Lab Officer/Assistant Lab Officer

Chieh Peng

Summary

The objectives of the expedition

Study the interactions between the growth of the Himalaya and Tibet, determine when the rifting of the eastern Arabian Sea occurred and its relation to Deccan volcanism, and to find out whether Deccan basalts extend offshore.

Operations

Two sites were accomplished and 8 holes were cored, including a short MBIO-dedicated hole (U1456B). Two holes had drilled-in casing but this didn't prevent the hole collapsing at deeper depths. We had to sever the pipe in U1456D after a bit change and a difficult re-entry. The VIT was problematic at times, resulting in some difficulty re-entering holes on several occasions. One camera failed during a re-entry operation; it was replaced and sent home to Dean Ferrell. One hole (U1456C) was logged but no VSP was performed.

Lab and Technical Services

General

• In general, there were no serious issues with instrumentation hampering normal core processing.
• A power outage during portcall resulted in a failed UPS for NGR, and the Gantry failed to find "home". All other instruments were tested for normal functioning after power returned.
• Surface sea water samples were collected on several occasions.

Core Lab

• The Minolta spectrophotometers were brought out as requested by co-chief Peter Clift, and used on cores starting U1456D-13H onwards. Data was collected and saved to DATA1. All data was saved by core numbers.
• The Pmag lab experienced the most instrument problems. We were able to work around them with caution. The SRM AF degaussing amp failed and we discovered demag problems on the X and Y axis at levels above 40 mT after replacing it with a refurbished amp. Both JR6A spinner magnetometers experienced failures, as well as an Icefield orientation tool. The Dtech 2000 demagnetizer continued to have problems despite the new power amp and replacement of several burned out connections by our ETs.
• A power supply failed on the SHMSL, and later a transformer on a PC board for SHIL also failed.
• A 4-5 cm offset in SHIL RGB data was found on images since EXP352 and issues were explored.

Focsle Deck

• There were lengthy communications between Weatherford and the chemistry technician for troubleshooting the SRA (Source Rock Analyzer). We have finally managed to bring the SRA back to full functionality.
• Erik was able to produce a reasonable calibration curve for the alternative tracer, PMDT (Perfluoro Methyldecalin).
• 22 thin sections were made, 13 of which were requested on the last day of coring. The Petrothin vacuum pump was not drawing sufficient vacuum. After investigation, we realized there is a built-in pump in Petrothin. We are not sure why it was not used. Once it was switched to the built-in vacuum the Petrothin performed without further problem.
• The hand held XRF was brought out at the very end of the cruise, and used for one hard rock core.
• PFT pumps were primed, O-rings replaced in pump A, but pump B also failed at end of the cruise. Two piston kits were ordered. They were set up but never used. Ethanol was pumped in plastic tubing.

Fantail

• GI gun was not used, and secured inside before reaching Mumbai.
• Compressed air valve on the starboard side was repaired. Air lines were realigned with a bracket.

Communications

• Internet activities remained high the entire cruise. Internet usage was restricted during most of the ship-to-shore videoconference events
• Ship-shore phone services were erratic after we switched satellites. Our MCS was able to work with Rignet and determined that the phone line priority rule was not enforced somehow. Once the priority rule was enforced, the phone service was back to normal clarity.
• Ex-LDEO office phone #233 is now shipboard internal phone only.

Computer and Data

• Discussion regarding Microsoft updates carried throughout most of the expedition. We found the smear slide PC had more than 1.2 Gb of updates pending. It took hours and several re-boots to finish the updates. The current practice is, for instrument host computers, only perform updates in the beginning and end of an expedition, and only if there is an operational break. If lab technicians need to "shut down" a computer for trouble shooting in the middle of operation, and there are updates pending, the MCS should be notified in case there is incompatibility issue. MCS will continue to monitor the update filter to ensure only security related updates are allowed.
• Raw data collected on each instrument host should be copied to DATA1 at the end of expedition. Further investigation is needed to see if there is an automatic method. However, it is the lab technician's responsibility to ensure copies of raw data are in DATA1 before end of cruise backups start.

Training

• Training were conducted for VSP endangered species watch for all technical staff. But no VSP was performed.
• Training for handling hazardous material spills was conducted; procedures and where to find spill kits were reviewed.
• Other training was conducted during EXP355T (details below)

Staff

Chieh Peng has sailed as LO and ALO. No other ALO sailed
Margaret Hastedt sailed as core lab senior tech and point of contact opposite to Chieh
David Houpt and Thomas Gorgas sailed as general core lab technicians
Adam Bogus sailed as program Aide in Underway/Geophysic lab
Aaron DeLoach and Aaron Mechler sailed in PP and T/S lab as permanent staff

Shipboard Facility

• A refrigerant survey revealed the small refrigerator in the core deck logging office has obsolete coolant and needed to be discarded. A replacement was ordered and should arrive for EXP356P in Fremantle. The portable A/C unit for the Rad Van also has obsolete refrigerant. However, the refrigerant in the A/C unit can be replaced without purchasing a new unit. It is added to tie-up list for Fremantle.
• Telephone in the core deck logging office was found to be classified as an "office" phone, which allowed users to dial an outside line. It was decided by shore managers that this number #233 will be shipboard internal phone only. It was reprogrammed as directed.
• Evaporator #2 in core reefer was found to be leaking coolant. It has been shut down and out of service since. It is added to the tie-up work list.
• Soft patch for elevator on bridge deck was serviced. All bolts were removed, cleaned, and dressed.

Anti-Piracy

On April 16 the general alarm sounded around 0800, due to a suspicious "fishing boat" approaching the JR directly and fast. "This is not a drill" captain announced. All personnel gathered in their indoor muster areas. We were then directed to our citadels. However, due to some miscommunication boat #4 personnel were stuck in the M-deck change room for an extra 5 minutes before safely making it to their citadel. It turned out that it was fishermen trying to scope out fish populations around the JR. After some post-event discussions a safer route was mapped for boat #4, and two more anti-piracy drills were conducted. Everyone feels more confident as to what to do.

Indian Navy

The Indian Navy boarded the JR on May 13, and notified us that we were in a military exercise zone. After one day of negotiation between Indian Administration and Navy, the Navy changed their exercise zone to exclude our location.

OPERATIONAL DATES

START

• Port : Colombo, Sri Lanka
• Crew change: March 31, 2015. Major problems with agent/immigration/port authority.
• Depart April 5, 2130

U1456 A/B/C/D/E

• Arrived April 9, 2015, around 1030
• Departed May 16, 2015, around 0800

U1457 A/B/C

• Arrived May 16, 2015, around 1300
• Departed May 29, 2015, around 2300

STOP

• Mumbai, India on May 31, 2015 at anchorage
• 28 PAX from science party departed. One scientist couldn't get the proper visa for India in time. He stayed aboard until Colombo.
• US Embassy staff visited the JR on June 1, 2015

END

• Port: Colombo, Sri Lanka, June 6, 2015
• Ship scheduled to arrive June 5, 2015

PORT CALL INFORMATION

March 31

• The 10am bus scheduled originally for on-coming crew never happened. Ten technical staff were selected to board via 2 small vans for cross over, one per lab. Didn't arrive at vessel until 1500.
• Off-going crew divided into 4 groups, but didn't start to depart the vessel until after 1500. The last group spent more than 2 hours at the port authority office and didn't arrive at the hotel until 0215 April 1^st .
• The rest of on-coming technical staff arrived onboard around 2200.

April 1

• EXP355 scientists came on a bus and arrived at the vessel around 1200
• Life at sea presentation
• No shipment activities due to personnel change difficulties
• No ALO nor curator came back to the ship due to difficulty obtaining a shore pass

April 2

• World Courier shipment, 11 frozen, 4 refrigerated samples (igloo) were offloaded. Due to elevator issues all samples were taken to the pier manually. Blue ice and dry ice were added on the pier.
• Started offloading the core shipment around 1800. All technical staff stayed and finished the offloading around 2030.

April 3

• Lab safety training and tour

April 4

• Brad J presented "ship is here" power point
• Offload the rest of the EXP354 shipment
• Ship moved 2 lots, our staff helped on the dock as line handlers
• Technical staff helped with food shipment
• Continued on-loading freight

April 5

• Continue help with food and IODP shipment
• Ship power went out unexpectedly around 1600. NGR UPS failed. Other instruments tested OK after power came back on
• Ship sailed 2130

TRANSIT ACTIVITIES

April 6-9

• 4 days transit from Colombo to first site U1456
• No towed magnetic data was collected due to international regulation
• Lab instruments were tested and calibrated
• Scientists were trained in individual labs and moved onto shifts
• GI gun was left on deck due to planned VSP at first site. It was inspected.
• PFT pump was primed with pump A not functioning. After changing out the piston O-ring it functioned properly.

June 1-5

• 5 days transit from Mumbai to Colombo
• Staff meetings at 0700 from June 2-5
• Training conducted including the use of AED by Dr. Gene, general training for shipping hazardous material with Dry Ice, and "what is AMS"
• Most staff submitted transit project lists, including reviewing SOP/UG/QSG, physical counts of inventory items, reviewing ROP/SL on inventory items, periodic maintenance of various instrument/equipment, cross training in chemistry, DESCLogik, Underway, and T/S labs
• Cores were palletized
• Unused staterooms on Upper Tween are locked

AMS/Inventory

• CT pointed out an inconsistency when running a report between Part Usage History and Usage Summary. Many items show different quantities using the same searching criteria. Saravanan replied that there is a calculation issue using the Usage History screen because of the "From Date". But the warehouse and inventory usage data is correct. So currently, if you are using Usage History you need to search with the default date which is 2003.
• Core Logistic spreadsheet is updated
• Suggestion for EXP356 bulk items shipment was sent
• EXP355 hazardous airfreight T35517a, didn't arrive for Colombo1 port call. Twelve gallons of acetone was purchased in Colombo.
• At the beginning of the expedition we could not locate any 10cc foam plug (LS0206). AMS indicates we should have 20 bags of 500 each. After email exchanges and global search, Maggie found them two days later buried under the shipment that came in during portcall. All 10cc foam plugs are now re-located in the blue plastic barrel and well labeled.

SHIPMENT

• F355_SURF1- contains Gas Racks, misc. empty K-boxes, 1 pallet of 19 boxes of core, and 1 pallet of 10 boxes of core plus 15 boxes of residues
• F355_SURF2 – contains 13 pallets of 19 boxes of cores/pallet. Core shipment goes to GCR.
• F355_FLAT – engineering items, including 2 rental mud motors
• F355_RAF – 2 yellow boxes of data, samples, and instruments, Icefield orientation tool, Schlumberger tool
• F355_FAF – 15 pieces
• World Courier shipment – 2 recipients, total of 7 frozen, and 3 refrigerated containers.

core description DESClogik

M. Hastedt

SUMMARY

DESClogik was reasonably well-behaved again this cruise. We actually had fewer core describers than usual and a smaller overall science party. We used Autosaves just a few times to recover after upload hangs, with one Autosave failure – for some reason the upload snapshot failed to capture the last 3 or 4 rows. I noticed that the progress bar associated with the Clear button this cruise had a habit of staying on-screen after the process finished, similar to what we frequently see with the Export button.
Internet slowdowns were problematic early in the cruise yet again, making it quite time-consuming to do additions and refreshes on our Google master lists. Unicode characters in some author references prevented successful imports into DESC until they were resolved in the Google lists. The Google lists handle the Unicode characters just fine but our database isn't nearly so tolerant.
One Internet-related problem arose very late in the cruise when the ship's Value List Manager (VLM) lost the ability to refresh straight from the DESC Google pages. The error message we see on this end is involved with account privileges being changed. Paraphrasing the developers it probably has something to do with the back-end processes of the VLM and the changes Google made to the DESC spreadsheets. Those spreadsheet changes were to be made by end of May and sure enough that is exactly when we started having real issues. So in the interim we download any value list or sublist sheet we need from Google and sync it offline using the Excel links feature of the VLM.
DESC's sample disambiguator (the function that asks you how to proceed when it sees multiple identical samples in the database for a single descriptive interval) still complains even when said duplicate samples have been canceled in LIME. It's cached the information somewhere. Developers are working on a fix for this. Note: once you complete a disambiguation DESC will honor it for the rest of your session until you log out.
The Margsaglia et al. smear slide collection were not signed out by the sedimentologists but they did find the PDF tutorials useful. Our smear slide specialist Sergio Ando may contribute another addendum focusing on heavy mineral recognition. Speaking of which, the smear slide scientists requested a further breakdown of the heavy mineral subassemblage within each slide's total grain population so that they could track changes in abundance of these minerals.
Per my usual habit I downloaded the most-used master lists from Google to Excel at cruise beginning and put them on Uservol as a 'shopping aid' for the scientists. This helped them avoid having to use the miserably slow Internet connections out here and edit their sublists more easily.
I added more Munsell GLEY-2 soil colors to our master color list in Google as only part of them were present. I also wrote a simple User Guide for how scientists (mainly the Paleos) can print extra sample labels as at least one scientist was re-entering his samples just to get another one! A copy has been placed at the root level of the "all things DESClogik" folder on IODP_Share. I began work on a document detailing how to work offline using an Excel export of a DESC template but it needs more work. It was an attempt to help a very DESC-averse scientist but ultimately turned out to be unnecessary. Getting a list of samples from a LIMS report and reformatting for pasting back into DESC is detail-oriented. I made a couple of macros in Excel to make things easier.

SEM

The SEM was not used very much this cruise, even though there were several days-long periods with no core. A number of sea water samples at surface, 5 m, 10 m, and 15 m were taken and yielded some assemblages of present-day diatoms and radiolarians. SEM images were taken in a few cases. The sea water samples were used to compare fauna found in the mudline samples since most of the rest of our sites were essentially barren for rads and diatoms.

Leica Sputterer

The sputter coater was not used this expedition.

