X390C Tech report Final

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Tech Reports (Individual) - EXP390C Technical Report (Final)

EXP390C TECHNICAL REPORT
Kristiansand Norway – Cape Town South Africa
Oct 5 – Dec 6, 2020








Table of Contents
LAB OFFICER 11
Summary11
Special projects 11
operation dates 11
ASSITANT LAB OFFICER 12
Overview 12
ALO Computer 12
Shipping12
Received 12
Offgoing 12
AMS/Inventory 12
Special projects 13
To Do List for Upcoming Tie-ups 13
Discussion 13
CURATION 14
Summary14
Shipments 14
Site Conversions 14
Site Summary14
Catwalk Sampling 15
Residues 16
Sample Request Codes and Numbers 16
Miscellaneous 17
CORE DESCRIPTION LAB 18
Summary18
Issues/Developments 18
DESClogik 18
Core Description Lab 18
Paleontology Wet Lab 20
Microscopes 20

• Performed routine maintenance (cleaning, corrections, alignment) to all microscopes 20

SEM 20
Thin Section Report Builder/Writer 20
Shipments 20
GEODESC 20
IMAGING & MICROSCOPES 22
Summary22
Equipment and Software Performance Summary22
LIST of General Imaging specalist's Duties 22
LIMS Files Produced 22
Documentation 22
SHIL testing and trooubleshooting23
Considerations of new LED lighting system 23
QP Card 10125
X-rite ColorChecker Mini25
PHYSICAL PROPERTIES LAB 37
Summary37
Confluence Updates 37
Pending Tasks 39
Logistics 39
Requisitions 39
Sent to shore 39
Individual Measurement Systems 39
Whole Round Multisensor Logger (WRMSL - AFT track) 39
P-Wave Velocity Logging (PWL) 39
Special Tasks Multisensor Logger (STMSL - FWD track) 40
X-RAY Imaging (XMSL)40
Natural Gamma Radiation (NGR) 42
Thermal Conductivity (TCON) 43
P-Wave Velocity Bayonet/ Caliper Gantry (PWB/PWC) 44
Shear Strength Station (AVS) 45
Section Half Multisensor Logger (SHMSL) 45
Section Half Image Logger (SHIL) 47
Moisture and Density (MAD) 49
PALEOMAGNETICS LAB 50
Summary50
Measurements 50
Core Orientation 50
SRM50
Core Liner Set Screws 51
Comments and Issues 51
SRM51
Magnetic Orientation Tools (MOTs) 52
Kappabridge 53
JR-653
D-2000 AF Demagnetizer 53
ACS Impulse Magnetizer 53
Thermal Demagnetizer 53
Haskris 53
Standards 54
Lab Computers 54
Mut Uploads 54
Data 55
CHEMISTRY LAB 56
Summary56
Ampulator 56
Balances 56
Carver Presses 56
Cary Spectrophotometer 56
Coulometer 57
Elemental Analyzer 57
Freeze-drYer 57
Fume hoods57
Gas Lines/manifold 58
NGA1/NGA2 58
Hydrogen generators 58
IC 58
ICP 59
Microbiology59
salinity59
SRA59
Pipettors 59
titrations 60
alkalinity60
Chloride 60
TOC 60
Water system 60
AMI Nitrogen Gas O2 Sensor 61
Misc61
Geochemists 62
Microbiologists 62
XRAY LAB 63
Summary63
Total Samples: 65963
XRD: Malvern and Bruker 63
Bruker D4 64
Haskris 65
MM400 Grinder 65
Beadmaker 67
Freeze dryer 67
XRD Safe 67
THIN SECTION LAB 68
Summary68
Logitech LP-50 68
PLJ2 jigs 68
Abrasive Cylinder Maintenance69
Logitech PM-5 69
Buehler PetroThin 69
Grain mount procedure 69
Soft sediment thin section procedure 70
Lab consumables 70
Cross-training 71
DOWNHOLE LOGGING (AKA THE CTD REPORT) 72
Summary72
System status 72
CTD 72
Items received 72
Items ordered 73
Methods and manual changes 73
UNDERWAY AND LOGGING GEOPHYSICS 74
Summary74
System STATUS 75
Navigation 75
Bathymetry 75
Magnetics 75
Items RECEIVED 77
Items ordered 77
Critical maintenance 77
Methods and manual changes 77
SONAR DOME 78
Report_1 in port_Kristiansand 78
Summary of issue encountered 80
Trouble shooting performed 80
Summarized between EXP384 and 390C80
Dome Removal preparation 81
ELECTRONIC INSTRUMENTATION SPECIALISTS 82
Summary82
Items Received 82
Items Ordered 82
Items to be sent back 83
Core Deck 83
ET Shop83
Paleo Lab 84
Gantry84
SHIL 84
Core Description 84
WRMSL85
Focsle Dec 85
Underway Lab 85
Fantail 86
RAD Van 86
Hallway86
LN2 Generator 86
Thin Section Lab 86
X-Ray Lab 87
Chem Lab 87
Lower Decks 87
GYM 87
SYSTEM MANAGERS 89
Servers (Microsoft): 89
Servers (Linux): 89
Servers (ODA): 89
Servers (VMware) 89
3PAR SAN: 89
Network 89
PC Workstations 89
Mac Workstations 90
Printers 90
Satellite/Internet/Phones 90
Other Equipment/Projects 90
APPLICATION DEVELOPER 92
Summary92
Special Projects 92
General Duties Performed 92
Change Summary92
Special Projects / Issues 93
Development Tooling and Infrastructure Changes93
Hardware and Server 94
LAB OFFICER Chieh Peng
SUMMARY

