TECHNICAL REPORTS
















Contents

LO – ALO Handover notes

William Mills, Lisa Crowder & Tim Bronk

Expedition 346- Asian Moonsoon:

Objective:
Onset and evolution of millennial-scale variability of Asian monsoon and its relation with Himalaya and Tibetan Plateau uplift.
Leaving from Valdez, Alaska, we completed a two-week transit to the seas west of Japan (Japan Sea, East Sea, East China Sea – take your pick). We recovered 6135 meters of core (IODP record) over the remaining 6 weeks (9 Sites and 30 Holes).

Operational Dates:

START

• Port: Valdez, Alaska (USA); Alaska Container Terminal
• Arrived: 29 July 2013 @ 1120
• Departed: 2 August 2013 @ 0718

END

• Port: Busan, South Korea
• Estimated Arrived: 27 September 2013 @ 0730

General Port CALL information

• 29^th: IODP-USIO staff and the expedition chief scientists arrived by chartered bus from Anchorage at 1530 hours and moved onto the ship on the 29th. Port call activities started with the IODP-USIO crew changes and cross-over.
• 30^TH: Completed the off-loading of the Expedition 341 cores and freight and began loading expedition supplies.
• 31^st: Completed logistic activities. Science Party arrived in the afternoon and completed a brief introduction to the ship.
• 32^nd: Welcomed science party onboard with staff introductions, and completed the SEIM Offshore and IODP safety presentations and tours. Staff and science party were given the afternoon to enjoy outdoor activities in one of Alaska's scenic ports.
• Administration staff completed an inventory of IODP equipment.

Transit activities

Expedition 346 started with a 2 week transit across the North Pacific into the Sea of Japan. With the exception of one strong gale, weather conditions were good. Routine bathymetric and magnetometer data were collected on the transit. Towards the end of the transit the magnetometer failed due to a compromised tow cable that allowed for sea water to infiltrate the tow head. The issue wasn't identified until our two board transceivers were damaged. The cable has been repaired and the damaged receivers returned for repair.
In the laboratory, technical staff prepared for the expected high core recovery. Tracks and lab instruments were calibrated and brought into working order and issues encountered during the previous expedition repaired. New software for the Image logger (SHIL) was tested and deployed. At the request of the science party we developed the capability to extract RGB data from the images. The RGB data was used for high resolution correlation between sites.
Completed Expedition safety inspections.

OFF-GOING ShipmentS

• All air shipments will be sent from Busan, Korea after 346. Core shipment will be sent to the KCC from Busan. No surface shipment to IODP.
• Routine Frozen Shipments utilizing World Courier
• Excepted Quantity Dangerous Goods shipment utilizing World Courier. The presence of Mercuric Chloride in water samples means they could be hazardous. HgCl2 is a 6.1 poison and while the amount of it is very small, we cannot exactly determine its toxicity. We determined it should fall under a PGIII and could send Excepted Quantity.
• A few items for the next surface shipment from Subic Bay have been placed in AMS pending.

AMS/Inventory

• Spot physical counts were performed on high-usage items
• Unable to upload address Excel file into AMS. Apparently it is a problem with the ship version and Saravanan is aware of it. Addresses were uploaded on shore

Miscellaneous

• Three temporary technicians sailed, Sebastian Cantarera (core lab), Justin Skootsky (core lab) and Darcy Lichlietner (chem lab).
• Materials for the Great Wall of Roy: Plywood covered and secured on roof top. Doors and 2x4s stored in the Science Pallet Area
• See Curation report for ALO's documentation of OSL special core handling.

AREA-BY-AREA SUMMARY

Core Deck

Core Entry:

• Operated Whole round tracks in parallel mode to double through but time. Technical staff rigged shielding around the MS loop to prevent significant cross talk.
• Re-cabled the WRMSL to relieve stress on communication and data cables. Installed a new shielded BNC cable between the pulsar and DAQ card producing a very clean signal.
• Installed new "thru beam" top-of-core sensors. New holders are being designed to replace the temporary setup.

Splitting Room:

• We were surprised to hear that we wrapping the cores as an expedition priority. This information did not find its way to the technical staff. Fortunately, we were able to scrounge enough miscellaneous materials left over from previous expedition to complete the tasks.

Core Description Lab:

• The new IMS version of the SHIL operating software was deployed.

Downhole Lab:

• Installed Core Rack from Hell to handle the 400+ meters of core backlog.

CryoMag:

• Cryo compressor recharged
• Replaced faulty Galil control board
• Replaced the drive coupling on the sample handler
• A faulty JR-6A Spinner is being returned for repairs

Fo'c'sle Deck

Chemistry Lab:

• Although we were able to complete all mission critical analysis, a number of instruments proved to be uncooperative with numerous minor issues to overcome. Because of the high volume of samples, there was little time to investigate. The SRA was sent home for repair along with the old coulometers.

LOWER TWEEN DECK

Lounge and Movie Room:
Gym:

• New exercise bikes installed.

Poop Deck

Underway Geophysics:

• A split in the magnetometer tow cable's outer jacket a meter above the connector, allowed water into the connector resulting in the loss of both transceivers before the problem was identified. The connector was opened and dried and then reassembled with Dow Corning 114 to act as a water block. The split in the jacket was packed with Dow Corning 114, laced closed, and sealed with multiple coats of ScotchCoat.

CORE LAB

Sebastian Cantarera
In general, core lab activities are running normally. This report presents minor changes and suggestions for common problems:

Core lab/Core entry:

The label printer often jams but is easily avoided by hitting "feed" after ripping off labels to allow for enough extra length to prevent paper getting stuck.
The laser engraver must be armed before beginning the labeling sequence. If it is not armed the sequence will continue to run however without actually engraving. The best way to deal with this is to finish the sequence with the laser disarmed and then start the sequence over.

Core Splitting/Boxing

We are no longer writing expedition and core information on the D-tubes. Printed labels on the D-tubes and the caps have been deemed sufficient.
Any sizable gaps in the curated cores after splitting can be filled with Styrofoam spacers labeled "Void" to prevent sediment from sliding.

Catwalk:

It is helpful to switch off core-catcher responsibilities to prevent injury from excessive hammering. The technician who doesn't prepare the core catcher can also set aside core cutters and spatulas in need of cleaning in between cores.
Added covers and shields to the drills used to release gas from the core liners to limit mud splatter into the drills.

CORE Description

Margaret Hastedt

Summary

Expedition 346 started out very slowly with a long transit (2 weeks) to the first site. The scientists stayed on days until just a few days before coring started. DESClogik was introduced early in the transit and template tweaking commenced almost immediately. As expected, most of the modifications had to do with adding species to the paleontological templates. Aside from these early efforts, pretty much everything afterwards revolved around core receiving and processing to the exclusion of just about everything else.

Issues

VCD log sheet templates (printed 11 x 17" sheets with images and columns for core descriptions) were edited per requests from the sedimentologists. Caution: there are differences between Excel and NI Report Generator coordinate systems - see the document at the end of this report. The sedimentologist quit printing and using the scratch sheets after the first site.
Old slide stock in the Upper Tween Stores from years ago (c. 304) although never opened, was obviously filmy and unsuitable for use unless washed. After review by a paleontologist we settled on using the new stock received at portcall for most paleontological slides, and reserved the old stock for foram smear slides or generic section scraping.
Bill Mills arranged for making hand-scrapers out of large spatulas (as opposed to using glass slides as in years past). These were popular, effective and heavily used by the sedimentologists on this cruise. Stainless steel versions have already been fabricated for use in future expeditions to forestall complaints from any paleomagnetists.
GoogleDocs site for DESC value lists and definitions is problematic over slow Internet connectivity. We had real problems with the DESC Googledocs datum_names list.  In fact, it became hopelessly tangled due to what we think was the very slow Internet out here (scientists were all on days at this point and were hammering the VSAT).  It's a huge (3300+ entry) list.  Refreshing is a real and time-consuming issue when you are trying to sort or add more entries.  We noticed at one point that a number of datum names were not matching the other information in the very same row in Google.  We were having terrible problems refreshing sub-lists with the Value List Manager because of the scrambling and the slow VSAT.  We believe that it may have scrambled due to repeated sorts and/or copy/pastes of new entries w/o it completing one task before another started due to the slow connection.  Possibly we shot ourselves in the foot in the course of our work, but it doesn't feel that way.
Using Undo in Googledocs didn't seem like an option since we would have a hard time telling how far back to go.  Fortunately, we had a nice clean backup from August 8th as we had downloaded the entire datums list to Excel to make it easier for the paleontologists to 'shop' their desired datums w/o having to go to a (slow) Internet host to do it.  So we took that backup, did a bit of cleanup (about a dozen duplicated entries overall), re-entered our own new datum additions from the scientists again, and then copied the whole thing back up to Google. Time-consuming, but worth the peace of mind. 
Bottom line:  it would behoove us to have periodically-refreshed static backups available out here.  A) for peace of mind, and B) for disaster recovery. We realize that we could have downloaded a copy of datum_names from Asman per the DESC Help pages... but the problem with that is that those downloads are only as good as the last VLM refresh.  If you've already refreshed on a hosed Googledocs list, then your Asman download is equally useless the way the VLM is structured now. 
Minor: remind scientists not to alter the default zero top/bottom offsets when selecting a smear slide in the DESC sample selector. It may look odd at first blush but the actual section interval is in the smear slide's name. If you change the top/bottom offsets then you're attempting to describe a sub-interval of the smear slide.
Check the following items if the SHIL VCD scratch pages fail to print, or print incorrectly

1. Make sure that the Excel template defaults to 11 x 17" paper and 0.5" margins on all sides in Print>Page Setup (Fig. 1). Check the margins setting on the VCD Scratch Setup page and ensure that they are also 0.5" on all sides (Fig. 2).

Fig. 1: Page Setup in Excel
Step 3Step 2Step 1
Figure 2: Configurable settings for VCD scratch pages in SHIL software, Utilities menu

1. Title and Label ID cell coordinates: There is a disconnect between how Excel denotes cell coordinates vs. what the VCD Scratch Setup uses. The yellow boxes in Fig. 3 below is where we want to put the Title (typically the expedition name) and the section's Label ID as read from the barcode. In Excel R1C1 (Row1Column1) notation the Title cell would have position R2C2 and the Label ID cell would be position R2C17. But the VCD Scratch Setup uses different coordinates. Its rows and columns start at zero, not one. Therefore, the same two cells mentioned above now will have coordinates of R1C1 and R1C16. Be sure these are correct in VCD Scratch Setup (Fig. 2). You may also want to double-check that the Title and Label ID cells in the Excel template are left-justified and Bolded.

Fig. 3: Title and Label ID cells in the Excel template, highlighted for clarity (normally empty).

1. Image cell coordinates and scaling: Similar to the Title and Label ID cells, images are placed in row 9 column 1 (Fig. 4). Scaling factor of 0.1151 was determined through trial and error.

Fig. 4: Cell location for cropped image from SHIL is highlighted in yellow.

1. Editing template headers: You can edit/add/delete any of the header cells you wish, as long as you avoid encroaching on the edges marked by the red No Change bars. Also, avoid changing the width of the image column to retain the scaling.

MAGNETICS LAB

Gabe Matson

Summary

The cruise consisted mostly of using the SRM for section half measurement and demagnetization up to 20 mT. All section halves from the primary hole (either A or B) at each site had the NRM measured followed by a demagnetization of 20mT and then another measurement. Section halves from the subsequent holes for each site were only demagnetized at 20mT and then measured. Discrete samples were processed as well, however these were demagnetized in fields up to 60 mT on three axes in the D-2000 Demagnetizer or the SRM, and then measured in SRM or JR-6A Spinner Magnetometer. We also used a routine aimed at preventing the acquisition of an ARM for some of the samples (see U1424 Site Report). Japanese style plastic cubes were used for discrete samples in sediments. A total of around 350 discrete samples were taken and about 200 of them were processed.
Margaret Hastedt and Emily Fisher also assisted in measuring archive section halves due to the fact that one of the paleomagnetists did not make it to the expedition. Their help was immensely appreciated.
The KappaBridge was used briefly to measure the AMS of about 30 cubes.
The FlexIT tools 36 and 38 were used on one hole at all nine sites. They performed well and had low standard deviations. I did notice several lines of zeros created by tool 36, yet this did not significantly affect the data.

Notes

Discrete Boat for the D-2000 Demagnetizer

A discrete holder was created so that Japanese cubes could easily be put into the D-2000 Demagnetizer and be put in three positions consistently. The boat created on X345 is still intact and remains available for discrete hard rock cubes.

Galil Motor Torque Issue

The Galil motor for the SRM was reported to be torqueing out during X341, though the issue was never fully resolved. After some analysis by Margaret Hastedt and myself, the issue was decidedly narrowed down to the motor running at a high voltage (~6V) even when it had just been initialized by the Galil Tools program but was not yet turning. After switching out the motors and changing axis on the amplifier – neither of which solved the problem, it appeared that the board in the computer was the issue. We first tried to return the board to factory settings in hopes this would solve the issue, but when it did not it seemed the board needed to be removed. ET Garrick Van Rensburg replaced this board with a new one sent from shore, after which the voltages started behaving properly. The original motor is still in use and the motor is still run through the x-axis. The old board will be sent back to College Station at the end of the expedition to the attention of Margaret Hastedt.

Changed Coupling on SRM Galil Motor

The rod that goes through the chain ring and the coupling that attaches this rod to the gear box were replaced. The original rod/coupling system had the tendency to loosen over time. After installation, the new system seems to work well. It was also discovered that there is a slight misalignment in the two bearings that hold the rod. This may have been the reason that the motor shows and eccentric motion while running loose from the bracket. Extra coupling parts, more of the new rod material, and the old rod are kept in the "Cryo Spares" drawer to the right of the Dtech monitor (middle monitor in the Pmag lab).