Misc

The Paleo Prep lab was especially busy and full this leg with four disciplines (nannos, rads, diatoms, and forams) all competing for countertop and hood space. One of the centrifuges was moved from the Chem lab upstairs for the diatom scientist. It will be returned at the end of the cruise.
Sedimentologists:
Boo-Keun Khim
Ravi Mishra
Sergio Ando
Anil Kumar
Kenta Suzuki
Huayu Lu
Zhaoki Xu
Mitch Lyle
Biostratigraphers:

PHYSICAL PROPERTIES lab

Aaron de Loach, Thomas Gorgas and David Houpt

Summary

Expedition 355 Physical Properties Lab ran successfully. Various errors occurred on most machines, and all but one problem persists. The descriptions of the errors, probable causes, and their resolutions are contained within this report.
Measurement Counts as of 05/31/15:

Velocity Gantry

Problems

1. The P-Wave station began malfunctioning after a 1 sec ship power failure. The Y-Bayonet would not home when the program was opened. After various efforts to correct the issue using the motion utility, no P-Wave bayonet or caliper was functioning, showing very slow or no response when the velocity program was opened. The drive file found in the file path below was loaded in Exlar, and normal function was restored.

C:\VELOCITY\Support\Exlar drive configs\VELOCITY-CALIPER\Drive Files
The various drive file directories were cleaned up to avoid mistaking the correct drive file for one of the out-of-date versions.

1. The position laser would not turn off, and a timeout error prevented the velocity and AVS programs operating. Powering off the laser was not sufficient. The developer used the PuTTY program to reset the laser, but additional problems with the laser readout were noted by the scientist. In the reset, it was necessary to set the laser range to the centimeter scale (its default is meters). This was done by the use of the command "SF 100," or Scale Factor 100, entered through the PuTTY terminal window.

Technical Service

Cleaning and calibration of Y/X bayonets and caliper with distilled water and acrylic cylinders was performed at the beginning and end of the expedition, and verification measurement were made throughout. At various times throughout the expedition the end caps were removed and both surfaces of transducers and end caps cleaned. A drop of propylene glycol contact solution was added to the surfaces to ensure good energy transmission throughout the various components of different materials (stainless steel end caps; piezo-material of transducers, etc.).

MOISTURE AND DENSITY (MAD)

MAD was run successfully.

Problems

1. The oven threw error #13 (over heating) continuously, but with the alarm turned off, it presented no problem. The error was identified as an open "Kilxon Contact," a faulty temperature sensor, requiring an exhaustive servicing of the oven to remedy. This was deemed unnecessary as the oven maintains temperature.
   1. The spare oven should be shipped to the ship and swapped out for this one, until this overheating issue is resolved.
2. Core material recovered at site U1456D required saturation. However, the material was not well lithified so the Aluminum cylinders were deployed. It was revealed during experimentation that an incorrect mass and volume were stored for container 20. The values were updated, and the data recovered. Further testing of the cylinders is planned during transit from Mumbai to Colombo.

Technical Service

New MAD residue labels were deployed which allow the labels to be placed directly on the vials for compact storage and shipment. The vials should be repacked in the original boxes.
The pycnometer cells were calibrated at various times and verification values entered into the Excel spreadsheet. The cell O-rings were cleaned and lubricated at the beginning and end of expedition.
NOTE: The helium cylinder in the splitting room has a pressure value of 350 psi, and it should be changed at 200 psi, or 10% of the cylinders normal fill pressure, according to David Houpt. The pressure dropped approximately 200 psi from beginning to end of expedition.

SHEAR STRENGTH STATION (AVS)

Problems

1. Shear Strength station data uploading remains problematic, usually the result of the operator improperly formatting of the file. A new version of MUT was installed initially at the beginning of the expedition, which prevented any files from uploading. The programmers released a new version of MUT and the issue was resolved.
2. The Pocket Penetrometer/Torvane read-out within the application and data display on LIMS were off by a scaling factor of 1,000 (kPa vs. Pa). The developers must change the unit within the LIMS report.

SPECIAL TASK MULTI SENSOR LOGGER (STMSL)

At the beginning of the expedition a new version of the MSL program, version 6.0, was deployed. The new version is equipped with a 2.0 cm sampling interval, and most of the measurements performed on the samples were done at this resolution; at times, the scientists used only a 5.0 cm interval.
Over the years it has been (repeatedly) recommended that it would be great to keep the data of last measured section (normally the H₂O Standard core) on the display window for longer than just the actual measurement run. Currently the data disappear as soon as the measurement cycle is completed, including the water standard. It would be better to allow the water standard data to be displayed long enough to study the data quality, for the case the operator does not watch the entire run but has step away to do something else. Another recommendation is that the scale of the graphical display can be modified during the run and also be retained on the screen.
These requests should be funneled into the IMS implementation that is planned for the Exp. 356P maintenance period.

Problems

1. STMSL was giving an error after scanning the sample and attempting to start the run. The bar code scanner wasn't separating the sample ID and text ID properly. The scanner was reset several times. The bar codes rules are stored in the Phys Props Tech Manual (white binder located bottom left cabinet of T-Con station).
2. The MS system was giving a NaN value approximately once per 200 measurements, caused by the failure of serial communications between the PC and the Bartington MS2 meter. Switching out the MS2 meter had no effect (with the exception of some confusion because of an older unit with different communication settings (see #4, below).The NaN values persisted. Various combinations of MS loops, meters and measurement iterations were tried with no effect. Ultimately, a RS232 serial card, Startec, was replaced in the STMSL CPU. The frequency of the NaN value was reduced to approximately one per 2,000 measurements, at which it remains.
   1. Per Change Hardware Notification it was stated: "The serial connection on the STMSL was demonstrating occasional faults (dropped data points on magnetic susceptibility (MS)) and the meter, loop, cables, etc. were ruled out as the cause. The Startec serial card was replaced with a National Instruments one and the problem appears to have been resolved." Actually, remains minimized.
3. It was determined that the calibration values of the P-wave and GRA will not take effect unless the program is closed and restarted after every calibration.
4. The older MS2 meter (which is restricted to 1200 baud communication speed, and also uses a different bit/stop setting) will be sent to shore to avoid confusion. All of the newer MS2 meters have variable communication settings, and can be set to the expected values.

The ability to recalibrate inside the software and not have to close and restart LabVIEW is another requirement that should be added to the IMS implementation if possible.

Technical Service

David Houpt ran a statistical analysis on the MS data between both track systems. The data shows an over correction an average of 9.213%, concluding that the correction factor should be lowered to 1.174 from 1.282. At the time of this report David Houpt was in communication with the manufacturer for additional input.
Cleaning and calibration of the instruments on the STMSL was performed periodically throughout the expedition (e.g., plastic shield emplaced above source hole; when this gets dirty, the density values for the water standard begin to rise above the allowed 1.02 g/mL value).

WHOLE ROUND MULTI SENSOR LOGGER (WRMSL)

At the beginning of the expedition a new version of the MSL program, version 6.0, was deployed. The new version is equipped with a 2.0 cm sampling interval.
The WRMSL ran with several minor errors.

Problems

1. Several times during the expedition the track motor would stop during measurement and give a GALIL error message. The pusher was homed and the sample was re-run after restarting the program. The problem was resolved. Operator error is suspected as the primary cause, such as scanning the sample label while the mouse cursor was outside of the sample ID field.
   1. The developers are aware of this issue, and some discussion was had about coding the WRMSL/STMSL to prevent this from happening; we expect that the IMS version will not have this problem, but Exp. 356 would benefit from this bug being fixed.
2. The GRA's lead/PFTE holder for the detector was extruding about 1 cm from the top of the metal casing as the assembly jammed and could not be replaced completely. The positioning nuts were also not fully engaged, allowing the detector assembly to be off-center (leading to some tedious and repeated recalibration efforts to attempt to get consistent results). The assembly was dis-assembled and the PFTE insert was lathed down a very small amount (as it was determined that the insert was the sticking point); the assembly went together completely after this.
3. It has been proposed that the rotational alignment of the NaI(Tl) sensor and its PMT and DigiBase is critical for proper calibration, but the NaI(Tl) sensor is radially symmetrical and the trouble with calibration and getting good reproducible values is probably not due to the rotational position of the NaI(Tl) sensor, but rather its positioning in the cross-core axis. The only calibration issues that I am aware of later in the cruise were due to mud on the protective shield.
4. At some point the measured values on sediments simply significantly drifted off (for example for cores between U1456A-52F-1 to U1456A-60F-3), which consequently was visible in markedly higher density values (up to 2-3 g/cm³) than the cores below or above that core interval. Re-measuring the actual cores to see whether they consistently reproduced much higher values on the same core material was only semi-successful because the cores have been split already. But ultimately this weirdness in data behavior was related to the fact that the GRA sensor wandered off from the normally expected value range (as observed in the typical 1.0 g/cm³ +/- 5% value range for the H₂O Standard Core) to some higher values. We were not able to reproduce such values at any time throughout the expedition, nor has it been observed to that extent in the past. It remains entirely speculation whether this was caused by something questionable, like "Installing Updates". Generally speaking, the WRMSL seems to behave a bit more erratic than the STMSL (in terms of "accuracy" and "precision"), and it might be worthwhile to investigate a bit more why that is.
   1. I also have no explanation for this short-term drift from accepted values, as the mere presence of some mud on the protective shield only increases values by a very small percentage. The problem did not recur, and the more important issue is that the questionable values should have been caught prior to splitting. The STMSL was run on all cores after this point, even though it wasn't needed for correlation, in the case that the WRMSL values again "wandered away" from reasonable, but this proved unnecessary.

5. The MS-Loop (WRMSL only) showcased a whopping value range to [-20] - which for our materials (any we measure?) do not exist. Furthermore, the MS-Point sensor on the SMHSL measured very reasonable values in the range of expectation for the corresponding material (U1456E-4R-4). Most likely, these rather unusual values were caused by an operator forgetting to remove a core section out of the loop prior to zeroing the meter and causing a significant negative offset.

6. At the start of the expedition the P-wave was configured such that the software was not selecting the first arrival peak, even on the water standards. The stacking and threshold voltages were increased to 0.0025 and -0.0002 respectively. After the P-Wave logger was idle for 2 weeks, the same problem reoccurred. The stack and threshold voltages were increased to 0.01 and -0.001 respectively. The problem did not reoccur.
   1. It should be noted that the core sections were quite gassy and highly fragmented and that many of the samples did not give (and were never going to give) good p-wave data. Eventually, the scientists chose to discontinue p-wave measurements, as the higher stacking value led to quite long measurement times each time the p-wave signal was poor.
7. For measurements on hard rock, often only the top portion of the core liner is filled with specimen, while the bottom portion remains empty (e.g., material fills core liner to 120 cm while the core section liner is by convention always the full 150 cm length of a normal section). This causes the "empty" portion to produce spurious values, but checking past expeditions' data in the shore database shows that this has occurred historically.
8. LIMSPEAK issue: The LIMSPEAK program uses created length to display the section boundaries, not curated length. This is problematic when hard rock sections are analyzed, as the data positioning is shown against the curated depths + offsets, creating a somewhat confusing data display. LIMSPEAK (or its replacement) should be changed to use curated length for its display of section boundaries, as no context exists to show created length when the curated length is different. This problem exists with re-curated sedimentary sections, but these are much rarer and usually of small magnitude (e.g., 1-3 cm) so it's not as obvious.

Technical Service

Cleaning/lubrication of P-Wave caliper with silicon spray and DI water was performed periodically. At various times throughout the expedition the end caps were removed and both surfaces of transducers and end caps cleaned. A drop of propylene glycol coupling agent was added to the surfaces to ensure good energy transmission throughout the various components of different materials (stainless steel end caps; piezo-material of transducers, etc.). Periodic calibrations were also performed on the GRA and P-Wave.

SECTION HALF IMAGE LOGGER (SHIL)

The SHIL continues to have an issue writing the RGB data file. The RGB file is inconsistently shifted down by a few centimeters, a problem confirmed to have begun during Expedition 352. The result is the top few centimeters of the section is not recorded and the area past the section is being added. Efforts by a working group to correct the issue were still underway at the time of this report.

Problems

1. The MDrive (motor control) failed late in the expedition. There was no power being supplied to the motor, although the 75V power supply was functioning. The armature could move freely, and no error message was displayed. The problem was traced to a failed regulator in the PC motor board. The board was fixed by the ETs replacing the regulator, thus avoiding changing the entire board.
   1. Per Change-Hardware Notification it is stated: "After working well for most of the cruise, the SHIL's MDrive went dead (no indicator lights; actuator was free to move). The 75V power supply was functioning properly, so Etienne traced the problem, finding that the power PC board for the MDrive had failed. Removing it, he further determined that the transformer component (edit: this was a regulator, not a transformer) had failed (the rest of the PC board unit, fuses and relays, appears to be okay). We located a spare PC board (it had been mounted on the SHMSL in preparation for its eventual conversion to MDrive configuration, but not used) and installed it on the SHIL, returning the logger to normal function. To be considered:1. Are these components not robust enough for the shipboard environment and the load being placed on them?2. Did this failure occur because of power surges, similar to the two failed personal computers (PCs), one of which was a power supply, and other electrically-related issues during the cruise?3. Assuming the components are robust enough, is it cheaper to order additional transformers (these screw onto the board and are easily switched out) or additional boards with transformers attached?4. If upon consideration, we think the transformer's too weak, can we buy a higher-rated one in the same form factor?5. In the supplies Bill Mills has acquired and shipped for the whole round logger IMS conversion, are there sufficient additional power boards to serve as the needed spares? Or do we need to acquire more boards (or transformers) and get them into A/F for Colombo or Freemantle? Bill (Mills), if you could advise as to whether you think we need to invest in a heartier transformer, and whether buying just the transformers or the entire board including the transformers is cheaper, we'd appreciate it."

Technical Service

Cleaning and calibration was performed by Bill Crawford.

SECTION HALF MULTI SENSOR LOGGER (SHMSL)

The SHMSL functioned well throughout the expedition.

Technical Service

Both bulbs were replaced in the Ocean Optics during this expedition. Some difficulty was experienced at first as the set screw location (under the cooling fan) was not remembered.
The white Spectralon standard was cleaned and polished twice. Set screws were added to allow the advancement of the standard material out of the aluminum holder for polishing; this extends the lifetime of the standard considerably.
When cutting Glad wrap, the band saw will melt the ends together making the roll difficult or unable to peel. After band sawing, the melted ends should be trimmed with a knife or hacksaw.