• EXP390C is a preparation project for EXP390 and EXP393. We retrieved cores from 4 out of planned 6 sites and installed re-entry systems for these 4 sites.
• We transited from Kristiansand under COVID mitigation rules to Las Palmas for fueling
• COVID mitigation plan lifted 14 days after quarantine started in hotel in Kristiansand and no COVID case is detected onboard.
• Confirmed that COPE document is a guidelines, shipboard captain, Lab officer, and Operation Superintendent can make modified decision base upon situation to relax or tighten the rules
• All oncoming staff, including SIEM, were quarantined in hotel for 5 days with 3 negative COVID tests before boarding the vessel
• End port is changed to Cape Town mid-cruise as South Africa is open while Europe is applying more travel restriction.
• No portcall nor shipment was conducted/received in Kristiansand as a one month tie-up was held prior to 390C.

SPECIAL PROJECTS

• Trouble shooting 3.5 kHz transducer and Bathy echosounder issues, after lost 3.5 kHz completely within 24 hours of operation.
• Repaired towed magnetometer cable after it was found twisted and damaged
• Replaced the main drain line in splitting room
• SHIL testing with new light system. Developed calibration procedure
• In XRD lab, installed new Haskris and repair the old one. The old one is stored onboard as backup
• CTD deployed 3 times successfully
• EXP390C To Do list is listed in Confluence under Lab Notebook/390C
• Confluence Lab notebook page was cleaned up. Several missing links were repaired. New pages for archived tech reports, Chemistry, and Physical Property were created and replaced.
• An upright incubator was removed from RadVan to TBULK
• Diagram of N2 flow from the N2 generator is created and palced in Confluence under N2 generator

OPERATION DATES
START

• Port : Kristiansand, Norway
• Crew change: October 5, 2020
• Depart: October 7, 2020 END
• Port: Cape Town, South Africa
• Crew Change: Dec 6, 2020

ASSITANT LAB OFFICER
Heather Barnes and Eric Moortgat
OVERVIEW
EXP390C Port Calls Kristiansand (Oct 4th, 2020) and Cape Town (Dec. 6th, 2020). EXP390C was dedicated to installing reentry cones at 6 sites for EXP390 and EXP393 with sediment and minor basement coring. No scientists sailed. Full suite of technical staff sailed.
Important Note: Whole round basement sections recovered on EXP390C are remaining onboard. They are boxed and secured in the HRS.
ALO COMPUTER
Updated Password. In Safe.
SHIPPING
(Note: all paper work and diagrams are available in Confluence ALO Notebook Shipping)

RECEIVED

All X390C shipments were received onboard prior to boarding on Oct 4th.
2 Cardboard K-boxes X390R AIR are due to arrive on the vessel Dec. 5th. We will remove the Knudsen sonar dome testing tool and stage the K-boxes in TBULK for the oncoming crew to unpack.

