X363 Technical Report PDF File

LAB OFFICER REPORT

Roy Davis

General Leg Information

Expedition 363, Indo-Pacific Warm Pool commenced on October 6, 2016 at Singapore with the boarding of the marine specialists at 09:30 hrs. The science party boarded the following day. The vessel got underway for Guam on December 6, 2016 at 05:00 with an ETA of 08:00 December 8, 2016.
The Expedition recovered 6,956 meters of core.

Port Call Activities Overview

Singapore

Loading of

• 60 ST of Barite
• 160 ST of Sepiolite
• 50 T of Cement
• 2 ea. 40' flats w/drilling equipment( 1ea screened 10.75" casing & 2 ea core liner boxes
• 3 ea 40'dry containers with misc. lab supplies
• Regular air freight

Offloading of

• 1 ea 40' refer container of Core for KCC
• 1 ea 40' container for return surface freight
• 1 ea 40' flat with mud motors and misc. supplies
• 1 ea 40' IODP surface freight
• Regular Air Freight, Foreign Air Freight, World Courier frozen and refrigerated

Guam

Offloading of

• 1042 boxes of core (54 pallets of core)
• World Courier
  • 7 Frozen (JOHN) and 3 Refrigerated (JOHN) and 3 Refrigerated (ROSE) – may change after last SITE.
• SURF
  • 5 gas racks, 1 kbox, 1 Schlumberger item, gator box hardware
• RAF & FAF
  • samples

ASSISTANT LAB OFFICERS REPORT

Heather Barnes, Chieh Peng

Summary

Expedition 363 sailed from Singapore and concluded in Guam.
EXP363 was a high recovery sediment expedition with two week long transits at the very beginning allowing us to test out various instruments and perform physical counts in all labs.
Ty Cobb and Alexis Armstrong are hired as permeant marine technicians. They are excellent addition to the technical staff. Jan Jurie Kotz, or young Jurie (JJ), sailed as an ET in place of his father, the other Jan Jurie Kotz. JJ has proved himself to be an excellent marine technician, in addition to his ET duty, he helped out on the catwalk and in the core lab. We are very impressed and happy to have him for the expedition. If future opportunity arises, we would love to see him onboard again.

AMS/Inventory

• Physical counts performed on UTS and various labs.
• There were several items that had not been checked out, resulting in a low or depleted quantity on board. Please review again with technical staff the importance of "checking items out".
• We started using Chrome for AMS, especially for printing check-out sheet. It doesn't cut off the dates and titles.

Special projects

• Cryovac shrink wrap film was purchased and used for 2 sites. The material is less permeable and is used in the GCR. A heat roller was also purchased to seal the sides. Various special adapters were made and bought for the heat gun. We wrapped all cores from the first 2 Papua New Guinea sites (U1484 and U1485) with the Cryovac, along with one oxygen absorber per section. We ran out of the cryovac film towards the end, and started using our regular shrink wrap. We double wrapped the cores with Glad Wrap before shrink wrap, and we used 2 oxygen absorbers in each section.
• In the middle of U1488, we noticed the "new" core liners have darker lines, but the lines are not align perpendicular to each other. It is decided by the Pmag scientist(s), that we will split cores with double lines (Working side) on top, and ignore the split line.
• With the "new" core liner, we also notice the outside diameter is slightly larger, resulting in some difficulty fitting end caps over with a specula.

Shipment

• It is decided that we will use 19 boxes of core as per pallet from now on (when possible).
• All sites are from various countries/territories. Therefore cores are boxed according to sites.

U1482/U1483 –box 1-175, Australia, orange
U1484/U1485/U1486/U1487 – box 176-352, Papua New Guinea, red
U1488/U1489/U1490 – box 353-XXX, Federated States of Micronesia, no paint (note that there are a few on the middle shelf on top that are Micronesia).
3 boxes of Legacy cores.

• We will need to pallet these cores according to country – a detailed Visio and list is provided.
• World Courier: 7 Frozen (JOHN) and 3 Refrigerated (JOHN) and 3 Refrigerated (ROSE) – may change after last SITE.
• Surface freight (5 gas racks, 1 kbox, 1 Schlumberger item, gator box hardware).
• RAF as usual, FAF as usual.

Special notes

• Need to purchase in Guam : Blue ice? Acetone?
• The water cover for the Supersaw has several deficiencies
  • It is hard to see the blade
  • It is hard to see the core material
  • It is hard to clean
  • It doesn't reduce the amount of the water spraying out
  • It doesn't reduce the noise, not noticeable
  • It is hard to replace blade
  • The water volume cannot be adjusted
  • The spray direction cannot be adjusted

CORE LAB

Maggie Hastedt & Alexis Armstrong

Summary

Arbor Press was sandblasted and painted. The clamping bar, a new hose, and a new spray nozzle were replaced on the core splitter. Shrink wrap (both thin sheet-style non-permeable and the thicker hard rock tube type) were used extensively at the Papua New Guinea sites, techniques and issues are discussed below. Faulty core liners with mis-oriented split lines were sent to the ship, techniques used for correct splitting are discussed herein.

Equipment Notes

catwalk arbor press

Etienne and Siem orchestrated cleaning and refurbishing the core catcher Arbor Press. The Press was cleaned using a sonic bath, before being sandblasted, primed and painted. Since its maintenance, the Arbor Press has remained virtually rust free.

zebra label printers

We had sporadic issues with printing labels. Although we used new label stock, we did have issues with extensive adhesive material on the label bar causing labels to drag and misprint, wrap up, and/or be misaligned. Routine cleaning, and manually unwrapping stuck labels were our solutions to this problem.

Splitting room – installed new splitting bar & replaced hose and spray nozzle

The water hose and spray nozzle for cleaning the wire cutter and splitting bench were replaced. While splitting we were having consistent error in width discrepancy between the archive and working halves. To solve this problem Etienne and Jurie replaced the splitter bar completely and refitted the bar positioning. For more information see the ET tech report.

SHRINK WRAPPING

Shrink wrapping was used to increase the preservation potential of calcareous fossils at our Papua New Guinea sites. In order to expedite this process we created shrink wrapping stations and benches in the splitting room. Two stations were created. One station was created by flipping over the delrin section racks on the mobile table; the other was created by fitting a piece of plywood to the top of the central white sink-table. In the middle of the two benches, two rolls of shrink wrap were mounted onto a spool and affixed to the wall.
One main issue of the shrink wrapping is that we ran out of original non-permeable material, and were forced to use semi-permeable shrink wrap used for hard rock cruises. Depending on the shrink wrap used, two methods exist.
Non-permeable shrink wrap: First wrap each section in glad wrap. Add in an oxygen scrubber. Cut out your desired length of shrink wrap (the wrap is in sheets on a roll, not tubes). Roll the section in shrink wrap until the end of the wrap is in line with liner (it is important that the end of the wrap does NOT line up with the core material). Seal the ends with a heated crimper. Use the heat roller to create a seal along the length of the core were the roller can press against the plastic liner. Use a heat gun to do the final shrinking.
Permeable shrink wrap: Double wrap each section in glad wrap. Add in two oxygen scrubbers. Cut out your desired length of shrink wrap (shrink wrap is in a tube). Glide core section into shrink wrap tube. Using a spatula and a heat gun, melt and fold in ends of tubes. Use heat gun to heat the shrink wrap and create a seal. Shrink in a sweeping motion to prevent bumps and holes in the wrap.
Oxygen Scrubbers: These react very quickly, and within minutes will be unusable. Originally we could not use the scrubbers' quick enough, and if a package was opened and left, scrubbers were rendered useless. To solve this problem we individually packaged seven to eight scrubbers within ordinary IODP sample bags and individually sealed them.

misaligned core liners

Two alligator boxes of skewed core liners were sent to the ship. These new liners are thicker and are differentiated by thicker, darker black lines. The split lines are not straight, are not of equal distance and are visibly skewed. In order to maintain proper orientation, while splitting, we oriented each section with working lines straight up, and did not use the split line at all.

PHYSICAL PROPERTIES

Ty Cobb

Summary

Expedition 363 saw issues with the WRMSL, NGR, Gantry, and SHMSL, the 5 day transit to Site U1482 was used to resolve most issues with extensive effort from the Technical Staff and Developers, but some issues remained throughout the duration of the cruise. The NGR continues to have above normal Plastic counts, although the issue has been tested and found to be mainly Plastics detector 5. Also, the boat is running with a busted weld with no available spare, so extreme caution is being taken while in use. The Thermal Conductivity and Moisture and Density stations ran without any major issues throughout the cruise.
All archived/uploaded data for Expedition 363 has been removed from the local host and placed in S:\data1. This procedure should be done at the end of each expedition before the oncoming scientist are on board. On 363 this was completed by the PP technician. I am suggesting that this become part of the PP SOP for each Expedition.

Individual Measurement Systems

Moisture and Density (MAD)

The MAD station ran successfully and no major issues were reported. MadMax crashed a few times during the expedition and had to be restarted, the cause of this remains unknown.
MAD vials were taken for Paleo use as they ran out of unlabeled vials, additional vials will be sent out for X366.

Technical Service

Cleaning and calibration were performed throughout the expedition. The standard Sphere_10 was measured as a sample throughout the expedition, and an Excel sheet was saved on the desktop of the MAD computer station to check the calibration of the pycnometer and track any drift within the cells. Note: The volume for the spheres was corrected in the spread sheet from 10.2 to 10.255.
The new desiccator was installed at the beginning of the expedition. The increased efficiency of this device was seen throughout the expedition as 1 large bottle of drierite lasted the entire expedition.

Natural Gamma Radiation (NGR)

The NGR ran with some problems. There was an issue with the Plastics counts being out of range, but it remained within statistically acceptable error throughout the expedition. Additionally, the boat is being used with extreme caution as the weld on the load bearing end busted and has been rotated.

Problems

At the beginning of the expedition one of the two cooling fans (the fan closest to the bulk head) failed and had to be replaced. It was determined that it was being run at too high of a speed and was reduced to only run at normal while the other cooling fan was kept at max.
The above normal Plastic counts persisted throughout the cruise and were extensively tested during transit between Site U1483 and Site U1484, it was determined to be detector 5 that was causing much of the issue. The noise that was being seen can directly be related to the M-Drive motors on the WRMSL and also the NGR. After careful observation, it was noted that as the motors operate at full speed the Plastic counts jump to >20,000 counts. An attempt to block the noise from the WRMSL was unsuccessfully attempted using aluminum plating. After much discussion with David Houpt it was determined that the error caused by this issue was negligible as long as it did not reach 100,000 counts.

Technical Service

Energy calibrations were performed at every Site and the channels adjusted according to peak positions. A request for a new Co standard was submitted to the Lab Officer at the beginning of the expedition.
The actuator was greased at the end of November.
In the last two weeks of the cruise the weld on the load bearing end of the boat partially busted. To temporarily bandage the issue the boat was rotated 180° to remove as much stress as possible from the rupture. The spare boat is missing an end so therefore it will be sent back to College Station to have the end attached. This means that the busted boat will still be in use for Expedition 366, unless it is able to be fixed while in Guam.

Section Half Image Logger (SHIL)

The SHIL was used to measure section halves at each Site with minor errors throughout the expedition. See Imaging Specialist reports regarding color calibrations.