SRM Positioning Tests

Several tests were run to test the positioning of the SRM. A discrete sample was place on a known spot on the section half tray and run at a small interval in the section half program 10 times. The spike in intensity was measured consistently 0.5 cm off from where it was place on the boat. The motor was also tested to see if number of counts per millimeter has changed at all over time. Results show that the motor runs at 125.39 counts per mm of travel – which is very close to what the previously measured ratio was (125.74 counts per mm).

JR-6A Spinner Magnetometer Exchange

The old spinner magnetometer was put away and the new spinner was brought out into use due to a report of an overflow error during the holder correction routine. This issue has been ongoing, and happened frequently on X345. The issue brought to Agico's attention during X341P/S and they suggested cleaning and optical sensor. After performing this, the overflow error ceased, but has now returned. The old spinner will be sent back to College Station to the Attention of David Houpt following this expedition.

Charged Compressor

The compressor was still running at a low pressure ever since the cold head exchange in May 2013. Margaret Hastedt gave instruction and assistance in charging the compressor from a ~255psi to ~280psi.

SRM Time Out Error

An error occurred 4 times in a 24 hour period and twice afterwards. The errors appeared during the beginning of the 20mT degmagnetizing sequence. Screen shots of the errors can be seen below. This error has been seen in the past, but the high frequency was concerning. After monitoring by the developers and analysis of the limit switches by the ET's, nothing definitive could be pointed to as the issue for this alert. It did not disrupt the measurement enough to warrant more investigation on such a busy expedition.Second Error Message First Error Message !worddav6efc47fc8205cff5bd001b70018be912.png|height=128,width=175!h1. Paleo Prep LAB
EMILY FISHER

Summary

Scientist looked at some bugs.

Special projects

Repaired the heat sealer by replacing the non-stick film.

Problems encountered

(Old) Microscope slides (precleaned) used for smear slides catalog no. 12-550A are too dirty for use. (New) Microscope slides catalog no. 12-550A3 are good to go and nice and clean.

Miscellaneous

Super nice scientist.
Used Rose Bengal and Methanol disposed of in the Chem lab.

PHYSICAL PROPERTY LAB

Thomas Gorgas

Summary

EXP346 was probably one of the most successful expeditions in the history of IODP. The recovery was high (around 6km) and the workflow through our core laboratory nothing but excellent. We worked 24/7 collectively as a team, including both IODP staff (and our valid Temp-Tech's!) and scientists.
In this environment of harmony and diligence a few important "Firsts" were accomplished:

• For the first time RGB (Red-Green-Blue) data were recorded and extracted from the line scan imagery produced by the Section Half Image Logger in its latest version (SHIL – IMS 7.0 aka SHIL 3.0).
• We ran both Whole-Round-Multi-Sensory Loggers (WRMSL & STMSL), commonly called "MST", in a novel parallel-running mode. It required several modifications and upgrades to accomplish this task.
• NGR data were acquired only at POSITION-II for a maximum allowable counting time (300-420 seconds of LIVE TIME); this running mode produced very smooth data without the typical "notches" from edge effects.
• A NGR calibration was performed almost in between every new site to maintain a maximum proximity of our energy channels, being tied to the expected energy bins of Cs/Co standards.
• For the first time we also recorded data on our new "U-238" (IODP-produced) standards, supplemented by data acquired on (IPL-produced) "Th-232" and "K-40" standard cores.
• Whenever there was enough time in between sites (or even holes), we cleaned the floors of the core lab and rid it off the excessive dust accumulation that comes along with the core processing. This might sound a bit like "cleaning over-kill", but it minimizes the risk of cross-contamination for our specimen. It also reduces the negative impact on people's health, which an over-abundance of dust accumulation can cause (allergies; respiratory systems, etc.). Normally we clean underneath the blue mats half way through an expedition; during EXP346 our team got so fast that we accomplished this task within 45 minutes.

In sum, we achieved to collect an enormous amount of high quality data. One important cross-check for our data quality was the logging data, which, for example, showcased a strong correspondence between GRAPE and NGR data sets, also for Thermal Heat profiles (in conjunction with our Therm-Con data). Magnetic Susceptibility laboratory and logging data were sometimes divergent, which might have been related to the fact that our material was often exhibiting very low values. It might be worthwhile to look more into the details of that difference in the future.
Below follows a summary for the individual instruments that we used during EXP346 to collect high-quality physical property data.

WRMSL-STMSL:

The WRMSL/STSML systems worked overall very well without causing too much grief. For example, the PWL sensors did work well on the mostly soft and well-saturated sediments. In some cases, PWL was measured even below 300 mbsf!
It was one several "Firsts" in IODP's expedition history to run both STMSL and WRMSL in parallel and thus generating a "real-time" record of the stratigraphic correlation using GRAPE and/or MagSus data.
For this purpose, the step of temperature equilibration was skipped after it was demonstrated - with obtaining and analyzing data at the first site (via Dr.S.Clemens) - that it indeed does not make much difference whether the cores have been equilibrated for several hours or not. This "parallel" operation mode allowed our scientists to produce stratigraphic correlation profiles alongside with the coring, and thus to identify the sub-seabed layers and horizons, which define stratigraphic units and also drill depth.
However, some hardware modifications were necessary due to the unusual and unprecedented simultaneous "Parallel Mode" operation of both WRMSL/STMSL. When exchanging the 70-mm MagSus-Bartington loop on the WRMSL with the 90-mm MagSus sensor loop – and now operating two 90-mm loops at the same time – we noticed "offset" jumps in the downhole MagSus profiles. This phenomenon was caused by an unwarranted "Cross-Talk" between the two 90-mm loops (see: more details below).

General changes and modifications:

• Time/Distance-Sensors: The mechanical trigger, which replaced the former laser trigger, has been now replaced by a fiber-optic cable-fed light-source trigger. The sensors worked well, without causing any significant "downhole advancement" issues - i.e., the downhole depth accuracy and precision of the core section advancement was high.

A typical "overshoot" error occurred during the high-speed, low-res runs (10-cm advancement):










This was a typical and frequent occurrence, and so we eventually decided to remove the limit-switch (via developer D.Fackler). In most cases we ran both tracks in a "parallel mode" at 5 cm-resolution where "overshoot" problems never occurred.
At first the mechanical components of the light-sensors were too fragile and prone to be moved with every single touch (or bang with a core section); this required a "find top-of-the-sensor" run to re-adjust the exact distance between sensor and home switch. At some point throughout the expedition, we poured some epoxy around the top sensor of each track to reduce the fragility of the sensor position. We still recommend to paying attention to this detail of operation to avoid possible and erroneous distance recordings and advancement issues. According to our EXP346-correlator scientists, who extensively worked with the data, no depth-issues in our track data were noticed.

• H2O Standard Cores: We also produced several new H2O Standard cores, which are readily to be used. One of those new cores features one of the new acrylic end caps. The acrylic end cap (with the Teflon nut for H2O-refills) was tightened down with a hose clamp; this procedure ensures an equal-force squeeze on the end cap while the acetone was melting the two acrylic/plastic surfaces (end cap-to-core liner) together. Both surfaces were pre-prepared with a coarse sandpaper to enhance the interlocking of the two plastic surfaces during the acetone bonding process.

• STMSL Motion Control: With the ongoing expedition, we noticed on the STMSL a screeching sound during some runs of the pusher toward the limit switch. We interpreted this occasionally emitted sound being caused by the "Actuator Screw", which most likely requires some greasing due to the dryness of the environment and constant use of the logger. For the "Actuator Screw" we highly recommend to remove the front panel of the actuator and grease it up.

GRAPE (Gamma Ray Attenuation Porosity Evaluator)

• Following the procedures from EXP344S ("Baffin Bay"), we regularly produced acceptable calibrations for the WRMSL GRAPE (e.g. for the first site on 08/17/2013).

The STMLS track rarely needed to be calibrated since the expected values were so close to the measured data on distilled water. However, we repeated our calibration measurements consistently after every site (if warranted) to reduce the amount of drift, which is normally observed in our GRAPE data after continuously running the tracks for a while. Checking the H2O Standard QAQC data during data acquisition on site regularly allowed us to keep track of the reliability and reproducibility of our measurements throughout the entire expedition.

MS (Magnetic Susceptibility)

• Following the recommendation and wishes of our stratigraphic-correlator scientists, we replaced the WRMSL-70-mm loop with a 90-mm loop for 1) to allow a safe passing of expanded core sections through larger-diameter loops, and 2) to record consistent data by going through the same-diameter sized loops.

!worddav3cca9e07ecb798a5f97c871035e9544b.png|height=219,width=77!We noticed that both loops (of 90 mm) exhibited a severe cross-talk behavior, which caused an unwarranted "off-set" of both MS and GRAPE data in an uncontrollable fashion. We solved this problem by creating a "Faraday"-type of contraption around the STMSL loop, using scrap aluminum pieces. This make-shift construct shielded the two electro-magnetic fields from each other, and thus reduced the observed data disturbance from 8Δ SI units to Δ1 SI units.
The only reason why we even could observe and study this phenomenon was because we ran the two tracks in parallel (to accommodate a warranted "real-time" stratigraphic correlation), plus a very low magnetic susceptibility of the sediments; it was just high enough to be detected as a real signal (see: screen shot above).







Albeit we were able to "fix" this issue by installing an aluminum contraption from several pieces of scrap metal (see: photo to the right), our "technical solution" is considered to be only a temporary correction of the problem.
Ultimately, we like to see either a more permanent and well-developed "fixture" for this "loop cross-interference" issue - perhaps in form of a "μ-metal"-type of magnetic shielding, or in form of some "frequency adjustment" of the two loops. The latter could be either provided by BARTINGTON, or in form of some self-made electronics attached to the loops.

PWL (P-Wave Logger – on WRMSL only)

• In general, the signal waveform of the PWL was good, and in some cases we recorded P-wave energy and measured ultrasonic sound speed throughout the entire hole to 300 mbsf and deeper (with APC-ing to Core 50H and deeper) – a very good result overall, albeit the variance in values was more prominent in the logging data (probably due to the typical differences between in-situ vs. laboratory ultrasonic data).

Issues:

• • Sometimes we experienced mechanically-induced issues with the PWL transducers, and thus frequently sprayed silicon onto the mechanical moving parts of the instrument to avoid an unwarranted clamping behavior of the transducer mechanics onto the core liner.
  • When running the first test core (during transit), the PWL sensors did not work at all. To investigate the problem, we ran the Exlar Tritex application and obtained a read-out on drive's internal status. The diagnostics panel indicated a "low bus voltage" condition.

To clear the error, do the following using the Tritex application:

1. Pressed the "Reset" button to clear the fault.
2. Switched to the Control panel tab: tested the "open" (Move1) and "close" (Move2) motions: Ok.
3. Shutdown Exlar Tritex application.

Launched WRMSL.

1. Verified that the PWL now properly was opening and closing.
2. Taking readings.
3. Calibrating system with both acrylic rods.

After fixing this problem, the PWL ran without any problems throughout most of the remainder of EXP346, showcasing good waveforms (see: screenshot below). We only kept the moving mechanical parts properly intact by spraying silicon onto those components.
Measurements were taken throughout expedition w/o re-calibration. Checking data with measuring sound speed on H2O calibration standard cores confirmed values around 1,500m/s, which is in the range of expectation for our lab-temperature

• • Toward the end of the expedition, a weak signal on core material was initially interpreted as a weak coupling of the transducer energy to the core liner and specimen. We disconnected the transducer ends caps and lubricated the interface between transducers and end caps. For this matter, it turned out that the weak signal was indeed due to the material properties as with a change of material the signal reappeared. However, a higher noise content started to reduce the signal quality over the course of the next few hours, which triggered a whole slew of activities (from removing the transducers entirely, to discovering that one clamp screw of one transducer plate was basically stripped and un-removable, to re-armoring the RF-cable and cleaning up the cable chaos around/associated with the WRMSL-PC).
  • We recommend to add again some mechanism, which allows to keep the core liner/transducer end cap interface wet at all times (as we did create such a mechanism during EXP344S; unfortunately, this mechanism was dismantled with the next expedition).

NGR (Natural Gamma Radiation):

In general, the NGR performed rather well. The noise protective shielding on the NGR (as installed by AOL T. Bronk during EXP345) has had a very positive influence on the working environment around the NGR. It allowed us to work comfortably right next to the instrument without wearing ear-protective gear at all times (as one of the Tech's did during EXP345).
As one of several "Firsts" for all IODP-EXP's (see: WRMST/STMSL summary), we re-calibrated the NGR several times throughout the 2-month long expedition, primarily to verify and study the drift behavior of the instrument and thereby making sure that the energy channels remain in alignment from site to site. The results of the repeated calibration runs showed a minimal drift, whilst helping to optimize the final output and data quality. The LIVE COUNT time for each calibration run was 120 seconds, and most measurements on sediment core sections were performed between 300 and 420 seconds.
The results of our measurements were generally corresponding well with those from the logging operation (as they were for GRAPE and other data).
Issues

• Very occasionally the NGR started its total counting on its way into the tube. We interpreted this observation to be related to some erroneous triggering within the software application. The negative effect of this phenomenon is probably minimal as it only takes a few seconds to move the titanium boat from the out-to-the inside of the NGR tube. Nevertheless, this misbehavior ought to be fixed during the next tie-up period.
• Prior to our first drill site we wanted to verify how much the relative position of the specimen-titanium boat-detector systems really has. We did this primarily after receiving some conflicting messages during EXP341 in that respect. After running sub-cm position tests while acquiring data for 60 and 300 seconds (LIVE TIME counting), we concluded that the reported "issues" as were not really problematic.

