updated and fine-tuned throughout the Expedition as new data were recorded.
Figure 1 Expedition 352 VCD templates/headers.

The software programs used to create the VCD's were:

• • Lims2Excel version 10
  • DESC Logik version 8.0.0.0
  • Strater 4.1.1156 (64-bit)
  • Microsoft Excel + macros for pre-processing data

Software comments: The core images for the VCD's were downloaded using L2E and an images .xml file. This file was updated (from previous cruise .xml's) to include a "flag" option. This adds a line in the xml: flag = "true". With the "flag = true", only 1 core image, per core, is downloaded (instead of 3-4.) The correct image for display is flagged "true" by the scientists in DESC Logik.

Report Tracking

The Expedition Report has 5 chapters:

1. Methods
2. U1439
3. U1440
4. U1441
5. U1442

Each chapter has eleven sections (listed below), except U1441which has ten (no Downhole logging section.) The sections are:

1. Background and Objectives (Introduction for Methods chapter)
2. Operations
3. Sedimentology
4. Biostratigraphy
5. Fluid geochemistry
6. Petrology
7. Rock geochemistry
8. Structural geology
9. Physical properties
10. Paleomagnetism
11. Downhole logging.

The text, figures and tables were collected and tracked during the cruise. The preliminary number of pages (in Word+Figure/Table captions), figures and tables submitted, as of 25-Sep-2014, are listed in Table 2.
Table 2 Preliminary page, figure and table count for Expedition Report 352 (as of 25-Sep-2014.)

The majority of Site Chapter U1442 has not been submitted at this time. The total number of pages, figures and tables is expected to increase by the end of the Expedition.

YEOP Summary

General duties were performed for 28 scientists on Expedition 352. This included:

• Regular communication with the Radio Operator (e.g. gathering passports, verifying number of science and technical staff onboard, assisting with Customs/Immigration forms and travel visas
• Distribution and collection of expedition paperwork (communications policy, photo releases, copyright forms and lab training forms
• Preparation of Birthday cards and ordering cakes from the Catering Staff;
• Coordination of provisioning proper immersion suit sizes;
• Coordination of cabin room deficiencies/maintenance requests;
• Collection of Scientist address changes/updates for correspondence and shipping;
• Miscellaneous graphics work (modify log sheets, sample stickers, etc
• Coordination of a T-shirt contest;
• Communication with IODP Travel Administrator for hotels in Taiwan.

Suggestions from Scientists:

• Sell postcards with pictures of the JR (e.g. similar to the Birthday card pictures of JR.)
• Post VCD's on the ship's web. Include a large link on the front page.

DEVELOPER'S REPORT

ALGIE MORGAN and WIlliam Mills

Overview

This document highlights changes to the JOIDES Resolution laboratory data management environment during Expedition 352.
Selected issues are highlighted, but not reviewed in exhaustive detail. In general, see the ship activity log and Pending pages of various products on the developer site for additional detail: https://sites.google.com/a/scientific-ocean-drilling.org/developer-page. The title of each product section is a link to the release notes for that product on the development Google Site.
Note that as of this report we no longer include all software packages managed and maintained by IODP application developers; this report only contains information about software packages that were updated or had important issues reported. For a complete list of applications maintained by Applications Developers see the Applications section of the developer site.

WORK IN PROGRESS

During 352 the shipboard developer actively participated in development of a new Correlation development project. The revision in correlation tools permits more efficient correlation by providing a new set of software tools and implements new affine and splice interval tables in the LIMS database that gives correlators greater control and flexibility in creating affines and splices.

Curation and Core Handling

SampleMaster

Changed. Operating at release 6.

• Piece Entry:
  • Prepend "0" to pieces with single digits: e.g., "01", "02", etc.
  • Removed "auto-split" option column; according to Curator pieces should always be split.
  • Make "oriented" column auto-fill; i.e., clicking column header toggles auto-fill / no auto-fill behavior.
• Reinstated calculation of old-depths (recalculate depths logs both "old" and "new" style depths). This was done because DESClogik looks up and displays piece information using old depth model.