Problems

1. As per Log of the MCS's, it is stated: "Power supply failed in PC52715 SHMSL, symptom was 4 beep with 2 second pause then repeat with a red indicator on power switch instead of normal blue indicator. Unplugged all cards and peripherals except motherboard, still got beeps. Pulled P/S from PC52714 for exchange, plugged up bad P/S so as to know how to replace when replacement arrives." The suspicion is that a power surge killed the power supply, coinciding with other technical problems in the lab around the same time (somewhat erratic therm-con measurements of a brand-new half-space probe on the MACOR Standard; a light bulb burning out on one of the microscopes; another Lab-PC having trouble). This could also explain and be the reason for a power supply failure on the SHIL toward the end of the expedition (note: this is all speculation and not substantiated by any evidence.)

Additional Details/Observations

At the request of Peter Clift, the Minolta was used to collect reflectance spectra for some of the sediment cores as time allowed. Analysis by David Houpt of the RSC data showed a potential for identifying Hematite (H) and Goethite (G) from the ratio of the first derivative of the 565, 535, and 435 nm wavelengths. See reference list at the end of the report.
Minolta data obtained on several cores showed a distinct peak in the ratio discussed which could then be used to identify areas where the minerals might be present. The presence of these minerals were tentatively confirmed by P-Mag measurements of the hematite (obtained by thermal demagnetization experiments). These exercises are not recommended for a high recovery cruise.
Comparing the SHMSL RSC values for the same cores does not yield an as distinct peak, which was the initial cause of the displeasure expressed by one co-chief scientist (Prof. Peter Clift). His insistence on the faulty data quality for this particular waveband interval triggered a whole range of methodical instrument and data analysis experiments, which eventually led to the conclusion that the SHSML is incapable of producing data for aforementioned mineral detection on H and G. The heavy noise in the blue end of the spectrum is likely a result of the halogen bulbs used in the Ocean Optics system.
Management must determine if the color reflectance spectra and the first derivative of those spectra are important enough to warrant improvement of the color reflectance system. The CIELAB L*a*b* and Tristimulus XYZ data obtained from the Ocean Optics system compare reasonably well with those values from the Minoltas. This is because the power functions for these color space values integrate over a very wide range of wavelengths and are both relatively insensitive to the blue end of the spectrum. Further, in a qualitative sense, the raw spectra are also comparable (the overlaid graph of diffuse color tiles, below, shows this behavior). Differences between the Minolta and Ocean Optics color tile spectra, as well as the slight differences in a* and b*, can be attributed to the fact that the Minolta is calibrated against a glossy color target and the Ocean Optics against a diffuse color target.

Fig. 1: Minolta (10 nm bins, diamond markers) vs Ocean Optics (2 nm bins, round markers) for diffuse color targets
Fig. 2: Minolta (diamond markers) vs Ocean Optics (round markers) for Tristimulus X.
Fig. 3: Minolta (diamond markers) vs Ocean Optics (round markers) for Tristimulus Y

Fig. 4: Minolta (diamond markers) vs Ocean Optics (round markers) for first derivative plot; note that the peaks at 435 and 535 nm are indicative of goethite and the one at 565 is indicative of hematite. Note also that the Ocean Optics peak at 435 is missing (the rise to the left of that is due to signal noise) and the peaks at 535 and 565 are significantly reduced.

NATURAL GAMMA RAY (NGR)

The NGR functioned well throughout the expedition. A few minor issues arose as a result of operator error.

Problems

1. When scanning the core sections, if the cursor is not within the label ID window when the operator scans the section label, and then clicks the measure button, the experiment will proceed as if normal, but no file to save the measurements in will be created. Thus no data will be recorded and the section will have to be rescanned. As always, the data should be checked before splitting using LIMSPEAK and by selecting the SYMBOL option of the application to display the data. This is because LIMSPEAK draws a line between data points, and it may not be possible to see that data are missing without displaying symbols. It is recommended that a check list be created by the Physical Properties technician to assure the data is collected, and is within the expected range for the given material.
2. At the beginning of the expedition (around April 4^th) a power outage caused the NGR to shut down. Powering the system back up thereafter following standard procedures showed no signs of problems. The ET's have suggested the purchase of a different type of UPS to protect against a recurrence; this type feeds A/C power from its batteries at all times and line power merely charges the battery, so the A/C power output is completely isolated from the input.

Additional Details/Observations

A background was run upon or near the arrival of the ship at each of the sites. A calibration was verified at each site and performed as deemed necessary. Cleaning can be more easily performed if the rear door of the NGR is lifted with the use of a vacuum and the "NGR Cleaner" rod, which was performed at the beginning of the expedition. The users were sufficiently careful about muddy/wet core sections that the acrylic tube did not need cleaning mid-cruise (but this is unusual and the tube should be checked regularly).
The user manual for the NGR has been edited, but it has not been updated. The manual should be updated.

THERMCON

The Thermcon was run successfully throughout the expedition. Communicating with TeKa, Berlin, allowed us to implement a data cleaning work protocol within the software application, which further enhanced the overall data quality.

Problems

1. Serval times the data files were created with an improper name, so they were not uploaded to LIMS (due to operator error). The file names were changed manually and the files could then be uploaded.
2. One time a scientist stuck the needle probe first into the core, and then directly into the MACOR standard material. ET soaked and blew out the dirt from the needle probe to restore the original material property of the MACOR standard.

Additional Details/Observations

There are a number of ways the experiment can be altered to produce results and better quality data. If the results are poor or the program will not give a result, a good first step is to try lowering the heating power. A heating power as low as 0.5 W is likely the lower reliable limit for the small-sized pucks. A heating power of 1 W is still the recommended starting point for the small-sized pucks, whereas for the larger pucks and/or needle probes higher heating powers might be a good choice (1.5 -> 2 W/m²). An additional way to improve the success rate of the measurement is to cleaning the probe or puck and applying a very thin coating of thermal compound and wiping it off.
Boundaries within the test section as well as the size of the core can effect results dramatically. Moving the puck over several centimeters to a section with a greater diameter or less cracks can give a good result, where the previous section did not. In general, it is worth experimenting with the various parameters.
Evaluating data in the TK04 graph program is aided by a pilot project conducted by one of our developers (Algie Morgan) during EXP350, which allows the renaming and reformatting of the original files such that they are easier to identify (per actual EXP-Hole-Exp Label ID vs. its corresponding Text ID). The reformatting portion is important to allow all files to be displayed properly by TeKa Graph and thereby check the data quality post-measurement. Testing of this program (Thermconfileconverter) code should continue. It can be found in the following link;
http://web.ship.iodp.tamu.edu/tasapps/thermconfileconverter/

GENERAL

1. Several cores were split without having checked the WRMSL data, only the STMSL data was verified which is typically not equilibrated. No data was lost. The Limspeak displays for the STMSL and WRMSL are nearly identical making this mistake likely to reoccur. A good way to reduce the risk of data loss due to premature splitting would be to have all whole round track data displayed on one Limspeak window. This would also reduce the number of Lims windows open across the Core Lab.

It would also be advisable to use the curated length to display such data so that all data will not display the often large portions of empty core liner scanned when running hard rock. It is the standard technique to use full section liners when curating hard rock throughout the history of the program.

1. A method for removing duplicate data has been developed and an instruction sheet has been stored in the physical properties folder.

SHIPMENT TO SHORE

1. Logging sheets for all instruments, and Phys. Props. Scientists' notebook

PALEOMAGNETICS LAB

Edwin Garrett

Summary

The paleomagnetics lab was experienced quite a few technical issues this leg, but we were able to work around most of them and some of them were resolved during the leg. The SRM AF degaussing amp failed and we discovered demag problems on the X and Y axis at levels above 40 mt. Both JR6A spinner magnetometers experienced failures, as well as an Icefield orientation tool. The Dtech 2000 demagnetizer continued to have problems despite the new power amp and replacement of several burned out connections by our ETs. There were also some problems with core quality (sand, small XCB biscuits, voids) that precluded the use of the SRM and so discrete samples were taken one per section (assuming the section had reasonable material).

The D-Tech AF demagnetizer

The D-Tech AF demagnetizer amp was switched out with a new crest amp, but this did not resolve problems with the unit. The ETs serviced the D-Tech controller and replaced some burned out part, and this seemed to help for a while, but problems returned. It would still hang up during the demag cycle. At random times the program would freeze and all the lights on the Dtech would go off, but on several occasions power was still being delivered to the coil, which started to overheat. The Dtech would need to be power cycled to work again. Turning it off for a while seemed to help. Also for most of the leg we only used the A channel of the amp and did not have it at full power. The scientists measured the field delivered and altered their inputs to get the desired field delivered. We still ran it off the laptop which helped a little to reduce the frequency of problems. The scientists also shut down the amplifier and the Dtech controller between each set of experiments (at least once forgetting to do so, repeating the overheating behavior).

Kappabridge

Kappabridge was returned this leg and none of the errors experienced on previous legs occurred, so most likely the replaced serial card in the computer had been the problem. However the scientists complained that the data from the Kappabridge and the JR6 spinner magnetometer was not uploaded to the LIMS database, and this was a serious deficiency. David Fackler spoke with them and looked in to the issue but had no time during the leg to add this functionality.
There have been on-going issues with the naming convention used for samples measure with the Kappabridge and the JR6A. Since both programs are 3^rd party programs not linked to our database, no naming convention is enforced. In addition the JR6A has a limitation of 8 characters that can be saved in the data file even though it allows more than that to be entered. It was decided to use the scan code printed on the sample cube labels as the sample name. Two additional scanners were obtained and each was programmed to scan the sample cube ID into the name field in the Kappabridge and JR6A programs. We need to order an additional scanner as one was borrowed from the computer specialists.

JR6A minispin magnetometers

During the leg both JR6A minispin magnetometers failed. The first failed during port call because it would not perform a holder correction at high speed. We replaced it with the spare JR6A. The manufacturer was contacted and sent instructions to disassemble the unit for cleaning and for downloading a command line test program, JR6SERVR.EXE. The program and instructions were copied to V:\IODP_Share\PMAG_Documents\JR6A spinner. During the cleaning the shaft came loose. The set screw was not tight enough. This appeared to be the reason it did not function on high speed. Maggie put it back on and tightened it. It worked properly for a week or so but failed again for the same reason. The ET re-attached the shaft and used lock-tight on the set screw so it wouldn't come loose again. It required re-alignment using the procedure in the manual. The spare JR6A also failed when the manipulator stuck and would not move. The ETs found that a wire to the sensor had come loose and replaced it. It worked for a while but failed again when another wire came loose. The ETs then replaced all the wires to the sensors because they were too short and the filaments too thin. It functioned properly the rest of the leg. For testing purposes the JR6A program was installed on the temperature probe computer in the logging area.

Icefield orientation tools

All three Icefield orientation tools were used, but on Hole U1457A the scientists reported that the data from cores 7 to 12 looked bad. Tool 2007 was used for those cores. Subsequent tests and comparisons to the other tools showed that the tool was not functioning properly. The data returned was erratic and the earth's magnetic field was reported at only a small fraction of what it should be. This tool took a severe jolt at the very end of leg 353 and seemed to function OK afterward, but this may have been the root cause of the problem. This tool will be air-freighted to shore for repair.

SRM AF demag

The SRM AF demag amp died during the leg. Something, probably age, caused several resistors to burn (although it was coincident with other electrical failures (e.g., SHMSL host power supply failure) that occurred early in the cruise, so it may have been power surge related coupled with aging components). It was not repairable because it was old and the ETs did not have parts for it. They repaired the A channel of the old D-Tech amp and we used it to replace the burned out unit. We tested it to make sure it had enough power and that the AF fields produced were accurate. We used the hall probes placed inside foam inside a core liner. In checking the X, Y, and Z axis we found that all functioned properly and accurately up to 40 mT. Above that, however, the X and Y axis to ramp up to just above 45 mT then quickly ramp down to about 20 mT even though the controller showed them still ramped up. We thought the amp might not have enough power, however, the Z axis had no problems. We tested above 80 mT and got a stable and accurate field on the Z. We thought the problem had been caused by the failed amp, but then a pmag scientist reported that he had some unusual/erratic data points from samples that had been degaussed above 40 mT before the amp had failed, so this could have been a pre-existing condition. We called Applied Physics and Frank said that first, after replacing the amp it needed to be tuned to the coils and second, if there was a problem it could take an experienced technician a day or more to troubleshoot it. A new CA12 amp was ordered and the techs and ETs will investigate the tuning procedure during the transit.

Cryo Magnetometer

At the start of the leg the cryo cooling absorber was changed. Since they should last at least a year, it should not need changing before the new magnetometer is delivered. Also it was determined that the cryo might not have enough liquid helium to last until replacement, so a helium refill has been scheduled for the tie up period.

Cryomag readings

CURATORIAL REPORT

Chad Broyles

SUMMARY

Samples

A total of 6,571 samples were taken on Expedition 355. This included 4,430 shipboard samples, and 2,140 personal samples. 1,721.58 meters of core material was recovered during the expedition with 65% average recovery.
Personal samples were limited to: Geochemistry (Bendle, Bratenkov, Clift, Griffith, Gurumurthy, Liddy, Tiwari), Microbiology (Kumar, Subbarao), Paleontology (Saraswat), and Sedimentology (Ando, Lyle, Pandey). Any additional personal sampling will occur at a sample party held at the Gulf Coast Repository (GCR) in August, 2015. I am including an excel spreadsheet with the sample information in the email that includes this report (355 LIMS Download Curator Report.xlsx).