We modified the distance/offset position to its original setting again (it was shifted by about 1 cm from its original to another position), and showed that the difference in counting time alone can produce a "shift" in peak detection by 1 cm. Plotting the results as COUNTS/MINUTES for both a 60-sec and 300-sec count time as a function of relative position of detector and specimen highlights the limits in "precision" and "accuracy" for our measurement. Note: the GREEN DOTTED LINE represents the 300 counts, adjusted to a 1-minute count time record (i.e., original data divided by "5"). The RED SOLID CURVE represents a run at 60-sec count time.

• We noticed that the (K-40) peak at Detector #6 was always shifted toward a higher energy channel compared to all other detectors. We wondered whether this was related to "Drifting", but could not verify any out-of-the-ordinary behavior during our repeated calibration tests. Our recalibration experiments consistently showed a stable situation, with all energy channels in close proximity to their expected values.
• After two high-recovery expeditions, we highly recommend that the NGR-tube will be cleaned during the tie-up period because of the high risk of unavoidable sediment/water contamination from such heavy use of the NGR instrument.
• When looking at the core data prior to splitting, we always (ALWAYS!) ended up plotted the data per "Symbol" onto the screen – after noticing that the traditional "Line" display does not necessarily show the existence of the data. THIS IS A BUG THAT NEEDS TO BE FIXED! We discovered this bug upon splitting a core WITHOUT having the data, and then realizing later that the data were actually not in the data base. Consequently, we needed to retrieve the core from the repository and putting the core back together with tape (shrink wrap would have done an even better job…). Ditto: To be absolutely sure that data are in place, checking the LIMS REPORT is always a good idea (of course), but realistically speaking – during a high-recovery expedition like EXP346 this is easily overlooked. We never had this issue again after plotting the data ALWAYS as "Symbols" onto the screen.
• Uranium Standard Core measurements: Another "First" accomplishment during EXP346 was measurements on our new Uranium standards (R-and-C-Grade). We performed those experiments without applying any processing to the acquired data, as we did not have the background data yet when we ran our tests. This can be produced via post-expedition processing using the background data obtained at the first drill site.

Thus, the results of our measurements currently show only the spectral files, but not the xls-summary files. This experiment can be repeated at any time and/or completed via reprocessing the data by incorporating the background data. Below is a screen shot of the final state of the test run on Uranium (C-Grade @ 60,000 seconds Live Time). The measurements will be useful for post-EXP346 research in conjunction with geochemcical analysis at Boston University (via Prof. Richard Murray et al.) and at other institutes (e.g. via Dr.GwankSoo Lee, Korea).
Measurements on the U-Standard cores were followed by corresponding test runs on the Th-&-K standards. Low counts for both K-40 and Th-232 experiments were observed on Detector #2. We show a screenshot for the K-40 experiment, with a prominent peak around the expected K-energy bins (except for Detector #2; see: RED CIRCLE).
Another screenshot (below) shows the energy spectra distribution for the Th-232 experiment, with discernible peaks for the lower energy channels, especially for Detectors # 6 through 8 (note: the standard core is only 45-cm long and pushed against the 0-cm offset position and thus producing high peaks on those detectors, which are close to this particular position). Note: As above, Detector #2 does not depict a prominent K-40 peak (see: RED CIRCLE in schreenshot).

TeKa (Thermal Conductivity):

No prominent issues were reported during the expedition.
As always, we measured thermal conductivity on sediments with the full-space needle probe. We chose V11035 as our preferred needle.
However, this time we kept the probe in a pool of the "Thermal Joint Compound" and swiped the cream off right before each measurement. We did not want to contaminate the sediment material with the compound, but the cream might have helped to couple the probe better to the sediment at times. Maybe an invisible micro-film of the compound remained on the probe, thereby causing this positive outcome perhaps more often than expected (that expectation is based on many sediment measurements in the past).
Below is an example of measurements on a core section from the upper part of the drill hole. We applied heating powers between 2-6 [W/m]. TeKa's SAM model analysis produced results, which were consistent with the logging data (via Dr.J.Lofi).



Another example is shown (right) from measurements conducted on core sections from the lower part of the hole, with a similar positive outcome - a very good result from our experimental work!




In general, we ran the TeKa System from the "Blue Socket" power power (aka: "Clean Ship's Power") and performed our experiments inside the "Coffin" to reduce the effects of temperature fluctuations during every measurement.
During the transit we tested the measurement output when running the system from the battery (UPS) system alone, but did not recognize any significant differences in the result.
Issues:

• Toward the end of the expedition, the keyboard did not work anymore. As a result, the keyboard was replaced and also USB connections to the PC checked. It turned out that the USB connectors on the PC-side were also partly faulty. We recommend to investigating this issue during tie-up. We coined this incident "unresolved USB connection issues".

MADMAX (Mass-Density and Porosity):

As expected the system worked very well, albeit one mishap did occur.
Issues:

• The first tray of beakers was not properly logged into the data base, with the effect that the weight of the dry beaker was not subtracted from the wet/dry measurements. Thus, first few data points needed to be recalculated after re-measuring those beakers. The following steps were executed to correct the error:
• We cleaned the beakers in a sink with warm water and afterward in a sonic bath. Then the beakers were dried for 2 hours in the oven and then re-measured on the METTLER Balance system. As a final step, the re-generated data needed to re-calculated, now taking into account the dry mass of the beakers. Comparing our data with comparable data from ODP Leg 127 & 128, we know that the recalculations produced reasonable results (probably within the +/- 2-5 % variation range - perhaps better).
• We then identified the beakers, which were measured and logged properly onshore and continued with our measurements with those beakers, without experiencing any additional issues thereafter.
• It was mostly extra-work for the developers to deal with the re-calculations, and we were lucky that this issue could be resolved relatively quickly (big "Thanks" to David and James!)
• Consequently, the onshore process of weighing and logging the MAD vial beakers requires further attention and diligence to avoid mishaps of that kind in the future.

GANTRY P-Wave Caliper:

Albeit the PWave Caliper and/or Bayonet system was not used by the scientists during EXP346, we want to report our findings from testing the system during the transit from Alaska to the Sea of Japan.

• The GANTRY station received a new OLYMPUS 5077PR square wave pulser/receiver. All the settings were the same as we had chosen in the past, except that this time we selected an amplification of +20db (and not –dB). It was a good compromise between enhancing the appearance of the first signal arrival vs. over-amplifying also the noise on the signal.
• Attempting to take a P-Wave Caliper measurement without any coupling liquid in between transducer and steel end caps fails. The energy is not transferred properly through the material boundaries, no matter how hard we squeeze the specimen. It also does not matter whether some coupling (normally distilled water) is added to the surface of the specimen – because there is simply no energy transferred from one medium across a hard boundary into another medium.

The screenshot above shows a signal produced without any coupling, which reflects a zero-energy transfer through the transducer components. The signal is simply noise.
By contrast, the energy is easily transferred through the "specimen/metal end cap/transducer" interfaces with only a one drop of "Couplant A" Propylen Glycol. For the test experiment depicted on the screenshot below, we did not even use any distilled water as a coupling between specimen and steel end cap.












For that reason we decided to utilize the Z-BAYONET transducer pair for the few measurements that were taken during EXP346. The signal in water consistently provided a near-perfect calibration signal and (fast) result, and therefore was the most reliable and best choice among all three transducer pairs.
Shown is a screenshot of the ultrasonic signal pulse recorded in a soft mud sample of an "EXP341 Play Core", revealing a good quality signal and very reasonable acoustic sound speed obtained with Z-Bayonet transducer pair.
Improvements: To avoid a massive destruction of the sediment material upon pulling the Z-Bayonet transducers out of the specimen, we constructed a plastic plate, which covers the entire core section width, while also allowing each transducer to glide in and throughout a corresponding notch. A test with the plate being attached to the transducers with a rubber band did reproduce the same water sound speed during control measurement. (Below is a photo of the plastic board to perform this type of measurement).
Our scientists opted not to use this system in the end. Thus, it wants to be tested during a future sediment-retrieving expedition. We'll keep this plastic board inside the "Standard" drawer.

ASV (Automated Shear Vane):

We do not report any issues with the instrument. To ensure running the experiments smoothly at all times we sprayed some silicone onto the high-friction mechanical components of the machine.
Sometimes our scientists had problems with one particular working step where the Text_ID needs to be scanned into one cell of the XLS spreadsheet after recording the data; this cell content (YELLOW in color) wants to be modified in a certain way to allow the MUT-uploader to identify the file name in order to upload the file properly.
If the user is doing something wrong during that step (i.e. not "cleaning" the Text_ID dialog cell on the XLS spreadsheet properly), MUT needs to be closed and re-started. By opening the actual data file and cleaning the corresponding Text_ID information, MUT will identify the file properly and readily upload it into LIMS.

SHIL

SHIL has undergone several re-designs and re-builds since EXP320 and is now routinely collecting Linescan Images and RGB data. Note: RGB-data are placed in the "Auxiliary Data" subdirectory C:\AUX_DATA\LSIMG\RGB .
Collecting RGB data is another "First" for IODP expeditions accomplished during EXP346. According to our correlator scientists (via Dr.S.Clemens) "the data are spectacular and the best I've ever worked with". Scientists were able to correlate corresponding data from site to site and created essentially "on-the-fly" a site map for the entire research region.
Since the RGB data are extracted per line, SHIL produces an ultra-high resolution data set, which also will scientists allow the study of high-frequency cyclicity (aka: "Heinrich-Events" on the millennium scale).
Despite the successful implementation of the new SHIL software (plus a few hardware innovations – via Developer B.Mills et al.), some issues bogged down the data acquisition at times.
Issues:

• It appears that setting the exposure rates to small (higher speed) will induce ripples in the image. The high speed of the camera motion caused the triggering signal ("Newall Encoder") and crowded the safe exposure/shutter-cycling response time on the JAI CV107CL. Exposure rates were increases until the ripple effect disappeared which relates to a scan speed of 9cm/sec. The final rate was set to 8cm/sec to eliminate line drops.
• Initially, users could crop the image without setting a crop box. Without a crop box defined, the trimmed jpeg image was un-trimmed and no RGB dataset was generated. The code was changed to disable the crop button unless a crop box was set.

Other than that, it seems that the users were happy with the operation and output of the instrument. SHIL is super-fast in terms of data acquisition speed, while the image quality has been coined to be very good (via Image Specialist B.Crawford).
Furthermore, the system (with this added feature of producing RGB data) is a true innovation to the Phys-Props Lab on the JR and will add more value to the science community from here on.
As with the SHMSL, it has been proposed to collaborate with other prestigious labs (e.g., WHOI) to compare and continue developing the instrument (via Developer Bill Mills et al). This deserves truly applause as a good step in the right direction.

SHMSL:

Our scientists performed several important tests on the SHMSL, of which one demonstrated the good transmission and low reflectivity properties of the "Glad Wrap" that is regularly used for our experiments. (Additional information and results from such experiments are available in form of an XLS spreadsheet and/or a pdf – via Dr.T.Irino). Another experiment tracked the color reflectivity spectral power of our control-run color standards (labsphere Teflon Disks). We only started this experiment during our transit and prior to the first site. Unfortunately, we had to terminate our efforts due to the high recovery of sediment cores. Nevertheless, it was a first and important step toward acquiring regularly "Verification Measurements" using industrially-produced, color-calibrated standards.
Issues:

• One of our Phys-Props scientists demonstrated the high noise level of the instrument at its current state of development; according to his expertise the noise is relatively high compared to what the Minolta spectrometers formerly generated as IODP's color reflectivity instrument (via Dr.L.Giosan).
• Another source of noise is caused by the use of Glad Wrap on the core. When an optically clear contact is made between the wrap and core surface (wet clayey core) high quality measurements can be obtained. However, any air gap between the wrap (or a wrinkle in the wrap) will cause a small percentage of the light source to be reflected back into the sensor causing the L value to jump and the a and b values to washout. The solution is to only use the wrap when necessary and use de-ionized water to insure a optically clear contact is made. Unfortunately, this does not work on sand or ash.
• Dirty white calibration standard resulted in an offset in the calibration values. In general the science party was good at keeping the standard clean. Possibly, an automated cover is in order.
• For the Point Source Magnetic Susceptibility measurements, running the sensor at a resolution of 2.5 cm (GREEN CIRCLES in screenshot below) produced an unwarranted artifact in the data compared to running the SHMSL at 2.0 cm resolution. When switching back to 2 cm of resolution (GREEN TRIANGLES in screenshot below) this phenomenon disappeared. Test showed that this was not an artifact of the software as the SHMSL program was capturing the data as sent by the MS meter. The reason for this behavior is unknown.
• Toward the end of the cruise, the USB connections to both the Phidget relay control (light power) and the OCEAN OPTICS sensor disconnected. In addition, we lost both keyboard and mouse after rebooting the system. After the second reboot the USB connects where remade. This appears to be an instrument host problem. During the expedition we saw similar issues on the SHIL and Thermcon PCs.
• The light bulbs were exchanged once during EXP346 when the "Integration Time" started to reach "1-second".

Summary

• The SHMSL performed overall according to the expectation and the status-quo of its design and development.
• We like to note that we do not observe those radical offsets and drifts anymore as we had since EXP340 (e.g. via Dr.M.McCanta-EXP340; Dr.P.Ferretti-EXP344S; Dr.B.Ildefonse-EXP345); those rifts and offsets had been formerly identified as thermal and calibration-setting problems and correspondingly addressed (via developer B.Mills).
• However, EXP346 scientists have been less enthusiastic about L*, a*, b* data than about the (SHIL 7.0.) RGB data. We suggest further diligent testing of the SHMSL instrument and data quality, improving the instrument's data acquisition, and also a more rigorous data processing and verification work flow using our new labsphere Teflon Disks standards.