OFFGOING

1 x 40ft Refrigerated containing core and surf. Note: the MBIO mixed gas rack contains 'full' bottles and must be emptied before shipping and the whole-round sections (basement/sediment interface) will remain onboard (secured in HRS).
1 x Flat Rack
1 x RAF, yellow box air freight going to IODP
5 x FAF, foreign air freight going to scientists (samples)
1 x Hand Delivery to Agent in Cape Town, Pelican Case containing Tension Force Gauge (Drill Floor), going for calibration.
Old Liquid Scintillation Counter is shipping back to IODP
AMS/INVENTORY
AMS will time out after 15 minutes if inactivity. There is a timer in the bottom right hand corner.
GB1237 MBIO mix 95% N2, 5% H2 is stored in TBULK by the gas monitoring unit (by blue logistic lockers), in case someone is looking for it.
SPECIAL PROJECTS
New Core Cutters suggestions for improvements: 1. The cutter with the aluminum blade holder needs to be modified so that it fits the blades we have in stock. Currently we have to cut the back end of the blade as well as the side of the blade because the shape of the blade holder is not designed for our blades. In addition, the blade holder does not allow the blade to protrude enough to consistently cut the liner. This is especially for XCB cores where the core material does not fill the liner and the cutter compresses the liner into an oval-like shape, such that the blade does not dig into the liner to cut it; and 2. The other cutter has a 3D printed white blade holder, and it is working well, but it would be ideal if both cutters had modified aluminum blade holders.
Smear Slide Station moved to the FWD table. This frees up space in the far stbd corner. If you would like to move it or have any suggestions please do as you see necessary.
Dual monitor stands for description tables 1 and 2, and 2 new computer screens for description table 1 are ordered.
TO DO LIST FOR UPCOMING TIE-UPS
Move Argon bottle GB1154 from the N2 reservoir to Argon rack GR0026.
Gel Coat the splitting table. The hardener is attached to the gallon mix in BFLM.
Floor outside the Paleo lab and working half rack and in Microscope lab has many cracks that can be repaired. New rotozip bits for sanding out the cracks and Red Hand for filling cracks should be onboard.
Painting the floor outside the Splitting room. Paint is patchy between splitting room and door to stairwell.
Section of Floor in FCL by the tech desk gets condensation and slippery. It should be painted with "non- slip" grit powder
DISCUSSION
n/a
CURATION
Brittany Martinez
SUMMARY
A total of 1,594 samples were taken on Expedition 390C. 865 meters of core material was recovered during the expedition with 86% total recovery.
Only samples for shipboard analysis were taken onboard. PAL WRNDs were separated into eight samples and the splits will be shipped to Expeditions 390 and 393 paleontologists. No samples were taken from the section halves.
SHIPMENTS
9 pallets of 14 core boxes and 1 pallet of residues will be shipped from Cape Town to the Gulf Coast Repository (GCR) in College Station, Texas. 5 boxes of whole-round basement cores will be left onboard to be split on Expedition 390.
The core boxes were divided into Archive and Working pallets. Each core box is labeled by the box number followed by an 'A' (Archive) or 'W' (Working) to denote the section halves in the box. All cores were boxed in order, however, please refer to the Core Box Inventory sheets. The pallet inventory will be sent to the GCR by the oncoming JRSO crew.
All split sections were wrapped in Glad Clingwrap. Cores that contained the sediment/basement contact and basement were flushed with nitrogen and sealed in aluminum bags, and remain onboard.
SITE CONVERSIONS
The conversion between pre-site to site identifiers are listed below:

SITE SUMMARY

U1556

Hole A: APC/XCB to 283.8 m

U1557

Hole A: APC to 9.5 m (missed mudline)
Hole B: APC/XCB to 574 m Hole C: Jet-in test
Hole D: Partial casing and reentry system installation

U1558

Hole A: APC/XCB to 163.9 m
Hole B: Failed casing and reentry system installation Hole C: Failed casing and reentry system installation Hole D: Casing and reentry system installation

U1559

Hole A: APC/XCB to 66.2 m
Hole B: Casing and reentry system installation


CATWALK SAMPLING
The Expedition 390C Catwalk Sampling Strategy is shown below. The following samples were routinely taken:
Head Space (HS) – (1) 5 cc syringe per core Interstitial Water (IW) – (1) 5 - 10 cm WRND per core Paleontology (PAL) – (1) 5 cm WRND per core



RESIDUES
The residue distribution is as follows:

SAMPLE REQUEST CODES AND NUMBERS
Below is a list of the samples requests that were approved by the Expedition 390C SAC and their respective Sample Request Codes:

MISCELLANEOUS
Archive Half Scrapings: Archive half scrapings were bagged and labeled by section. They will be sent to the GCR for storage.






CORE DESCRIPTION LAB
Alexis Armstrong
SUMMARY
Expedition 390C was a re-entry focused expedition; which cored, cased, and deployed re-entry systems for the postponed expedition 390. Core material collected was minimal, and consisted of both sediment and hard rock. Sediment cores were split, scrapped, and ran through the section-half tracks; whereas hard rock and material at the sediment/hard-rock interface were not processed. No material, either sediment nor hard-rock, was described; no templates were created. Sediment cores will be brought to the ship and described at the time of expedition 390. Hard-rock sections will stay on the ship until 390; they will then be curated, split, ran through the section-half tracks and described.
ISSUES/DEVELOPMENTS

DESCLOGIK

Current Version: 16.2.0.0.
DESClogik was not used. DESClogik was opened, tested (performing normal functions), and confirmed to be working.

Updates

No updates to report.

Issues

No issues to report

CORE DESCRIPTION LAB

The smear-slide (SS) station was moved to the forward table of the Core Description area. The SS station consists of the Axio microscope, hot-plate, UV box, Zebra printer, Slide making supplies, and reference slides.
To accommodate reference slides, a custom drawer was created. To accommodate slide making supplies, and generic lab storage, a Vidmar cabinet was moved underneath the SS station counter.
A secondary monitor was mounted above the auxiliary table, to be used as a LIVE display monitor.
The location of the UV box has been placed underneath the secondary description table; whereas, the Zebra printer is located underneath the third or auxiliary description table. The hotplate is located on the SS station benchtop, as it can be a hazard if placed out of line of sight.
All placement of equipment can be changed. Please look over the SS station and access if any changes need
to be made. If this station stays in its current position, future modifications proposed are: 1) Shielding for the hot plate (concern has been made about the placement of the hot-plate and the computer monitor cables), 2) a wooden tray to hold the basics needed for SS creation (to sit atop of the benchtop), 3) a proper foot rest to alleviate lower back pain (useful for smaller microscope users), and 4) a proper bench-top height chair.
Following photos showing the new SS station:

PALEONTOLOGY WET LAB

• Both faucets were replaced.
• Performed physical counts and inventory of the sieves
• Performed physical counts and inventory of all accessory equipment stored and used in the Paleo wet lab. Full inventory list can be found at: +http://confluence.ship.iodp.tamu.edu:8090/pages/viewpage.action?pageId=63767790+
• Performed a routine check of the chemicals and solutions stored within the wet lab. Disposed of any discolored containers, old solutions and un-labelled solutions

MICROSCOPES

• Performed routine maintenance (cleaning, corrections, alignment) to all microscopes

SEM

The SEM and Sputter Coater were turned on and confirmed to be working. No issues to report

THIN SECTION REPORT BUILDER/WRITER

No thin sections were described. The Report Builder and Writer were not used. No issues to report.
SHIPMENTS
No shipments were received
GEODESC
Geodesc is in full development, with a focus on Template Manager, Data Capture, Data Access, and Taxa File Checker. Implementation and testing are active for both Template Manager and Data Capture.
Changes in testing schedule and methods have been implemented, with each application in testing (TM and DC) released on a staggered bi-weekly schedule (TM is scheduled for the 3rd, with DC scheduled for the 10th). The normal schedule will be put on hold for the holidays, with the next release of TM (version 15) scheduled for January 14th 2021. On the Monday of the scheduled release week, the lead developer emails the respective test plan manager to inform them of upcoming changes. This allows the test plan manager to edit the test plan, and to try to stay as up to date as possible.
An overview "Testing" document was created, and can be found at: {+}https://docs.google.com/document/d/1Q98CRwa2cDZhS7T8YGHmiI8_IGyepKNj-DpBQT93kXI/edit+
This document explains how to test, how to write a test plan, how to assign testers, how to create an issue report, etc.








IMAGING & MICROSCOPES
Sarah Kachovich
SUMMARY
Expedition 390C's four-week long transit before reaching the first sites allowed for extensive testing and troubleshooting of the SHIL. Once we were coring, the focus of my work turned to normal Imaging Specialist's responsibilities, with the added duties of running sections through the SHIL and SHMSL. Other added responsibilities included: outreach on social media, adding missing logos to the stairwell, photographing empty labs for the JRSO website, updating headshots for the JRSO directory, gathering new B-roll footage of operations for USSSP, gathering safety information for the production of new safety videos and cross-training peers in the SHIL calibration, paleo prep and preparation of the new SEM/EDS.
EQUIPMENT AND SOFTWARE PERFORMANCE SUMMARY
All equipment under the Imaging Specialist's lab performed well, unless listed below:

• Faulty SD card identified. This card was the cause of multiple lost files, including some of the NGR training videos from the San Diego port call. The card has been labelled and removed from rotation.
• Extensive SHIL testing was performed. First to understand the best scanning parameters to help rewrite the SHIL manual, and secondarily, to troubleshoot calibration issues and new parameters with the LED lighting system.
• SHIL's IMS has some lags, and caution need to been taking into consideration when navigating around and calibrating the camera. The worse IMS software issue was that the 'cancel' button, on two of the windows were functioning as a 'save' function. This has since been corrected, see developer's tech report for more details.

LIST OF GENERAL IMAGING SPECALIST'S DUTIES

• Generated the headshot posters (used a new design)
• Downloaded and proofed all of the line scan core images.
• Shot close-ups
• Production and editing of the weekly photos.
• Produced all of the group photos.
• Printed the T-shirt stencils and coordinated the competition and ironing party.
• Detailed cleaning and alignment of the Core Lab microscopes.

LIMS FILES PRODUCED
1 Close-up Image
714 Line Scan Images


DOCUMENTATION

• Started a new IMGAGING/MICROSCOPY LAB NOTEBOOK in Confluence (sections still under construction, but feel free to add and edit). The main aim was to organize (the Chemistry Lab

Notebook format was chosen to keep the labs consistent. Phys props Lab Notebook has done the same), add missing information and to rewrite the SHIL calibration methods. The old notebook should remain in Confluence until the new notebook has been completed and reviewed.

SHIL TESTING AND TROOUBLESHOOTING
The rest of this tech report will be focused on the testing and troubleshooting of the SHIL. Please also see the Phys Prop's and developer's tech report for a complete documentation of the SHIL during expedition 390C.

Disclosure: Please note that the SHIL is operational. The troubleshooting and testing were done to help rewrite the SHIL manual, figure out the scanning parameters under the new LED lighting system, help make suggestions for improvements.

CONSIDERATIONS OF NEW LED LIGHTING SYSTEM

1. 1. Reflectance issue

There are two new considerations that need to be further observed to assess the cause: (1) random reflectance in the red bar (Figure 1), and (2) the reflectance pattern of the circle light on reflective (wet) surfaces (Figure 2).