Shipments

Core-Approximately 15 pallets of 276 core boxes will be shipped from Colombo following the expedition to the GCR in College Station, TX. The core boxes will be divided into Working and Archive pallets. The electronic Core Box Inventory is being sent via email with this report (EXP 355 Core Box Inventory 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 355 Core Box Inventory Handwritten Archive.pdf & Exp 355 Core Box Inventory Handwritten Working.pdf)
Frozen and Refrigerated Samples-Frozen and refrigerated shipments are being sent via World Courier during port call in Singapore.
5 frozen coolers and 2 refrigerated coolers for Ganesh Kumar (KUMA) are being sent to:
Dr. Ganesh Kumar
Marine Biotechnology, National Institute of Ocean Technology,
Velachery-tambaram high road, Pallikaranai
Chennai
TamilNadu
India
600100
email: microganesh@yahoo.com
phone: 08870576212
1 refrigerated and 2 frozen coolers for Gowtham Subbarao (SUBB) are being sent to:

Dr. Gowtham Subbarao c/o Yvonne Bohan
Scripps Institution of Oceanography
University of California, San Diego
8750 Biological Grade, room 4200Marine Biology Research DivisionLa Jolla, CA 92037, USATel: (858) 534 1607.
E-mail: gsubbarao@ucsd.eduAlternate Tel: 001 858 334 3605

Residues

The residue distribution is as follows:

Thin Sections

21 thin sections were prepared by Aaron Mechler on Expedition 355.
The thin section inventory is being sent via email with this report. (Exp 355 Thin Section Inventory.xlsx). There were 10 sedimentary sections made during the cruise 11 igneous thin sections were made during the transit from Mumbai to Colombo. Please see the Action Items section regarding the igneous thin sections.

Smear Slides

The sedimentologists prepared and described 946 smear slides. All smear slides are being sent to the GCR. A complete list of smear slides is being sent via email with this document to the GCR. (Exp 355 Smear Slide Inventory.xlsx). Dr. Sergio Ando and Anil Kumar have requested made on the expedition. The smear slides will first go to the GCR and be forwarded to them for a period of one year. After this time expires, they will be returned to the KCC. The Smear Slide Inventory contains a tab detailing which smear slides each scientist would like to request.

Core Preservation

All core sections, both Archive and Working were wrapped in Glad Wrap. For lithified sediment we used shrink wrap.

CURATION AND SAMPLING

Pre-site to Site Conversion

Catwalk Sampling U1456A

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.
Geochemistry
The following plan was implemented:
Interstitial Water (IW)

• 1 per Core. 1 every other Core for ½ APC.
• 0-300m, 1x5 cm whole round (WRND)
• 300m-415m, 1x10 cm WRND every other Core.

Head Space (HS) Gas

• 1 per Core.
• 5cc plug
• Below IW.

Microbiology (MBIO )
Microbiology samples were taken for Dr. Ganesh Kumar (KUMA, 21074IODP). The general sampling plan for MBIO was as follows:

• 0-384m, 1 x 5cm WRND every core (APC/XCB), every other core for ½ APC.
• 0-384m, KUMA, 2 x 5mL syringes, 1 x 50mL syringe above KUMA WRND

Paleontology (PAL)

• 5 cm Whole Round (WRND)
• Taken from bottom of Core Catcher (CC)
• Dhananjai Pandey (PAND) 10 cc split from PAL sample.

Catwalk Sampling U1456B (Microbiology Hole)

The general plan for catwalk sampling is outlined in Figure 2. The primary sample types taken on the catwalk were for Geochemistry, Microbiology, and Paleontology.
Geochemistry
The following plan was implemented:
Interstitial Water (IW)

• 1 per Section
• 1 x 5 cm WRND

Microbiology (MBIO )
Microbiology samples were taken for Ganesh Kumar (KUMA, 21074IODP), and Gowtham Subbarrao (SUBB, 21755IODP).
The general sampling plan for MBIO was as follows:
Ganesh Kumar (KUMA) Samples

• 1 x 5cm WRND every Section.
• 1 x 10 cm WRND every Section.
• 2 x 5mL syringes, 1 x 50mL syringe from 10 cm WRND.

Gowtham Subbarao (SUBB) Samples

• 1 x 5cm WRND every Section.
• 1 x 10 cm WRND every Section.
• 2 x 5mL syringes, 1 x 10mL syringe from 10 cm WRND.

Paleontology (PAL)

• 5 cm Whole Round (WRND)
• Taken from bottom of Core Catcher (CC)
• Dhananjai Pandey (PAND) 10 cc split from PAL sample.

Catwalk Sampling U1456C

Microbiology (MBIO )
One microbiology samples was taken for Dr. Ganesh Kumar (KUMA, 21074IODP) from 41X-2. It followed the same plan from Figure 1.
Paleontology (PAL)

• 5 cm Whole Round (WRND)
• Taken from bottom of Core Catcher (CC)
• Dhananjai Pandey (PAND) 10 cc split from PAL sample.

Catwalk Sampling U1456D

The following plan was implemented:
Geochemistry
Interstitial Water (IW)

• 1 per Core (where recovery was greater than 50%) to 864 meters.
• 10-15 cm WRND.

Head Space (HS) Gas

• 1 per Core.
• 5cc piece
• Below IW.

Bulk Geochemistry Sample (BEND)

• 43% of IW Squeeze Cake.
• 5 cm WRND above PAL sample in Core Catcher.
• Recorded under James Bendle's sample request (BEND, 20189IODP)
• Divided between geochemists for pilot studies to refine their sample requests.

Paleontology (PAL)

• 5 cm Whole Round (WRND)
• Taken from bottom of Core Catcher (CC)
• Dhananjai Pandey (PAND) 10 cc split from PAL sample.

Catwalk Sampling U1456E

The following plan was implemented:
Bulk Geochemistry Sample

• 5 cm WRND above PAL sample in Core Catcher.
• Recorded under James Bendle's sample request (BEND, 20189IODP)
• Divided between geochemists for pilot studies to refine their sample requests.

Paleontology (PAL)

• 5 cm Whole Round (WRND)
• Taken from bottom of Core Catcher (CC)
• Dhananjai Pandey (PAND) 10 cc split from PAL sample.

Catwalk Sampling U1457A

The sample plan for U1457A followed the same pattern as U1456A (Figure 1).

Catwalk Sampling U1457B

The following plan was implemented:
Geochemistry
Interstitial Water (IW)

• 1 per Core to 194 meters.
• 10-15 cm WRND.

Head Space (HS) Gas

• 1 per Core.
• 5cc piece
• Below IW.

Paleontology (PAL)

• 5 cm Whole Round (WRND)
• Taken from bottom of Core Catcher (CC)
• Additional holes sampled to fill in recovery gaps.
• Dhananjai Pandey (PAND) 10 cc split from PAL sample.

In addition, one 5 cm microbiology whole round (KUMA) was taken from 13H-3

Catwalk Sampling U1457C

The following plan was implemented:
Geochemistry
Interstitial Water (IW)

• 1 per Core to 857 meters.
• 10-15 cm WRND.

Head Space (HS) Gas

• 1 per Core.
• 5cc piece

Paleontology (PAL)

• 5 cm Whole Round (WRND)
• Taken from bottom of Core Catcher (CC)
• Additional holes sampled to fill in recovery gaps.
• Dhananjai Pandey (PAND) 10 cc split from PAL sample.

In addition 3 Bulk Geochemistry samples were taken from core 93R to 95R.

Section Half Sampling

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

• 1 per section.
• Picked by paleomagnetists.
• Japanese style cubes only (7cc).
• Cubes cut with saw in lithified material.
• Additional samples taken as needed.

Moisture and Density (MAD)

• 3 per core.
• Usually Sections 2, 4, & 6.

X-Ray Diffraction (XRD)

• Picked as needed by sedimentologists.

Carbonate Analysis (CARB)

• Taken from IW squeeze cake residue.

Nanno Fossils (NANNO)

• As needed
• Toothpick sample

Diatoms (DIAT)

• As needed
• Toothpick sample

PAL (Additional)

• As needed to refine ages.
• 10 cc for forams.
• Shared amongst all paleontologists for analysis.

ACTION ITEMS

Smear Slides-Sergio Ando and Anil Kumar have requested smear slides made on the expedition.
The Smear Slide Inventory (Exp 355 Smear Slide Inventory.xlsx) details the smear slides that each person is requesting. These will be sent to the GCR and forwarded to them for a period of one year. After this time period, they will be sent to the KCC.
Igneous Thin Sections-We did not receive igneous core material until the last day of operations. We cut 11 Thin Section Billets and made the Thin Sections on the transit from Mumbai to Colombo. They still need to be described for the Shipboard Scientific Report. These 11 Thin Sections will be hand carried by me to the GCR. The GCR will need to forward them to Dr. Tallavejhala Radhakrishna at the following address:
Tallavejhala Radhakrishna Geosciences DivisionNational Centre for Earth Science StudiesAakkulam Trivandrum 695031India
radhakrishna.t@nic.in
tradha1@rediffmail.com
Tel: (91) 471-251-1657

PROBLEMS ENCOUNTERED

Crushed/Shattered liner. Several APC cores had shattered and crushed liner. We accommodated for this by using liner patch. In some cases the core material was extruded from the core barrel into half liners.

COMPUTER SOFTWARE

Dell Docking Station-My docking station malfunctioned during the first few days of the Expedition and the MCS did not have a spare. I hard wired my computer to the external monitors, keyboard, and mouse.




Figure 1: Catwalk Sampling Plan for U1456A. The same sample plan was followed for U1457A.

Figure 2: Catwalk Sampling Plan for U1456B.

geoChemistry Lab

Erik Moortgat & Vincent Percuoco

Ampulator

The ampoule sealer was not used. The awesome ampulator remains on board.

Balances

No issues to report for the Cahn & Mettler balances.

Carver Presses

No issues to report with the motor-packs/presses.

Cary Spectrophotometer

The Cary was used to analyze ammonium and phosphate concentrations and there were no issues.
We tested the Cary's Kinetics application to verify if the curing time for our phosphate and ammonium tests was accurate. There was about a -20% difference between absorbances measured 30 minutes and 1.5 hrs after mixing the reagents, after which the absorbances mostly stabilized. In the future we should wait ~1.5 hrs after mixing the reagents for the phosphate test to begin the analysis, as well as using drift standards every ~10 samples.

CHNS

Total carbon, nitrogen and sulfur were measured on the EA. There were no issues with the unit.
Residence times for nitrogen, carbon, and sulfur were 64, 100 and 640 seconds, respectively. In order to determine sulfur concentrations the analytical time for a sample must be set to ~900 seconds.
Sulfur concentrations were inconsistent over the life of the column. We ran out of pre-packed columns and, in the end, make our own.
We can delete out accumulated tests in CHNS Worklist Generator that are imported from the Cahn Balance by right clicking on a row, logging into the appearing LIMS splash screen, and then selecting "Cancel Partial Test."
We found that we are able to edit individual cells in the CHN Mutts Loader, and entered the term "Rejected" in place of an elemental concentration for samples that followed a running standard which had an analytical error greater than our QA/QC limits (User Guide: 10% for each element). This only displays "Rejected" in LIMS for that specific sample element, the raw data exported from the CHNS in the form of an excel file and uploaded to LIMS by MUTTs is still intact.

Coulometer

The coulometer is currently functioning normally.
The new spare arrived in the shipment to the JR and the old spare is being sent back to the beach.

Freeze-drier

There were no issues with the freeze-drier.

Fume hoods

No issues to report with the fume hoods.

Gas Lines/manifold

The TAS application Gas Bottle Status Review has been inoperable all Expedition. There has been no update/status from the Application Developers. This needs to be remedied ASAP.

GC3/NGA1

All headspace samples were analyzed on the GC3. There were no issues with the GC3.
When testing NGA1 at the beginning of the Expedition it appeared that no sample was getting to the column. Couple of things we noticed. First was that the top of the inlet glass liner was broken and second the column looked plugged with septa. The liner was replaced and the column cut-off below the obstruction and re-installed. Everything now looks normal.

Hydrogen generators

No issues with the hydrogen generators.

IC

Performed routine maintenance on the unit: changing AS ultrafiltration membrane, inline filter papers, H₂O scrubber, peristaltic pump tubing, cleaning AS probe, replacing guard columns. There were no issues to report.

ICP

The ICP was used to measure major and minor elements on the porewaters.
A spreadsheet was updated that lists our on-board rock standards, along with fantastic charts of element concentration .vs. standards.
There were no issues to report.

Microbiology

There was quite the flurry of activity in the Microbiology Lab at periods of times. Some of his requested chemicals never made it out to the vessel so certain fixations could not be done.
Microspheres were used at sites U1456A/B and U1457A [U1456B was a dedicated geochemistry/microbiology hole].
The GC2-PFT was calibrated for perfluoromethyldecalin ("PFMD") and perfluoromethylcyclohexane ("PFMCH"). During the calibration process, the needle kept bending during various stages of the process, between the agitator and injector. Gerstel was contacted and they recommended replacing the tension cords on the MPS2 injection head. Since we didn't have any spares, it was decided to replace the entire injection head with the one in the box being reserved for NGA2. This resolved the issue and tension cords were ordered for future use.
PFMCH density = 1.788 g/mLPFMD density = 1.972 g/mL

Notes: use a separate gas-tight 500 µL syringe for each PFMD level. PFMD standard concentrations are reported for the above recipes added into 20mL headspace vials.
: some of the syringe needles have lower flow rates so make sure that you have enough dwell time (~ 20 sec) when drawing up and dispensing the aliquot.
The COY chamber was successfully used.

salinity

The optical refractometer was used, no issues to report.

SRA

Continuing on the troubleshooting efforts done by Lisa Brandt on Exp 354, following the e-mails trails and notes in the instrument's blue book.
First was to resolve the erratic CO₂ readings. I replaced the CO₂ trap and the readings stabilized. Next was to stabilize the FID readings and I repositioned the pedestal per Bruno Leroux's instructions.
Now continues days of repeated issues with the FID not lighting, S1 too low or not appearing at all, very inconsistent CO/CO₂ readings. Many things were going on at the same time and I'm going to summarize what we did, what was changed and the current status of the machine. For details, the blue-book and binder (e-mail print outs) can be referenced.
After receiving numerous software crashes (Thermal Station Acquisition Run-Time Error '5'), it was suggested to put the SRA on the UPS. Since doing that, I have only encountered one crash, not every time the software ran a sequence. To be watched though.
Jurie found a very inconsistent current from the power supply to the FID glow plug and if we 'bypassed' the connection, the FID lit without a problem. I thus removed the suspect connection with a screw-down block. The FID jet was replaced as well. What Jurie also found was that the current that the glow-plug was receiving (1.49A) was just on the low-edge of what it was needing (1.5 – 2A) to light. He added two 10¿ resistors in parallel with the existing resistor so the glow-plug can now receive up to 1.75A with no issues.