IMAGING & MICROSCOPES

William Crawford

DIGITAL IMAGING TRACK (SHIL

Operational issues: During the previous tie-up period in Victoria, changes were made to hardware and software components of the SHIL. Hardware changes included a reconfiguring of the Galil gantry, camera and lighting mounts. Changes to the software were made to include all of the programs and controls needed to calibrate the camera and provided color and density correction tools for the generated files.
At the beginning of the cruise, I took the camera down to its factory default configuration and began adjustment and calibration from there. This also was an opportunity to work extensively with the newer software. Mr Mills has provided an interface which all of the necessary tools are now presented in tabs within one application. This saves time when busy with the task of adjustment and calibration. Although the application is not to the stage where generally accepted image calibration tools are available, with patience imaging calibration cards and standards, I arrived at a state of correction which within the confines of the tools available, which I was satisfied with. I feel a continued path towards integrating an ICC calibration of the raw file is necessary.
I understand some misunderstandings exist about what defines a Raw Image. All raw images, which are offered to consumers, have corrections applied. The state of the data directly from any digital sensor has been calibrated by the camera manufacture to correct the gamma curves. Raw files do reflect sensor data but with some help. Adding an "ICC" profile at the time the image is produced by the camera prior to the JPG correction is not altering the Raw data but merely completing the process which all camera manufactures provide. Typically "Raw" files appear flat and certain additional data such as While Balance and color spaces must be applied. At that point the file becomes a Tagged Information File Format (TIFF) style of file. These "Tags "give the computer and the monitor the information to deal with the file and present it correctly. The process of altering (ICC Calibration) the file (Raw) from the camera does not degrade but rather presents the data in a better manner. The file arrives at the correction process "half way" and then only needs minor adjustments to achieve visual approval. This is very important in the current workflow of the SHIL as we are lacking proper digital Imaging correction tools and must accept the limitations, which are associated. One path to provide the proper tools is to incorporate Photoshop in the process but there has been a hesitation to do so by IODP. Allowing the raw file to be presented in this manner would allow us to perhaps side step the introduction of Photoshop into the workflow of the SHIL.
The most recent version of the SHIL software had its growing pains but Mr Mills persistence was rewarded in a smoothly functioning system with added features which were embraced by the scientist, the foremost being the generation of RGB data.



Quality control: The images were constantly monitored and a calibration check was done between each site and hole. Serious interruption of data paths occurred early in the Expedition resulting in the re-scan of many images. To summarize, only a partial upload of image file types made their way to the database. The tiff or raw image had been omitted. The core was retrieved from the hold and mainly through the efforts of Mr. Mills and Lisa Crowder, each section was rescanned and re-wrapped. This help to ease the impact to the rest of the crew, which was already tasked by this high recovery Expedition. The images were downloaded each morning and visually checked. The use of Web Tabular's Image Summery was deployed to detect any core sections, which was missed and not scanned. Careful examination of the end caps revealed several cores which were scanned upside down. It is interesting to note, the Stratigraphic Correlators were quick to see the graphical mismatch of the RGB data when such an errant scan and its data was placed in LIMS.

MICROSCOPES

Configuration and alignment- The microscopes were configured as per the request of the users:
We were host to a full staff of Paleontologist. Microscopes were configured with heavy use of 100x, 63x oil and Phase. Lower power objectives provided for the smear section microscope. The new Zeiss Discovery V8 stereoscopes were well received.
One eyepiece tube was found to be defective and needs to be sent back for repairs. In all cases the LED ring light was removed from the stereoscope in favor of the flexible fiber optic illumination. Counters were requested and I was able to find two mechanical counters. One functioned properly and the other needed repair. Garrick and Clay were able to rob from Peter to pay Paul and brought the counter back in to service. Garrick successfully replaced the Pot adjustment on the MBIO microscope. It was found the scale generated by the Spot cam software is inaccurate. The scientist imaging a stage micrometer was able to adjust accordingly. This was discussed with the Applications Developers but a correction has not been done at the time of this writing. The images, which the corrections will be based, have been saved.
Micrograph imaging was non problematic. A newer spot camera was installed on an Axioplan II microscope. This completes the replacement of the older style spot cameras. One new Spot camera boxed and resides in the Imaging Office. There was one incidence of images being saved to a local folder but not uploaded to the server.
Overall Microscope Assessment- After configuring the microscopes for specific needs in the first few weeks after departure, the microscopes required little attention other than cleaning and minor adjustments.

SEM

The SEM was used frequently but no system has been put into place as to provide and upload with metadata to the database. This was discussed and explored by the Applications Developer. No progress to date. The Staff Scientist was advised and he took it upon himself to see the images were saved to Data 1 server.

Video and still efforts

Video efforts were limited to a very late request by one of the scientist to provide B-roll capture to be transmitted to shore via the internet. At the time of this writing the total effort of this project has yet to be determined. The video camera functioned well and the upload to Apple Final Cut Pro X was straight forward and with no problems.
A new Canon still camera was brought into service and the added capabilities is nothing short of amazing. The largest impact of feature improvement is an ISO range of 100 to 51,000!
Close up photography was in the form of downloaded SHIL images, edited and cropped as per requested. Most of the 100 or so requested was for the full 150 cm. Only two scientists had an interest in close up request.

shipping

Items to be shipped to shore:

• 1- Zeiss Discovery V-8 Stereo Microscope optical tube. Made in Germany. Serial number 435107-01 Shipped without oculars, camera or camera adaptor. Estimated value 1,500.00. USD
• 1-Canon 580ex Speedlight hot shoe mounted flash unit. Made in Japan. Serial number 548490 with case. Estimated Value 500.00 USD.
• 1-Canon EF 24-105mm zoom lens with UV filter. Serial number 635532. Needs repair. Estimated value 1500.00 USD Made in Japan
• I-Canon EOS-1DS MARK II DIGITAL camera body US Government property tag number 90594 Serial Number 338264 Made in Japan
• 1-Canon Battery Charger 0U0802 NI-MH charger NC-E2 100.00 USD
• 1-Canon camera battery made in China 100.00 USD
• 2-Calumet camera batteries Made in Japan 100.00 each USD
• 1-Canon A/C power adaptor PA-V16 00009050W K30120 120.00 USD

SummAry

• 6 Close-up Images
• 407 Micrograph Images
• 0 Thin Section Images
• 44.5 gb Raw Still Images
• 4877 Line scan images
• xxxx SEM Images

CHEMISTRY LAB TECHNICIANS REPORT

Lisa Brandt & Darcy Lichlyter

Ampulator

The new ampule sealer worked really well. Randy the ET built us a wooden stand for it that holds the propane bottles upright and has a gas cutoff valve on the side so that you don't have to reach over the flame.

Balances

The new Mettler microbalances are currently stowed in the cold lab. David had wanted us to test them out using new 9-bar weighing supports during the transit, but due to issues and time spent troubleshooting the GC's, we did not have time to test the balances. The new 9-bar weighing supports, part number 11106403 are currently stowed in the Mettler Supplies drawer under the Mettler balances.
No major problems on the Cahn's. The scientists had some issues with samples losing mass and thus being hard to weigh, but this was decided to be due to the sample matrixes.
No issues to report for the larger Mettler balances.

Carver Presses

We had some problems with the needles on the Motorpak control sticking, but we were usually able to just wiggle the needles loose. I believe we are replacing the Motorpaks during tie-up.

Cary Spectrophotometer

The Cary was used to analyze ammonium, phosphate, silica, and sulfide(HS) concentrations. We had a problem early on where the gear box that drives the pump broke. We had Garrick and Ken the rig mechanic look at it, and they were able to put a pin through the gears to make them turn correctly, and it had held up admirably throughout the cruise. We had a blockage develop in the tubing, which was noticed when the flow rate dropped down to only dispensing .5 mL of fluid, instead of about 2.5mL. We first thought that perhaps the pump was now turning more slowly and not dispensing enough fluid, but we then traced the flow path and found a clog in one of the lines. I trimmed the line and all was well.
We seemed to go through VIS lamp bulbs a high rate. We changed out the lamp midway through the cruise, and then had to replace it again a week later with a patented "Used but Good" lamp. Garrick thought that turning the Spec on and off was probably harder on the lamp than leaving it on continuously. After this, we have left the spec on non-stop, and have not had any more bulbs fry. I increased the stock level of VIS lamp bulbs on AMS.

CHNS

Carbon, Nitrogen, and Sulfur were measured on the CHNS, though the scientists felt the S peak was too broad and didn't report it as part of their datasets. We used sulfanilamide as the calibration and check standard, as the scientists did want to try to analyze sulfur. We ran about 110 samples per combustion column and ran a check standard every ten samples. We worked with David Fackler to fix the issue in LIMS Reports where the element values were being swapped with each other. Specifically sulfur and hydrogen values were being swapped. This turned out to be a parsing error from MUTT and has been fixed.

Coulometer

We had some issues where the data was not being saved after the user hit save. Not an operator error. Programmers are aware of the issue, no solution as of yet.

Freeze-drier

No issues reported. Heavily used.
Gas Lines/manifold
No issues to report.

GC3/NGA

We had some pretty major issues on the NGA that required a lot of help from shore to troubleshoot. It started with funkiness in the Methane peaks. We were getting poor reproducibility, on methane only. We shut down the NGA and powered it off to begin maybe looking at the column. When we powered it back on, the NGA would no longer talk to the computer. The IP addresses of the computer and both GC's looked fine, and it appeared that BootP, which is the server that that chemstation uses was running. We checked for physical problems, tried changing out the communication cables, tried plugging the GC's into different network ports. We finally figured out that BootP services weren't actually running. It looked like they were, because I could go into the Edit BootP settings, but I really had to go to Control Panel>Administrative Tools>Services>Agilent BootP Services, where BootP had had been disabled. I turned the server on and set it Automatic, so BootP should now automatically start.
After this, the NGA would talk to the computer. The next problem was that reconnecting the NGA made the software believe we had connected a new instrument. We kept getting error messages that said that the method trying to be loaded was created on a different instrument. I tried powering everything down and restarting, and contacted Agilent tech support, where they recommended disconnecting the NGA from our network and reconnecting it. This also did not work, chemstation kept thinking we were connecting a new instrument. When you connect a new instrument, Chemstation will try to transfer the method settings for you. After some trial and error, we made Chemstation just transfer the method settings to the "new" NGA. All settings appeared to transfer, except for the valve programming. I recreated the valve programming scheme. We were then getting a signal on the FID, but no peaks. We thought it might be a column problem, and trimmed 6 inches off the capillary column, still no peaks. Tried reversing the logic on Valve 1 thinking maybe we had reconnected the valve in an opposite alignment. Still no peaks. The FID was lit, ball on the injector was going up and down like usual. Tried measuring the gas flow out of the column using the flowmeter, and we determined that we were getting no flow out of the column. Then we decided that maybe we weren't getting a good seal using the flowmeter, so we bubbled the end of the column through a vial of methanol to see if we were getting flow. We did get flow into the column, but not out of the column. So we replaced the column.
After replacing the column, we baked it out for several hours at a temperature setting slightly higher than the highest setting in the method. We were now getting a random peak in the chromatogram, but it still did not look normal. Doublechecked all of the fittings. Still thought it was a leak. Went through all the method settings and then figured out that the Aux 3 He Line was not on, due to one of the settings that did not get transferred over when we were rebuilding the method on the "new" NGA. The Aux 3 He line is the one that pushes He through the loop into the column. After turning that on, and since we replaced the column, methane looked great.
No major problems on the GC3. At the very first site, it did develop an issue where no sample was being delivered to the column. We figured out that the Valve was firing, but had migrated down off the rotor shaft so the rotor wasn't actually turning. I pushed the black box back onto the rotor and it worked fine.

Hydrogen generators

A new Hydrogen Generator was installed in Valdez. No issues to report. I think there is a more in-depth maintenance kit for the Hydrogen generators that we can purchase. They are listed in the product manual. We currently just order the main cartridge, but there is another kit that contains more filters and things to replace. I did not get a chance to investigate and requisition and add these to AMS.
9-25 Addition note: Now have an issue to report. A couple days ago, the Hydrogen Generators started developing Overrun and Low Pressure errors. Not quite sure what was causing this. We might have developed a leak in the system. Since we were done with operations, and are sending the SRA home for maintenance and replacing the GC's, I just turned off the GC's and the Hydrogen generators.