Figure 1. Randomly appearing reflectance in the red bar during scans (?occurring every 20-30 scans). Initially thought to be a produced by the shutter speed being offset to scan rate (motor speed). Another potential cause is that the red bar is not secure and is wobbling/changing angles. Please make note if this occurs. Rescan if possible.

Figure 2. The pattern of the circle lights can be seen on any reflective surfaces. For now, be cautious of scanning wet cores. Try to dry the cores as much as possible before scanning to limit the reflectance. A possible solution is the addition of a diffusion plate.

The wiggle

The M-Drive motor seized, and we ended up replacing it for new one. Once we replaced it, a minor mechanical wobble in the camera at the start of the scan was noticed (Figure 3). We tried to tighten a few screws but couldn't fix it, please feel free to tinker. Due to time constraints, we went with the easy solution, by moving the QP card down 2 mm (Figure 3 –right). This artefact is more noticeable with slower scan rates.









Figure 3. (left) Two QP cards that were off-set from one another during a scan. Both showed movement during scanning, but more movement was observed with the top QP card. (right) New QP card placement with minor movement. QP card has been straightened and glue since this scan.

Caution with standards

Two considerations with the SHIL standards were investigated on expedition 390C: (1) changed values of the standards over the past few years, and (2) assessed the performance and fading of current standards.
After some research, it was found that the manufactures of our standards have changed their products and we think they haven't been noted.

QP CARD 101

The newer version (version 4) have near black and near white, instead of pure black and pure white (middle gray is the same), compared to the older versions. Know what version you are using! They have the L*ab color values for each patch printed on the back side, which can simply be converted to RBG (Table 1).

Table 1: QP 101 Version 4 values

X-RITE COLORCHECKER MINI

Apparently, the pigments on the ColorChecker used on the 3D standard, were modified in November 2014. Meaning that the currently available cards do not have exactly the same RGB values as the older ones. This needs to be investigated further to see if the values in IMS match the standards.

When the standards fade, some patches become brighter, where colors can also become washed out. Figure 4 shows the old and a new mini color standard. They were imaged on the same scan. Need to order more of the mini color checkers or design a neutral black and white/light grey heat resistant (silicone) standard.

Figure 4. Faded color standard (left) that was replaced at the start of Expedition 390C. Colors appear duller and white is too bright. The QP card 101 and the mini colorchecker needs to be compared (at least visually) before starting the calibration process for fading.

5. 4 Understanding the RGB curve when adjusting master gain and master black

Master gain changes the whites/high RGB values. You can use positive or negative values. Master black changes black/low RGB values. You can only input positive values for master black.
In figure 5, three scans with different master gain and master black values are compared to the known values of the standard. Do note, as you change master gain (MG) or master black (MB) you will need to change the red, green and blue exposures as well. For example, if you lower the master gain down to -131, you will be able to raise the overall exposure, and likely the red gain.
Without changing the gain values, the SHIL gives you a raw image with too high of a contrast. That is, whites are too bright, and blacks are too dark. You need to adjust the mid-tone and black level to achieve a good calibration. To do this, it is recommended to at least raise the master black. Lowering the master gain will help achieve a more ideal mid-tone, but be careful, because color can start to lose saturation and vibrancy when you do.
It is important to try and achieve the best possible raw image, with minimal post image acquisition corrections.



Figure 5. Gain levels on raw jpegs. Note the changing curve with changing gain values. The aim is to have perfectly linear values, with matching measured and given values.

5.5 Tiff post scanning process problem

This is a priority to get the .tiff images back to normal (Figure 6). The raw data and processed jpegs look great, but the .tiff processing is doing strange things. I am not sure what happened but this has suddenly happened to the scans half way through the transit.

Figure 6. Tiff image's black value is too high. I don't think there is currently an option to reset it. Shore has been notified but no solution has been mentioned.

5. 6 F-stop and the vignetting artefact

The f-stop is recommended to be set to 22 but there is no reasoning why it was recommended, so we performed a few quick tests to assess the quality of varying f-stops.
With a lower f-stop (wider aperture), means that more light can make it to the camera sensors, but you will have a worse depth of field. With a higher f-stop (closing the aperture), you will have a larger depth of field, but less light will get through to the sensors. The following figures are from the 'JAI Camera Setup' window in IMS.
Test 1: Higher f-stop of 32. Demonstrate the least amount of lens vignetting, but needs raised sensor exposure interval.
Test 2: Lower f-stop of 4. Demonstrates a lower sensor exposure interval, but a worsening lens vignetting.
Note that all lenses show some vignetting as a function of the field angle. Hence, even with homogeneous object illumination, the signal intensity of the image decreases with increasing image height. Shading correction (or flat field compensation) is used to compensate for lens vignetting as well as for inhomogeneity
in the illumination, but has the potential to cause gain artefacts (see section 5.1.7).




Figure 7. Changing sensor sensitivity with a varying f-stop, in the 'JAI Camera Set Up' window in IMS. You need to raise the sensor sensitivity (left) when working with a higher f-stop, because there is less light passing through the lens, due to the closed aperture. Question, is it better to raise the sensor's exposure interval, or have it lower?