Carried forward from version 5; this version was never deployed but all changes carried forward into version 6

• Hierarchy Search lists: revise sorting of pieces so they are ordered by depth. Revise sorting of samples below section half to sort by sample name, then depth.
• Clicking or double-clicking on empty region of some hierarchy search lists crashes SampleMaster. Fixed another case that allowed this to occur.
• Reinstate delete sample function.
• Add "Settings" menu item.
• Add "Notify After Label Print" option to Settings menu.
• Modify label print functions: if "notify after label print" setting is checked display notification after labels are printed, otherwise do not display notification

Outstanding Issues Reported on 352

• Operations Superintendent on 352 reported that while attempting to view information for a previously entered hole then to upload a new hole he inadvertently overwrote information for a previously entered hole. This happened twice during the expedition.

Work was begun to correct this bug but has not been completed. The changes have not been deployed nor committed to subversion library; work is in progress as of this writing.

Geology

Stratigraphic Correlation

Correlator

No change. Not used. Operating with release 1.695 since Exp 344. Release 1.7.0 was evaluated, but not used (native OSX 64-bit operation by switching to newer release of the python interpreter core).
Note: This section remains in the tech report for Expedition 352. Correlation was not performed on this expedition but there was significant work done on the new correlation tools on shore and by shipboard applications developer. As of this time the plan is to have all new correlation software tested and installed for use during Expedition 353 – Indian Monsoon.

[LIMS2Correlator

This effort reduced the frequency of the empty TIFFs but did not eliminate the problem.
Hoping to find something that could explain the problem, I started to look at the low level VIs in the IMAQ library. In the Call Library Function configuration window (for IMAQ Write TIFF File.vi), I noticed that the error message level was set to "Disable". I tried setting the level to "Maximum" but this broke the VI; but, I was able to set the error level "Default".


After making this change, we started to see "Out of Memory" errors after clicking the save button in the CROP window. It's in this section of the code where the application crops the JPEG, extracts RGB and saves the 3 image files. The "Out of Memory" error would occur in various IMAQ VIs (not just the Write TIFF File.vi). This would indicate to me that my action above changed some global setting in the IMAQ library. Regardless of where the error occurred, there was always empty TIFF file produced.
We all suspected that memory resources were involved, but now we had the smoking gun. Finally!
The decision was made to install LV 2013, 64-bit knowing this would open up more memory to the application and avoid any issues running under SysWOW64. Since the upgrade and have not seen a single error or empty TIFF file for the last half of the expedition.
Additional Changes to SHIL 8.3

1. Whole Round Imaging: Completed the following changes requested by the previous expedition:

• Only the TIF and consumer image should be generated. A cropped image is not required. The cropping process should not be required. DONE
• The header in the image should reflect the whole round surface scanning process—not split section processing. DONE
• The whole round surface images should be associated with the parent section (not the section half scanned from the D-tube end-cap. DONE
• RGB appears to NOT be desired for whole round surfaces. If it is, it too should be uploaded against the section rather than the section half. DONE
• VCD description templates should not be generated when whole round surface scanning is in effect. DONE
• Operators would like a stream-lined process where the sample is specified once, then the system pauses to allow setup for each of the four surface scans. DONE

1. VCD-S: With the upgrade to LV 64 we lost the Microsoft Excel reporting libraries which support the VCD-S Templates and printing process. Working with Maggie, we developed a process of using a LV VI's front panel decorations to create a print template. The VI is not part of the IMS code per se and is kept in the IMS Local/Resource folder. This VI is called using the VI server "call and forget" method allowing the SHIL to continue processing the image independent of the VCD-S printing process. This actually is a cleaner and faster method than using Excel dotNet calls. Maggie has written a user guide for the Description techs.