IC

First off, after uploading 700 some data points, I think we need to amend the way we upload data. I think there are ways to make the csv files display more chromatogram information so that we don't have to produce both a csv file and a pdf file.
Second Off: The email address for Priscilla the service rep, who I was in contact with regarding the Cations issues is applicationslab@metrohmusa.com
We had a couple major problems with the IC this cruise, one of which, cations issues, still needs to be fixed.
The other major problem, which we did fix, was that the software had a glitch that made it stop recognizing the autosampler rack. We would start up the MagiCNet software, and the rack would appear to initialize and find its home position, but then it would finish the initialization and then throw up an error saying we did not have a rack installed. We went in circles on this for several days. We tried:
Disconnecting the autosampler, removing it from the configuration in the software,then plug it back in to basically re-read it.  I did a complete power restart.  I shut down the software, unplugged the IC and autosampler, shutdown the PC, rebooted the PC, Plugged in the autosampler and IC, turned them on, and started the software.  Everything comes back ok, but I still get rack errors.  Another rep recommended that I unplug the autosampler from the computer and run it directly to the IC.  (Currently, there is a cable that runs from the Autosampler to the computer, and one that goes from the IC to the Computer.  I removed the USB extension cord on the Autosampler USB cable and connected it directly to the USB port on the back of the IC.)  After running the cable directly to the IC, I started everything back up, and still no rack connection.  Lots of hard restarts with the rack not installed.
I thought maybe the method we have been using got corrupted or something, and that's what causing the problems.  I tried to open the old method the service rep used when setting us up, and got a different error, which is attached,  which says the autosampler is not connected properly or is defective. 
Rolling back Windows updates to mid July. This did not help.
Tried cleaning the rack underside with windex, thinking maybe the magnet sensors were dirty.
We thought maybe the config file for the rack had gotten corrupted. We had the service rep send us a new config file. This did not work.
We took the Autosampler apart to check the magnetic sensor. It appeared fine.
Checked all USB cables to the computer. Fine.
We finally got the company rep to remote desktop into the computer. We found a software glitch that had caused the software to lose the location of our Special Beakers on the autosampler. The special beakers are the 3 big beakers. The biggest problem was that on install, we were not even configured to view the rack data and set the locations for the beakers. On the config tab, she went to View>Change Layout> and then selected the Rack Data to be a displayed subwindow. Until she did this, we could not even change the rack data. After enabling Rack Data, we could go to the rack data tab and tell it the rack was 6.2041.440. The glitch caused the special beaker locations to be set to 0, when special beakers 1,2,3 should be in positions 149, 150, and 151.
After entering the special beakers, I could initialize the rack. When I first tried running a sample, the sample needle jammed on the autosampler rack. It turns out a couple of other locations had re-set as well. In the config menu, under the 858 properties, on the tower tab, the external postions values had been defaulted to something weird.  We set external position 1 and 2 back to 116 and now it appears to be working. The "External Position" is the beige rinse drain on the side of the IC, which we have affectionately dubbed "The Spitoon."
The other problem we are having is that cations is not working properly. Sulfate was crucially important this cruise, and they took 650 samples, so there was very little downtime to try and trouble shoot cations. Early in the cruise, cations developed weird peaks in the middle of the chromatogram, even in blanks. I emailed the service rep, and they recommended de-gassing the eluent, and if that failed, regenerate or replace the column. I degassed the eluent, and saw no improvement. I didn't want to mess with regeneration, so I just replaced the column. After replacing the column, we developed a lot of pump pressure oscillation. It was oscillating between .4mPa to 1.6 mPa. The conductivity signal also had a sawtooth oscillation pattern. The service rep thought I might have to re-prime the pump. The instructions for this are on page 36-37 of the official Metrohm manual. I hooked a syringe to the port on the door that's connected to the cation pump, opened the pump valve a quarter turn, and pulled a vacuum. I did not see any bubbles. Also no improvement with the signals.
I was worried that perhaps I had crushed the inline filter piece when I was replacing the inline paper filter, so I tried replacing the inline filter with a regular coupling connector. I saw no change.
After this point, the scientists were so desperate for sulfate data that they didn't care about cations. I did not have a change to try and fix it.

ICP

We analyzed both Majors and Minors on the ICP. We slightly increased the sample uptake time since we saw some weirdness amongst the 4 replicates. No major issues to report.

salinity

The optical refractometer was used, no issues to report.

SRA

The SRA was not used to analyze samples. I fired it up at the beginning of the cruise in order to work on a staff scientist's project. Data values came in badly. I had a lot of problems getting the CO2 and CO values to stabilize in the IR cell calibration application. The lab then hit the GC problems, and shortly thereafter we got core, so I didn't get back to working on the SRA until mid September. The CO2 values seemed much more stable this time around. I might have just needed to give the IC more time to stabilize. After a few weeks, the CO2 values had stabilized, but the S2 and S3 values were very high, outside of the acceptance range, and were not repeatable. Tried troubleshooting more by emailing the contact person at Weatherford, and also tried some of the maintenance procedures that were outlined in an official maintenance document in the SRA folder on the computer that I did not know existed.
I tried the following:
The split flow assembly, which is the swag-lok assembly on the side of the FID, seemed to be a little loose. Also you are supposed to take it apart and clean it every 6 months or so, and we've never done that. Took it apart, sonicated it in Methanol, and put it back on the FID. Still got cruddy results.
Connected to the CO2 cell in the main body of the SRA is a Teflon piece called a flow restrictor assembly. We are supposed to change this out every 6 months, I don't believe it has ever been changed. We had a spare, so I swapped that out. Still bad repeatability and too high s2 and s3 values.
After trying these solutions I emailed Weatherford Labs about the problems and sent them my files. They thought the split flow values were too high. The split flow is indicated by the ball indicator and is adjusted by the black thumbscrew on the back of the instrument, on the left side if you are looking directly at the back. It is supposed to be 40 ml/min, we had it at about 60. I dialed it down to 40 and tried another run. Still too high and bad reproducibility.
I then replaced the FID. The old FID did not appear to be clogged, but it was basically the only thing left to replace. I have not had time to see if this solution worked.
My contact person at Weatherford had mentioned that there was a firmware upgrade for the IR cells on the SRA. We decided to ship the SRA home to get this upgrade.
My contact person at Weatherford Labs is Simone Young. Simone Young's email at Weatherford is simone.young@weatherfordlabs. com

Pipettors

Pipettors were used; no issues reported. We received several new pipets at the Valdez port call but did not use them.

titrations

alkalinity

No major issues to report. Alkalinity was heavily used.

Chloride

Chloride titrations were done. Only software problem was that the "Measurement Done" pop-up message on the Cl titrator software can be minimized if you have alt-tabbed out of the program, for example, when you're also performing alkalinity titrations. If the "Measurement Done" box has been minimized and is hidden and you go to do something else in the software, it causes a crash. This issue was discussed at the most recent Chem LWG meeting on shore and has been punted to the programmers to be fixed.
We had a problem halfway through the cruise where the titration would not reach its end point. The titrator was adding the maximum amount of Silver Nitrate to the titration solution (6mL) and never reaching the end point, just maxxing out. I had Fackler helping us, to see if it was a software problem. It did not appear to be anything wrong with the application. I did not see any damage to the electrode. I did notice that the silver ring on the electrode was quite tarnished, and I cleaned it with some toothpaste, as recommended by the Metrohm manual that came with the electrode. This did not help. Fackler and I finally replaced the electrode and cable that connects to the titrator body. The new electrode worked. It looked like the connector actually might have been the problem, but I didn't have time to troubleshoot that. We might want to add the cable to AMS separately. Currently it just comes with a new electrode.

Water system

No issues to report.

TOC

The scientists were interested in using the TOC to get DIC data. I fired up the gas generator, and that took several hours to build up to the required psi. I then turned on the TOC, and did some preliminary testing. The TOC analyzer hasn't been used since Expedition 329, South Pacific Gyre. When I did the self-test on the hardware, I got a failure on the CO2 detector. The manual with the instrument does not tell you what to do when the instrument fails self-checks. I got Rachel to email tech support, got the contact information for their TOC service rep:
guillermo.jimenez@xyleminc.com, and our reference # is 957564
I basically ran out of time to continue troubleshooting this instrument. The issues with the IC took priority. The scientist took a preserved DIC split home.

Misc

• We think it would be a good idea to put the Cary and IC on separate computers. Due to the high sample load this cruise, both instruments were heavily used and it was sometimes difficult to get onto the IC since the scientists were using the SPEC.
• We stole 4 of the black/yellow anti-fatigue mats that they use up in the core lab. We put them in front of the splitting fume hood, the sink where we clean squeezers, and directly in front of the presses. We found they helped a lot with alleviating general fatigue. We cleaned them using the power washer on the catwalk and have stored them for chem lab use in the MBIO cold room.
• ToDo List: You might want to do a physical counts at some point.
• Cations on IC
• Add Hydrogen Generator kits to AMS and order them.
• Troubleshoot H2 generators.

XRD & ICP SAMPLE PREP LABS

Kristin BRONK

Summary

This expedition was a high recovery sediment cruise with 341 XRD samples. The majority of samples were powdered by hand, with a few requiring the mixer mill. All equipment functioned well on the expedition.
XRD samples: 341

Methods

The Bruker Diffractometer ran without problem. The parameters for the scans were:

• 40 kV, 40 mA
• Scan angles: 4 – 70° 2 ¿
• Step Size: 0.0087
• Scan Speed: .2 s/step
• Div Slit: 0.3° = 0.6 mm

In general, one sample was taken from every core. In the case of half cores, one sample was taken every other core. Per the co-chiefs request at two sites, we took XRD samples from the core catcher on the catwalk to quickly determine when we hit an opal boundary. These samples were placed in the oven for one hour at 90C, powdered and run as usual.

Equipment and Software

• Two new LOI trays were received this expedition. They fit in the furnace but were too long for the desiccator lid to close. The machinist was able to cut the trays down about three inches and they fit well. The new trays have not yet been ignited. We now have two new trays and three 'old/flaky' trays in the lab.
• The freeze dryer vacuum pump oil was changed twice.
• A requisition was made for three new Spex tungsten carbide containers for the shatter box.
• New platinum crucibles should be arriving in the Philippines.

Problems/Issues

None! Just a lot of samples and a lot of core.

THIN SECTION LAB

EMILY FISHER

Summary

There were a total of 6 thin sections consisting of dolomite and sandstone.

Special projects

Repaired ceramic knife with epoxy.

Problems encountered

None

Miscellaneous

Routine equipment maintenance as needed.

UNDERWAY GEOPHYSICS & FANTAIL REPORT

Matthew Knight

Summary

This was a high recovery sediment leg that started off with a two-week transit from Valdez, Alaska to site U1422 in the Sea of Japan. We initially planned to run the magnetometer for the entirety of the transit until we reached the high traffic area near the Tsugaru Strait, however, the magnetometer failed due to electrical current overload most likely caused by seawater intrusion into the tow cable. The PDR was operated during each transit of the expedition with no significant problems. WinFrog was operated on the WinFrog1 computer for the entire expedition.

Navigational Data

Transits:

• Valdez to U1422(L1T = 3413 mi)
• U1422 to U1423(L2T = 125 mi)
• U1423 to U1424(L3T = 98 mi)
• U1424 to U1425(L4T = 180 mi)
• U1425 to U1426(L5T = 148 mi)
• U1426 to U1427(L6T = 66 mi)
• U1427 to U1428(L7T = 240 mi)
• U1428 to U1429(L8T = 4 mi)
• U1429 to U1428(L9T = 4 mi)
• U1428 to U1430(L10T = 430 mi)
• U1430 to U1427(L11T = 182 mi)

Sites:

• U1422 (Holes A, B, C, D, E)
• U1423 (Holes A, B, C)
• U1424 (Holes A, B, C)
• U1425 (Holes A, B, C, D, and E)
• U1426 (Holes A, B, C, D)
• U1427 (Holes A,B, and C)
• U1428 (Holes A and B)
• U1429 (Holes A, B, and C)
• U1430 (Holes A, B, and C)

Site fixes were performed at every hole and WinFrog event fixes were gathered every thirty seconds during transits and while on-site.

Equipment Performance

Bathy 2010

The PDR and the Bathy 2010 software were run for the entirety of all transits and used to calculate drilling depths at every site. No issues to report, and in fact the software seemed to be writing SEGY files correctly.

G. Guns

The G. guns were overhauled on August 15^th in anticipation of planned V.S.P. logging at our second to last site. In the end the guns were never used because the site was abandoned earlier than planned.

Seaspy Magnetometer

The magnetometer was deployed shortly after our departure from Valdez with the intention of towing it for the majority of our two week transit. However, on August 4^th, the SeaLink software displayed an "output overload" error message and said that it had shut down the tow system. Garrick suggested that there might be a bad connection to the winch slip ring, so we cleaned the connector and reattached it. This seemed to fix the problem and the magnetometer continued to operate for another 3 days with proper supply voltages below 200 mA (often below even 50 mA).
On August 12^th, SeaLink displayed another output overload message, this time unrelated to the slip ring connector. Garrick and I suspected that it was a power supply issue so we checked the isolation transceiver and found problems with the LED indicators: the power indicator was red when the magnetometer was connected and green when disconnected. We also installed our own power supply which showed us that current was only about 70 mA, not enough to actually cause an overload. We then plugged in a spare transceiver we have onboard and found the same problem.
We then brought the magnetometer back onboard so that we could test and inspect the tow cable. The tow cable had a dead short when we inspected it with a meger and we found that there was significant corrosion inside the cable head connector (the end that connects to the mag) and cleaned it out. Inspection of the cable itself revealed a damaged section of the insulation about 1 meter above the bend restrictor with water present inside the cable (we presume the water made its way to the connector head).
Lastly, we bench tested the magnetometer by connecting the electronics module directly to the isolation transceiver but we got the same "output overload" message. We even tried a spare electronics module we have... again it shut down immediately.
I contacted Michael Daffern at Marine Magnetics, the manufacturer of the magnetometer, for advice on how to proceed. He suggested that because there was damage to the tow cable that included seawater intrusion, that Garrick and I might have inadvertently overloaded the isolation transceivers and damaged a specific low-resistance resistor in each of them during our troubleshooting. He suggested that we ship them back to the manufacturer for repair.
The magnetometer was inoperative for the rest of the trip, however most of our transits in the Sea of Japan were in high-traffic areas where the magnetometer would not have been deployed anyways.

Winch/Slip Ring

Garrick and I cleaned out the slip ring connectors during our troubleshooting of the magnetometer and re-taped the connector in such a way as to keep the cord out of the way in the small passageway in between the winch and the port rail. Garrick did mention that he thinks the connectors are too small for the current load they handle over protracted periods of time (multiple days to weeks of continuous use). He suggested we replace them with larger connectors that could handle loads of 2 amps.

Level Wind

No issues to report.

WinFrog

WinFrog was used for the collection of all navigational, bathymetric, and magnetics data during the expedition at 30-second intervals.
During the transit from Valdez to our first site I edited and revised a WinFrog Startup Manual that Bill Mills created. This is a work-in-progress for the use of future Underway technicians. It can be found under the name "WinFrog Lab Specialist's Guide" in: \\JR1\IODP_Share\UW

Miscellaneous

It would be advisable to reevaluate our method for deployment and retrieval of the magnetometer. Our method for deployment currently involves hooking up the magnetometer on the deck and then lowering the cable by hand over the rail until it reaches the water. Retrieval involves a similar step of hauling in the magnetometer close to the ship with the winch and then pulling up the cable by hand over the rail. A lot of strain is put on the end of the cable and the cable's insulation as it is hauled over that rail and it is probably no coincidence that the tear we found in the tow cable early in the cruise was located on a part of the cable that experiences that stress from the rail (tear was found about 1 meter from the cable head). One idea that has been discussed at length during this expedition is the installation of some sort of rounded extension on the rail that the cable could feed through in order to reduce the pressure put on cable as it feeds over that rail.