Figure 8. Lens vignetting with a changing f-stop, in the 'JAI Camera Set Up' window in IMS. The

This artefact (when shading correction is turned off) is interpreted here to be vignette because of the (1) diffracting pattern of the different spectra (red has a longest wavelength here), and (2) when you compare the illumination pattern with a reflective surface (Figure 1, 2 and 9), the two outer circle lights do not seem to match the reduced brightness nearer the periphery of the image (Figure 9). It was previous recommended to add more illumination closer to the left-hand side of the line scan, but after the f-stop tests, it appears that the shading is more likely caused by the lens. Further thought and investigation needs to be achieved to find the optimal camera and lens configuration. Will play around with the shore SHIL on this.




Figure 9. Lens vignetting vs the LED light reflectance pattern. At the top of the figure is a compilation of the live displays of the 'image grab' in the 'JAI Camera Set Up' window, in IMS. The top image grab is a non- reflective light gray surface, where the image grab underneath is of a piece of steel to show the LED's reflectance pattern. The graph below, plots the RGB values from both tests. Note that the middle LED is
centered to the of the lens. The two outer LED positions do not seem to be affecting the periphery dimming curve at all.
The biggest issue with the observed vignetting is that the red spectra is significantly less dispersed (at a different angle) towards the periphery. When the gain correction is applied (shading correction), the sensitivity of the red, green and blue at the periphery have different multipliers to one another. One would predict this would cause color inaccuracies in these regions of the scan. Need to investigate more.
The cause of this vignetting/shading can be split into two groups; those primarily caused by the lens and those caused by the sensor. (1) All lenses are influenced by what is called Cos4 vignetting which is caused by the fact that the light has to travel a further distance to the edge of the image and reaches the sensor at a shallow angle (Figure 10). This can be avoided, or reduced if the lens is stepped down by two f-stops. Need to research more about sensor vignetting to understand if this has an effect in our system.

Figure 10. Diagram of Cos4 vignetting of lens from https://www.sukhamburg.com/documents/LineScanCameras_06-2019_E_web.pdf

5. 7 Understanding how much to defocusing the lens during calibration

This test was sparked by Beth's question "how much do you defocus the lens during calibration". Answer: as little as possible (see Figure 11).

Figure 11. Results of a focus vs defocused lens (under and over focused demonstrated here) on the flat field (shading) correction. The results are from a flat field correction done on a gray scale card with a focused lens (middle results). Then the camera was defocused to show how the lens (also topography) impacts the effectiveness of the flat field correction in the areas that needs the most compensation for vignetting.

5. 8 Stabilization of the LED lights and thermal management

A lot of time and effort was put into understanding the new LED light's operational parameters to achieve the optimal performance. Initially, we were under the impression that the temperature of the lights was impacting the illumination performance, but after a more careful inspection and research, it appears that temperature is just a proxy for the stabilization time of LEDs.
We ran multiple tests, but only the last test is shown here. The test used two of the k-thermocouple sensors and the live display in the 'JAI Camera Set up'. Temperature and the RGB intensity values were collected every second on the light gray patch of the QP card 101 v4 (true RBG value of this patch is 235, 235, 235). The results clearly demonstrated the response of the LEDs stabilizing (Figure 12), and thermal management (Figure 13).

Figure 12. The LED's stabilization curve for the scanning parameters used on expedition 390C. The LEDs reached the calibration (RGB of 235) set for expedition 390C at 19 seconds and was too far out of calibration after 2 minutes and 12 seconds. Note that the lights get brighter over time, and in time, the divergence of the blue intensity causes a color change when scanning light objects (see figure 14).

The LED's manual (Cree XLamp CXB3590 LED, uploaded to Confluence) recommends to stabilize the lights and run them at an optimal temp of 85 °C. The problem isn't the heat sink for the LEDs, but with the temperatures under the lights. The temperature sensor placed at the core height, reach 100 °C at only 2 minutes and 27 seconds. Moreover, the experiment was stopped at 11 minutes as the temperatures under the lights were getting too extreme (max temp recorded at 135 °C). I fear that the high temperatures will easily vaporize something under the lights and damage the lens or camera above it. It is also, highly likely the scientists will be very concerned to know about the temperatures under the lights.

Figure 13. The LED's thermal response when left on and stationary. The temperature under the LED's, at the core surface, reached 100 °C after just 2 minutes and 27 seconds.


In an ideal situation, it would be best to have the lights stabilized, but there is currently no safe solution to get the lights to that level without damaging the camera, track or cores, due to poor thermal management solutions underneath the lights. For Expedition 390C, it was decided to calibrate the LEDs while they had been off for a while, and by the end of the expedition we realized we needed to do a blank scan before (if the SHIL's lights hadn't been on for over an hour) and also allow 5 minutes downtime between scans, so that the LEDs would keep within an acceptable calibration. The QP cards were monitored and rescanned if the light gray card patch on the QP card 101 showed too much variation from the RGB intensity value of 235 (Figure 14).