Problems

The SHIL IMS was set to draw the created length from LIMS as opposed to the curated length, this was causing issues when trying to scan sections that had either expanded or shortened based on curation. This issue was corrected in the IMS code by Maggie and not seen again.
Several times during the expedition the SHIL lost its color calibration completely and had to be recalibrated by the Imaging Specialist. This issue was directly related to IMS system crashes that occurred several times throughout the expedition, the cause for these crashes is still unknown and need to be carefully monitored.
Scientist continually reported that the camera would take an image and then would give nothing in return to crop, i.e., the user interface to crop the image would appear with a blank selection.
The Imaging Specialist discovered that the QP grey card was varying in size on images throughout the expedition, this was not causing sections to need rescan, but it does indicate that the camera isn't initializing capture at the some point for each image.
A continued issues is the failure to write TIFF files once the SHIL computer hard drive is near capacity, the solution to this is to clean up the drive about half-way through a cruise to ensure the issue does not occur.
While the database is running "slow" there is an error that occurs while trying to image sections. This is due to the call to LIMS being too aggressive, Developers say that there isn't much to be done without touching the code. For now the work around has been to simply dismiss the error and continue, this causes no loss of images and only occurs at the beginning of a scan after scanning a previous section.

Technical Service

All technical services were performed by the Imaging Specialist.

Section Half MultiSensor Logger (SHMSL)

The SHMSL ran successfully throughout the expedition, with several work arounds to persistent issues that were unable to be resolved. At the beginning of the expedition the SHMSL QSG was updated and sent to David Houpt for review, this has not yet been returned.

Problems

There were several persistent problems during the expedition that were unable to be resolved. The first was a continuous 2 cm offset when the core section was measured, this required the scientist to continuously subtract 2 cm from the laser measured core length to make sure that the instrument beginning measuring at the true end of section. The apparent reason for this is due to the home and load position being equal, although they should not be and attempts to change them failed.
Another ongoing issue occurred after each calibration of the USB4000, when the instrument would turn off the light sources it would only turn the LED source back on. This issue was determined to be due to the Fhidget and because there are no spares on board, the work around for this was to close out of IMS and restart the program, with calibration only occurring every six hours this was of little hassle.

Technical Service

The halogen light sources were changed twice during the expedition and will require changing on the 15^th of December 2016. The white standard for the spectrometer was cleaned four times during the expedition.

Recommendations

With the Fhidgets it would be recommended to have at least two spares on board and to start an in lab inventory of each type of Fhidget that is on board. This will help prevent future problems if we are able to confidently say we have a backup.

Special Track MultiSensor Logger (STMSL)

The STMSL was used extensively throughout the expedition with no major issues. For each Site only sections from Holes B and onward were run for correlation purposes. At the beginning of the expedition the correction factor for the MS loop had to be adjusted to 1.174 as it was only set to 1, this was causing a major offset between the WRMSL MS Loop and the STMSL loop.

Recommendations

The pusher section is only measuring one point, it was noticed that this decreases precision on the water standard (although when measured completely precision was within acceptable range). It would be more advantages to measure multiple points instead of just one to ensure that precision is still being preserved.

Shear Strength Station

The AVS system was not used during the expedition.

Thermal Conductivity

Thermal Conductivity ran successfully for the entire expedition. Needle probe V11062 was used extensively on the soft sediment for the expedition. In the more lithified sediment the mini half-space probe (H51016) was used on split core sections. At the beginning of the expedition needle probe V10702 was used unsuccessfully and was subsequently changed out. Note: 2 additional battery packs were order for the drill

Problems

The two issues that occurred during this expedition was the power effect on measurements and the drift control set being original set too high. A continued problem the power affecting measurements was found on the expedition to only effect the mini-puck, while using the needle probe the instrument remained plugged into the white power connections. For the drift control the parameter was originally set to 40 and was lowered to 10 as is normal operating procedure for TEKA.

Whole Round Image Logger (WRIL)

The dedicated WRIL was not used during this expedition.

Whole Round MultiSensor Logger (WRMSL)

The WRMSL had several issues towards the beginning of the cruise, and continuous issues throughout the extent of the expedition. Ultimately, it was worked through and ran well enough to provide the needed analysis for the science party.

Problems

There were several issues with the WRMSL throughout the expedition. The most notable was during the 5 day transit to Site U1482 the M-Drive failed and needed to be replaced and subsequently IMS lost communication with the M-Drive and the P-Wave Tritex. To resolve this issue David Fackler had to reprogram IMS to recognize both devices, this took several days. The Tritex system port configurations were reset during the issue (occurred due to board removal and driver reinstallation) and after discussion with Bill Mills it was found that the port configurations had to be switched to match the new positions of the boards. Once, this issue was fixed the P-Wave logger was adjusted to only just make contact with the core section as opposed to squeezing extremely tight, this produced much better measurements.
Throughout the expedition the P-Wave logger repeatedly lost communication with IMS and had to be powered down and unplugged completely to regain communication. A quick fix for this before restarting the computer is to use the Tritex software to move the P-wave logger, reinitializing from this software seems to get the machine to start "talking" again.
An additional issue is when the software or the individual P-Wave instrument in shutdown the peristaltic pump remains on and has to manually be turned off.

Recommendations

Keep the current contact settings for the P-Wave as they are, express to scientist that contact tighter than a slight decompression will cause a skew in the recorded data.
The pusher section is only measuring one point, it was noticed that this decreases precision on the water standard (although when measured completely precision was within acceptable values). It would be more advantages to measure multiple points instead of just one to ensure that precision is still being preserved.

Velocity Gantry

The Velocity Gantry system was used to measure the X and Z axis velocities of sections halves. The Gantry ran with minimal issues throughout the cruise, but had a few hardware failures.

Problems

Expedition 363 saw issues with serial communication between the laser and the computer being lost, the gas strut failing, and the laser failing to find the end of the core section. The issue with the serial communication was resolved by simply removing power to the laser and letting it rebut, this problem only occurred once.
The gas strut failed about half-way through the expedition and was replaced with a spare with the help of the ET's.
The major issue that occurred during the expedition was the inability for the laser to determine the end of the core section, this was determined to be because of the differences in color of the blue end caps, the only solution that was found for this was to place a more solid piece of material on the end of the section (e.g., a piece of paper).

Technical Service

The Gantry calipers were disassembled, cleaned, and lubricated at the beginning of the expedition and twice during; the X bayonet was lubricated twice during the expedition and Y bayonet was not used. The gas strut has been replaced on the calipers.

General

• The water tank for the peristaltic pump for the P-wave logger on WRMSL should be change as needed, with a very small amount (one capful) of bleach added to discourage bacteria growth.

Shipment

To Shore

Air Freight/Surface

1. Desiccators – 2 individual, replaced at beginning of expedition
2. Pycnometer water chiller, no longer being used
3. NGR spare boat to add end piece

To Ship

1. Additional treys for the Desiccator
2. Additional MAD vials (12 boxes)

PALEOMAGNETICS LAB

Edwin Garrett

Summary

The paleomagnetics lab was used extensively for this high recovery sediment expedition. The SRM functioned fairly well and there were few technical difficulties. The orientation tools were deployed on every hole, with over 30 runs so far. They still had the issue of being 180 degrees off on orientation direction. Over 370 cubes were taken for shipboard analysis, close to 5000 meters of core has been measured in the SRM with varying demag levels. The intensity and quality of core magnetization varied, with some holes/cores giving excellent results, and some having almost no magnetization (white carbonates). IRM was also used on some cube samples, and the Kappabridge was used for bulk susceptibility with the DOS Sufar program. At port call there was a helium refill and a replacement of the cold head. 2G came to perform both and there were no significant problems. This is anticipated to be the last expedition for the liquid helium 2G magnetometer, as the new one should be installed during the Guam port call. At the end of the expedition we will begin to prepare the paleomag lab for the new installation, time permitting, as there is a short transit from the last site to Guam and a likely backlog of cores to measure.

Issues

• The D-Tech AF demagnetizer functioned mostly without problems. However, on one occasion it appeared that it stopped demagnetizing samples though it reported no error. The scientists restarted everything and it worked properly. This was early in the expedition and the problem never reoccurred.
• Kappabridge functioned without incident. In order to use the Sufar bulk susceptibility program, the DOSbox program had to be run, with the following commands to start up Sufar: mount y c:\sufar <CR>, y: <CR>, sufar <CR>
• Orientation tools were used on every hole. We have had 30 runs so far with orientation picks for over 450 cores. We started using the Flexit tools to check them, then switched to the Icefield. Both still reported orientations that were off by 180 degrees. Early in the expedition we observed on the rig floor how the tools were assembled for APC coring, and we looked at drawings of the system from Kevin Grigar, but it did not help resolve the problems. Otherwise, the tools had few problems. We had one partial failure of an orientation tool due to battery failure. I tested the batteries before putting them in the tool, but the voltage reported after starting was less than expected and it stopped recording after a few hours. Unfortunately the tool does not report the battery voltage until after you start the run, and on this occasion we left a tool for the ALO to start because Maggie and I would both be off shift when it was needed. Fortunately they were just spot coring a hole C and the data was not critical. We will let the ALO's know that anything below 9.2v should not be run if we are not on shift for deployment. Also a scientists was suspicious of data from Icefield tool 2007. Although it performed as expected during tests, the data seemed clustered, so we stopped using it at his request. And during the expedition there were some cores in 2 holes that showed a 90 degree offset instead of 180. We have not had time to look into this. Figure 1 (courtesy of Rob) shows the oriented core data in normal and reversed periods, the grey area was just noise from poorly magnetized core. The 180 and 90 issues can be seen, but the figure may need to be expanded to view this (figure stored on DATA1). Also we could not upload the Icefield data using the Kappabridge computer. It would sync time, date, etc but not transfer the data. The downhole computer would not sync at all unless rebooted. Maggie's computer is the only one that always transferred without issues.
• The new IRM was used with no problems.
• There was still an issue with the new JR6 MUT upload program and the way the scientists planned to record and process their data. They wanted a naming scheme that directly related to the sample location, but the upload program needed the cube ID. David Fackler altered the pmag cube printer to print 2 scan labels, one with the cube ID, and one with a human readable ID that would work with the Remasoft program. He tried to put both into the label ID, but the cube number was truncated in the JR6 file. In order to be uploaded, the JR6 files will have to be edited if the cube number is not used as the sample name. It was also discussed that all the relevant data is in 1 JR6 file, yet the upload requires 4 files, making it complex and prone to errors that are hard to track down. A better version of the MUT program is needed.
• During the leg the JR6A was used for all cube samples and performed well.
• The SRM functioned well. There were variable problems with flux jumps that could not be associated with a site, hole, heading or anything tangible. At the beginning of the leg, the new SRM software was tested. There seemed to be some positioning issues, as we put a magnetized pin at a known location and measured in 1cm increments. Depending on the tray offset entered in the config file, the squid center was offset 1 to 2 cm in the measurement. After some emails to shore we were able to get the measurement area centered under the squids, but it was unclear as to why the offset we used worked. Overall the new software was more user friendly than the old, but of course there are still various addition and/or modifications that might be desirable.
• The thermal demagnetizer was not used.

Figure 1

Cryomag readings

CORE DESCRIPTION AND MICROPALEONTOLOGY PREPARATION LABORATORY

Rachel Gray

Summary

Expedition 363 was a high-recovery sediment expedition. The science party included eight core describers and seven paleontologists, with expertise in planktonic foraminifera, benthic foraminifera, and nannofossils. Templates were created for each microfossil discipline.
The core describers used a description scheme which involved combining multiple prefixes (e.g., foraminifer-bearing clay-rich). They briefly toyed with the idea of using a workaround to create multiple prefix columns, but ultimately settled on generating a list of all possible prefix combinations in Excel and adding them to the value list. Subsequently, the prefix value list is very long.
The SEM was heavily used, for both micropaleontology and lithology imaging.
The Micropaleontology Wet Laboratory was used for all paleontological disciplines.
BugWin was not used.