Data Backups

• \\JR1\DATA\data1\1.5 Ops Navigation
• \\JR1\DATA\data1\1.6 Ops Bathymetry - PDR pulse depth recorder
• \\JR1\DATA\data1\1.7 Ops Magnetics

ET REPORT

Garrick Van Rensburg & Randy GjesvolD

Summary:

This was a two week transit and high core recovery near Japan Expedition

ET Shop

Conducted Basic Electronics and Arduino training. Found the ET Shop Stereo Amplifier to be significantly damaged. A new one has been ordered.

DHML:

• Sanded and varnished the two damaged spots on the big workbench.
• Broke out and tested the APCT-3 Tools.
• Tools 1858004C and 1858007C were used as primary and backup.
• Tools 1858022C and 1858005C were bench tested. Tested sat.
• Ran Tool 1858004C in hole:
• U1422C core 04, 07, 10 and 13.
• U1423A core 04, 07, 10 and 13.
• U1424A core 04.
• U1425B core 04, 07, and 10.
• U1426A core 04, 07, 10 and 13.
• U1427A core 04, 07, 10 and 13.
• U1428A core 04, 07, 10 and 13.
• U1429A core 04, 07, 10 and 13.
• U1430A core 04, 07, 10 and 13.

• Cleaned and inspected the rest of the steel cases. Some are showing signs of wear. Sending 3 of them back to the engineers for examination.

Paleo Lab:

• Black light failed. Repaired fittings and replaced light bulb. Hotplate power switch began to flicker. Cleaned out the switch and tightened it on the case.

Core Lab:

• On the SHIL the trigger circuit wiring would eventually work loose and cause intermittent problems. Installed terminals and torqued the wiring down on the circuit board.
• Added a few drops of oil to the impeller of the Pycnometer water cooler RM6 Lauda Brinkman.
• Installed the Olympus 5077PR Square Wave Pulsar/Receiver above the Core Gantry.
• Installed new Ocean Optics Bulbs on the SHMSL at the beginning of the expedition. Changed out the Ocean Optics Halogen Lights prior to running cores for Site U1426 on the SHMSL.
• Installed the shaft for the position Sensor for the SHMSL.
• Temporarily installed a Photoelectric Switch Fiber Unit on the fast track for testing. Testing worked well so a second unit was installed on the WHMSL.
• Repaired Cryomag Reverse Limit Switch wiring in the harness. It had shorted out.
• Trimmed and fit a shaft for the Cryomag motor.
• Installed a new mount for the High Resolution Surface Scanning Sensor on the SHMSL.
• Removed, cleaned out and re installed the Integrating Sphere on the SHMSL.
• Mounted a USB Hub inside the cover over the power supply on the SHMSL.
• Disassembled the camera system on the SHIL and installed new mount for the camera. It was then re installed.
• Replaced a broken CW limit switch. Re adjusted the CCW limit switch for end of travel. Removed broken screws and replaced them in the mount for the Logging Sensor on the WRMSL.
• Middle description table lifting columns began to have issues rising and lowering. Wiring checks out OK. During investigation found the reed sensor in one of the columns had failed. This was replaced.
• Blacked out half of the LED light above the SHIL to prevent glare on the track.
• The Gantry started returning incorrect data. Cleaned out the sensor and re applied the lubrication compound.
• Catwalk drills began to malfunction. Ended up disassembling two to make one work. Drills were brought in several times for servicing. Usually just had to clean the mud and sand out of them and oil the moving parts and the bit latching system.

Core Splitting Room:

• Installed Amphenol Connectors on the saws.
• Large heat sealer was knocked off the table and damaged. Glued the damaged parts back together. Runs Sat. Two more of the heat sealers were damaged later on in the expedition. These were both repaired. The temperature control was moved farther down the cord to prevent its weight from pulling the heat sealers off of the table.

Liquid N₂ Gen:

• Monitored during the run. Ran on Aug 6-8, Aug 20-21, Sept 2-3 and Sept 18-19.
• -80Freezer: Cleaned out the filter. Installed a battery pack and installed new batteries for the alarm.

Chem Lab:

• Replaced potentiometer in the microscope at the back of the lab.
• Pump for the Spectrophotometer failed. Motor still trying to turn but can't spin the impeller for the pump. Removed the gear box from the motor and cleaned it with Acetone and then added turbine oil to lubricate it. Still having issues. Removed it again and disassembled the gear box. Two of the gears were slipping. Took them back to the ships machinist and had a pin installed to stop the slipping. These were then re installed. Works sat.
• Manufactured a table for the sealing Pipettes area.

Hold Reefer:

Ultima II -40 Chest Freezer ceased to function. The wiring is in good working order and the compressor runs but it is buried in core and not accessible for repair. The machine is scheduled to be serviced in Subic Bay.

Gym:

• Added air to the Speed Bag.
• Repaired the Bicycle Pump.
• Assembled two new Stationary Bicycles. Aligned the wheel on one of them.
• Cleaned and greased the Elliptical trainer.
• Cleaned and lubricated the Universal Gym.
• Repaired the back plastic guards to the large treadmill. Repaired two dry soldier joints on the big treadmill.
• MP3 player audio jack was damaged. This was repaired and re enforced.

Science Lounge Movie Room:

• Conducted a deep clean of the projector.
• Cleaned out the UPS. Removed the Interrupter Protected Power strip and replaced it with a standard power strip for the A/V system. Found that the power strip in the overhead that goes to the Black Lights had been turned off. This was turned on.
• Popcorn media player fan began to make noise and overheat the player. The fan was removed and replaced.
• Small couch was digging into the carpet when moved. The center slider was bent and the edge worn away to expose a metal edge that was digging into the carpet. This was removed and a bolt put in place as a temporary repair.

Fantail:

• Assisted in Magnetometer deployment and retrieval.
• Added a light coat of oil to the slide bar before deployment.
• On Sept 11 the slide bars and upper sensor assembly were cleaned and a heavy coat of grease applied to preserve the system for the upcoming stand down. The port reel was then covered.
• Prepped the Seismic Air Guns for a VSP.

Underway:

• Magnetometer power supply began tripping on overcurrent. During investigation found out that the Amphenol Connecter for the Slip-rings was working loose and causing a bad connection. The A and B pins were shifted. Cleaned out the contacts on the power supply and the problem cleared for a few hours. During further investigation found the tow cable to be compromised. Sea water was getting into the cable head assembly causing an intermittent short circuit condition. A temporary repair was made to keep the water out. NOTE: Slip-ring needs to be of a shorter type or a guard put around it to prevent damage as personnel pass bye.

Misc:

• Manufactured "Rain Gutters" for the Schlumberger Telemetry Lab window and the Bridge level Conference Room. During a storm on Aug 6 they began to leak severely.

CURATORIAL REPORT

Chad Broyles

SUMMARY

Samples

A total of 10,319 samples were taken for Expedition 346. 8,053 shipboard samples, and 2,266 personal samples were taken. 1,148 shipboard sample residues were requested as personal samples. 6135 meters of core material was recovered during the expedition with 102% total recovery.
Personal samples were limited to: Microbiology (Yuki Morono, 4535-IODP; Nan Xiao, 4169IODP), Geochemistry (Jerry Dickens, 4405-IODP; Ann Dunlea, 4793-IODP; Rick Murray, 4883-IODP ), Volcanic tephra stratigraphy study (Yasufumi Satoguchi, 4166-IODP), Color study (Liviu Giosan, 4744-IODP), Oxygen isotope study (Kyung Un Lee, 4684-IODP), Opal-CT study (Gwangsoo Lee, 4586-IODP), Thin section study (Martin Ziegler, 4477-IODP).
All other personal sampling will occur at a sample party held at the Kochi Core Center (KCC) in Kochi, Japan held March 16-24, 2014. I am including an excel spreadsheet with the sample information in the email that includes this report.

SHIPMENTS

Core-Approximately 44 pallets of 932 core boxes will be shipped from Busan, Korea following the expedition to the KCC in Kochi, Japan. The core boxes were divided into Working and Archive pallets. A Core Box Inventory is being sent via email to the KCC with this report. Please note that U1428B was drilled out of sequence and is found in boxes 360-371 Working and Archive. U1427C was drilled out of sequence and is found in boxes 428-458. U1425 E is found in boxes 458-466. The electronic Core Box Inventory is being sent via email with this report (EXP_346_CORE_BOX_INVENTORY_FOR_ELECTRONIC.xlsx). The handwritten Core Box Inventory was scanned as a pdf file and is being sent via email with this document for cross referencing (EXP_346_CORE_BOX_INVENTORY_HANDWRITTEN_ARCHIVE.pdf & EXP_346_CORE_BOX_INVENTORY_HANDWRITTEN_WORKING.pdf)
Frozen and Refrigerated Samples-Frozen and refrigerated shipments are being sent via World Courier during port call in Busan, Korea.

• 4 frozen and one refrigerated cooler are being sent to:

Dr. Yuki Morono Geomicrobiology Group, Kochi Institute for Core Sample ResearchJapan Agency for Marine-Earth Science and Technology (JAMSTEC) Monobe B200, Nankoku, Kochi 783-8502
Japan Phone : +81-88-878-2198Fax: +81-88-878-2192
E-mail: morono@jamstec.go.jp

• 1 frozen cooler is being sent to:

Dr. Liviu Giosan
Woods Hole Oceanographic Institute
266 Woods Hole Rd.
Woods Hole, 02543
USA
Phone: +1 508 289 2257
E-mail: lgiosan@whoi.edu

Residues

The residue distribution is as follows:

I assigned requested residues to the sample request numbers (designated in the table above) in the LIMS database.
Thin Sections – A total of 6 thin sections were prepared by Emily on Expedition 346.
The thin section inventory is being sent via email with this report. (EXP_346_THIN_SECTION_INVENTORY.xlsx).
The following table is a list of all thin sections produced:

Smear Slides- The sedimentologists prepared and described 1,910 Smear Slides. A complete list of smear slides is being sent via email with this document to the KCC. (EXP_346_SMEAR_SLIDE_INVENTORY.xlsx).

CURATION & SAMPLING

Pre-site to Site Conversion

Catwalk Sampling

The general plan for catwalk sampling is outlined in Figure 1. The primary sample types taken on the catwalk were for Geochemistry, Microbiology, and Paleontology. This plan was followed for Sites U1422, U1423, U1424, U1425, and U1426. Modifications were made to each additional Site depending on how fast we were receiving the core and the work load on the Chemistry Lab.

Mudline

Water from every mudline core acquired on Expedition 346 was collected in a bucket, logged into the database and processed by the paleontologists. These samples provide valuable insight into microorganisms that live at the seafloor (e.g. benthic foraminifera). The geochemists also collected a 50 cc syringe of this water for Interstitial Water (IW) analysis.

Microbiology (MBIO )

Microbiology samples were taken for Dr. Yuki Morono (4535-IODP, MORO), and the KCC (4169-IODP, XIAO) at all sites except for U1427. In general the following plan was implemented. Minor modifications were made depending on the Geochemistry sample plan as Dr. Morono will incorporate IW analysis into his study.

• Odd numbered cores (1H, 3H, 5H, etc.) to APC refusal.
• Taken from the bottom of Section 1.
• 2.5 cc syringe from the bottom of Section 1 (MORO).
• 5 cm whole round (WR) from the bottom of section 1, shared between Morono and Xiao (XIAO_MORO).
• MBIO WR sample taken above IW WR.

Geochemistry

In general the following plan was implemented with minor modifications depending on the rate at which we received cores. This is outlined in the following figure on the next page.

Interstitial Water (IW)

• Mudline Core IW (If < 3 meters, 1 IW; > 3 meters, as approved by co-chief on duty)
• 2 per Core to APC refusal. {1 per core depending on recovery
• (approved by co-chief on duty)}.
• Bottom of Sections 1 and 4.
• 1 per core for ½ APC cores (Section 1).
• 5 cm Whole Round.

• 1 per core after APC refusal (Section 1) [Length/size as approved by co-chief on duty].

Carbonate Analysis

• The Carbonate analysis (CARB) sample was taken from the IW squeeze cakes.
• Head Space (HS) Gas
• 2 per Core.
• 2 plugs (5cc).
• Top of Sections 2 and 5 (Near IWs from bottom of Sections 1 & 4).
• 1 per core for ½ APC cores (Section 2).

Outline above is the general template used for catwalk sampling during Expedition 346. Minor modifications were made to this plan depending on core recovery and in cases where ½ APC cores were taken.

Rhizon Sampling

• Rhizons were taken in addition to the traditional Interstitial Water (IW) whole rounds and Head Space (HS) sampling. Rhizons were taken on all sites in the upper 100 meters of core material (Figure 2). Splits were made from the liquids for shipboard analysis, Dr. Jerry Dickens sample request (4405-IODP, DICK), and Dr. Kyung Un Lee's sample request (4684-IODP, LEE_KYUNG) . The Rhizon sample plan varied from site to site. The following is a list of Rhizons taken on Exp. 346.

Paleontology (PAL)

• 5 cm Whole Round
• Taken from bottom of Core Catcher (CC)
• Primarily from the first successfully drilled hole.
• Additional holes sampled to fill in recovery gaps.