Figure 14. QP card monitoring at Site U1558B, down hole. Averaged RGB intensity values were extracted from each of the QP card patches at the top of every scan. Notice that the variation of the RGB intensities were only noticeable in the high values (>~220). The time stamps were extracted from the metadata. Rescans were only preformed when the light gray patch varied by more than 15 (small red circles highlight rescans).

5. 9 RGB monitoring of expedition 390C cores

Alexis scanned and processed RGB data from various tests with the cores from expedition 390C. The data and results can be found under:
IODP_Share > PhysProps > Testing and Calibration Notes > SHIL > 390C SHIL testing
In this report, I will make a quick comment on two of the tests: (1) RGB's of the rescans, and (2) the same section being scanned multiple times.
Alexis clearly showed that, while we had variation in the high intensity values in the light gray, QP card 101 patch, the RGB variation in the core was of no significance. This raises the question of what is acceptable variation in values? Imaging Specialists require input from the LWG about this. During the continuous scanning of the same section, the RGB values reflected figure 12's LED light's stabilization curve. Here the most variation was seen during the first few scans, but the RGB values within the core did not vary significantly enough, even between the first and the last scan.

10 Green aberration after high contrast areas

The green streak in the QP card and in areas in high contrast were once again observed, more at the first two sites. It was removed for a bit, but think it came back due to the pixel gain correction being performed again.
Current thought is that this artefact is due to gain corrections, or blooming.
Blooming in line scan cameras
When the line sensor is saturated from excessive illumination and cannot accumulate more charges, the overloaded pixels transfer some of the excess charge to adjacent pixels − an effect termed blooming.
Blooming leads to the corruption of the geometrical assignment of both the signal and the image generated by the line sensor. Over-exposure caused by too large an integration time leads to severe signal and data corruption when using line scan cameras without anti- blooming. Since the light travels the shortest to the green senor in the camera, I think this could be a cause. This effect should be looked into more. Ran out of steam and time on expedition 390C.
PHYSICAL PROPERTIES LAB
DORIS PINERO LAJAS
SUMMARY
Emily Estes was the only scientist onboard during this expedition. Approximately 800 m of core was processed in the PP laboratory.
For further information please visit the X390C Physical Properties Lab Notebook, ETs Report and Imaging Specialist report for X390C.

CONFLUENCE UPDATES

• • Physical Properties Notebook page was updated on Confluence. Following the recommendations of LOs, ALOs, technicians and previous tech reports the Phys Props page was reviewed and updated. This page needs to be reviewed by the oncoming crew.
  • The "old" PP Page was saved and Archived under 'Info for Physical Properties Technicians'. If the original notebook PP page is to be recovered, v340 should be used (March 4, 2020), after this date structural changes were implemented.
  • During the past months two different PP Notebook pages has been used. All the changes in both of them were compiled into the current page.
  • In order to unify and standardize the format of the Laboratory pages, the current Notebook PP Page follows the Chemistry Lab Page (designed by Johanna Suhonen).
  • Current page allows clear view of tracks' status and an easy way to find laboratory related information. Main difference with the initial PP page is that each track has each own page, before all the lab information was listed in the same page. Mentioned division allows the user to find the related information efficiently. Each track is listed on the left side of the main page. In the page, the information is organized by expedition and date. Newer information is at the top. On the right side of the page user could find links to instrument user guides, vendor manuals, tests and other resources.
  • Important related laboratory information can be found on the right side of the main page. The follow are the different sections:
  • ´Expedition Specific Physical Properties Notes´: It is designed to add expedition general notes that could be compiled on the Technical Report. It is also organized by expedition.
  • 'Info for Physical Properties technicians': Useful information for the technician cam be found here, like vendor manuals, laboratory templates, configuration files , IMS , other software resources, laboratory resources, archived information and inventories.
  • At present the following inventories are compiled: Bartington MS Detectors and Sensors Laser QEPro spectrometers

NI items inventory (under construction) Teledyne, X-Ray Imager sources SHIL cameras Pycnometer cells
TCON needles and probes Radioactive sources

• • 'Physical Properties Laboratory Task List': Reserved for pending tasks at the end of the expedition. It is way to communicate with the technician in charge on the next expedition.
  • 'Physical Properties Laboratory Issues': Links to Physical Properties Software Issues table and to the link to report new software issues.

• • 'Tech Reports': Links to 'Archived Tech Reports' page.
  • 'Physical Properties Books and References': Assigned for useful information for scientists, like published articles and formally referenced academic works.
  • 'Vendor's Troubleshooting Information': See further information above.
  • Following the recommendation of Eric Moortgat, NI (National Instruments) inventory was added to the list of inventories (Under 'Info for Physical Properties Technicians'). This inventory contains model, serial number and location information of the item, and also its inputs and outputs and alternative models for items that is no longer available by the vendor. As well, it is useful for understanding how each station works, and for troubleshooting. (Note: this inventory is under construction).