ISSUES/To BE noted

Scientists, particularly the planktonic foram paleontologists, had occasional issues with duplicated rows upon downloading data. This issues was compounded by the fact that the planktonic foram template had several columns in which data from one column was autofilled (by use of a formula) into a second column elsewhere in the template. This often caused the duplicate rows to "come back" after being deleted.
Uploading value lists in the pre-2007 Excel format (.xls) caused an error message from the Value List Manager. All values lists still in .xls format were re-saved in the newer .xlsx format, which solved the problem. (The VLM still accepts sublists in the .xls format).
The SEM filament was replaced twice during the expedition.

Data Backup

All DESClogik data was exported to excel and saved on a hole-by-hole and template-by-template basis to data1/10.1 Core description.
All smear slide sheets and core description log sheets were scanned and saved to data1/10.1 Core description.
All SEM files (jpg, tiff and txt) were saved to data1/25.1 SEM and uploaded to LIMS (by the scientists).
In order to sync all google value lists on ship/shore all current value lists (main and sub), were copied from "All things DESC" on IODP Share to data1/10.1 Core description.

CURATORIAL REPORT

Chad Broyles

SUMMARY

Samples

A total of 18,545 samples were taken for Expedition 363. This included 7,499 shipboard samples, and 11,046 personal samples. 77 shipboard samples were requested and assigned sample request numbers and codes. 6,956 meters of core material was recovered during the expedition with 100% average recovery.

Shipments

Core-Approximately 54 pallets of 1,042 core boxes will be shipped from Guam following the expedition. These will be shipped 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. The pallet inventory will be sent to the GCR by the oncoming JRSO crew after Exp. 363.
Frozen and Refrigerated
Frozen and refrigerated shipments will go to the following locations:
Daniel L. Johnson (JOHN)
Department of Geological and Planetary Sciences
California Institute of Technology
1200 E. California Boulevard
Pasadena CA 91125
USA
Tel: 815-494-0523
d.johnson@caltech.edu
Yair Rosenthal (ROSE)
Institute of Marine and Coastal Sciences
Rutgers, The State University of New Jersey
71 Dudley Road
New Brunswick NJ 08901-8521
USA
Tel: 848-932-3402
rosentha@marine.rutgers.edu

Total JOHN Frozen Bags: 6
Total JOHN Refrigerated Boxes: 3
Total ROSE Refrigerated Boxes: 3
13 Total World Courier Boxes.
Residues
27 Boxes (1 pallet) of residues are being sent to the GCR with the core shipment.
The residue distribution is as follows:

Smear Slides- The sedimentologists prepared and described 1,122 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.
Thin Sections- Seth Frank prepared 4 Thin Sections on Exp. 363. The thin section inventory is being sent via email with this document to the GCR.

CURATION AND SAMPLING

Pre-site to Site Conversion

CATWALK SAMPLING
The catwalk sample plan for U1482, U1483, U1484 and U1487 is listed below.
Mudline Sample

• A mudline sample was collected in a bucket for all mudlines.

Interstitial Water (IW) Samples

• Figure 1 details the IW sample plan.
• This sampling was performed on single holes, usually Hole A.
• Cores 1H-3H, 5 cm Whole Round (WRND) bottom of Sections 3 and 6.
• Core 4H to TD, 10 cm WRND bottom of Section 6.
• Every other core for ½ APC Cores.
• Increased to 10-15 cm when water content decreased.
• Bottom of Section 6. If interval was found to be disturbed, the sample location was adjusted.
• If another Hole was drilled deeper then IW sampling picked up in that Hole.

Head Space (HS) Sample

• Taken below IW sample
• 5cc plug.
• Small pieces were taken for lithified material.

PAL Sample

• 5 cm Whole Round (WRND) from bottom of Core Catcher.
• Splits were taken for foraminifera and nannofossils.

The catwalk sample plan for U1485 is listed below.
Mudline Sample

• A mudline sample was collected in a bucket for all mudlines.

Interstitial Water (IW) Samples

• Figure 2 details the IW sample plan.
• This sampling was performed on single holes, usually Hole A.
• Core 1H-6H, 5 cm WRND bottom of sections 1, 2, 4, and 5.

10 cm WRND bottom of Sections 3 & 6.

• Core 6H to TD, 10 cm WRND bottom of Section 6.
• Every other core for ½ APC Cores.
• Increased to 15 cm when water content decreased.
• Bottom of Section 6. If interval was found to be disturbed, the sample location was adjusted.
• If another Hole was drilled deeper then IW sampling picked up in that Hole.

Head Space (HS) Sample

• Taken below IW sample
• 5cc plug.
• Small pieces were taken for lithified material.

PAL Sample

• 5 cm Whole Round (WRND) from bottom of Core Catcher.
• Splits were taken for foraminifera and nannofossils.

The catwalk sample plan for U1486, U1488, U1489, and U1490 is listed below.
Mudline Sample

• A mudline sample was collected in a bucket for all mudlines.

Interstitial Water (IW) Samples

• Figure 3 details the IW sample plan.
• This sampling was performed on single holes, usually Hole A.
• 0-150m, 5 cm WRND bottom of sections 1, 2, 4, and 5.

10 cm WRND bottom of Sections 3 & 6.

• 150m to TD, 10 cm WRND bottom of Section 6.
• Every other core for ½ APC Cores.
• Increased to 15 cm when water content decreased.
• Bottom of Section 6. If interval was found to be disturbed, the sample location was adjusted.
• If another Hole was drilled deeper then IW sampling picked up in that Hole.

Head Space (HS) Sample

• Taken below IW sample
• 5cc plug.
• Small pieces were taken for lithified material.

PAL Sample

• 5 cm Whole Round (WRND) from bottom of Core Catcher.

Splits were taken for foraminifera and nannofossils.
SAMPLE TABLE SAMPLING
The general shipboard sample plan for Exp. 363 is listed below. Slight variations were made for individual sites depending on recovery and core flow.
Shipboard Analysis (Working Half)

1. Carbonate (CARB)

• 2-3 sample per Core.
• Picked and taken by sedimentologists.

1. Moisture and Density (MAD)

• 3 per Core.
• Every Other Section.

1. Nannofossils (NANNO)

• Toothpick Sample.
• 1 per Section.

1. Paleomagnetism (PMAG)

• 3 per Core
• Taken by PMAG scientist.

1. Paleontology (FORAM)

• 3 per Core
• 10 cc large Tube (TUBE_L)

1. XRD

• As needed by the sedimentologists.
• 5 cc tube.

1. SEM

• As needed by sedimentologists for volcanic ash

Additional Sampling (Archive Half)
1. Smear slides (SED)

• Toothpick Sample.
• As needed.
• Taken by sedimentologists.

1. Personal Samples for Ann Holbourn and Yair Rosenthal.

The co-chiefs requested additional samples from U1490B-23H-26H for a quick publication post expedition. This was approved by the SAC. This was recorded in the LIMS database under their respective personal research proposals (41901IODP and 41159IODP) Below is the research proposal description from Dr. Holbourn.
Dear Chad,
Here is a brief description of the proposed research for the samples taken yesterday.
We have taken shipboard samples from U1490B-23H-26H for preliminary benthic foraminifer isotopes (Holbourn), and for Nd isotopes, TOC and CaCO3 and grain size analyses (Rosenthal in collaboration with Aiello and Ravelo). At Site U1490 we found lithologic (e.g., clay content, grain size), geochemical (%CaCO3) and faunal (foraminifer assemblages) changes suggesting a major change in water currents at the estimated age of ~14 Ma. The apparent change in current direction/velocity likely reflects larger changes in the Pacific meridional circulation. The preliminary data, when combined with the shipboard measurements, will help us better document this apparent change in circulation and its possible links to the middle Miocene glaciation of east Antarctica and associated sea level fall. While a more rigorous study will be required to validate these initial observations, given the uniqueness of the new record and the scarcity of similar records in the western Pacific, we think that a quick publication is warranted. We propose to submit to a high impact journal a paper co-authored by shipboard participants, which will document this finding.

Please let me know if you have further questions. Thank you for your help with this,
Ann

CORE PRESERVATION

All archive and working half sections were wrapped in Glad Wrap. For sites U1484 and U1485 we also used Cryovac shrink film on both working and archive halves. These sites were near the coast of Papua New Guinea. At these sites, the sedimentation rate and organic content in the core material acquired was very high. The shrink wrap was requested by co-chief in order to preserve carbonate micro and nanno fossils.

ACTION ITEMS

Legacy Cores-Three boxes of legacy cores were sent to the ship for X363. This will be included in the X363 core shipment. The following is a core box inventory for this core material.

problems encountered

New Core Liner-We started using a box of new core liner mid-expedition. These originate from a new manufacturer. We found that the working half double lines, the archive half single line, and the two split lines are not evenly space around the circumference of the core liner. All lines are not spaced 90 degrees from one another. Therefore when splitting you cannot depend on the split line for even spacing. We tried centering the working half double line on the top when splitting core, since the double line was used for APC core orientation.
Drilled Intervals-Sample Master does not update the 'Catwalk Length' in the Core tab when there is a drilled interval. The application should populate this field with a zero, since you do not recover core material. To work around this you need to Edit the Core Tab for a specific Hole, update the 'Catwalk Length' to a zero value for drilled intervals, and recalculate the depth for the entire Hole.










!worddav7a28ff330c7af426c5b56f8f999b410f.png|height=520,width=630!h1. IMAGING LAB and MICROSCOPES
William Crawford

Still Cameras

The Canon EOS IDS, Hasselblad, and both Canon EOS 5D cameras as well as the Nikon and a variety of lenses were employed with no issues to report. The sensor on the Canon was cleaned. The new lens is a welcome addition to our lens set. It allows a more unique stylish image, which is sometimes preferred in publications. It was a joy to use.

Video Camera

No video usage.

Epson printer

The Epson printer continues to impress me with the ink savings between the previous model. The amount of ink usage has gone down at least 50 percent. The advent of roll paper has allowed a larger image to be produced which helps clarity on the group photos when the head size of the individual is small due to group size. We did have a roll of paper damaged in shipment and 1/3 of the roll was not usable.

Close-up Imaging

The Close-up Station was found to be inoperable due to upgrades in software by the programmers. The links between the image files were pointed incorrectly and therefore inoperable. It took some time to sort out the problem but in the end the system worked well. This being a high recovery sediment expedition, the Close-up Station was not heavily used.

Petrographic Image Capture and Archiving Tool (PICAT)

The PICAT system worked without requiring additional attention. Again, this being a sediment-dominated expedition very few Thin Sections was generated.