The connectors for the drierite tube were replaced with metal ones to hopefully get better seals and limit sources of leaks.
The oxidation purge time was increased from 5 to 8 minutes.
One 'fix' that is troubling Bruno, and this is something still not 100% explained, that we are getting great traces with the split-flow reduced from ~ 40 mL/min to ~ 25 – 28 mL/min.
We are now getting good FID/CO/CO₂ profiles, albeit with a bit of a low S1 peak and a 'new' peak before S4, on the CO₂ trace. Bruno said that there is not much we can do for the S1 peak and the peak before S4 is not affecting the other values. This may be something to look at in the future though. The IR baseline (~ 50mV) is also looking very good as well.

Pipettors

No issues to report with any of the pipettors.

titrations

alkalinity

No issues to report.

Chloride

The Scientists did not want to use IW split water for the extra chloride measurement via titration.

Water system

No issues to report other than changing the carbon filter.

Misc

Birmingham molecular climatology

J. Bendle (Oct 2014)
1. Freeze drying

• All sediment samples must be freeze-dried before analysis.
• Freeze samples at least 24-hr prior to freeze-drying.

2. Cleaning glassware (COSHH No. ENS00210)

• Remove labels from glassware and scrub sediments out of the vials
• Pre-soak all glassware in HCl bath over-night.
• Rinse and dry (oven)
• All glassware, except volumetric glassware, should be combusted at 450°C for 8-hrs prior to use. Cover openings with foil.
• As an alternative to furnacing, glassware can be cleaned with 3x 5mL n-Hexane and then 3x 5mL of Dichloromethane (DCM)

3. Extraction of Total Lipid Extract (TLE) (COSHH No. ENS))209)

1. Homogenize the freeze-dried sediment with solvent-cleaned agate mortar and pestle. For lithified sediments use the ball mill. Be sure to clean tools to avoid cross contamination. Take ca. 0.5cc sub-sample for TOC into a GC-vial.
2. Place homogonized, freeze-dried sediment into a pre-weighed 30mL test tube. Record the dry sediment mass.
3. Add 30mL of DCM:MeOH (3:1) to the test tube and cap.
4. Mix using the vortexer.
5. Ultrasonicate for 20 minutes, then heat in heating block at ~ 50°C for 1 hour. Make sure you measure the temperature by placing a solvent cleaned thermometer in the blank block. The temperature should not rise above 50°C.
6. Remove from heating block and centrifuge for 3 minutes at 3300rpm.
7. Pipette the supernatant (solvent sitting on top of the sediment) into the polyvap test tubes (or 100mL round bottom flasks).
8. Add 10mL 3:1 Dichloromethane (DCM):Methanol (MeOH) to the sediments in the 30mL test tube.
9. Mix on vortexer (may have to use a spatula) to ensure all sediment is re-suspended.
10. Ultrasonicate for 20 minutes (if necessary heat again for 1 hour at 50°C)
11. Centrifuge for 3 minutes at 3300rpm.
12. Pipette off solvents into polyvap test tube (or 100mL round bottom flask)
13. Repeat steps h) to l) until the extract containing the solvent is clear (but at least 2 more times).
14. Dry the TLE using the polyvap or the rotary evaporator.

15. Transfer the TLE using a small amount of DCM:MeOH [9:1] into pre-weighed vials (GC or 7mL vials). Dry down under nitrogen. Weight and record the TLE (COSHH No. ENS00213).

Note: after step m) you may need to filter through your TLE to remove fine sediments and/or residual water. Fill a pasteur pipette with 4cm of Na₂SO₄ on glass wool. Condition with 2mL of DCM:MEOH [9:1]. Redissolve your sample in DCM:MeOH [9:1] and transfer it over the Na_aSO₄ column until the solvent is clear. This depends on the sample type. It requires a judgement call and may/may not be needed.
4. Filtration of TLE split for GDGT analyses (COSHH No.ENS00216)

• Re-dissolve your TLE split fraction (that should be in the GC vial) in 200µL of n-hexane:i-propanol [99:1]. Filter the sample using a 0.45µm syringe filter, attached to a 1mL syringe.

• Filter into an insert in a GC vial.

IODP  #00454 Rotary Evaporator with Bath and Jack (Rotavap)

X-RAY DIFFRACTION LAB

Susan Boehm

Summary

At the start of the expedition I disassembled the cooling lines to the xray tube and removed and cleaned the tube and tube stand to the best of my ability. After sending pictures of the tube to Bruker technicians is was deemed necessary to order a new one to be installed before Expedition 356. The current one is around 7 years old (the original one installed) and average life span is 4 years. Water flow is now back up to over 5.5 l/minute which is very good. A full QAQC was performed as well as detector calibration. Procedures such as detector calibration and tube conditioning will be added to the user manual. A preventative maintenance schedule will be posted in the lab. The handheld XRF was set up in the downhole lab on the last day of sampling to analyze a section of basalt. However the XRF data were not ultimately included in the scientific reports.

Total Samples

XRD: 145
ICP: 0
XRF: 20

X-ray Diffractometer

Backwards flushing of the Haskris and rinsing with a weak acetic acid solution did not increase the flow rate enough. There is a small screen inside the x-ray tube housing underneath the spray nozzle that needed to be cleaned out. I put it in a beaker of a weak acetic acid solution and sonicated for 30 minutes to remove the build-up (lots).
Pictures of the x-ray tube and housing:

Screen underneath spray nozzle sits in the center.
We had spare small o-rings but not of the larger one, so I replaced those with a small amount of silicone grease. With alcohol and cotton swabs I cleaned off the rest of the tube. The mylar sleeve was replaced with a spare. Bruker technicians said the plastic coating probably melted due to our past over-heating issues. Water flow remained at over 5.5 l/minute for the remainder of the expedition. I think the small filter screen was the main culprit for our water flow issues. I also removed quite a bit of debris from the Haskris tank, which should only be filled with pure DI water.
A full QAQC was run without a need for a Z correction. I also did a detector calibration which showed it had been running within the detector limits. That procedure will now be included with the QAQC. Tube conditioning is described in the manufacturer manual but will be included also in our User Guide as it is good to do if the x-ray tube has been off for an extended period of time which happens to us regularly. It will help extend the life of the new x-ray tube. I have decided during tie ups or extended periods of not using the D4 we should completely drain the Haskris and cooling tubes to reduce any growth or buildup in the cooling system.
The bar code scanner is reprogramed so when entering sample ID's into the Commander program it automatically fills in all the information with underscores instead of entering only the text ID. Keep this in mind if going into sample master and scanning labels. Instructions on how to get the scanner to go back to its previous setting of only entering the text ID are on the computer desktop. This might be useful in the future for entering LOI samples into excel.
I replaced the thermometer in the furnace in the x-ray lab.
A maintenance schedule will be posted in the x-ray lab to keep track of the D4 vital signs and when various filters get replaced.

ICP Preparation

The filter in the bead maker water supply has been replaced. When doing this in the future remember to turn off the valve to the water in the thin section lab. A sticker indicating this is on the filter now. The bead maker turned on normally but I did not make any beads.

Thin Section Lab

Aaron Mechler

Summary

21 thin sections were made. 10 of them were of calcarenite, conglomerate, sandstone, breccia, and limestone; 7 of these were full impregnations. The other 11 thin sections were of basalt.

Special Projects

None

problems encountered

The Vacuum pump connected to the glass Logitech system on the wall had some problems where it would stop working and wouldn't pull vacuum after being on for a short time. The ET's replaced the vacuum pump with a new one which fixed the problem for now. They think the real problem may be with the glass chamber system on the wall that may need to be replaced with some other in line filter system in the future.
Had an issue with one of the sediment traps that wouldn't stop leaking at the connection with the outgoing pipe. After taking it apart and reconnecting it multiple times and making sure everything was correct and connected properly, it still had a slow leak. I finally added some water resistant lube/sealant to the connections which stopped the remaining leaking.

Miscellaneous

Routine equipment maintenance and cleaning was done as needed.

Imaging LaB

William Crawford

Still Camera's

The Canon EOS IDS, Hasselblad, and both Canon EOS 5D cameras and a variety of lenses were employed with no issues to report. The Canon EOS ID Mark X has a spec of dirt on the viewfinder and the sensor has minor debris. The sensor will be cleaned at the end of the expedition.

Video camera

No video services were requested during Expedition 355. The equipment is in excellent condition. We lump the audio equipment with the reports for the video. The remote microphone was fitted to the core lab music system. This allowed voice amplification used during the science cross over meetings.

Epson printer

The printer performed well with only one head cleaning required. Experimentation with the new roll paper feed capability revealed a larger size of group photo could be produced. This was welcome. The settings for the printer and the photograph are stored in the meta data. It will be a simple matter of referring back to the last printed image to harvest the printer settings. Images of that nature are archived onboard with layers so all of the print data, type style and format etc. can be played forward to the next Expeditions Imaging Specialist.
I also found the printing heads can be "cleaned" in pairs. The system allows precise "head clog" information and identification. The problem heads then can be cleaned separately saving time and ink.
I am very pleased and our customers are very pleased and understand the images produced from this printer are archival in nature and a part of their personal history and legacy.

Close-up imaging

The Close-up Station was used daily throughout the cruise. Although the Section Half Imaging Logger (SHIL) was producing the best images to date, close up images are still required even during primarily sediment recovery Expeditions. Our Close-up station has the capability to illuminate the sample from the bottom as well as the top. This gives us a cleaner surface (photographically speaking) with no shadows cast from the object itself. The images therefore can be separated as needed from the ruler, photographed label and gray card calibration scale. I had to opportunity to listen and see some of the lectures and talks from scientist who utilized the requested Close-up images. What I saw was pleasing in the consistency of density and color kept throughout the expedition.

Petrographic Image Capture and Archiving tool (picat)

Twenty one Thin Sections Images were produced from 9 thin sections. The light source light socket was replaced. No issues to report with the PICAT and related systems. At the time of this writing, 11 more Thin Section Slides have been ordered. This was due to the success of the drilling efforts and reaching the hard rock basement. These will be imaged and completed as planned before reaching Colombo, Sri Lanka on our transit.

FLIR CAMERA

The cameras was checked and cleaned by Adam Bogus and myself. Operational but not used during this expedition. Adam has completed the Users guide and Operation manual. This has been sent for review. The document is also stored on IODP Shared> Imaging Lab.

QA/QC

The system by which the images are downloaded and checked has been totally redone. Each day and during high recovery Expeditions, sometimes twice per day the Imaging Specialist downloads the images produced by the SHIL for inspection.
This is done to check the photographic quality and the health of the SHIL. We check for cropping errors and to make sure the surface of the sample is prepped to yield the best quality of image. Should the sample be wet or dry? Were there any indications of marks or debris on the surface? What the sample tilted or askew? In addition the Imaging Specialist has been tasked with checking the Whole Round (WRND) samples taken on the Cat Walk during that process. The length and type of sample or who requested the sample is recorded in the image itself and this data must be checked against curatorial records.
This data has historically been found in several different reports and required a bit of juggling to gather what was needed.
The programmers and others have been working on the reporting system to replace the current one. During this process the workflow of the Imaging Specialist was taken into consideration.
The programmers and or teams have generated three new reports. QAQC, LIMS Reports online report portal and a new LIMS Report meant for the general science user.
QA/QC at a glance gives the imaging specialist data on:
Length mismatch,
Missing Images,
Whole round sample length (WRND), label, kind and who had requested the sample.
LIMS REPORTS
Allows more complete WRND data viewing,
Core composite Images (all the sections of the entire core arranged in one photograph),
Core Close ups,
Photomicrographs (all images taken with a light microscope),
Thin section images created by the Petrographic Image Capture and Archiving system (PICAT),
This data is accessible by the scientist with the exception of the larger Tiff Images generated by the SHIL.
Those images must be downloaded by the Imaging Specialist daily by a separate program called Image Grabber. Now we are able to do this within the three new data viewers.
Many thanks to David Fackler for patiently studying work flow elements and to Rui Wang who was on the other shift working to see the changes gets done.
Chad Broyles, the Curatorial Specialist and I worked well together on the daily checks from Images generated from the SHIL. He was a pleasure to work with.

SHIPPED to shore

No items were shipped to shore from the Imaging Specialist.

Image summary

LSIMG 1575 Core Sections
Close-up 391
Micrographs 2317
Thin Section 21
Still Images 101gb
Video 0

Microscopes

The microscopes were set up as needed for Nannos, Radiolarian and Foraminifera in the main lab and for Smear slide in the descriptions area. The microscopes were in need of additional cleaning which was expected because of the short transit times and the amount of recovery from the last expedition.
I had the opportunity to set up a microscope for Differential Interference Contrast (DIC). This was the first time in my 11 years that I have been asked to do this. I found the parts and pieces needed and with the help of reference materials, I was successful. I learned a lot and was pleased with the results. In installing the equipment, I found the condenser stage was misshapen. It looked as those it had taken an impact. I disassembled the unit as far as I could so not to damage the optics and Etienne Claasen using a micrometer gently pulled the metal back in alignment. I am certain this was a shipping or moving mishandling and up until now the critical use of the condenser stage was not noticed.
There was one disturbing problem with the newer microscopes. The tab, which holds the bulb housing, was of plastic. The plastic failed on one lamp house. The bulb housing which is a slider unit within the main housing is spring loaded. This allowed the electrical contact to separate and the bulb subsequently would not burn. Once again Etienne fabricated a simple but elegant rotating clamp to hold the slider in against the spring. David Houpt was as equally disappointed in the engineering of the lamp house. Three additional replacements have been ordered in case of future failures. The fix is fairly simple and can be done onboard. I am surprised that a part which is subjected to stress and heat cycles was made of plastic and not metal.
To close, the microscope lab equipment available and overall layout of the lab is strong and well suited. One of the unused stereo microscopes was removed and stored in the Imaging Office to allow more desk space.
The microscope at the end of the paleolab is a little office unto itself. The air circulation is low and the temperatures tend to be higher than the rest of the lab. I borrowed a air fan from the splitting room and this relieved a bit of the circulation problem. I would recommend a fan be ordered and placed presently. This might be advisable for the Mbio microscope area also in the chemistry lab.
There was a bit more than usual trouble with some getting used to equipment that is not in the users personal lab. There was a call for more of a projection type of systems where the user did not rely on the occur view as much. This need diminished as the user gained familiarity with the Zeiss Microscope and the Spot Camera Imaging systems.
All in all with multiple daily checks the operators of the microscopes seemed satisfied. I am particularly happy with the installation and success of the DIC set up.