The memory optimization changes mentioned at the beginning of this section where left in place.
All changes have been committed to SVN and copied to the DEPLOY folder.Discrete sample systems

Discrete sample systems

Thermal conductivity (TCON)

Released beta version of utility ThermconFileConverter. This utility is used for post processing to copy the data files produced by ThermconUploader to a set of folders with "human readable" names that include the sample label-id, and to modify the encoding of the files from Unicode to ANSI 8-bit encoding so that TKGraph will read the files. Note that no changes are made in the process of measuring thermal conductivity and uploading the data to the LIMS database; this application only copies data to a separate set of folders so that it is easily identified by users and can be used in post-processing analysis. This application remains in beta phase pending final acceptance by the physical properties technicians and approval by the Geophysics Lab Working Group.

Underway GeophyICS

JRNav-Google Earth and JRData SERVER

Changed. Initial release 352 for both applications.
JRNav Google Earth (JRNav GE) is a LabView application that takes real time navigational information from the JRData Server and creates a KML file (Keyhole Markup Language) that provides instructions to Google Earth to display the JR's navigational track and position. This data is used Google Earth running on the Ship' Information PC and transferred to shore for presentation in the IODP web site.
JRData Server is a LabView application that collects information from various sources and makes that data available to multiple client applications in real-time. In its initial deployment, only navigational data from WinFrog and waypoint data is currently available.
To provide data across the shipboard network, this application uses the LabView's Shared Variable Engine (SVE). SVE is based on National Instrument's Publish-Subscribe-Protocol, which is a form of the User Datagram Protocol (UDP) communication. Basically, the JRData sever publishes a list of variables (data) and the client application selectively subscribes to one or more of those variables. For further information see the following link: http://zone.ni.com/reference/en-XX/help/371361K-01/lvconcepts/ni_psp/
SVN: Both Applications have been committed to SVN. A copy of the development projects is in the DML folder and the installers in DEPLOY. Note: Both applications must use the installer to register external resources with the Window's Operating System. More details are in the User' Guide which can be found in the project resources in DML.
Future changes: JRData Server replaces direct TCP/IP calls to WinFrog which often fail when WinFrog is moved to the backup PC or when client applications compete for the same port number. JRData Server supports many clients on the same data stream and takes the responsibility of maintaining the connection to WinFrog. This greatly reduces the complexity of the client coding. As time allows the following JRNav applications will be updated to use the JRData Server:

• JRNav HDG: Supplies heading information to the Pmag lab
• JRNav EPC: Controls the EPC thermal Printers
• JRNav Site Fix: Determines final hole positions
• JRNav Navigator: Ship' Information display

Bonus: Scalar data (text, numbers) provided by JRData Server can be viewed using NI Dashboard app on both iOS and Android devices. The app is free.

Geochemistry

Alkalinity

Waiting on input from the Chemistry LWG regarding ALK 3.0. Still operating on 2.0

dATA uPLOADERS

SpreadSheet Uploader

Changed. Upgraded to version 4.

• Added "Display Flag" column so that uploaded tests can be uploaded with flag explicitly set "T" (TRUE) or "F" (FALSE).
• Corrects bug that caused it to display an error to the user when file was uploaded without any additional components, even though file uploaded normally.

Development Tools and Frameworks

LabVIEW

Changed. SHIl / IMS8.3 upgraded to LabVIEW 2013 64-bit. Currently all remaining production LabVIEW applications are built with LabView 2011. Exceptions: Laser Engraver and Alkalinity 4.0 are using LabView 2013.

IMS Common tool box

Carried forward. No change.
The IMS Common Tool box is currently in the middle of an important update. Full reconciliation with all IMS applications planned for X354. If you need to work on the code during X353, you'll need to work on the local host or make sure you have done the following before working in your development environment:

• Delete any copies of IMS Common Toolbox from the LabView User's library folder.
• Copy from the host (or the particular deployment snapshot), the IMS Common Toolbox to your local LabView User's library folder. Don't forget you'll need the Open-G and the i3 JASON libraries, as well
• When done, copy the changes to the track code and the IMS Common Toolbox back to the instrument host. Don't forget to back-up the host …just in case.