Challenges

By far the biggest challenge was the Section Half Imaging Scanner. The scanner suffered from unknown changes, which set in motion a series of event, errors, and crashes, which plagued the entire length of the expedition. Initially the scanner was found in an inoperable state due to loss of its calibration data. The buffer of the Tiff image displayed as the image was acquired with the corrected jpg displayed as a dark unremarkable unusable image. Jay Miller met with me and we discussed this issue along with encouraging me to write an operation and calibration manual, which I concentrated on and wrote extensive notes throughout the cruise.
Having recalibrated and brought t the scanner into operation during the 6-day transit, the frequency of errors and crashes were more prevalent with the IMS than we have ever witnessed. On the positive side of this, we had the best people on board with the skills to chase down most of these issues and either solve or work around them.
One of the most troubling would occur after an error or re-start of the IMS program. The IMS would refer back to an old calibration without notice. Such an error may or may not be apparent to the operator and it caused cores to be rescanned. David Fackler working with Margret Hastedt chased down the problem to duplicate Configuration files. "Green Flashes" we common also.
On a positive note, due to the attention the IMS required, this allowed me to dive deeper into the processes and develop a much better understanding of its operation.
There was an attempt to do a Camtasia screen capture video, highlighting an explanation of some of the more complicated processes but an interruption of work flow and the chance of erasing the calibration, would have been prohibitive. This will be continued with the shore based SHIL.
The first site was dominated by darker core and the last site was core having a density brighter than our control swatches. Photographing darker core and extreme white core presented its own set of challenges.
Monitoring the scanner output and reacting to the quality of images efforts increased as the Expedition progressed. I do feel this is some of the better images we have produced considering such challenging ranges of core luminances. Having said so, the scanners calibration were shifted to the conservative side due to the unpredictability of the core's reflectance densities.

While such attention was turned to the Shil I took the opportunity to add improvements to the system. The QP Card calibration platform was leveled to that of the tray. Working with Etienne Claassen, a gray cardholder was created to ensure the gray card target was being held flat and level when placed on the section tray. The calibration of the sensor is very sensitive to even slight variations in illumination and this helped in that problem. An evaluation of several of the gray cards reveled a enough of a variety in color that it was affecting the outcome of certain phases of calibration. The Graytag McBeth gray card proved the most neutral and this card was fitted to the new gray cardholder. A new approach to the Pixel Gain and the Shadow correction calibration procedures also proved fruitful. All of these small adjustments allowed a finer more accurate calibration and a much better side-to-side consistency and evenness of lighting and reproduction.
I came away from the Expedition with a much greater understanding and will gladly share this within the pages of the manual to be written. Life is good.

.

Shipped to Shore

No items were shipped to shore from the Imaging Specialist.

Image Summary

LSIMG 5333 Core Sections
Close-up 17
Micrographs 1806
Thin Section 6
Still Images 98 Gb (55 Gb Raw)
Video 0
SEM 701 uploaded

Microscopes

The microscopes were cleaned, configured and adjusted during the fortunately long transit. The systems and the cameras worked well.
The microscopes were set up for Nanno fossils and Forams.
There were little problems with the microscopes once the operators understood the camera functions and the microscope controls.
Only common issues such as bulb changes occurred. One of the new lamp houses needed attention. This is the same issue with the lamp drawer coming unlatched. No repair was necessary and we have plenty of spares.
All of the users of the microscopes users were experienced and required little attention from us.
We were witness to a new method of viewing nannos using Circular Polarization introduced by Luc Beaufort (Paleontologist, Centre National de la Recherche Scientifique [CNRS], France). This method "unmasked" the dominance of the birefringence affects of the cross polarization to peek at the actual body of the nanno also. We are low however on the stock of adequate wave plates to take full advantage of this technique in the future. I found this exciting and fascinating.

SEM

The SEM was heavily used. I believe the technical staff, lead by Rachael Gray, Zenon Mateo and Margaret Hastedt, installed three carbon filaments. The Splutterer was used heavily as well. There were some issues with the differences operation between the Micrograph image up loader and the SEM Imaging uploaded which lead to some confusion. To date 701 SEM images were uploaded.

X-RAY DIFFRACTION, ICP PREPARATION

Ben Daniel

Summary

Moderate number of XRD samples processed. No ICP samples processed. Mostly bulk and carbonate free scans. Some Clay separations, but did not get good quality data from these runs. Major issue with the water chiller for the D4 encountered, solved with assistance from ETs and LO. Resolved by cannibalizing impeller pump from water chiller for the Cryo-Mag. 2 New pumps ordered and on route to the ship.

Total Samples

XRD: 98
ICP: 0
MBIO: 0

X-ray Diffractometer

A full QAQC at the beginning of the expedition showed no need for adjustment. Subsequent runs of the NIST1976 throughout the expedition also showed no need for any adjustment. Water flow rate from the Haskris began at 6.53 l/min. Haskris pump noise changed noticeably on November 12, but flow to the D4 was normal. At some point on Nov 12-13, the haskris pump seized, haskris shut itself off and all flow to D4 stopped on November 13. D4 flow alarm tripped, and machine automatically shut down per protocol. The ET and I took apart the haskris and tried to unbind frozen pump by sonicating and exercising the pump by hand. After putting device back together, flow returned briefly, but pump soon seized again. After fully disassembling the pump, it was found that the impeller had a major fracture, and that several of the blades had been ground into pebbles. Completely irreparable. We then replaced the original pump with a spare, slightly smaller pump from the haskris for the Cryo-mag. Though we were able to get internal flow in the haskris, the D4 was still showing minimal flow, and giving a low flow alarm.
LO and ET reversed the direction of flow to the machine, and removed a significant amount of debris from the D4. It seemed to be more pieces of the disintegrated impeller. After returning the direction of flow to normal, the D4 showed flow in the normal operating range of ~6.40 l/min. Water quality was monitored closely for a few days to ensure that any more debris was removed from system, and that flow remained normal. No further issues have been encountered. New pumps are ordered, but LO thinks that repair job may be sufficient for the foreseeable future. It was discovered that the filter on the ship's chill water is unnecessary. Water from ship never enters the haskris/D4 system. Rather, it remains isolated in the heat exchanger/ship circuit. The debris that was reported periodically in the haskris reservoir is likely from the impeller blades slowly breaking down. (Fine, dark grey, silty material; and larger black grains). Clay separations did not give good quality results when fallowing the procedure from Kitty Milliken at UT-Austin. Clay content was likely too low, and not enough material was present in the supernatant after the final centrifuging. To compensate for this, settling by gravity was allowed in a final wash of DI water, (rather than 1% borax). The upper layer of the settled material was sampled by pipet and run on a low background quartz disk as in the original procedure. This was referred to as carbonate removal, rather than true clay separation. X-ray tube conditioning should still be recorded and monitored for any changes.

ICP Prep

No ICP prep was done on this cruise.

Thin Section Lab

Seth 'Sparky' Frank

Summary

1. Word of the expedition
2. Work /w¿¿k/
3. noun
4. 1. activity involving mental or physical effort done in order to achieve a result, to work.
5. 3 thin section requests. Grain mounts, mostly sand, some clay, one rubble bin filled with olivine and other materials. These were especially difficult to work with on large format slides as the amount of pressure applied unevenly across the surface would cause cracks to form. Also with large format grain mounts, the epoxy would flex the sample as a whole and provide quite a challenge for the petrothin cutting phase and final hand sanding on sandpaper. Recommendations from this tech is to perform handmade thin sections in small format only to prevent loss of time & hair tearing out.

LP-50

While frosting slides in preparation for this expedition and the next, the vacuum pump connected to the LP50 wouldn't engage. I took it apart and it looked as though it hadn't been cleaned or oil changed in years. I cleaned it as much to my knowledge as possible, and then replaced the oil. When I reconnected it to the LP50 system, and turned the pump on using the switch on the LP50, the entire thing shut off, LP50 and vacuum pump. Currently unable to establish exactly the cause. The ET's determined a fuse was blown from overwork caused by blockage on that vacuum pump through the system.

Took the pump completely apart except for the motor. The amount of corrosion and rust on the inside was unacceptable. Sonicated the metal parts to remove what could be removed and then put back together, replaced with the oil, now pulling excellent vacuum. Replaced blown fuse as well on LP50.
It is the recommendation of this tech to make it a practice to clean the vacuum pump at least once a month. Help is appreciated and required in order to complete this task in a timely manner.

Petrothin

No problems with the petrothin itself. I had a problem with the large format thin sections achieving adequate vacuum, though this was due to the samples being attached to those slides, causing slight warping. The petrothin system had no problems otherwise achieving vacuum. The oil was replaced on the appropriate vacuum pump 11/16/2016.

WG-2 Polisher

The WG2 polisher head has the replacement piston put in, but the head does not spin. Tried a variety of fixes to see if I could get it to respond properly and nothing worked. Recommend replacing the head and sending the old one back to Logitech to get repaired. There is a video on the T/S computer showing exactly the problem.
The polisher is now officially being sent back to get repaired and a replacement is being sent out post 363 for future expeditions.
I modified a polisher slideholder to accommodate a slide for making thin sections by hand. Old methods were destructive to fingertips, and less effective since uneven pressure is put on a slide during hand sanding methods. The polisher holder evenly distributed pressure across the whole thin section and removed your fingers from direct contact with sandpaper making hand sanding a far more effective method than before. This polisher holder is marked specifically with paint on the back so it is unmistakable.

Samples and methods

There is no change to the methods I made this cruise. I followed some of the methods set up in the Cookbook and some that were described in the 362 tech report. But there were no major changes made to any current operating procedure besides regular maintenance on the vacuum pumps.

Miscellaneous

Nothing to report on miscellaneous items.
Recommend performing physical counts of consumables in this lab to ensure adequate amounts of materials for future expeditions.

ELECTRONIC TECHNICIANS REPORT

Jurie Kotze, Etienne Claassen

Labs

Chem lab

ICP Auto sampler

The ICP auto sampler were not getting the same slot, we had a look at it and found a few thing wrong with it, the cable did not have enough tension it we tension the cable but the problem still uncured, we remove the motor and the shaft and discover the shaft were not secure to the motor with its crib screw, we remove everything and refit it back on the motor, we rewind the cable as the cable was running over one another because of the tension. We install all components and test, we realign the sampler and it was working as prescribe, we need spares for the instrument, like new motor and a new cable, but we have to look at order spares or replacing the sampler with a new sampler.

Core laB

Mad stasion

The oven in the mad station area was not working it had no power, we removed it to the workshop to fault find, we found the fuse was blown on the 115 v line in we replace the fuse and the oven is working, we install the oven again, we are monitor the oven to see why the fuse blown.

NGR

The fan rack on the left had one fan going down, we replace the fan rack with a new rack and test the faulty rack, there is only the one fan not working and it is not the controller but the fan, we did talk to Brad and Garrick and they will order new replacement fans for the rack.
The rack on the right also are having issues and we decided to leave it in and run is at full speed, it works on full speed, but new fans are on order.
The titanium boat end broke of, we turned the boat around and reattach it to the rod, we had a look at the spare boat but it is also broken off, we are arranging for a welding shop to weld the ends as we don't have the equipment to weld titanium on the ship.

WRMSL

The WRMSL went down the motor stop working, we work with the programmers and replace the motor and the controller board, we end up replacing everything and the programmers reprogrammed everything, and we got the track running again, after look the coms cables re found that the cable inner was cut probably when cable was made up this course the motor to burn and trigger the programming problem.

Cable wire cut Cable close up

Cable close up

Splitter room

We had a shrink sealer that broke and after stripping it to be repaired the bake lite handle fell apart, we decided to remove it from use and to order a new sealer.
We still have problems with the supper saw cutting uneven pieces and cutting from thin to thick when using the wire cutter.
We took a few measurements, and found that the cradle the core are lying in is moved and that accounts for the core splitting uneven, we did made a few changes but if we don't fix the cradle this will be a accruing problem until me fix this. We made a new bar for the supper saw as it was thought to be bend, the old bar is in the splitter room.

LaSer Engraver

We replace the airflow sensor, it got clogged up and we did clean a few times but it could not be cleaned anymore and we replaced it, we set the low air flow and to the High air flow.