Publication Specialist

Keith Dupuis

summary

Visual core descriptions (VCDs) were created for two sites on Expedition 355. A total of 332 VCDs, or individual barrel sheets, were created from eight holes. Table 1 lists the number of VCD's per hole by type (e.g. Sediment or Hard rock) and the core labels. The drilled intervals are also listed.
Table 1 Number of Sediment and Hard rock VCD's created for each hole. The core labels (the range) are also listed with drilled intervals and zero recoveries indicated.

Core description and track data were downloaded and plotted to create the Visual Core Descriptions (VCDs.) The data were plotted daily and posted to Uservol on the Ship's Server as .pdf files. A Methods / Legend was created for the VCD patterns and symbols. Hole summaries and recovery plots were produced for each hole.
The Sediment and Hard Rock VCD templates are shown in Figures 1 and 2. The scientists chose the layouts. They used a graphical list of previous Expedition VCDs to communicate their preferences. The VCD layout was updated and fine-tuned throughout the Expedition as new data were recorded.<ac:structured-macro ac:name="anchor" ac:schema-version="1" ac:macro-id="fb073fbd-437c-4088-b896-78369708954f"><ac:parameter ac:name="">_Ref273248979</ac:parameter></ac:structured-macro> Figures 1 and 2 also map the descriptive data logs to the corresponding DESClogik tab and column name. For example, the dark brown bar in Figure 1 (the Bioturbation intensity log) is mapped to the DESClogik "sediment" tab, and the Bioturbation intensity rank column.




Figure 1 VCD Sample with Desclogik data mapping key. The data logs plotted using descriptive data are colored separately and matched to the corresponding DESCLogic spreadsheet tab and column name used to plot the log (e.g. DESC: <tab name>: [column name].)

Figure 2 DESClogik mapping key for the Igneous VCD plot (similar to Figure 1.)
The software programs used to create the VCD's were:

• Lims2Excel version 10
• DESC Logik version 8.0.0.0
• Strater 4.1.1156 (64-bit)
• Microsoft Excel + macros for pre-processing data
  Software comments:
  A new version of DESCLogik was available mid-way through the cruise. I did not install it.

  Report Tracking

  The Expedition Report has 3 chapters:

1. Methods
2. U1456
3. U1457

Each chapter has eleven sections:

1. Background and Objectives (Introduction for Methods chapter)
2. Operations
3. Lithostratigraphy
4. Biostratigraphy
5. Stratigraphic correlation
6. Igneous Petrology
7. Geochemistry
8. Microbiology
9. Paleomagnetism
10. Physical properties
11. Downhole measurements.

The text, figures and tables were collected and tracked at the end of the cruise. The preliminary number of pages (in Word+Figure/Table captions), figures and tables are listed in Table 2 (Methods – Introduction and U1457-Operations are not included here.)
Table 2 Preliminary page, figure and table count for Expedition Report 355

YEOP Summary

General duties were performed for 29 scientists on Expedition 355. This included:

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

ELECTRONIC TECHNICIANS

Jurie Kotze, Etienne Claassen

Chem lab

Bio-lab

Zeiss Microscope power supply & lens filter controller failure in port (Colombo) while tech team was taking scientists for a pre-cruise informational lab session.
The unit was removed in port and taken to ET shop for repairs. Faulty electronic components were replaced and tested okay again. Power supply assembly was replaced and the microscope worked without any further problems for the rest of the expedition.

SRA

The Rock analyzer had a problem with the sample gas combustion. The techs worked with the vendor to do tests and located gas line problems but we found that the gas ignition glow plug seemed to be a little cold by looking at the glow. By measuring the current in the glow plug line we found that the 1 ohm resistor was actually slightly higher than 1 ohm and caused the current drawn by the glow plug to be on the low end of its window. It is supposed to draw between 1.5 and 2 amps but it actually draws 1.49 Amps. A 5ohm parallel resistor was soldered over the 1 ohm load resistor to increase the current to 1.75 Amps that places it comfortably in the window. The glow plug connector was replaced with a better type of connector as well, it looked a bit corroded. The instrument works well again.

Carver press

We strip both remaining carver press rams that have not been repaired this year as maintenance and training, we trained Vinnie on removing dissemble clean and rebuild on the carver press rams, both are back in use and are working to specifications.

Core lab

Laser engraver

The techs got caught out a couple of times with laser lockouts due to a new emergency lockout switch. This switch was installed presumably during the previous expedition and sits at an angle about shoulder height and it gets bumped by people coming round the unit on their way to the WRMSL track without noticing it. We will install a LED warning light as we did on the other tracks earlier after the cores are all processed.

SHiL

M-Drive power regulator board V1.4 failed. The 12V/5V disappeared. The regulator block is fed by a 75V DC input and gives out 12 and 5 Volts regulated. The failure is most probably caused by the fact that the regulator can handle 76V max on the input, this makes it very vulnerable for voltage spikes. The unit was replaced with a new regulator block and put back to service.
If this tendency stays we will have to lower the input voltage via a pre-regulator to lower the input voltage to the block regulator making it less vulnerable. We will keep a watch on this. It is doubtful that it failed during a real circuit fault.

PaleoMagnetic Lab

Pmag amp en D2000

The D Tech crest amp was removed and replaced with a new crest amp, the old amp was taken to the ET shop for repairs and maintenance. The PC board and various components were burnt and corroded due to many years of service, two extra fans were installed to help with cooling of the electronics, (it was installed later when SRM amp failed as well.) All the wires and connectors between the amp and high voltage capacitor bank on D Tech were stripped out and replaced with new and thicker cables to carry 1000Watts of power. The HT power plug on the D tech was removed and a new robust connector was fitted as well. The D-Tech worked without further problems during the expedition. The HV capacitors were given a high voltage leak test on the bench and they are in good condition.
The Crest amp for the SRM failed as well later in the Exp. and was removed for repairs, one channel's "mosfet bank" power transistors went short circuit (12 of them), they normally tend to fail as in a domino effect, if one fails the rest just follows suit, the biasing circuit around the transistors are normally the culprit in such a case and it showed severe burns on the components due to presumably temperature fatigue over many years as well, 19 years in this case. The spare repaired amp was installed and is still in use with the SRM, the amp was retired and documentation was done with help on shore. Two new amps were ordered and will be sent to port in Freemantle.

Agico spinners

Both the Agico spinners had to be repaired, the one in use's shaft became loose and was repaired by the Tech but came back days later with the same problem, we stripped it again and Loctite used to secure the shaft set screw, this meant that we had to align the up and down shaft movement. Kept as spare while the other one is in use now. No.2 spinner's wires came loose as well on the angular cross travel and was soldered as well, it is currently in use.

Thin section lab

The vacuum pump that serves vacuum to the working surface plate and coupled to the cutting saw blade sample holder lost vacuum over time and became too weak to do the job properly due to running surface being worn down. We looked through our old stash of small pumps that we try to keep up and running as backup but all of the 5 were so worn that we could not find a proper replacement to get in good working order again. We installed a bigger new welch pump to help out and ordered a new vacuum pump for the thin section lab plus one or two spare ones on standby.

X-RAY LAB

We replaced the filter in the Haskris cooling water circulation system with the XRD tech, the date was written on the filter and we will replace it every year now since we had the water algae problem recently.

DHML lab

Ran APCT3 tools no. 1858022C on Hole U1456A, during core 4 the tool came back flooded, it was reported to College station and will be sent back with the shoe and sleeve, no obvious reasons for this was found as everything looked normal, we used tool 1858004C to complete the outstanding core's 7,10,13, no problems further. This tool was used during the rest of the expedition. The failed shoe and sleeve was given a pressure test while APC coring with no logger inside and it flooded again during its second run. It will be inspected on shore for possible manufacturing problems.

Rigwatch

Rigwatch had a few problems, we had problems with the pipe counter, we replaced the optical switches and rebuilt all the fittings on the pipe stabber, we will have to make some changes to the back plate on top of the pipe stabber as well, rust have gotten into it, causing a rocking/unstable fixture and not solid as it should be, we will make it a tie up project when it's not in use. A new backing plate will be manufactured and fitted.
The core counter overlay went off more than once and we found that the every time we restarted rigwatch we had to reset the program or restart the Star-tech 485 communications device.
The VIT overlay also did not work and the MCS's made some changes on the DOW comms program and it worked again but not on the TV monitors, we'll have to look into this more with Dean F.
The DVR sub-Sea system will be removed and sent back to College station as requested.

Fantail

No work was done on the fantail itself but we plan to do a lubrication service on the magnetometer drum and carriage and a thorough test run to check its operation on route to Colombo for the upcoming transit to Freemantle with the next crew. All should still be in good shape but we will check it anyway.

Entertainment

Movie room

No problems was reported in the movie room.

Gym

No problems was reported in the Gym.

GENERAL

-80 Forma Freezer

The reconditioned Unit was reinstalled in the pallet store (after a service call in College Station) during port call and it is functioning well.

Radvan

The last of the ground fault interrupters outstanding, a 220V "Square D" Unit was installed with the help of the SIEM electricians and the 2 X 220V outlets that was mounted right above the water faucet was shifted to a safe position to the left side, away from spillage danger.

Fridges & Freezer CFC gas audit

A refrigeration CFC gas audit had to be done for SIEM following a new regulation for ABS. All freezers and fridgerators on board used by IODP had to be put on record with all specifications attached. This was done and handed to Siem Engineer for their records.

Computer user room

The Brewtus coffee machine was removed to the ET shop and the received retrofit kit was installed after a problem with the previous software programmer for the two boilers. The retrofit kit works very well and it is being used ever since. The new unit is very simple to set up with no software involved.

UPS issues

Four new UPS's was ordered and will be delivered in Freemantle. All four of them are new "double conversion" type Ups's. One, a 2750VA with extra battery pack is for the NGR and 3 smaller ones for the most critical tracks that needs them after the old UPS's fitted now needs replacement. Upon reception a final decision will be made where the most appropriate positions will be.
We had a total power loss in Colombo following an electrical fault somewhere in the ship system which had a couple of UPS's tripping out. It must have been a fairly violent mains fluctuation as a couple of the UPS's tripped after that, including the NGR's UPS. The power failure lasted a couple of minutes after which it was restored.
The 50kVA UPS (in the koomey-room) for the lab uninterruptable power outlets lost 2 X ventilation fans, it has 5 X 150mm fans in the cabinet roof. An order will be made out for replacements.

Power Tool and chords

SIEM did their scheduled electrical GFI safety measurements and inspections on all IODP power tool and mains related shop equipment

Software Developer

David Fackler, Rui Wang

Overview

This document highlights changes to the software configuration of the JOIDES Resolution laboratory data management environment during Expedition 355. This is intended to be a summary. More exhaustive detail may be found: at the links in the title of each section, and in the resources section at the end of this section.

Curation and Core Handling

SampleMaster

No change. Operating at release 6.0. Rolled back from release 9.
Expecting to distribute release 10 during transit to Colombo--after additional testing and feedback from technical staff.

• Added label print option to set a default label (chemistry request).
• Removed sample delete functionality.
• Removed unused menu item Configure.

Release 9 would not print labels from the Sample Table tab. Regression tested to code changes in release 8.
A series of bugs related to processing result data associated with samples. Not resolved.

• Editing a MAD sample container number fails to display the updated value in SampleMaster displays, though you can see the edit in the database.
• Driller edits to sparsely populated drilling parameters usually save and display, but not always. When a parameter is preceded by an unpopulated entry, it is more likely to not display.
• The services which retrieve result data (like containers number, drilling parameters, piece orientation) retrieve both canceled and un-canceled results. The also results in unexpected sample master display errors. Partial cancelation of test results is not handled well by current queries in this sub-system. The queries are widely used and configurable. A fix requires extensive testing.

Laser Engraver

No change. Operating with release 3 since Exp 350.
Issues the technical staff would like addressed:
Waking the instrument host from screen save mode will start the engraver if you happen to tap that portion of the screen.
Do not lock-out the empty section selectors. Sometimes a section is held aside for alternate processing, then is engraved out of sequence.
Feature request: Have the refresh button also reset the engraving logo to "Full". Operators tend to forget to set it back.

LIME (LIMS Editor)

Changed. Operating with LIME 5.1 in production. Repairs a specific condition that prevented the site list from updating.
Most requested feature changes:

• Cancel/Uncancel Test: Support for operating on more than one test. Not unlimited, but something more realistic than one. Errors do not come singly, they cluster.
• Chemistry: Ability to cancel/reject result replicates. Particularly applicable to ICPAES, CHNS analyses.
• Remember hierarchy browser state between menu item context switches.
• Enable handling large batches of cancellations without overwhelming the audit log facility.

Geology

DESCLogik

Changed. Operating with release 12. Repairs library (LIMS.dll) failure to filter out canceled samples. The library change affects these applications when they are rebuilt: SampleMaster, MUT, ClAutotitrator, Janus2Lims. The method affected looks up samples based on label content (GetSamplesFromLabelID).
These following changes are pending as release 13 after further technical staff review, feedback, and approval.

• Close button on Asset uploader dialog repositioned to the upper-left corner of the window.
• Generate XLSX files that do not result in yaps about malformed files.