IMS 8 Upgrade deployment plan:

• The IMS 7 and the Common Tool Box will not be moved with the LV upgrade but stay behind with LV2011 making a clean break. That means LaserKatjie 3.0 and Alkalinity 3.0 which are using the final version of IMS 8 Common Tool Box, are developed in LV 2013. Copies of LV13 are these hosts.
• SHIL has been moved to a preliminary version IMS 8 to support the Image Length project (JASON Libraries were needed), but the SHIL code is not running on the final version of the IMS 8 and therefore, still running under LV2011.
• On X352 all IMS based applications (especially the SHIL and SHMSL) will move to the final version IMS 8. Also, at that time we'll attempt to integrate the code into SVN using the new tools available.

Current Status of IMS based applications for X351:

• Gantry-IMS7: SVN
• SHMSL-IMS7 > R:\AD\DEPLOY\JR\LabVIEW\IMS 7\SHMSL use me JAN 23
• SHIL-IMS8 > R:\AD\DEPLOY\JR\LabVIEW\IMS 8 -SHIL ONLY
• LazerKatjie 3.0-IMS8 > R:\AD\DEPLOY\JR\LabVIEW\lazerkatjie\3.0
• Alkalinity 4.0-IMS8 >R:\AD\DEPLOY\JR\LabVIEW\alkalinity\ALKALINITY 4.0

Subversion Repositoryhttps://sites.google.com/a/scientific-ocean-drilling.org/developer-page/applications/-net-c/data-loaders/spreadsheet-loader/spreadsheet-uploader-release-notes

A new subversion repository was created at URL https://build.ship.iodp.tamu.edu/svn/jrlv. This will become the primary repository for storing and versioning all LabVIEW projects. As of this writing the repository contains the latest versions of:

• IMS 8. Common library
• SHIL (version that has been running circa 20 August 2014)
• SHMSL
• Alkalinity

We will store other LabVIEW applications and libraries as development work progresses on those tools.

Other

Drill Report

CHANGED. Operating with release 3.

• Fixed bug that caused night shift operator to be shifted to day shift. Modified so that we deploy using Tomcat WAR file instead of manually copying html / js / css files to web folder.

SYSTEM MANAGER'S REPORT

Mike Hodge and Thomas Wick

Summary:

• Departed Yokohama Japan on August 3, 2014 with all IT systems up and running including all scientific instrument PCs and servers in working order.
• We encountered issues with the VSAT system with 2 blown fuses and 2 outages on RigNet side, one voice outage and other a data outage. Other than those issues, all of our below and above deck VSAT equipment worked properly with internet and phones services normal.
• Still having ongoing issue with data center MGE UPS located in Koomey room and is scheduled to be resolved during Subic Bay tie up period X353P.
• Minimal problems with VIT black and white camera work around using DSL modems with cooper wiring after final fiber cable broke prior to our last drill site. The work around using the copper for the DSL modems was very slow to normalize when powering system up cold.
• Shil_B was rebuilt with new version of Labview 2013 X64 installed. Captured image of Shil_B from prior expedition for the developers as a failsafe but, Shil_b has performed as intended this expedition after Labview memory issues were resolved.
• Discovered new BBWC (Battery Backup Write Cache) memory cache and battery bad out of the box from HP. Will replace with new one during Subic Bay tie-up.
• Sharp copier is on its last cycles of 60,000 rotations on color print drum and developer and is to be serviced in Subic Bay. iPrint was reconfigured to support the degraded state of the printer/copier so that scientists and staff could continue to use it.
• We uninstalled Skype from the Userroom and Conference Room workstations. Official video conferencing software is Zoom. The fuser unit was replaced on the HP printers for Science Office and Tool Pusher shop.
• Bill Mills created Labview software for transferring JR_NAV Google Earth KML files to shore so that shore users can get updated JR location positions.
• Driver updates were applied to our 3-node VMware cluster to resolve various server crashes.