Dedicated Holes for Geochemistry and OSL Sampling

Samples for OSL dating were taken on Sites U1424 and U1425 for Dr. Saiko Sugisaki (4849-IODP). Cores 1H, 2H, and 3H were dedicated for this study from both sites. Dedicatd OSL cores are being sent to the KCC for sampling and processing. The remaining material from these cores will be available to the science party for future sampling. Dedicated OSL cores were shot during the night so sunlight could not penetrate them which would erase the signal. Lighting on the catwalk was also minimized. The following protocol was implemented for OSL sampling:

• 3 Cores dedicated to OSL sampling.
• Core taken during night (Ideally during Saiko's shift).
• Immediately put into opaque Mylar bags and sealed.
• Write Site, Hole, Core, Section information on wine bags with up arrow (red marker).
• Core section data uploaded to LIMS, labels printed, placed on wine bags.
• Double label and tape over label to ensure labels are not lost.
• Cores will not be run through shipboard whole round track systems.

Tim Bronk and Lisa Crowder (Assistant Lab Officers) were on shift during OSL sampling. They documented the process in the following section.
X346 Optically Stimulated Luminescence (OSL) Core Curation Procedure
The technical staff was requested to curate (3-4) entire cores from two sites in a way that would minimize exposure to light. This occurred at dedicated holes, at night.
Preparation: Prior to the expedition Dr. Sugisaki (Primary Investigator) was informed that IODP had Light-proof Mylar bags long enough to fit sections if needed. Black Shrink wrap was brought by Dr. Sugisaki. It was determined that the use of the Mylar bags would be used exclusively as the black Shrink wrap was not completely opaque.
We asked the bridge to turn off the catwalk lights. The emergency fluorescent lights on the forward end of the catwalk remained on. The rig floor personnel also turned off the lights on the rig floor and derrick (the emergency fluorescents remained on). This provided considerable darkness but enough light to work comfortably.
As all of our work would happen on the rig floor we provided ourselves with a 5-gallon bucket with clear & blue end-caps, Mylar bags, acetone, markers and spatulas. We had a rain-coat to drape over the exposed end of the core liner once the core barrel was laid horizontal.
Procedure: The drill crew was made aware of what we wanted to do (i.e. collect 150cm long sections with minimal exposure to light).
After the core barrel was laid out, a rain-coat was draped over the core-catcher end. The core catcher was removed while covered and handed to a technician. The Technician attempted to process the core catcher under minimal light using a raincoat. After completion, the core catcher was placed in a Mylar bag.
The arm of the rain-coat was threaded over the end of the core barrel and a clear end-cap was acetoned onto the core liner. The core liner was pushed through into the open end of a Mylar bag and ~150 cm was measured out with a meter stick held to the outside of the bag. (Figures 3&4) A compressed air line was used to pre-inflate the Mylar bags to make it easier to push the section into the bag. At the same time a Roman number or a letter was written on the Mylar bag to note which section was being cut (the first section out was labeled I or A, then II or B, then III, or C, etc. Once we had all the sections cut we knew how many sections were actually in place). The core liner was cut with a core liner cutter and a blue end cap was quickly acetoned on. At that point the Mylar bag was folded over and taken to the catwalk platform where blue end-caps were acetoned on.
After all the sections were cut on the catwalk the sections were re-measured and the information entered into Sample Master. The Archive and Working labels were put on the core sections per usual and an additional set of labels were stuck to the Mylar bag. At this point the bags were brought inside and had the ends crimped shut with the wine bag sealer (high heat, hold for 10+ seconds) or taped closed. Note: all of the core catcher sections were contained in one Mylar bag.
The un-split sections were put in a waxed core box with additional split liners to fill up and stabilize the boxes for stacking. Information about the contents was written on the box itself.

Geochemistry Holes

Hole U1424C (Cores 4H-7H) and Site U1426B was used for high resolution geochemistry sampling (1 IW per Section). These cores were not exclusively dedicated to geochemistry and the remaining material was tracked through the core lab, split, and described.

Section Half Sampling

The following information is the general outline that was followed for section half sampling.
Working Halves
Paleomagnetism (PMAG)

• 1 per core
• Picked by Dr. Saiko Sugisaki, Paleomagnetist
• Japanese style cubes only (7cc)

Moisture and Density (MAD)

• 2 per core for 1H to 4H (~40m mbsf).
• Upper part of Sections 2 & 5 (to be near IW from Sections 1 & 4).
• 1 per core 5H to TD.
• Upper part of Section 5 (to be near IW from Section 4).
• 10 cc syringe (all samples).
• Additional samples across areas of interest (e.g. dark/light), 1 per core max.

X-Ray Diffraction (XRD)

• 1 per core (routine sampling).
• ½ of a 5 cc tube.
• Section 1 (next to PMAG sample, taken after PMAG sample)
• Additional samples picked by sedimentologists.
• Bulk analysis only.

Carbonate Analysis (CARB)

• Additional samples taken as needed to refine chemistry data.

Source Rock Analysis (SRA)

• Taken as needed to refine shipboard scientific data.

Nanno Fossils (NANNO)

• As needed
• Toothpick sample

Diatoms (DIAT)

• As needed
• Toothpick sample

PAL (Additional)

• As needed to refine ages.
• May use MAD residues (can be used routinely)

• 5cc [any additional volume approved by co-chief on duty].

• Any additional samples need to be approved by co-chief on duty.
• Shared amongst all paleontologists for analysis.

Archive Halves
Smear Slides (SS)

• Sedimentologists took toothpick samples as needed from archive halves for core description.

Core Preservation and Future Handling in the KCC

Section Half Core Wrapping

Core wrapping was a priority on Expedition 346 in order to preserve layering and to prevent the dissolution of calcareous fossils. This was a time intensive and laborious process. It was unclear how the co-chiefs specifically wanted this to be handled until we arrived on the ship in Alaska. We made due with the material that we had available on the ship. Figure 9 illustrates the core wrapping procedure, and it is detailed in the text below.
All archive halves need to be Shrink wrapped upon arrival at the KCC.

Working Halves

Glad Wrap & Shrink Wrap - For all Sites/Holes (U1422 through U1430) the top 100 meters of Working Half core material was wrapped in Glad Wrap and then Shrink wrapped (Figure 5). For Glad Wrap, we used a 1/3 cut roll to cover the top of the section half. We then completely wrapped the section half with Glad Wrap. The core material was then Shrink wrapped. This was to ensure layering in core material was preserved. The majority of quality Shrink wrap that was available on the ship was Cryovac that is a folded sheet of material that is used in the GCR core wrapping machine (Figure 6). This brought with it the challenge of side sealing the shrink film. Clayton Furman (Schlumberger engineer) assisted us in modifying a heat gun to side seal the material (Figure 7). A lesser quality tube type of 3mm Shrink wrap was also available. This was used for Shrink wrapping below 100 meters.
U1422, U1423, U1424 were Glad Wrapped and Shrink wrapped to 100 meters. From 100 meters to Total Depth (TD) the sections were Glad Wrapped.
For U1425 and U1426 oxygen absorbers were placed underneath the Glad Wrapped core liner and then Shrink wrapped for the upper 100m. From 100 meters to TD the section halves were Glad Wrapped. For Site U1426 the scientists helped us with this process to 200 meters, as calcareous fossils were abundant, and we were receiving core every 25 minutes.
Site U1427A & B provided many calcareous fossils. For the top 100m we Glad Wrapped and Shrink wrapped with an oxygen absorber inside the wrap. For 100-200 meters we followed the same wrapping procedure without the oxygen absorbers. This site was in 327 meters of water and at times we were receiving a new core every 15 minutes. The scientists requested to wrap below 200 meters, and assisted us with the wrapping. Carlos (Staff Scientist) assigned them wrapping shifts that helped greatly. For 200 meters to total depth (TD) we used the tube style Shrink wrap. The core section halves were Glad Wrapped as usual, and this outer layer of shink film helps prevent the Glad Wrap from tearing when inserted in the D-tube.
Site U1428A was Glad Wrapped and Shrink wrapped from 0-TD. Oxygen absorbers were used to 100 meters. Oxygen absorbers were not used on U1428B as we had a limited number and were saving them for U1430.
U1429A and U1429B were Glad Wrapped and Shrink wrapped from 0-TD. Oxygen absorbers were used in the upper 100 meters.
Site U1430 contained calcareous fossils in the top eight cores. For U1430A the core was wrapped in Glad Wrap, Shrink wrapped, with an oxygen absorber to 100 meters. U1430B was Glad Wrapped and Shrink wrapped without the oxygen absorber to 100 meters.
In general from 100 meters to Total Depth (TD) Working Halves were Glad wrapped.
From 100 meters to TD the working halves need to be vacuum sealed upon arrival at the KCC with the exception of Sites U1427, U1428, and U1429.
Archive Halves- All archive halves were wrapped in Glad Wrap. In all cases, a layer of this film was rolled onto the top of the section halves. The section halves were then completely Glad wrapped, and taped on each end.
All archive halves need to be Shrink wrapped upon arrival at the KCC.

Play Core

Jay Miller (Manager of Technical & Analytical Services, IODP-USIO) requested a play core for the Track Training Class (TOP) that will occur during dry dock in the Philippines. U1425A 1H-1 was a missed mudline and the co-chiefs donated this core to the JR.

PROBLEMS ENCOUNTERED

The Section Half Track Systems provided many problems during the first few weeks of operations.
Section Half Image Logger (SHIL)- The SHIL was not writing *.tiff files for many of the sections scanned. This caused us to reimage 300+ archive section halves. Many times we had to retrieve these from boxes in the reefer. Bill Mills (Lab Officer) helped to fix the software problems and assisted with the majority of the rescanning. Please see his report for further detail.
Section Half Multi Sensor Logger (SHMSL)-The core material retrieved was dark in color. This caused calibrations to be off, and we had to rescan many archive sections. Again Bill Mills helped with fixing any issues with this track system.
Core Rack Space- At a point during the cruise we realized that we would run out of space to place sectioned whole round core material. Two auxiliary racks were built during Expedition 323. These did not provide enough space. Bill Mills spearheaded a project to build a large rack in the downhole tools lab (Figure 8). This provided us with the storage space we needed for this core material.

COMPUTER SOFTWARE

Sample Maste - Sample Master was relatively well behaved during Expedition 346. Entering a comment during Section uploading sometimes causes the program not to print Section 1.
LIMS Editor (LIME)- LIME has been extremely useful on this expedition. I have successfully used it to re-parent batches of samples, delete incorrect Core entries from the drill floor, and to cancel large groups of samples.
Sample and Data Request (SaDR)-The new SaDR system that is used to submit sample requests was used for the first time on a IODP-USIO expedition. This system proved very robust, stable, and easy to use. It is also much faster than its predecessor even with the slow internet connection on the ship. I feel the system should be used on the ship for scientists to revise their requests at the end of an expedition (if time allows).
General LIMS Updates - Towards the end of the expedition I had the chance to work directly with David Fackler to add a new value in the 'Test List' field. Rhizon samples were a priority on this expedition and I did not have a practical way to extract this data from the database. We did h Rhizon as a 'Tool Name', but I am not able to search on tool name in any of our database search tools (LIMS Reports, and Web Tabular Report). David added the 'Test List' value of Rhizon and this helps me to extract this data. He also added the Rhizon Test List information to all of the Rhizon samples that had been taken previously.

This is a graphic representation of the core wrapping procedure that was implemented on Expedition 346. The wrapping methods include: (a) Glad Wrap + Shrink Wrap + Oxygen absorbers (b) Glad Wrap + Shrink Wrap (c) Glad Wrap only. !worddav76dcf4a358afea52a7fafc93aaef53e8.png|height=611,width=900!h1. PUBLICATIONS REPORT
TIM Alyssa Stephens

Summary

Expedition 346 has been a very high recovery and fast-paced, but successful expedition. The main focus of my work was to generate Visual Core Descriptions for sediment, and to proof, format, and track all volume materials (including text, figures, and tables). There are Visual Core Descriptions for nine sites and 29 holes at current, final count (9/22/13): U1422A, B, C, D & E; U1423A, B, C; U1424A, B, C; U1425B, D, E (projected); U1426A, B, C, D; U1427A, B, C (projected); U1428A, B; U1429A, B, C; U1430A, B, C. The volume materials collected cover nine sites: U1422, U1423, U1424, U1425, U1426, U1427, U1428, U1429, and U1430 + Methods and PR (Summary).
VCDs have been and will continue to be completed in a timely manner. For all holes with the exception of the last two added at the end (which we have yet to begin drilling) I have generated VCDs and hole summaries; these are complete. The final two holes' VCDs (U1425E & U1427C) will be generated promptly after coring finishes, well before we depart the ship. I foresee no issues with this.
Volume materials are being gathered. I have received nearly all materials for the first six sites, and am anticipating many reports will be turned in during the final few days. I anticipate some minor adjustments and/or new material to be added following the expedition, as the turnover time for the last few sites' volume materials is low.
Though we received high recovery, I was able to get my VCDs and other duties taken care of quickly and so was able to learn more about JR operations and assist in different capacities around the ship. I assisted with coring activities - helping on the catwalk, labeling/laser engraving, creating D-tubes, and splitting core.
Having sailed twice before, I had some experience on which I could draw, but even so, I encountered challenges (both anticipated and unanticipated), learning curves, and adjustments. However, this was mostly related to preparing VCDs and gathering volume materials for such a high recovery leg in a short time. Organization and time management were very helpful in this regard. In summation, everything went swimmingly, programs ran well, I was able to get my work done on time, and I was fortunate to sail with a very helpful group of people.
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 great extent.

Equipment & Software Performance Summary

I used Strater 3 to create my VCDs. I've used this on a previous expedition and on shore, so there was no real learning curve involved. It worked very well, with no issues arising. I also utilized Adobe Illustrator, PhotoShop, and Acrobat for some tasks. These all worked fine as expected.