X-RAY LAB

HasKris

The haskris in the XR lab stated making a noise and the XRD shut down, alarm show low or no water flow, after some fault finding we found the haskris pump were making the noise and were removed to be inspected.
The pump were open and pebble were found in the pump outlet, after inspecting the pump we found the impeller were worn down and pieces of the carbon housing were broken of inside the pump.
We is install a spare pump from the P Mag haskris, but the XRD still did not switch on, there were no flow to the instrument, and the thought was that the pump were too small.
We later inspect the haskris again and test the flow with a pipe looping out of the haskris and in again bypassing the instrument, the flow were 8 liters per minute, we again connect the instrument inline and found no flow, we open the inlet pipes going into the instrument, and found more pebbles in the inlet pipe, but still pebbles removed, we decrease the bypass flow and still no flow.
We switch the inlet and outlet pipes on the haskris and hope to flush any blockage out of the instrument and into the haskris, we test it again and fount the flow to be 4 + liters per minute, the instrument were switch on and came on immediately the flow on the instrument show 6.75.
This problem had to be started years ago and nobody notice it until now, if we see the water turning dark we have to look what is coursing it, we also have to install a filter inline in the inlet pipe to prevent this from happening again, and not on the ships cooling water.
Two new pumps have been ordered to replace the temporary punt that was install and used from the P Mag.

Thin section lab

The Logitech polisher head motor WG 2 stop working again, we have done some work on it, on Exp 360, we did get it working temporary, we had to soak it in the sonic bath on Exp 360, that we think course other problems, the motor sometimes work but draw so much amps that the instrument cannot handle it. On this Exp we do not need the polisher but it will be use on the next Exp, we had ordered a new motor for the instrument and will be sent to the next port call( Guam). There may be some work to be done inside the instrument but as soon as we have a replacement motor we will know more, the motor sometimes turn on the bench but not on the instrument, this can be course by the high amps the motor draw and the fact that the instrument cannot supply so much.

Entertainment

Movie room

The movie room amp stop working, at first we thought it was the Popcorn Hour that was having an issue but we remove the popcorn hour and still it had the same problem that the video goes blank only audio.
We swaped the HDMI cables but still the same, we checked the amp and found that some time for no reason the amp switch of the video, but as soon as you reset the amp it will work again, it looks like the HDMI in to the amp has been damage again, this is cause by people changing things on the amp without the ET'S knowledge.
Solution is to cover the sides of the amp like we have done before to prevent people from plugging their own equipment to the system, we have provided people bringing their own drives.
We Found the popcorn hour to stop working and was unstable, the video stop working but audio still work, we tested the popcorn player but it works, we cleaned the HDMI cable and the problem persisted , we removed pop corm hour feed and relocated to CBL/SAT HDMI port and the player worked, we think the HDMI got damage.

Gym

We had the tread mills going off constantly, the small 530 tread mill bushes were loose, this can be contributed to the impact from the running, and we remove the motor and repair the fault and put the tread mill back in use.
The bigger 750 hade a few issues the machine kept on going down in a training cycle, we clean the boards and found it working but the machine will go in to out of order and after a few call outs we found the memory back up wall mount supply under the machine were falling out. We moved the supply to the inside and it also stop doing this. We also remove the controller for the 750 clean the boards and found the cooling fan to be dirty and did not turn, we clean the fan and reinstall the controller.
The 530 T tread mill had an error 9, we removed the motor and ha to replace the brushes we notice that the commutators had some wear and spark of marks, we clean it with a brush stick and replace the brushes, the tread mill we put back in use.
The fan above the hatch did not switch of, the rotary switch was burned and we install an on/off switch.

Down hole lab

APC-T tool runs

We use APC-T instrument 1858005C for all our runs and run an APC-T for all the holes except on site U 1485.

GENERAL

Lights

In port call and at the begin of EXP we replace all emergency 2 x 4 lights and 2 x 2 lights in the core lab, chem lab, thin section X Ray lab, down hole, ET shop, underway, Palio prep and Tech office, we replace a total of twenty three LED emergency lights.
We also install ten 2x 2 led lights, with these lights install we have install all the lights in the labs all 33 lights.
jing

UPS

Four new Minute man UPS'S were received in the shipment at the beginning of EXP 363, we did not use it at this time as they are extra to cover the Chemistry lab and will be stored in the down hole until such time we can charge it and when we need to install it.

PUBLICATIONS SPECIALIST

Douglas Cummings

Summary

My duties included collection of publication materials from the scientists and generating the visual core descriptions (VCDs). I generated VCDs for eight sites and thirty holes, core recovery figures for each hole/site, and figures for the Methods chapter.
I distributed/collected shore passes, passports, and crew declaration forms from the scientists and technicians for port call activities. I also kept track of seagoing personnel using the check in/check out spreadsheet for port call.
Other expedition related administrative duties.
When I had free time, I made myself available to assist in other areas.

Equipment & Software Performance Summary

Software used: Strater 4, Acrobat, Illustrator CS6, Photoshop CS6, Excel, Word, Groupwise, FontCreator. Any issues with the software and the Yeop PC computer were addressed and corrected on the ship.

Database, entries, and data upload or downloaD

L2E was used to export depth, section, core scale, title, core images, samples, analysis data, and core composite photos. I experienced one problem early on with the software failing on write to file, but James corrected this.
DESC export was used for all core descriptive data. I experienced no problems.

Volume Materials

Chapters were collected as they were finished and I kept track of all material using the tracking logs for text, tables, and figures.
VCDs were updated once daily, in the beginning with both paper and electronic copies, but shortly afterwards it was decided to use just electronic copies as the paper copies began to cause change tracking issues.
Minor changes to the description/interpretation process necessitated some revision to the template and additions to pattern and symbol schemes as the expedition progressed and the re-plotting of several holes. Likewise, all holes were re-plotted once summaries had been finalized and ages and lithological units determined and added to DESC.
Hole Summaries may be an ongoing process following the expedition as that information has not been finalized and entered into DESC, and because the abundance of activity near the end of the expedition may require they be plotted on shore.

General Duties Performed

• Exported data using L2E, DESClogik, and Lims Reports; reviewed data for accuracy and ; plotted data using Strater software version 4; produced PDFs of the VCDs, and recovery plots; and distributed PDFs to the scientists for review.
• Worked with the scientists to ensure accurate data display in the VCDs. Corrected/modified VCDs, Strater schemes, templates, and Methods legend figure as needed.
• Collected, organized, and tracked all publication volume materials including text, figures, and tables in hard copy and electronic files.
• Assisted scientists with figure creation and in the use of the Adobe Illustrator software.
• Attended science cross-over meetings as needed.
• Provided administrative support to scientists and technical staff as needed, including providing supplies and assisting with travel arrangements.
• Distributed and collected necessary expedition paperwork - IODP communication policy, photo image release, manuscript and copyright forms, cabin repairs, personal safety equipment, and shipboard network access.
• Worked with the Radio Operator to ensure the science party and technical staff had appropriate documents for departure from Singapore and arrival in Guam.
• Kept track of seagoing personnel using the check in/check out spreadsheet for port call.
• Arranged birthday celebrations for 10 scientists and technicians.
• Communicated with shore staff regularly to provide updates.
• Restocked Publication supply cabinet as needed, and provide science party with supplies per request.
• Updated DVD and book libraries to reflect new acquisitions and donations.
• Led ship/shore even with a high school in WI as the EO was unavailable during that time slot.

Suggestions

It may be helpful to provide the pubs/yeoperson with scientists' and technicians' flight information from the destination port as it seems this information often needs to be given to the radio operator for transmission to immigration authorities in port to process entry, and collecting it from them again when we already have that on shore is needlessly redundant and often drags out longer than it need.

SYSTEM MANAGERS REPORT

Mike Cannon and Steven Thomas

Servers (Microsoft):

• Updated HPE Insight Remote Support to v. 7.7.0.0019 and updated plugins.
• The VMware vCenter server was updated with version 6.5. There are numerous improvements to the web console included in this release that benefit us.

Servers (Linux):

• We had one instance where the mail server's post office became unresponsive. A restart of the service brought the server back online. We had no further problems with the mail server. Logs indicate the server was running low on swap space. No corrective actions taken at this time as this appears to be an isolated incident.
• We had an issue early in the expedition where users reported they were experiencing problems connecting to the wireless network, VLAN50. We found that the DHCP server had assigned all addresses available in the VLAN50 pool and there were no free addresses available for new users. Many of these addresses were leased for users from the previous expedition and they had not been released yet. We manually refreshed the DHCP configuration file and modified the server's lease duration setting to 8 hours. The default settings was 8 days. We plan to monitor this new setting to determine if there are any unforeseen issues.
• We experienced a non-responsive condition on Novarupta twice early on. We could not log in to the server via SSH or console and we had to resort to a hard restart to restore functionality. We started a support case with our vendor and after looking at log files we sent them, they recommended to modify our LDAP configuration. After making the suggested changes we have not experienced a reoccurrence.

Servers (ODA):

• We reset the core switch during a short round of downtime and the reboot caused the database to become unresponsive. We contacted our DBA and they were able to restore functionality fairly quick. It appears the ODA interpreted the switch reboot as a database offline condition and attempted to start on the other node but the process did not complete successfully.

Servers (VMware):

• To coincide with the vCenter update, all the ESXi hosts were updated with version 6.5.

3PAR SAN:

• No issues or changes to report

Network:

• On Oct 10. we experienced intermittent, frequent internet outages. Upon examination we found that we could not communicate with our router or firewall in the VSAT locker. We determined there was an issue with the succeeding network switch. We replaced the switch from on board spares and reconfigured with captured settings from the original switch.
• The NetSight network management software and NAC appliance were updated to the latest software release, v. 7.0.6.27.

PC Workstations:

• We discovered there were too many installations of Kaliedagraph on the PC workstations. We are licensed for 10 instances and we found that there were 17 instances installed. Working with the EPM, we selected sever workstations and removed the software so bring us back in compliance.
• We created a Windows 7 virtual machine template and deployed two virtual workstations for the use of our physical properties scientists who had no workstation to perform data analysis in their work areas. The template will be kept and updated for future use in such instances.
• The Netscout Optiview was updated with the latest software release and patched with Windows updates.
• We found that the Optiview's batteries were bad and contacted our vendor to have replacements shipped to the next port call.

MAC Workstations:

• The VDU's were updated. XBMC (VDU media software) was updated to the latest stable release, now called Kodi. Our VDU image drive was simultaneously updated as it was severely out of date. We also performed similar updates to our Mac workstation image drive.
• With the new Kodi software, we experience a condition that causes the Apple remote to become unresponsive after reboot. We developed a startup script that remedies this issue by delaying Kodi initiation for a short time after initial log in.
• The VDU in Underway suffered a hard drive failure. We loaded the VDU image on a spare VDU Mac mini and installed the unit in Underway. The original Underway unit was tested and confirmed to have a defunct hard drive. The hard drive was removed and the unit was placed into spares inventory to be used for spare parts.
• The Yeop Mac workstation lost connectivity on Nov. 10. The cause was determined to be an incorrect configuration on the switch port that the mac was connected to. As the mac shares this port with the PC system in the office, it required multiauth users configured for that port.
• We have had an ongoing issue with our Mac workstations involving NAC agent. The agent will become unresponsive and cause the computer to be denied network access. We have been working with our vendor and they have reported that they have been able to reproduce the condition in their lab and are working on a solution. For now to get around this problem our Mac workstations have been bypassed from the agent verification.