Servers (Microsoft):

• Cumulus shore import to ship successfully. Encountered 3 Offline Asset (FOA) files. Contacted Karen Graber on shore who opened a ticket with Moksa. Support technician identified improper filenames and Karen resolved. Next import from shore should correct these files.
• Shore personnel upgraded their SQL Server for AMS to Service Pack 2 (SP2) and requested ship to do same. Shore management decided this would be a project for Subic Bay tie-up period.
• During portcall replaced DIMM 4 module in St. Helens. Failed on last expedition.
• During portcall replaced RAID controller battery pack in Krakatoa. Failed on last expedition.
• During portcall replaced RAID controller battery pack in Erebus. Failed on last expedition.

Servers (OES):

• OES server Ararat hung on Aug 8^th. Power cycled server restore server operational. Attempted to investigate log files but they had either rotated before, during or after hang and had a gap in entries during time of the hang.
• Noticed backups failing on Ararat on Aug 10^th. Contacted Novell and opened support ticket concerning Storage Management Services (SMS) not running on Ararat. SMS is what services our backup software CommVault uses on the server to backup local files and directories. Worked with several Novell support technicians but, was unsuccessful at restoring backup services. On August 23^rd while responding to more action items from Novell discovered not able to login into the root account on server. Initiated a reboot of the server and discovered after reboot SMS services restored. Backup services started working again.

Servers (Solaris):

• During portcall swapped out failed fiber HBA (host bus adapter) on server Etna successfully. HBA failed during Expedition 351.

SERVERS (VMware esxi):

• Early in this expedition 2 of our 3 node VMWare cluster had PSOD (Purple Screen of Death - crashed), Vesuvius and Kilauea. All services were running on 3^rd node Tambora. Initiated call to VMWare support for analysis of the crashes. Vesuvius required driver and firmware updates for FCoE (Fiber Channel over Ethernet) adapter and Kilauea required HPSA (HP Smart Array controller) firmware. Installed updates on all three nodes remedied problem. No further incidents for the expedition.
• BBWC (Battery Backup Write Cache) memory cache and battery was ordered on Expedition 351 for installation in vCenter server Fuji's raid controller on Expedition 352. Upon installation server would not boot to OS. POST showed addition of memory cache but, no drive indicators from OS boot. Pulled cache and battery and server booted up. Initiated service call to HP and they confirmed bad parts. They are to send replacement parts for installation during tie-up at Subic Bay.

EVA4000 Storage:

• No issues to report.

NETWork:

• Configured D2 switch for DP named D2-DP. This was in preparation for installation of new Subsea DVR in DP.
• Implement fiber/copper run from Bridge Planning Area (lan port B49-014) to F-18 VSAT cabinet for Subictel DSL land-line circuit during tie-up period in Subic Bay.

PC Workstations:

• Encountered serial communication issues on Dtech PC52700. Replaced serial interface card which resolved the immediate issue. However, discovered when running Dtech and D2000 instruments at same time, encountered serial communication issues again. Loaned a Dell D630 laptop with serial interface for Dtech instrument and segregate instruments. It is our understanding that Dtech instrument to be replaced during Subic Bay tie-up period.
• SHIL PCs Corelab:
  • At the beginning of this expedition SHIL_a (PC52591) was missing its data disk RAID pair due to failure of one of the drives from last expedition. The remaining disk was made the boot disk. Found and restored factory 256GB drives as RAID 1 boot disks and installed two new 2TB data drives. As a test for this expedition installed a Samsung 840EVO 500GB SSD for data disk. Performance outstanding. What took ~50 seconds before to write ~150MB image files to data disks now takes about 5 seconds.
  • SHIL_b PC52515 was use for LabView 64-bit upgrade and testing to resolve a memory issue with LabView 32-bit version. After remediation of memory issue the SSD drive installed in SHIL_a (PC52591) was extracted and installed in SHIL_b. All of Expedition 352 ran on SHIL_b reliably and successfully.
• Discovered XRF PC51559 disk space minimal, 2GB free disk space and performance poor. Investigated and found 25GB of XRF how-to videos on root drive. Installed two additional spare 80GB drives in raid 1 setup and moved videos to this additional disk space. PC working normal.