Database, entries, and data upload or download related

Lims2Excel performed flawlessly. Having heard the issues reported with L2E on Expedition 341, I was interested to see how it would fare. However, we rolled back to a previous version (that I had used on Expedition 344) and I found that, just as before, it offered a fast and excellent data retrieval.
DESC also worked perfectly. Using it to extract data or fact check my L2E data was seamless. I also had no trouble exporting whole data sheets (smear slides) from DESC > Excel.

Volume Materials

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

General Duties Performed

• Collected and organized all volume materials, to include text, figures, tables (both print and electronic copies).
• Provided administrative support. This includes: assisting the scientists with various tasks, getting supplies, helping with travel issues.
• Provided graphics and publications support throughout the expedition. This includes proofing, formatting, editing and tracking all volume materials. Also, providing assistance with drawing of figures.
• Distributed and completed necessary expedition paperwork. This includes: communication policy, lab release, photo release, manuscript and copyright forms.
• Collaborated with the Staff Scientist to create server directories for the scientists, as well as creating the Publication directory for transfer of volume material to shore.
• Worked with DESCLogik administrator to create accurate data reports for use with VCDs, thin sections, and smear slides.
• Worked with L2E programmer to test, and to identify problems so that future users of L2E will not experience these.
• Worked with science party: in my creation of VCDs to ensure that the data they wish to be represented was, and that it was scientifically accurate and aesthetically pleasing.
• Provided support for methods figures and core recovery summary figures.
• Modified initial shore-created Strater templates and Methods figure during the expedition to display specific patterns, symbols, and plots. Continued to update these as needed.
• Assisted and coordinated social events, including: birthdays, expedition t-shirt contest, kite contest, and parties.

Additional duties

• Assisted in the core lab with labeling/laser engraving, and where needed.
• Selected weekly web photos each week.
• Communicated with shore staff regularly to provide updates and seek expertise.
• Restocked Publication supply cabinet as needed, and provide science party with supplies per request.

Suggestions

There was only one issue to speak of. It would be helpful to ensure that there remains a limited set of lithology selections in DESC. I'm not sure what happens during the creation/description process, but my data set will pull many different descriptors that all signify the same thing. For example: "silty clay," "silty clay," "silty clay [exp339], "Silty Clay." This may not seem like the worst problem, however, because of the way Strater (the software I use to create VCDs) is set up, it is a very time-consuming issue. Lithology patterns are set up at the beginning of an expedition, and they must be mapped to a specific keyword; Strater will only recognize that specific keyword. Any variance in spelling, spacing, capitalization, etc. renders my scheme useless for that variant entry and I must then go through and search the lithology data for each variance of the pattern and map that to the appropriate lithology. There was one site where I had to remap nearly all lithology patterns because of this issue.

DEVELOPER'S REPORT

Zhao, Fackler, Mills,

Overview

This document highlights changes to the JOIDES Resolution laboratory data management environment during Expedition 346.
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.

Curation and Core Handling

SampleMaster

CHANGED. Operating with release 2.2.4.5 since Exp 346.
Fixed that Sample Master failed to update formatted_entry when user edit component. Revised and distributed in the last week of the expedition. Used for the last site.

LaserEngraver aka LazerKatjie

No change since 341P switch to Z420 hardware. Operational with release 2.1.0.2 since Exp 342.

LIME (LIMS Editor)

CHANGED. Operating with LIME release 1.0.0, its web-services resteasy-lime release 1.0.2, and authorization component Auther release 1.0.0. First distribution in the shipboard environment. Applied routinely by the curator for sample management. Applied on a provisional basis by some technical staff for test cancellation in preference to Lims-on-Line.

Geology

DESCLogik

No change. Operating with release 3.23.7.1 since Exp 344.

Virtual core composite generation

No change. Operating with release 2.0.3.2 since Exp 336.

Stratigraphic Correlation

Correlator

No change. 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). Spent the transit clarifying bugs observed with the Lamont Borehole group. Expect to evaluate a release before the end of the expedition. A "new" correlator station with faster processor, more cores, current MacOSX 10.8.4, and increased memory was installed, but made not difference to the stability of the software.

[ LIMS2Correlator

Release 3.0.2.2 distributed in compiled form. Filed in R:\AD\DEPLOY\LabVIEW\msl\3.0.2.2.

Natural gamma (NGR)

No change. Operating with release 3.1.0.0 since Exp 341P.

[ NGR Profiling of Sensors

Additional reports of these known behaviors. Tracked down in code, but not yet fixed:

• Implicit conversion of floating point numbers from binary representation to decimal representation sometimes retains repeating decimals from the conversion process. Users would like the values rounded to 1 or 2 decimal places.
• Coreline runs totals are frequent "off" by 4-8 runs. Not clear at this time whether bug is procedural or code.

A test environment has been setup and populated to enable fuller evaluation of these issues without impacting production operations. Additional notes on the application "pending" page (development google site).

Culling Utility

No change.

Libraries

IODPUtils. No change.

Web Services

<ac:structured-macro ac:name="anchor" ac:schema-version="1" ac:macro-id="777bc549-6f28-4f9a-9541-571b9d0525c6"><ac:parameter ac:name="">_Toc367922896</ac:parameter></ac:structured-macro>SUSE OES Tomcat Servers [Ararat, Rainier, Shasta]

CHANGED. Revised server configurations to drop local access logging. Unnecessarily duplicates access logs and reporting overhead already retained centrally by the Apache HTTP server at Solaris cluster. For the duration of the expedition Ararat was removed from the production load-balancer configuration.
Restored as a production node at EOX 346.
ChangePassword. No change. Release unchanged since May 2012.
ReportOverview. No change. Operating at release 3.? since Exp 345.
WTR. No Change. Operating at release 3.0.1.0-PJR-20130720051136-hornbacher since Exp 341, last changed Exp 345.
depth-services. No change. Operating at release 2.5.1.2-PJR-b79-20110902153606-fackler.
lims-log. No change. Operating at release 1.1.0.1-PJR-b4-20110904210505-fackler.
ops. No change. Operating at release 2.0.1.0-PJR-b26-20110926101422-morgan.
probe. CHANGED. Operating at release ?. Removed from the production servers for Exp 346. Not reinstated at EOX.
resteasy-affinesplice-webservices. CHANGED. Operating at release 3.1 since Exp 346. Revised creating splice interval for new splice interval table.
resteasy-auther New deployment, at version 1.0.0-PJR- 0130730165957-zhao since Exp 346. First debut—official production release.
resteasy-desclogik-services. No change. Operating at release 1.6.8.7-PJR-20120914010615-fackler.
resteasy-drillreport. No change. Operating at release 1.0.0.5-PJR-20130718045129-howellsince Exp 341.
resteasy-error-reporting. No change. Operating at release 2.2.0.2-PJR-20120528164701-hornbacher.
resteasy-lims-sync. No change. Operating at release 0.9.5.2-PJR-b320-20120106055221-bennight. Every 4 hours trickles home currently available data.
resteasy-image-tiling. Removed on all SUSE nodes. Service can only be used on the system providing the file backing store: the Solaris cluster. No change. Operating at release 2.0.0.1-PJR-b12-20110905111358-fackler.
Observed. Image tiling process fails to complete in a percentage of cases. Not sure at this time whether it is a triggering issue or a process failure at the server. Image cancellation processes can also result in a tile set being invalidated, often without triggering the creation of a replacement image tile set.
resteasy-lime New deployment, at version 1.0.0-PJR-20130802180128-fackler.
Curator very satisfied with the new capability. Also made available on provisional basis the Cancel Test capability. Used by the developers and selected technical staff.
Outlined improvements to Cancel Test functionality for automatic, configurable provision of additional contextual cues that are necessary for conducting cancellation in some data sets. Back-burnered pending operational use of current test management capability.
resteasy-lims-webservices. Not changed. Operating at release 4.5.1.0-PJR-20130720064728-hornbacher since Exp 341.
Changes pending, some released on shore. Most related to furthering the use of the x_sample_depth model. Otherse driven by new and revised additions to services supporting the LIME product.
DEPRECATION notice. As of release 4.5.3.0, Lims-on-Line reparenting is no longer supported. Changes in web-service functionality break LOL functionality in favor of LIME. LOL reparenting functionality will not be repaired. LOL is retained for its printer management capability only.
resteasy-monitor. No change. Operating at release 1.0.0.1-PJR-b13-20110903171554-fackler
resteasy-printer. No change. Operating at release 2.0.1.5-PJR-b60-20110914204137-blaisdell
resteasy-reports. CHANGED. Operating at release 4.2-PJR-2013-08-30-06-51-10-zhao since Exp 346, last changed Exp 341. Corrects [again] the display of thermal conductivity offsets and depths. Incorporates changes to fix interval reporting.
resteasy-reqmgmt. No change. Operating at release 0.2.0.1-PJR-b33-20110905143055-fackler.
resteasy-role-management. No change. Operating at release 0.9.0.1-PJR-b182-20111103145826-bennight
sampling-services. No change. Operating at release 1.3.0.1-PJR-b9-20110905030644-fackler

Solaris Tomcat Server

Sites. Changed. Cumulus tool has moved to rosetta.ship.iodp.tamu.edu:8080/sites
labnotebookWebDav. Unchanged.
resteasy-asman. No change. Operating at release 2.5.0.1-PJR-b67-20111125070258-blaisdell
resteasy-image-tiling. No change. Operating at release 2.0.0.1-PJR-b12-20110905111358-fackler. Frequent failures to tile. Need to examine logs to see if there is an identifiable cause on the server side.

Developer Resources

Desktops

New monitors in place in the dev office. Miscellaneous software updates noted on developer site.

Servers

Load Balancing. CHANGED. Added proxy entries for web:8080. This will enable traffic for ASMAN and image-tiling to be captured in Apache HTTP logs. Implemented change in configuration, but did not restart Apache cluster service to apply the configuration change. To be tested during tie-up.
Tomcat 7 Java 7 SUSE Linux OES. No change in Java version. OES was updated to new version during last tie-up. Tomcat configuration has CHANGED—no longer recording Tomcat access logs as that information is concentrated at the Apache HTTP Server (as Tomcat redirectory/load balancer).
Subversion code repositories. No change in production configuration.
Subversion repository replication mechanism. No change.

SYSTEM MANAGER'S REPORT

Mike Hodge and James Cordray

Summary:

During expedition 346 the IT infrastructure performed as intended with minimal impact to operations.

Servers (Microsoft):

• AMS on McKinley upgraded to v1.60.

Servers (Solaris):

• The Solaris (SUN) servers performed as expected. No issues to report.

Servers (Novell):

• GroupWise WebAccess was completely stable during this expedition with no failed or hung services and no downtime.
• Continued effort on Novell case #10841431581 from last expedition concerning slow response of Novell sysadmin utility iManager. It takes approximately 15 minutes to migrate a service from one node to another node via iManager but, only a couple of minutes via command line method. Discovered from this that node Ararat was behind in updates verses nodes Rainier and Shasta. This led to investigating the Subscription Management Tool (SMT) application setup on Ararat which acts as a software update server (SUS) for all three nodes. Node Ararat was not configured to receive updates from its SMT SUS repository. The configuration was resolved and now has current updates available for install. Due to being a production environment, awaiting portcall to apply updates.

EVA4000 Storage:

• The SAN performed as expected.
• Noticed multiple emails concerning battery power low and a drive dropping offline. Contacted HP to investigate. Their analysis about battery emails concerns periodic battery discharge and recharge status, this is normal. The drive dropping offline was a one-time incident. The EVA corrected and brought the drive back online, no further actions required.

Network:

• The Network performed as expected. No issues to report.

PC Workstations:

• Performed a WalkAbout on all general purpose PCs implementing various updates. PC BIOS (v3.18), Firefox (v23.0.1), Java JREs (jre-7u25), Novell Client 2 SP3 and browser Flash add-ons or plug-ins (v11.8.800.168) were upgraded.
• Installed v2.0 Zoom upgrades on Panasonic laptops, Conference Room PC52524, PC52509 Userroom Skype station and T@Sea iPad.

MAC Workstations:

• Installed new MAC52767 Stratigraphic Correlator Mac successfully.
• Installed VDU MAC52690 in CTShop to alleviate application conflicts between RigWatch and Video Distribution video feed problems on RigWatch PC52494.
• Performed a WalkAbout on all Apple Macs implementing various updates. Firefox (v23.0.1), Java JREs (jre-7u25) and browser Flash add-ons or plug-ins (v11.8.800.168) were upgraded.

Printers:

• Sharp Copier encountered a front panel trouble code "Call for service code: F2-64". Manual says to replace "toner cartridge" but, no indication as to which to replace. Web interface stated all toner cartridges at acceptable levels. The magenta and yellow cartridges had recently been changed. This left cyan and black cartridges remaining and have not been replaced, a 50-50 chance choice. Replaced the black cartridge cleared the error message.

Satellite/Internet/Phones:

• On a couple of occasions we lost internet connectivity for a short period of time, duration was generally less than a minute. However, could observe the outage with SMTPTrafficGrapher utility. You could see the outage on both SIEM's and IODP's graph displays occurring at the same time. Causes were of unknown nature. These loss of connections were transparent to the end users.
• 08.31.2013 – multiple outages of short duration, cause due to weather conditions.
• 09.04.2013 – multiple outages of short duration, cause due to weather conditions.
• 09.21.2013 – lost satellite connection for 28 minutes, cause was a one-time pedestal error where radome lost communications with Antenna Control Unit. Power cycle of the dome and reset of the ACU cleared error condition. Equipment regained satellite connection.

Other:

• Received a new replacement tape drive for failed tape drive from last expedition. The new tape drive was defective, caused constant "Command transport failed" with biowait and bioerrors error messages. Also, caused another tape drive to malfunction on same bus. Pulled the replacement drive and reinstalled the original failed unit. Contacted HP and after verifying failed new drive had a replacement unit shipped to the office for future freight delivery to next portcall.
  • New HP case #: 4707538448
• Replaced hydraulic cylinder on Hermann Miller Aeron chair in MCS office.