Distribution targeted transit as several of this crew will return to sail with the changes on 356.

Stratigraphic Correlation

Correlator

Changed. Operating with release 2.0.1 since Exp 355. While used for learning and comparison, actual stratigraphic correlation work was conducted using the Igor Pro based system developed by Roy Wilkins.

[ SCORS Downloader

|https://sites.google.com/a/scientific-ocean-drilling.org/developer-page/applications/java/jnlp/scors-downloader] Changed. Operating with release 6 since Exp 355. Used routinely by the stratigrapher without issue.

Requests:

• If a given download in a batch fails, the program silently continues. Preferred behavior: notify the operator, though in a way that allows downloads to continue unattended.
• The feature to reload configuration state from a JSON control file was never implemented. Useful to have.
• Launch is extremely slow on the Mac. Timeout looking up certificates. Really need to white list internally provided applications in the shipboard environment.

SCORS UPLOADER

Changed. Operating with release 1 since Exp 354. Noted one splice upload failure for the last site (U1457A,B). SpliceFileFixer suggested "valid" section/offset changes to yield a successful upload. But the wide variance in the corrected vs. the provided splice file is unexplained. Need to obtain the stratigrapher's working data to trace the evolution.

Splice file fixer

Changed. Operating with release 8 since Exp 355.

• A JNLP-based application for validating affine, splice output from Correlator against LIMS. Intended to be used before SCORS Uploader is applied. User interface shown at the link above.

resteasy-scors

Changed. Operating with release 13 since Exp 355. Updated mid-expedition (v5.1) then at end of expedition (v13). Older version used once during Expedition. Then revisited usage during transit while verifying the source of offset discrepancies.

Geophysics

Whole core systems

Whole-round logger (WRMSL), Special task logger (STMSL)

Changed. Operating with release 6 since Exp 355. Added support for 2 cm measurement interval.

• Seen once. Starting up program fails to establish communication to the Exlar on COM6 used to communicate transducer open/close commands. Ended up rebooting the computer. Probably could have re-established communications more "softly" with a more careful review of running processes via the Task Manager.
• Seen once. Experienced multiple consecutive errors indicating the Abort clown-nose was triggered. Confirmed that it wasn't. Eventually cleared up and proceeded.
• PWL failing to achieve stable first arrival detection after change in material (and near a shift change). Dug up older configuration file with examples of higher thresholds and stacking voltage. The new values happen to work reliably for this material. Otherwise a longer search would have been required in the signal-to-noise-ratio space.
• STMSL only: Seeing occasional drop-outs on the MS observations: 1 in 2000 observations.
• Seen twice. Scanning into the Sample Entry sample ID field results in a successful run up until the system tries to create a file name with quotes embedded in it. Preventable?

Natural gamma (NGR)

No change. Operating with release 4 since 353P. Noted that scanning with a barcode gun before the sample entry dialog has been opened, will cause the dialog to open AND be incorrectly populated. Seen several times at the very beginning of the expedition.

Split core systems

Section half image logger (SHIL)

No change. Operating with release IMS 8.4 SHIL 354 since Exp 354.
Items to repair/improve:

• Offsets for RGB data sets are recorded that do not correspond to top-of-section. The code computes the offset relative to the top of the full image buffer. The end-users expect the RGB data to be referenced to the top of the selected crop region, not to the top of the entire scanned content. The disconnect presently occurs because RGB is computed as the image is captured, but an image crop selection is not made until after the RGB data has been computed. The precise location of where a scan starts is variable due to acceleration of the camera car.
• The parameters (top, left, right, bottom) for the crop region are not correctly recorded.

Discussion. Recommend that RGB generation be move to a post-processing step. Registering RGB offsets to the user-selected crop region is unambiguous. Post-processing enables the process to be repeated by anyone or any process having access to the raw image data (TIF file)—for data correction, or for alternative analytical purposes. About 4% of images are re-scanned (>1500 sections processed this expedition). Delaying production of the RGB dataset a day could avoid some of the data management re-work for that material.
Discussion. Most image re-scanning occurs to apply correctly labeled and ordered foam spacers reflecting catwalk sampling. It is possible to generate foam spacers electronically. Doing so entails access to database content. When not available, the automated process should gracefully degrade to an acceptable default—such as no modification to the acquired image. Value: avoid the effort (and risks) of cutting foam spacers; improve the accuracy of spacer labeling and placement; reduce re-imaging effort; improved capture of an ephemeral property by avoiding delays for some material.

Sonic velocity (GANTRY)

Changed. Operating with release 3 since Exp 355. Repaired software configuration that caused the system to attempt to use the same communications port for both the Y and Z Bayonets. Typically the Y They are now independently configured.
Noted. The latter three are straight-forward to repair.

• Seen once. PWB, PWC not communicating with Exlars after power out. The Exlars behave as expected when operated from the vendor software. Technical staff reloaded configuration files after locating a correct copy of the configuration settings.
• Seen several times consecutively. The sample entry dialog Sample ID field is a multi-line entry box. At least once an expedition, someone will manage to scan a label into that field and not see that there is additional text buried there that shouldn't be. Leads to upload failure at MUT. The error is preventable by ensuring the field is a single-line textual input.
• Seen multiple times. Laser flicks on and off outside of measurement cycle. Associated with behavior that interferes with normal operation of the equipment. Not demonstrated or repeated.
• Verified. If the laser distance window is closed via the red X, the laser is erroneously left on, in distance measuring mode. This causes communication interference in other segments of the program.

SpectroLog (Reflectance via Minolta system)

No change. One-off use for Exp 355. Then mothballed again. Data capture experiments were run during transit (Houpt, et al) to examine the MINOLTA color response; and to compare SHMSL and MINOLTA system response.
The Minolta system was run on all archive half split sections.

Discrete sample systems

Thermal conductivity (TCON)

No change. Third party acquisition software. Operating with vendor TCON release 5.0.0 build 7 since Exp 335.

Thermcon Uploader

No change. Operating with release 1.3.1.0 since 341S.
Seen several times. Experimental results would contain file sets that varied in name from the start of the run to the end of the run. Example: 4R01, 4R02, 4$03 4$04. Appears to be related to some programmatic operational variance. Specific steps to repeat not identified. The fix: rename the DWL, DWG files to match the names consistently recorded in TC-LIST.dat.

Moisture and density (MAD)

No change. Operating with release 2.0.0.9 since Exp 344. Display shows different version than available in the distribution site.
Discussion. It is challenging to correct errors in the entry of container numbers. If caught immediately, the error can be corrected before upload of the sample record in SampleMaster. If caught later, knowledge of specific features of MADMax and LIME are required. SampleMaster supports editing the container number, but does not do so reliably—no positive feedback is supplied indicating that the container change was successful. Improvement desirable in software. In the mean-time ameliorate with early and clear training of end-users.
Noted:

• Seen once. Pyc cell controller throwing error then generating random numbers returned as volumes to MADMax. Abort all cells. Shutdown MADMax. Re-start. Cancel the random values, setup the experiment again. Error not repeated after restart.
• Computations against CONT_Al_20 coming out wrong. Why? Because there's another container CONT_20g getting used instead. Repaired.
• Revisited above. Aluminum container entry and formatted entry do not match for volume component. Volume component is suspect as the density - mass - volume values don't fit the equation d = m / v with any great precision. Further measurements to be conducted during transit to repair these values.

Paleomagnetics

Kappa Bridge KLY-4S

No change. Operating with AMSPIN unchanged since Exp 335. Did modify the barcode scanner rules several time for better annotation of samples in the raw output files.
Desired modifications to support integration of this dataset into LIMS systems

• Modify the sample entry dialog to support handling of content scanned from labels. Avoid having to specially re-program the barcode guns (repeatedly if they get borrowed for other uses).
• Ensure that sample identification in the raw files output includes text ID and label. The former aids automation of data upload. The latter aids human readability.
• Add support to the program to raise and lower the sample holder. Silly to have separate utilities to do this.

Superconducting magnetometer (SRM section)

No change. Operating with release 318 since Apr 2011.

Superconducting magnetometer (SRM discrete)

No change. Operating with release 318 since Nov 2011.
Bug noted:

• Seen once. Program concatenates treatment, treatment level and a comment for display purposes. Then that comment is (incorrectly in some cases) distributed to incorrect fields in the uploader input file. Seen for discrete program. Behavior dependent on comment content. Worked around by editing resulting files manually.

Geochemistry

Alkalinity

No change. Operations continued with release 3.0 of the software. Release 4.0 was mothballed. Not modified. Other development activities were given priority over moving this item forward.

CHNS

No change. Operating with vendor FLASH_EA 3000 since 341P; and MUT 2.1.0.1 [TEST] since Exp 346.
Expecting to apply MUT 10 during transit for evaluation. Repair CHNS file recognition in cases where blank lines are embedded in the data stream.

ICPAnalyzer

No change. Operating with release 2.1 since Exp 355. Re-released due to credential changes hard-coded in the software.
Expecting to release 4 during transit to Colombo for review and testing by staff.

• Revise parsing of reference material names and units. Presently these are being uploaded incorrectly. Data is re-worked after the fact to correct it (SQLDeveloper). When reading from the raw (Salsa output file) CSV, trim spaces off a number of fields when present—do not preserve in content upload.
• Added login dialog. Removed hard-coded credentials.
• Revise text displayed on login boilerplate.

X-ray fluorescence

No change. The XRF hand-held device was demonstrated for use for the hard-rock recovered at the end of the expedition. Additional testing and training will be done with the device during transit to Colombo. No data was acquired specifically for Exp 355.

Rig instrumentation system

Depth Overlay and WITS Communication

No change. Operating with release B6 since 353T. During 353T revisions were made to the application: to support forwarding of VIT depth to RigWatch; and to forward Schlumberger depth and tension to RigWatch displays. A specific item for cross-over. The documentation in the Operations Engineer manual and its electronic sources requires update. Developers have a different documentation cache than do the ETs and Ops Engineers.
Added screen snapshots here for expected VIT configuration: \\JR1\VOL1\TAS\AD\DEPLOY\JR\configuration\DOWCOMM.

Downhole Measurements LAB (DHML)

DAQ_MRU (heave, heave acceleration capture)

Changed. Operating at release 2 since Exp 355. Captured source code to development Subversion repository. Re-distributed in compiled form after determining which subset of code from that box went with this application.

WPD-WITS (Schlumberger logging wireline depth and tension)

Changed. But not yet functional. Captured source code to development Subversion. Will continue working with Schlumberger and Engineering during transit to restore functionality see functional during 353T. Added notes to the development site regarding the tools and data feeds.

Data Loaders

MegaUploadaTron5001 (MUT)

Changed. Operating with release 9 since Exp 355.

• Repaired recognition of AVS files.

Pending change for release with MUT 10:

• Revised CHNS file check: ignore blank lines. The older version of the loader contains the same bug.

Expect that the old unique copy of MUT applied in chemistry for CHNS will be removed and replaced with the current version during transit to Colombo.
Specifications were discussed for SPINNER (Agico JR6A), KAPPA (Agico KLY-4S) content and file formats. Improvements are specified for the orientation tool upload. We'll push these further forward during the transit.

Reporting Systems

Thin Section Report

No change. Operating at release 1 of THSReport (the tool to generate the reports based on collected data). Operating at release 2 of RDB (report definition builder). Used to create reports for sedimentary thin sections.

Image QAQC Report

Changed. Operating with release 8 since Exp 355. The report was revised to improve its utility for the image review process.
Particularly:

• Aid the check of spacer correctness by including information about catwalk samples. Applied to the checks for NO ARCHIVE IMAGE and LENGTH MISMATCH.
• Include the display of drilled intervals in the NO ARCHIVE IMAGE check. Provides positive confirmation where images are not to be expected.
• Enabled control to adjust the page size.
• Enabled control to filter for rows containing specified text.

Interface usage notes. The core list allows for multiple selection. On a Windows system hold down the Shift or Control key while selecting additional cores. If useful, a multi-column sort may be done: click in a column header to sort that column; then hold the shift key and click in the header of another column. To use the search field, supply a word or text. The rows of the table will be filtered to display only those including the specified text.

LORE

Changed. Operating with LORE 1.2 since Exp 355.
Distributed at the beginning and middle of the expedition to carry over production-ready changes from shore. Minor modifications made on ship and folded into code and report definitions:

• Some data was processed client-side as if it all was to be converted to numbers. Resulted in NaN (not a number) being written in place of expected text strings. Repaired. Noted when reviewing modified versions of the CHNS, IW reports.
• Revised the CHNS report definition so that row breaks would be determined by more than just section and offset. Now also checking hole and core.

Distributed several sets of reports based on shore project progress during the expedition.

• Added special reports: hole, core, section summary.
• Added special reports including hole, core, section, hole list.
• Fixed hole summary report rounding problem.
• Added curator report.

Distributed these reports for evaluation and review. Not accepted yet for production use.

• Added mixed samples and shipboard samples reports.
• Added all cores drilling summary.

Added reports on an evaluation basis for all ANALYSIS and COMPONENTS in LIMS. The report definitions are auto-generated and provide lookup capability equivalent to that provided by web tabular reports. As the project proceeds on shore, a sub-set of these are being integrated into the LORE standard menus.
Discussion. The LIMS Reports are presently linked from the home page.

LIMS2Excel

No change. Operating at release 9 since Expedition 349. Seen twice. Download of raw RSC spectra failed twice. Root cause is a data variance. Several core catchers were uploaded, but were too short to actually acquire RSC data, so no offset-indexed content was ever uploaded. Code change desirable, but handled for the moment by canceling the "bad" RSC records.

Drill Report

Changed. Operating with release 3 since Exp 355. Editing night tour report data, then approving it, had the unwanted side effect of reseting core line run data. Corrected by a change to the underlying web-service. No change to the user interface.