MAC Workstations:

• Uninstalled Adobe CS5 from all Mac VDU systems during last portcall. This was per management's request because of licensing issues. Adobe is changing their licensing method which will entail more expenses to license this product for systems that do not use it.

Printers:

• During expedition the Sharp copier announced error message stating "Maintenance required. Codes: CA DC DM DY VC VM VY". After researching these error codes by MCS and shore personnel it was determined that copier could not be serviced by ship personnel. A vendor in Philippines has been contacted and scheduled for servicing the copier at Subic Bay during tie-up period.
• Workstations around the ship and especially on Fos'cle deck that use iPrint services stopped printing to copier after it latched error codes. Researched iPrint server configuration and was able to allow printing to copier regardless of copier status.
• Output smudging on StafSci HP5550 printer in Staff Scientist's office. Replaced fuser assembly remedied problem.
• Core Tech Shop HP5200 printer smudging print output, light print. Replaced fuser assembly remedied problem.

SATELLite/internet/phones:

• VSAT outage for 30 minutes on Sept.14^th due to heavy rains.
• VSAT Bow dome dropped offline during heavy rains on Sept.13^th. After weather cleared discovered blown fuse in Bow dome's Codan Converter. Replaced fuse brought dome back online.
• Incurred a VSAT outage for 2 hours on Sept. 11^th due to Aft dome derrick obstructed and Bow dome not passing traffic. Power cycled Bow circuit from dome to BDE (Below Deck Equipment) cleared Bow circuitry and started passing traffic.
• Encountered VSAT outage on Aug. 27^th for 20 minutes until Aft dome was not derrick obstructed. Bow dome would not track satellite. Investigated Bow dome and discovered blown fuse in Bow dome's Codan Converter. Replaced fuse brought dome back online.
• Incurred a VSAT outage on Siem's circuit on Aug. 23^rd, IODP circuit not affected. Outage duration ~1hour and 13 minutes.
• Incurred phone outage on Aug. 16^th at ~9PM. Outage lasted 16h30m. Rignet reset a voice gateway device in Houston restored phone services.
• TAMU had a campus wide internet outage on Aug. 8^th that affects the ship, duration ~15 minutes.
• Discovered during portcall extensive damage to Bow dome dish and pedestal from prior expedition. Adjusted elevation stops on Bow dish to prevent contact with pedestal.

other equipment/projects:

• Replaced failed flat panel RF52304 in CoreTech Shop.
• Replaced failed Samsung VDU flat panel RF52304 in Microscopy Lab.
• Aux AC unit for LTDAT broke a belt on Aug. 18^th. Contacted ECR who promptly replaced belt, downtime about 15 minutes. LTDAT temperatures reached 104F before stabilizing back to 72F after belt replacement.
• Aux AC system electrical tripped off on Aug. 11^th. Problem identified to red fire box door in Upper Tween slightly ajar. Re-closed door cleared alarm condition and allowed electrical power to resume for AC.
• Mark Reagan (Expedition 352 Co-Chief) came down and thanked both MCSs for his 2 hour zoom session on Aug 8^th as part of a thesis defense panel he was on. He stated that he was surprised and amazed that he was able to stay connected for 2 hours without issues and thanked us.
• Per instructions from Jim Rosser, uninstall Skype software from Userroom and Conference Room PCs. Zoom is considered official shipboard video conferencing software.
• Encountered one incident of Tape Library LCD display none responsive, no display. Power cycled tape library returned LCD function.