Printers:

• The core deck color printer's network port was damaged during a previous expedition and a replacement system board was ordered. We installed the replacement board, updated the firmware and re-configured the printer back to previous settings.
• We encountered an issue with the core deck color printer where it would seem to stop processing documents queued to print. This happened on a couple of occasions. We noted in each instance the problem seemed to occur when a technician printed a very large image file. We could find no error in the printer logs to indicate a cause for this. Clearing the large job immediately fixed the problem and the technician was able to successfully print the document later.
• The Ops Office printer had an issue where it would jam with an error code 59.40. This error indicates a fault in the drive system. We determined the toner cartridge was the cause and replaced it. No problems from this printer after that.
• The Open office printer developed an issue where the printer would it would jam when printing multiple page documents. After running paper path tests it was noted that the printer was feeding an extra sheet through after printing the document, for example, if 10 copies were requested, the printer would print 10 copies and then feed an additional sheet through the printer. The fault was a sticking paper pickup solenoid. The printer was disassembled and the solenoid was cleaned and reassembled. The problem has not returned.
• The Core Entry label printer was replaced with a spare Zebra this expedition. The printer would produce an out-of-media error when the staff attempted to print labels for new core. They would have to clear the error and un-pause the printer and it would print the labels until the next core arrived, where the error would re-occur. We took the printer to our office and examined it. We found a label stuck in the media path as well as adhesive residue. We also found a spring clip disconnected from a media guide plate. We cleaned the unit thoroughly and reset the spring clip properly. The printer has tested good and we are placing it into spares inventory.

Satellite/Internet/Phones:

• We found a fault code on the cooling unit in the aft radome, code HPF. This code indicates a high Freon pressure usually caused by insufficient airflow through the condenser. We had the filters cleaned and so far the error has not reoccurred.
• On Oct 20. we transitioned space vehicles, moving from IS-902 to IS-18. No issues and the process was completed with little downtime.

Other Equipment/Projects:

• We selected two participants to become pilot users of the onboard exchange server. Kevin Grigar and David Fackler agreed to use Exchange/Outlook for the last half of the expedition. So far, feedback has been positive. Questions have arisen regarding the Outlook equivalent of various functions in GroupWise, such as how to get read receipts etc.
• The Siem Telemedicine system had issues connecting off site test centers. Since it is connected to our network we were approached by Siem staff to assist in troubleshooting the issue. We found some incorrect settings in the video conference appliance's network configuration as well as the PC computer's network configuration. The correct settings were set and the system was tested again. The doctor was able to complete several test calls.
• One of the monitors in the Pubs office suffered a failure. The monitor was replaced with a spare from our inventory and the failed monitor has been marked to return to College Station.
• David Fackler attempted to access SHIL-A for testing purposes (SHIL-B is in service) but was unable to connect to the computer remotely. He reported that the computer had no network connectivity. This was confirmed and it was discovered that the premise run between SHIL-A and the Core deck network locker (C42-065) was faulty. Testing the cable run indicated the faulty portion may be in the connector by the computer. We will make note of this to examine and repair at a later time, possibly during a tie-up. To get SHIL-A connected we installed a small desktop switch in SHIL-B's network port and plugged both SHIL-A and B into the small switch. The corresponding port on the switch was reconfigured for multiauth users.
• While troubleshooting the cable run mentioned above we discovered that the Fluke Networks Cable IQ tester was unable to accurately test any cable we plugged into it when we used the end run adapter. After troubleshooting with Fluke tech support we discovered the adapter was bad. A replacement has been purchased and will come out at the next port call.

SOFTWARE DEVELOPERS TECH REPORT

David Fackler, Rui Wang

Overview

This document highlights changes to the JOIDES Resolution laboratory data management environment during Expedition 363.
Selected issues are highlighted, but not reviewed in exhaustive detail. In general, see the ship activity log and product pages on the developer site for additional detail
http://build.iodp.tamu.edu:8090/display/DEV/Developer+Home+Page https://sites.google.com/a/scientific-ocean-drilling.org/developer-page
Note that the latter site is being retired. Corporate knowledge from developers regarding product, process, workflow, and code are now being captured to the first site.

WORK IN PROGRESS

During 363 the developers actively participated in

• routine expedition support
• Limspeak replacement efforts
• clarification of what a comprehensive laboratory data acquisition framework should do for IODP and its customers
• infrastructure and tooling changes

CHange Summary

Applications, services, instrument software.

Outstanding Issues

Oustanding items here are tracked by development in a system called Trello. Items that have not changed are not listed.

SampleMaster

• Though numerous validation errors were addressed by changed in v12.3, this one lingers on. Annoyance validation error persists on section entry. Tripped by sections extending beyond the drillers advancement. The annoyance is due to the extra click required for sample upload when validation errors trigger.

DESCLogik

• See issues outlined in Trello. Have some rough repeatability cases for upload errors seen in micropaleontology (most often) and occasionally in sediment description. Repeatability data is retained in SHIPTEST from Exp 363 for additional debugging cycles on this content.

Stratigraphic Correlation - Scors aFFINE/SPLICE uPLOADER

• Revised, but only distributed in the test environment. Displays an edge case behavior: the first time affine or splice file validation is conducted, the UI fails to enable the upload button. Proceeds successfully on a later pass.
• Current version shows timing issues that can sometimes cause the validation and uploads to fail. Current version also fails when file is already uploaded to LIMS: they cannot handle the messages supplied by ASMAN services in this case. Shore repair to the new version. Another round of careful testing required in conjunction with the changes above.

ImageGRABBER

• Not used by the photographer in its current state. Will reconsider if this feature addition is made: support core range selector similar to that supported by LORE, e.g. "1-3", "2,6,15". Downloading the 9 cores processed last shift is much more efficient than downloading the entire hole.
• Product gained a following in Physical Properties. Participants used the product to feed an alternate stratigraphic correlation package (Wilkins) that happens to stitch images together to provide a visual rendering of the splice.

Whole-round logger (WRMSL)

No software changes over IMS 9.2 release during Exp 362. Ditto for STMSL.

• Noted. For the PWL utility to function correctly, the PWL module must successfully open and close the PWL calipers via the Exlar motion control. If the Exlar motion control drivers encounter an error (most typically an "in current limit" fault) then the whole module will fail to initialize properly and cause a variety of domino failures in the PWL subsystem.
• Seen once. Calibration of GRA sub-system was completed, then a run conducted. Measurements of the run were taking 10 sec. Under some condition the measurement duration from the calibration step can once in an unqualified "while" bleed over into the experiment on unknowns. Shutdown and restart of the system cleared the issue.
• Noted. Though not fatal, system shows unexpected ordering of experiment operations. For example running all three sensors results in this behavior on WRMSL: move to measurement position; GRA measurement fires and completes; two MS measurements fire and complete; PWL caliper closes; PWL measurement taken; PWL caliper opens; last MS measurement is taken; MS average computed; … repeat. Previous systems all MS measurements to be averaged were taken together.
• Noted. About once per week LabVIEW will hard crash. This is triggered in the PWL sub-system which communicates with USB-5133 oscilloscope device. Under some condition the 32-bit niscope_32.dll crashes on close. This only occurs on WRMSL. The same behavior does not occur in 64-bit handling of oscilloscope data (on the basis of continuous use of the Velocity Gantry). STMSL is not affected. It does not support this device.
• Noted. If the power supply for the M-drive motor system is shut down. IMS must be restarted twice. Initialization of the system fails the first time. Going into the motion control utility verifies that the sub-system is usable. Then a subsequent restart initializes completely, without error.
• Noted. If the end-of-travel switch is left depressed too long, the system times out and aborts the run. The operators would prefer the system wait indefinitely—until the operator clears the completed material.

Hardware and driver changes

• M-drive replaced. Burned out components on integrated controller circuit. Associated power cable retired too. Occurred during analyses to identify sources for NGR scintillator noise. Root cause: nicked wiring allowed short to occur.
• Removed unused serial ports from the system. Installed current NI serial drivers. Caused number of the serial ports to renumber.
• When the DigiBASE USB was connected via ports on the back of the system, it would not recognize or communicate. Move the DigiBASE to a CPU front USB port, move the barcode scanner to the opened slot on the back. That arrangement worked.
• Removed Galil motion control board. Uninstalled associated driver.

Special Task Multi-sensor Logger (STMSL)

Hardware and driver changes. Applied to retain similarity of hardware and software configuration between WRMSL and STMSL at the time of the above WRMSL changes.

• Removed unused serial poerts from the system. Installed current NI serial drivers. Caused renumbering of serial ports.
• Removed unused analog to digital I/O board once applied for an alternatemagnetic susceptibility implementation.
• Removed Galil motion control board. Uninstalled associated driver.

Section half image logger (SHIL)

• Noted. If a run is aborted, the lights stay on. They are not cleared until a routine run is completed OR the utility menu is used to turn the lights off.
• The software on SHILa is different than SHILb. Repairs to some of the issues listed in Trello were made in the code on SHILa and then vetted by swapping boxes. SHILb was in use for the duration of the expedition.
• Repaired. JAI-CV-L107CL Camera DAQ Calibrate.vi retained constant reference to configuration in c:\IMS System Local\IMS CONFIG\CURRENT rather than c:\IMS\CONFIG\CURRENT. Led to unexpected resetting of camera-related configurations when that dialog was opened. The c:\IMS System Local directory is expunged from both SHILb and SHILa.
• If an operator uses the LIMS browser, subsequent invocations of the Sample Information screen apply the very first section in the LIMS browser list. The leads to repetitive errors where operators thought they scanned the end-cap, but actually recorded yet another image as 363-U1482A-1H-1-A.
• Because of current timing of when the lights are turned on (before external triggering is slaved to motion) the CCD is accruing charge that takes several discharge cycles to bleed off. The discharge shows up as a green hue overlaid on the image color card. The effect can be prevented by triggering the CCD to discharge while the camera is idle.
• It is preferable that the lights be turned on just before motion starts. Motion should not begin until ALL banks of lights are on.
• Seen multiple variants in one sitting. At a point of high traffic on the network, SHILb experienced intermittent difficulty connecting to the web-services. In one case, caused IMS to offer to turn off LIMS connectivity. In another variant, failed to lookup sample length (or use the one from the label) and resulted in a minimum scan (0 + a fixed amount of overrun).
• Hard crashes of LabVIEW continue to occur on this system. They are all associated with points in the code that manage disposal of image buffers.
• Sample Information. Check box intended to enable acquisition of unmodified content from the camera for calibration purposes has no effect. Software adjustments are always applied.

Sonic velocity (GANTRY)

• Seen once. The Acuity Laser stopped communicating. Re-established by unplugging the power supply to the laser control/serial port junction. Then re-connect power. Worked normally after that.
• On numerous occasions the laser would provide faulty distance readings. Participants observed that the reflectivity/translucence of some end-caps was the cause. In further cases where the distance observation was "flakey" a guaranteed reflective target—like a blank label—was affixed to the end-cap.

Reflectance and susceptibility (SHMSL)

• There is a 1 to 2 cm offset between the laser profiles nominal position and theabsolute position with respect to top of core. Re-initializing the motion control, and homing the system cleared it temporarily. But some later activity in routine operation resets it.

Moisture and density (MAD)

Outstanding change requests.

• Enable operators to edit MAD test comments from within the program. Retire the unused MAD_MASS, PYC result comments which were never fully implemented. Can be worked around by giving operators permission in LIME to edit MAD comments.
• Close the loop on container edits. If a sample was accidentally assigned the wrong container, must change the container in MAD, and edit the sample name via SampleMaster. Preferrable to do this in one place.