Web Services

<ac:structured-macro ac:name="anchor" ac:schema-version="1" ac:macro-id="d686e210-f266-40a2-95b5-2efda2aad8cd"><ac:parameter ac:name="">_Toc421004644</ac:parameter></ac:structured-macro><ac:structured-macro ac:name="anchor" ac:schema-version="1" ac:macro-id="73996c06-32a2-47eb-b9a4-42dc8b758e1c"><ac:parameter ac:name="">_Toc421004892</ac:parameter></ac:structured-macro><ac:structured-macro ac:name="anchor" ac:schema-version="1" ac:macro-id="ee42798f-78b0-4c2a-8784-36fd645f2a53"><ac:parameter ac:name="">_Toc421171772</ac:parameter></ac:structured-macro>SUSE OES Tomcat Servers [Ararat, Rainier, Shasta, BUILD]

Auther: No change. Operating with Version 1.1 since Expedition 349. ChangePassword: No change. Release 3-PJR-20140115231410-hornbacher during tie-up 349P. DR: No change. RDB: No change. Not used. Report Definition Builder operating with release 2 since Exp 350. ReportOverview: No change. UWQ: No change. Operating at release 7 since Expedition 349. WTR: No change. Operating at release 6-AGNOSTIC-20140205004809-fackler since Expedition 349. depth-services: No change. Operating at release 2.5.1.2-PJR-b79-20110902153606-fackler. resteasy-auther: No change. Operating at version 1.1.0-PJR-20140113074315-morgan since tie-up 349P. resteasy-desclogik-services: No change. Operating at release 2-PJR-20140225223735-fackler since Exp 349; last changed Exp 345. resteasy-drillreport: Updated. Operating at release. As previously noted in the Drill Report section. resteasy-error-reporting: No change. Operating at release 2.2.0.2-PJR-20120528164701-hornbacher. resteasy-lims-sync. Updated. Operating at release 3-PJR-20141219191802-dev. Revise change in tables being transported. Old affine splice content was removed. resteasy-qaqc. Updated. See Image QAQC report above. resteasy-lime: No change. Operating at release 1.0.8-PJR-20140419043130-zhao since tieup 349P. resteasy-lims-webservices: No change. Operating at release 11-PJR-20140405175545-morgan since Exp 350. resteasy-lore: Updated. Operating at release 2-PJR-20150508153147-wang since Exp 355. See also LORE reports above. resteasy-monitor. No change. Operating at release 3-PJR-20141024123333-fackler since tieup 353P. resteasy-printer. Updated. Operating at release 5-PJR-20150504092341-fackler since Exp 355. Added support for using the substitution variable ${sample_number} within label format definitions. Supports newly added MAD label. resteasy-reports. No change. Operating at release 9.2-PJR-20140521232150-zhao_h since Exp 350. resteasy-reqmgmt. No change. Operating at release 0.2.0.1-PJR-b33-20110905143055-fackler. resteasy-scors: Updated. Operating at release 10-PJR-20150402042557-wang since Exp 355. See resteasy-scors above. sampling-services. No change. Operating at release 2-PJR-20141016034418-fackler since tieup 353P.

Solaris Tomcat Server

Sites. No change. labnotebookWebDav. No change. 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. Removed on all SUSE nodes. Service can only be used on the system providing the file backing store: the Solaris cluster.
Image tiling is triggered by MUT and Image Capture for the various image sets. Both are hardcoded for a given environment--remember to revise it at build-time.
Important note: when a sufficiently large batch of image tiles (greater than 3-5) is submitted, the Tomcat at Solaris can become non-responsive and starts "flapping". This causes a series of MUT data upload failures throughout a busy labstack. If this keeps recurring, it is Ok to disable the image tiling service until a more quiescent period of operations is reached in the labstack. This has direct impact on image displays in LIMSpeak. Be aware of it. Learn to manage it. Changes are in the works to move image tiling off of the solaris box.

Development Tools and Frameworks

LabVIEW

Currently all production LabVIEW applications are built or run via LabView 2014. Upgraded the BuildJR box to carry NI-MAX 14.5, and SP1 (aka 14.0.1) updates to both 32-bit and 64-bit versions of LabVIEW.

SQL Developer

Updated. Operating with version 4.1.0.18 since Exp 355. Distributed to development systems. Most valuable features: much improved export to Excel; improved stability.

LIMS Configuration

Barcode scanner rules. Barcode scanner rules have moved. The formal location for recording these is: \\JR1\VOL1\TAS\AD\DEPLOY\JR\configuration\barcode rules. Technical staff are widely familiar with the tools and modify these as required for specific purposes.
Analysis and component snapshots. Created storage for snapshots of LIMS configurations: ANALYSIS, COMPONENT, INSTRUMENTS, LIMS_CONSTANTS, LIST, LIST_ENTRY, PRINTERDEFAULTS, PRINTERLABELS, PRINTERS, UNITS, X_REPORTLINK. All are exported as Excel files. Created to aide backup and recovery in case of unwanted changes. Accessible to all technical staff for reference purposes at this location: \\JR1\VOL1\TAS\AD\DEPLOY\JR\configuration\LIMS
A new label format was added to support direct labeling of MAD vials.
In the process of reviewing data to be made visible via LORE reports (LIMS Reports III), numerous unused analyses and components were removed from all database environments. The scope of the changes may be reviewed by comparing the beginning and end of expedition LIMS configuration snapshots for ANALYSIS and COMPONENT.

Libraries

LIMS.dll

Updated. Revised a service wrapper (GetSamplesFromLabelID) to exclude canceled samples when returning content.

Developer Resources

Office Space

Updated. Stowed the laptop shelf by the desk. Laptop was slipping off. Not re-engineered at this time.

Desktops

Changed. Software updates largely mirroring BuildJR updates. Notably: SQLDeveloper 4.1.0.18, LabVIEW 2014 SP1 (aka 14.0.1), Java 8u4, Firefox 37.0.2.

Servers

Tomcat 7 Java 7 SUSE Linux OES. No change in Java version. OES was updated to new version during last tie-up.
Tomcat 7 on Build. Changed. Upgraded to Tomcat 7.0.56.
Software updates. Changed. See the shipboard deployment log. Look for occurrences of BuildJR. Notably: SQLDeveloper 4.1.0.18, VisualSVNServer 3.3.1, LabVIEW 2014 SP1 (aka 14.0.1), Firefox 38.0.1.

Applications Retired

These applications are removed from distribution, and source code retired.
AffineSpliceParserAffineSpliceCSV2XMLConverterAffineSpliceUploaderCullingUtilityJanusReportOverviewLims2Correlatorresteasy-affinespliceReportOverview

Resources

The products above have web-pages and release notes associated with them. Have a particular interest? Take a look. Not finding what you were looking for? Contact a developer: programmers@iodp.tamu.edu

• Application development notes are housed here: https://sites.google.com/a/scientific-ocean-drilling.org/developer-page/home. Keyword search is available.
• Activity logs indicate where current development is focused:
  • https://sites.google.com/a/scientific-ocean-drilling.org/developer-page/home/working-on/ship-activity-log
  • https://sites.google.com/a/scientific-ocean-drilling.org/developer-page/home/working-on/shore-activity-log

Systems Manager

Mike Hodge & Steven Thomas

Servers (Microsoft):

• On Expedition 353 server McKinley notified HP of a memory cache battery failure and HP auto sent replacement battery to IODP. Battery was replaced during portcall and hand carried by Phil back to shore.
• Was discovered on Expedition 354 that HP System Insight Manager was not operational on server Pelee. Problem was related to administrator password change. Made configuration changes to reflect new password restored HP SIM operational.
• HP Insight Remote Support (IRS) software on server Pelee was updated to version 7.2. Registered all HP servers Support Agreement IDs (SAID) current except for two Novell OES servers pending required IRS software installation on these two servers.
• Incurred multiple instances where functions with AMS not working. Contacted Saravanan and issues were resolved. Created AMSService account for users to use in uploading documents into AMS.

Servers (linux):

• HP IRS requires hp-snmp-agents to be installed on Ararat and Shasta before HP IRS can register SAID contract. Agents are dependent on Novell OES patches being implemented before agent installation.
• OES server patch updates are pending non-production time and are scheduled for installation during transit period between Mumbai and Colombo.
• Mac users are experiencing problems editing files directly on servers. Some user's experience is to copy a file from the server locally and close connection to servers before editing file. Novell states that our servers need to be patch updated to take advantage of improvements in CIFS and AFP protocols. Novell has strongly encouraged us to patch our servers' current before troubleshooting file editing issues with our servers.
• Novell server Shasta lost CIFS and AFP protocols configuration files, reasons unknown. Recreated configuration files resolved issues and allows PC and Mac users to access files on this server.

Servers (solaris):

• Swapped FAN Tray 1 assembly in Sun server Etna with replacement unit successfully. This resolved error indicator on server and constant error logging in system log file. Assembly failed on a prior expedition and replacement unit was obtained from vendor.
• No other issues to report on Sun servers for expedition.

Servers {VMware):

• No incidents with any of the ESXi servers or virtuals (VMs) running on servers to report. Checked periodically during expedition and no errors or alerts.

EVA4000 SAN:

• No incidents with the EVA to report. Checked periodically during expedition and no errors or alerts.

NEtwork:

• Updated our Fluke license thru Feb 2016.

PC Workstations:

• Upgraded five workstations to Starter v4 per shore request. All VCD stations and Pubs PC.
• Power supply failed in PC52715 SHMSL. Replaced with p/s out of PC52714. Contacted HP and arranged for replacement unit. To arrive portcall for Exp356T.
• Inspected LT51107 LSC-Cahn laptop in RadVan and brought up to date and current operational standards per shore request.
• Replaced parallel card in PC52648 DHML due to failure and not recognizing Rigwatch security dongle.
• Replaced Startech serial card in PC52701 STMSL due to experiencing communications errors.
• Upgraded memory DIMM modules to 32GB on both SHIL_A PC52591 and SHIL_B PC52515.

MAC workstations:

• Updated all ship's VDUs and Userroom Mac-minis to OS-X 10.10 (Yosemite).
• After updating Userroom Mac-minis to OS-X 10.10 discovered NAC agent stops and prevents Mac from accessing network until agent is restarted or reboot of Mac. Suspect this will be resolved with next NAC upgrade scheduled for tie-up period.

printers:

• No incidents with any shipboard printers to report. Just routine servicing such as out of paper or toner cartridge replacements.

satellite/internet/phones:

• Migrated from satellite IS-906 to IS-902 successfully per Rignet's request on April 21^st. Satellite owner wanted to rebalance services on both satellites.
• On April 27^th observed satellite connection dropping offline multiple times. Inspected equipment and noticed AGC power had dropped to Threshold limit causing equipment to switch/search between the domes. Adjusted threshold level to compensate for new AGC values resolved issue. Notice on May 1^st that AGC levels had restored to prior levels and adjusted threshold levels back to their original settings.
• Incurred VSAT outage due to planned maintenance on May 1^st. Duration about 4 hours.
• Router that services the JR's satellite traffic at Land Earth Station (LES) in Germany was replaced on May 1^st. QoS rules were not applied to new router which affected JR phone services until omission was discovered. QoS rules reapplied and phone service was restored to normal operations on May 6^th.

other equipment/projects:

• Auxiliary AC belt replaced on April 14^th and on May 7^th.
• Replaced tape drive #1 in tape library with new replacement unit from HP successfully. No further issues with tape drive during expedition.

UNDERWAY GEOPHYSICS LAB

J. Adam Bogus

Summary

Navigational data were collected through WinFrog during all transits and at each site. The magnetometer was not deployed during any transit due to regulations within transit waters. Bathymetric data were collected on all transits as well as a precision depth recording (PDR) at each site.

Data Summary

Expedition 355 consisted of three transits and two sites.
Transits:Colombo, Sri Lanka to U1456(L1T ≈ 941 nm)
U1456 to U1457 (L2T ≈ 61.6 nm)
U1457 to Mumbai, India (L3T ≈ 309 nm)
Sites: U1456 (Holes: A, B, C, D, E)
U1457 (Holes: A, B, C)
Site fixes were performed at each site/hole
Event data points were gathered every sixty seconds when underway and at site locations.

Equipment Performance Summary:

WinFrog

WinFrog1 station was used for primary navigation acquisition. No issues to report.

Trimble GPS

The aft/forward Trimble GPSs were the primary GPSs used for the duration of the Expedition. During port call in Colombo, the forward Trimble lost connectivity with satellites and had to be rebooted to reconnect. Intermittent outages continued during port call, however the issues disappeared when we left port and did not resurface. There were no observed issues with the HDOP of either Trimble GPS.

Bathy 2010

WinFrog 2 was used as the host to run the Bathy 2010 software. The only issue arose when trying to obtain a PDR at the second site, U1457. After arriving on site and beginning dynamic positioning, we obtained a corrected PDR depth of 3515.3 meters, which was about ~125 meters shallower than expected. A second measurement confirmed a measured PDR depth of 3517.3 meters. However, there was an extraordinary amount of noise in the sonar signal. After confirming bottom depth by tripping pipe and shooting the mudline with APC, the noise in the signal went away approximately 9 hours after the first PDR measurement. The disappearance of noise did not coincide directly with any operational changes (such as ending pipe tripping or beginning to core), and the reason for the noise remains uncertain.
Figure 1.
After second PDR measurement; with a large signal in shallow water (~150m - 450m) and a few discontinuities in signal
Figure 2.
4 hours after second measurement, normal start of site/hole operations including DPing, tripping pipe down, etc.

Figure 3.
9 hours after second measurement, normal coring operations, noise and discontinuities have disappeared.
*Note-
Gain has been changed to "Auto" in screenshot, but was changed after noise disappeared.

Magnetometer

The magnetometer was not used during any transits due to regulatory complications within transiting waters.

VSP

The GI Gun and Gun Cluster were assembled during the Expedition 354 with the expectation of performing VSP at site U1456. The guns were left secured and covered on the fantail for the duration of the expedition in anticipation of being used. However, the guns were not used at the site due to hole conditions, and new GI Gun chain (6+ meters in length) has still yet to be deployed and have the actual length measured.

Data Backups

Data files for the Expedition were copied to:
\\JR1\DATA\data1\1.5 Ops Navigation
\\JR1\DATA\data1\1.6 Ops Bathymetry - PDR pulse depth recorder