Paleomagnetics - JR6A SPINNER MAGNETOMETER

• Training and communication required to sell the use of text_ids in this data set. Convenience for participant recognition of samples vs. convenience for technician support of upload are at odds.
• If you have operators that insist on using human readable identifiers, there is a cube label format "jr6a cube" that provides two barcodes – the left is the text_id, the right is a human readable identifier (presently an aggregation of core, section, offset, e.g. 10-1-102-103).
• If human readable identifiers are used, the upload process becomes labor intensive due to the number of places in which the identifiers need to be replaced with text_id.

Paleomagnetics – Superconducting magnetometer (SRM)

• A number of cosmetic changes were made to the SQUID monitor component to label axes and identify units. These changes are captured to Subversion.

ICP Data Reduction

• An Excel-basedNo change. Operating with release ??? since Exp 362T.
• Outstanding issue: software is not subtracting the signal for the BLANK analysis from the signal for an unknown—as documented in p 35 of the manual.
• The last applied drift correction is wildly negative. Implies that software is applying an incorrect factor.
• Request that calibration plots include dashed 95% confidence lines bracketing the existing calibration lines.

Gas bottle monitoring

• The gas monitor upload software continues to fail on an occasional basis. On neither occasion did the stale data alert trip as expected. An assessment of each data points age is returned when the last data points are retrieved. But that didn't address the failure to alert. Try again.
• Glyphs indicating gas status are now visible again. The fonts used were being mangled by a product build step (Maven filtering). Filtering is now explicitly disabled for that content.
• The product name is now appropriately applied rather than showing a never-replaced substitution variable.

ALKALINITY

• Repaired the Rate Manager and Standard Manager dialogs. The display were unusable without the Ok and Cancel buttons visible.

MegaUploadaTron5001 (MUT)

No changes. But a variety of observations made with an eye toward future improvements.

• At SHIL, roughly 2% of the uploads fail with one or more of the images failing to be cataloged to LIMS. This occurs with RGB and LSIMG file sets. Technically this is not MUTs fault, this is indicative of an occasional systemic failure at Olympus. Work-around is to pull the *.roi, *.rgb files that do get placed in the error folder and simply upload them again. Similar could be achieved in MUT by having it back off and retry after an ASMAN file upload failure.
• The ORIENT loader module displays erratic behavior when more than one file set is queued for upload. On two occasions, files sets for hole A and B were queued to together. In the first occurrence the orientation data for the first core of hole A uploaded. No further cores from a were uploaded. All data from hole B uploaded successfully, except where matching core numbers from hole A were present—then there were two instances of the hole B data. In the second occurrence, no data from hole A loaded. All data for hole B were loaded in duplicate.
• GC3 loader module after an extended period of time just stops uploading. It acts like it is processing the files and generates no errors, but ceases to load any content to LIMS. This is on a 32-bit Windows XP system. Resolve by stopping and restarting MUT. Then the data files must be dropped in from the source HP-Chem folder (c:\Chem32\2\DATA
  {EXP}—each folder here corresponds to a single sample run).
• Seen once at Velocity Gantry. MUT consistently crashed hard. Removal and reinstall would not repair it. Root cause and resolution. Some event on the system caused the MUT Settings.xml file to be zeroed (completely emptied). Deleting the Settings.xml file allowed MUT to restore a working baseline Settings.xml copy. From there MUT could be run and properly configured for this system again. Chain of events that caused the Settings.xml file to be blanked—unknown.

• Seen twice. Once at the very beginning of the expedition. And once later after lingering Exp 362 content was removed from ASMAN. For all the track systems, configuration files are uploaded in addition to the data for the current run. If the ASMAN files are cleaned, but not all of the associated LIMS.FILES a situation can occur [with track configuration files that change very slowly] where ASMAN will hash the configuration file, find the LIMS.FILES record, and fail on actual lookup of the file because it was cleaned out as part of BOX. All you see in MUT is an error that the ASMAN file doesn't exist on disk and refusal to upload otherwise perfectly well-formed files.

LORE

Several outstanding requests to be addressed.

• Splice search. Fails to trim data on sections which participate in the splice but contain the boundaries for the splice segment. Revise the code to trim instrument data outside the boundaries of each splice segment.
• DH_TEMP report does not show bottom depth drilled.
• Core section summary. When a section has 11 or more sections, those sections in double digits sort literally rather than numerically.
• Revise Core summary report to provide totals for as many columns as is reasonable.
• A report akin to the Core summary, but ordered and organized like the whiteboard is desirable for curatorial convenience.
• Affine and Splice detail reports were repaired according to scheme previously identified on shore. The report type was set to AFFINEDETAIL and SPLICEDETAIL for the respective detail reports. A regression from sync'ing JR and HQ configs.
• Report changes are now captured in Subversion (http://build.ship.iodp.tamu.edu/svn/wapps/Apps/LORE/definitions/) and then distributed to all affected target environments.

Depths

• CSF-B. Sample tops and bottoms are properly computed and displayed (were for part of the expedition). Lots of sediment expansion was observed this expedition. It was appropriately recorded in the various summary LORE reports. Offsets for instrument observations are NOT normalized to the CSF-B depth scale. This asymmetry and inconsistency was left unresolved as this depth model is not being used in the shipboard environment.
• CSF-B. As of Nov 11, section offsets computed for 363-U1485B-4H-1 and below are computed incorrectly. Noticed and reported on Nov 30. Start in time backtraced, but root cause not yet identified.

Development Tooling and Infrastructure changes

SQL Developer

• A new version of SQL Developer is available. V4.1.5 is Ok to use. Avoid V4.2.0 – its handles of CLOBS improperly (e.g. inappropriately truncates display of LORE report and DQ template definitions beyond 75 characters).

Visual Studio 2015

• Visual Studio 2015 should be installed by now on all developer laptops.
• BuildHQ now carries Visual Studio 2015.
• BuildJR DOES NOT SUPPORT VISUAL STUDIO 2015. It will be retained at Visual Studio 2010 until an operating system upgrade and move of services can be effected.
• The package manager NuGet is used in conjunction with Visual Studio and Nexus to manage .NET dependencies. While very useful for 3^rd party dependencies; looking for other solutions for IODPUtils as it presently must frequently change when services change. So the cycle of troubleshooting, debug, fix as applied with NuGet is neither as familiar nor as convenient as extern'd source attached to the project.

Build JR

Notable software updates

• ImageMagick 7 64-bit
• Notepad++ 7.2 64-bit
• IrfanVIew 64-bit
• Msys64 – GNU'ish tools for Windows 64-bit (less, sed, awk, grep, etc.)
• Nexus 2.14.0-01 – Maven, NuGet artifact/dependency management repository.
• Jenkins 2.24 – A facility to enable automated build of checked in code and product.

Build HQ

• Migration of Confluence content to Oracle back-end.
• Trickle documentation from Google Site to Confluence—manual cut'n'paste as needed. Content deleted from Google Site once moved. If not desired at all just deleted from Google Site.

Office

• Developers are moved to the technical staff office off of the downhole tools lab on Core Deck. Development equipment and monitors are staged at the first desk segment to the right of the doorway.
• The drawers to the right contain developer storage (travel drives, international plugs, locker keys, software CDs).
• Miscellaneous content from the Dungeon vidmar cabinets are staged in the top locker adjacent to the User Room sink/coffee bar.

Hardware and Server

SHIP TEST Environment

• The ship test environment server (uluru) is pointed at the production database. The DQVIEW (Limspeak replacement) product is staged there and widely available via the applications index page.

Redirector

• Redirector configuration was modified to
  • Add support for DQVIEW application and the dqview thumbnail directory.
  • Remove support for UWQ, lowercase invocations of gasstatus, qaqc.

Tomcat File Servers

• Production and ship test Tomcats were modified to support distribution of thumbnails content for DQVIEW by exposing the directory /asman/dqview (and its children) to HTTP access.

Subversion repositorIES

• TheIODP_OFFICIAL/IODP_DOCUMENTS directory is now effectively a working directory for repository jrdocs. Similar to how AD/DEPLOY/products is a working directory for the Subversion products instance. But minus the rules for change management.

Novell shared directory changes

• Individual user homes in R:\AD are moved to R:\AD\people\

Desktops

• CHANGED. The Mac Mini was replaced during Exp 362. It is configured as a typical Mac OSX desktop. If you need administrative access to install software, make arrangements with the MCS. A copy of the complete Windows 7 development environment is installed here via Virtual Box should an alternative to a laptop or the build box be needed. Keep track of its. Its not locked to a wall bracket and can easily walk.
• CHANGED. The Dev Desktop is now primarily kin to the typical workstations in the laboratory environment. MATLAB was installed here. All development tools were moved off the base machine to a VirtualBox VM hosted there.

Servers

• SHIPTEST. This database environment now includes content from Expeditions 118, 179, 360, 361, and 363.

CHEMISTRY LAB

Erik Moortgat & Vincent Percuoco

(as of 23h00 2 Dec 2016)

Ampulator

The ampoule sealer worked great.

Balances

No issues to report for the Cahn & Mettler balances.

Carver Presses

There were no issues with the Carver presses.
One of the gauge face plates was cracked so a REQ went in to get some new face plates made in B-CS. Carver does not sell the face plates separate from the gauges.

Cary Spectrophotometer

The spectrophotometer was used to measure ammonium and phosphate concentrations in the porewaters.
The Cary unit itself did not have any issues but we had a couple of issues with the autosampler.
We started by doubling our liquid volumes so we wouldn't have any aspiration issues (dead volume/air gaps). We aspirated for 40 seconds and waited 5 seconds to take a reading. The rinse was left at 100 seconds. We had high ammonium values for the majority of the sites and had to dilute our samples up to a factor of four. We also tried having higher calibration standards but this caused problems with future aspirations, inconsistent uptakes most likely attributed to the makeup of the ammonium standards causing flow issues in the tube connected to the flow cell. If higher standards are needed it is recommended to put them at the end of the sequence and put a DI aspiration between them. Agilent was contacted and they recommended a larger ID probe (1.3 vs 1.0 mm) because of our reagent makeup. A couple were put on order for future use.
We also had intermittent problems with the probe coming in contact with the tube (Z-axis error), forcing the sequence to crash and needing to be restarted. A new custom rack was made, with new x/y co-ordinates for the vials, and this has limited the problem with the probe not properly aligned with the centre of the vials.

CHNS

Total nitrogen and carbon were measured on the EA.
Initially the Soil CHNS Reference material (PWDR5968501) was used but then we switched to the Buffalo River Sediment standard after some inconsistent checks were measured with PWDR5968501. We did this because the 'original' bottle of reference material became depleted so we started to use a new two bottle batch. Almost immediately we began to have issues with our samples and checks (check concentrations would gradually decrease over time in the sequence). We do not have a definitive cause as it could have been an issue with the sample matrix. This only occurred at one site and since then there have been no issues with the samples nor checks. Time constraints and disinterest from the Scientists did not allow us rerun those questionable samples from the one site.

Coulometer

There were no issues with the coulometer.

Freeze-drier

One scientist commented on the smell of vacuum pump oil after initial freeze dryer startup. A temporary exhaust line was connected to the pump and vented to fume hood one. In addition, requests were made for additional oil mist exhaust filters.

Fume hoods

A new eco-foil was ordered for the acid hood.

Gas Lines/manifold

There were no issues with the gas system.

GC3/NGA1

There were no issues with GC3.
NGA : We worked on the optimizing the procedure for low molecular weight hydrocarbons at the beginning of the expedition. It was discovered that the valves timings were erroneous and were permanently venting analytes instead of sending them to the TCD. The timings were corrected, a new temperature regime was created, and both the FID and TCD are generating reproducible results. We were under the impression that the NGA setup allowed separation of hydrogen sulfide, however the column literature didn't list this as a separable component. The new H2S standards received this expedition we run, but no distinguishable peaks were observed that correlated with the standard concentrations. Chromatograms from previous expeditions, as well as any generated during the initial instrument setup, do not indicate this has been done before.

Hydrogen generators

No issues with the hydrogen generators.

IC

There were no major issues to report aside from basic PM. Both sets of peristaltic pump tubing were replaced. The guard columns were replaced to try to get a better baseline around K and Mg and eventually the cation separation column was replaced.

ICP

A backup of the Salsa database was made at the beginning of the Exp (db_backup_8Oct2016). Only IW minors were run this expedition.
We had problem with the autosampler on the first run. Etienne and Erik found that the wire which controls movement of the sampler needle was misaligned/angled on its spindle. It was re-aligned, and is currently working great. Teledyne was contacted while it was being fixed and they sent a document which explains how to recalibrate the needle-to-vial alignment, if need be. A request was made for some autosampler parts (wire, motor, probe holder). We started using a new program based in excel to do the ICP data reduction. There are no problems to report. A few bugs were worked out at the beginning of the expedition, but it has been generating good results. There is a guide currently being updated that walks the user through the procedure. Uploading to the database with spreadsheet uploader has been straightforward.

Microbiology

There was no microbiological sampling/analyses this Expedition.

salinity

There were no issues with the optical refractometer.

SRA

The repaired SRA was not received in the on-coming shipment.

Pipettors

No issues to report with any of the pipettors.
Before our last site we ran out of the 'blue pipette tips' for 500-1000µL dispenses. We had to therefore use the electronic pipettor, with the 5000µL tips, to dispense 500 µL amounts.

titrations

alkalinity

There were no issues with the alkalinity titration system.

Chloride

There were no issues with the chloride titration system.

TOC

The TOC was turned on and calibrated but very high %RSD were encountered. Requests for information were sent to Xylem but no responses were received. Time constraints did not allow further troubleshooting.

Water system

The carbon filter on the RO unit was changed and both final filters on the DI unit.

Misc

A new microbio fridge was received and installed.
During the high resolution IW sampling sites, whole-rounds were kept in a nitrogen disposable glove-bag until ready to be squeezed.

Geochemists

Tali Babila (inorganic) Department of Earth and Planetary Sciences
University of California, Santa Cruz, CA, USA
Germain Bayon (inorganic) Unité Géosciences Marine
Institut Francaise de Recherche pour l'Exploitation de la Mer (IFREMER), Plouzané, France
Kelly Gibson (inorganic) Department of Earth and Ocean Sciences
University of South Carolina, Columbia, SC, USA
Dan Johnson (inorganic)
Department of Geological and Planetary Sciences
California Institute of Technology, Pasadena, CA, USA
Masanobu Yamamoto (organic)
Faculty of Environmental Earth Science
Hokkaido University, Sapporo, Japan
Yige Zhang (organic)
Department of Geosciences
Texas A&M University, College Station, TX, USA

WIRELINE LOGGING & DOWNHOLE TOOLS

Zenon R. P. Mateo

Summary

Expedition 363 consists of six sites distributed across the region of the Western Pacific Warm Pool, from the Scott Plateau in the Timor Sea to the Caroline Basin north of Papua New Guinea. Given the spread of the sites and the allotted time for the expedition, wireline logging is scheduled only for the last hole of first site (U1482C). Only two runs were conducted:

1. Triple combo (MSS/HRLA/HLDS/HNGS/EDTC/LEHMT)
2. FMS/GPIT/DSI/HNGS/EDTC/LEHMT

Prior to reaching the first site, a Petrel project file was created to include the available multichannel industry and site survey seismic profiles from Greg Mountain. This project file was saved in the desktop of both logging workstations for the logging scientists to peruse and use as needed, either remotely or in the workstation itself. Greg Mountain and Anais Schmitt are the logging scientists for Expedition 363 and Kerry Swain is the Logging Engineer.
Logging was conducted from 23-24 October 2016. After playback and initial pre-processing of the data by Kerry Swain, the raw data was sent to Lamont-Doherty BRG and received back on October 27 and 28, 2016.
The APCT-3 (tool number: 1858005C) was deployed by E Claassen and J. Kotze 38 times in all sites, and returned decent data from 36 runs. Wintemp v 5.1.0.0 and TPFit v. 1.0 were used in initiating the instrument and in downloading and processing the data. In TPFit, final time picks and temperature derivation and eventual uploading to LIMS were made by Anais Schmitt.

Together with the thermal conductivity measurements, the downhole formation temperature data were used to calculate the thermal resistivity, heat flow and approximate crustal age of the site. An excel template was modified from Pribnow et al. (2000) to calculate these parameters and resides in the IODP Share drive for future use.
Using Petrel, additional support was extended to the science party by plotting key physical property data (GRA, PWL, MSL), core description and biostratigraphic datum against the seismic profiles. A trial but successful exercise was also made in calculating a time-depth chart or velocity model using the PWL data.

Details

1. LIMS Reports: Downhole temperature

In the standard report for downhole temperatures, the column on Depth DSF (m) is currently not populated. Also, in the Expanded DH_TEMP report, the tool_serial_number is missing, though it appears as the first part of the name in all files uploaded for a particular test. The column on temperature_uncertainty is also reported as being zero, whereas "the nominal accuracy of the APCT-3 is reported to be ±0.05°C, with a total error of 0.1°–0.5°C" (http://publications.iodp.org/proceedings/342/102/102_9.htm)

2. Heat Flow and Lithosperic Age calculations

During this expedition, the scientists were assisted in calculating the heat flow for the six sites, using the downhole temperature measured using the APCT-3 and the thermal conductivity values. The work by Pribnow et al. (2000) was used as a reference and the Excel workbooks that came with the article were used as a template. The modified worksheet includes annotations about the parameters and, when applicable, an estimate of the lithosphere age based on the GDH1 model of Stein and Stein (1992) and PSM equation by Parson and Sclater (1977), and were compared to the global oceanic crust isochrons of Muller et al. (2008).
For possible need in future expeditions, a sample copy of this spreadsheet and related references are located in IODP_Share\Logging\Heat Flow. The spreadsheet contains the three possible methods of calculating the bulk and matrix thermal conductivity, the last involving porosity data. For the porosity-related approach, Kaleidagraph was used in fitting a rising exponential function to the depth vs. in situ thermal conductivity values. Details about the methods and equations can be found in the accompanying article of Pribnow et al. (2000).

3. Loading SEG-Y files to Petrel

Several multi-channel seismic profiles in SEG-Y format were loaded into Petrel to provide geometrical information about the cored sequences and to correlate adjacent sites such as U1484 and U1485. The manual loading involved the use of separate (i.e. not embedded) navigation files, and detailed time-depth values from Greg Mountain for use in plotting core data against the seismic profile. Physical property data, lithology and biostratigraphic data were then plotted to synthesize and integrate both sites. Printed plots were displayed on the whiteboard near the NGR. Additional assistance was given to the scientists who were interested in more detailed and user-interactive observation of the seismic profiles in Petrel, as an aid in interpreting the nature of the deposits. As per Greg's suggestion, plots of the seismic profile, hole trace and depth markings were also provided prior to starting a new site in order to give the scientists a 2D view of the stratal geometry, sediment thickness and basement topography.
Using the procedure developed in the previous expedition (362), some of the Bathy2000 chirper sub-bottom profile were also loaded into Petrel.

4. Core-seismic tie: Direct time-depth conversion using PWL and PWC data

In Site U1489, permission was given to extend coring to 5 sec TWT along a particular 2D seismic profile, thereby requiring for the equivalent total depth to be calculated. A time-depth table was derived from the seismic data before the expedition (Figure 1). However, in the core data plot against the seismic profile, there was an apparent offset between the features of the physical property data and reflection characteristics and geometry (Figure 2, left panel). This was despite using a second, "slower" time-depth curve from the previous site.
Figure 1: Time-Depth charts for the various sites occupied for Expedition 363. Note the difference between the "fast" velocity model for WP4 (blue) and the "slow" velocity curve derived from the PWL data (yellow).

In the absence of a VSI data or any downhole logging data, a trial exercise was done to create a time-depth chart using the PWL data from Hole U1489C. Most seismic processing experts caution the use of transducer-measured sonic velocity due to the difference between laboratory and in situ pressure conditions. However, in this instance, despite being used as a last resort, the resulting time-depth chart proved very useful in providing a more (qualitatively) accurate core-seismic tie. This exercise proves the utility of the PWL in providing an alternative and potentially reliable velocity model during and after an expedition, and should be explored further. Exploratory exercise should include using the PWC and PWB data, especially velocity along the z-axis, which is more appropriate representative of the vertical velocity component that is required, but being aware of the potential errors due to the use of a bayonet probe. However, additional work needs to be done in normalizing the resolution of the log and seismic profile, and to complete the calculation of interval and average velocity and the calibration curve, either manually or using Petrel and with due consideration to matching data resolution.
Figure 2: Seismic-core tie using seismic normal moveout (NMO) velocity model (left) and the TD table derived using the PWL data (right) [Note: Data labels omitted on purpose.]

5. Downhole Temperature Uploader v 4.1.0.1

The user encountered a recurring problem with uploading downhole temperature data because the archive directory is not updated and the uploader cannot transfer a folder with the same name as an existing one. Although this is mainly a user error, several other solutions can be implemented: (1) Make the folder names unique by using the usual site-hole-core-type combination instead of just using "Core 4" as the folder name. (2) Request for a change in the application to handle duplications by automatically appending a numeric to the name [i.e. Core 4(1)]

Data Backups

Logging data files for the Expedition 363 were copied to: \\JR1\DATA\data1\27.1 Logging and also at S:\Uservol\Logging

UNDERWAY GEOPHYSICS LAB

Eric Moortgat

Summary

Navigational data was logged by the WinFrog software on WinFrog1 computer during all transits and at each site (site fix).
Bathymetric data was logged by the Bathy2010 software (3.5kHz) on WinFrog2 during the transits and seafloor depth determinations.
Magnetics data was not collected during any of the transits.

Transits

Bathymetry Data

Hardware/Software Issues

When we boarded for Exp363 it was discovered that the WinFrog2 computer, which was replaced during Exp362, could not communicate with the intranet (separate subnet, IP stack), thus WinFrog1 could not send position data to it nor could WinFrog2 send water depths to WinFrog1. The Marine Computer Specialists rebooted the unit and all communications returned.
There was also an issue that both WinFrog 1 & 2 were 'rebooted' during one transit, losing both navigation and bathymetric logging for a period of time. There was no definitive reason for this aside from assuming that it was a Windows update that forced the PCs to restart. This cannot happen in the future and those units should be taken off of the auto-update registry.
When making a picture from the Coastline Extractor/Makepic programs, make sure that the file that Winfrog reads (*.pic) has the following in the first row, or else the coastline picture may not appear in the graphic:
2,COAST,7,0,0

FANTAIL

Roy Davis

Summary

Bathymetry and navigation data were routinely collected throughout the expedition.

Problems Encountered

None

Miscellaneous

Performed routine checks and maintenance to air manifolds and regulators as needed.

PHOTOS

Science Party

IODP Staff

Ship's Staff

Catering Crew

Expedition 363 PhotoS