• • 'Vendor's Troubleshooting Information' page was created to provide information on an instrument that was sent to a vendor for repair. This list contains the description of the problem, dates when the instrument was sent and received and as much information as possible about vendor's diagnosis and repair. It would be useful to add any communication emails with the vendor. Information should be added by the technician onboard if the repair information is received on the ship, or by someone onshore, if they have the contact with the vendor or the information was received together with the instrument onshore.

• • WRMSL/STMSL, NGR, XMSL, SHMSL, GANTRY and SHIL checklists were reviewed and added to Confluence. Heather Barnes, Brittany Martinez and Luan Heywood reviewed the checklists.
  • Along with Alexis Armstrong and Heather Barnes onboard, and Alejandro Avila and Aaron Deloach onshore, WRMSL/STMSL, NGR, XMSL, SHMSL, GANTRY and SHIL Quick Start Guides were reviewed and added to Confluence. The QSG provides the steps the user needs to accomplish correct measurements, upload and review the data. Deeper theory and information about the station will be found on the User Guides (review in process).
  • Reviewed SHMSL User Guide including the changes made during X387P is added to Confluence. It will be Under the SHMSL page for further review before adding it to the User Guide´s page.

PENDING TASKS

• • Test AVS.
  • Review PP check lists and add final comments.
  • Review PP Notebook Page to establish the final version.
  • Edit TCON, AVS and MAD Quick Start Guides, to standardize their format. Continue NI items inventory.
  • Continue adding Vendor's troubleshooting info to the Confluence Page.
  • Gantry, NGR and WRMSL/STMSL User Guides are in process, will be finished during next expedition (Feb-Mar 2021). Fix the bolt holes on the X-Ray source door.

LOGISTICS

REQUISITIONS

100 ft of 1/8" black lifting rope. To use on the X-Ray Imager and other required purposes. 3ft of high- temperature silicon o-ring cord stock for the SHMSL sensors (PN 96505K24).

SENT TO SHORE

TCON Half-Space Puck sn H11040 for recalibration. Reported low values during October 2020 test (See Thermal Conductivity section).
INDIVIDUAL MEASUREMENT SYSTEMS

WHOLE ROUND MULTISENSOR LOGGER (WRMSL - AFT TRACK)

WRMSL/STMSL QSG and instrument checklist were reviewed and updated in Confluence.

P-WAVE VELOCITY LOGGING (PWL)

The water pump (sn P305133) of the PWave station stops every 15 seconds during U1558, it was necessary to hit re-start every 15 seconds. To solve the problem and continue with the measurements the water pump was replaced, sn P303417 was installed. ETs found the problem was related with a configuration setting, it was set to a volume of 10.00 ml, but it should be set to OFF in order to operate continuously. Rate should be set at 40 ml/min. Sn P305133 is installed again on the PWave station.
During previous expeditions if the track was not used during a period of time, the P-wave system was not closing the first two-three times. Jurie Kotze cleaned and grease the guides-brakes of the P-Wave hydraulic system. We've continued to grease it during the expedition when the station was in use. We still notice that if the station doesn't work for a period of time, it will fail the first measurement, but after that it will continue working ok. During next tide-up we are planning to open and clean the hydraulic motors.

SPECIAL TASKS MULTISENSOR LOGGER (STMSL - FWD TRACK)

WRMSL/STMSL QSG and instrument checklist were reviewed and updated in Confluence. GRA source was positioned and aligned. The amplitude now is around 1350.

Software Issues

During IMS opening a window with the message 'Failed to find Baud Rate. Cycle power on the AR700 and then click OK' pops up. There is no AR700 on the STMSL. If you click OK and 'continue' IMS starts properly and measurements could be taken correctly

RAY IMAGING (XMSL)

• • XMSL QSG and instrument checklist were reviewed and updated in Confluence.
  • Since the middle of the expedition four badges were placed to detect and measure any radiation around the station. The badges were located on the source's box, the screen of the PC, under the area monitor and on the upper NGR beam.
  • Safety test performed at the beginning of the expedition. Radiation values were within the range and safety procedures worked correctly. Background was around 0.8 kCPM. Low alarm on area monitor was set to 2.0 kCPM and the high alarm to 3.6 kCPM. New badges were set on the console and on the shield.
  • Taking the White Image when performing Calibration will activate the High Alarm on the area monitor, and X-Rays will be turn off. To avoid that behavior set the High Alarm a bit higher during the calibration, in this case we set it to 4.5 kCPM. This behavior was also reported on previous expeditions.
  • Some black images were obtained while measuring on the second site. To solve the problem, unplug and plug the source back in.
  • During measurements some over-exposed processed images were obtained. This occurred when measuring XCB cores. Raw images were ok.
  • It is important to consider during imaging that the processing image parameters are different for APC and XCB/RCB (rotary). The images obtained from the XCB cores, after processing, present two parallel lines in the same direction as the core liner. This is possibly due to processing parameters settings of small diameter rotary cores. For imaging XCB cores on hole U1559 the processing parameters for APC cores were used.

Cores obtained on hole U1559 were mainly composed by foraminifera, they were very light in color and its density was lower. Due to lighter color and lower density when we imaged with the same parameters that was used for darker and more dense cores the images for the foram rich cores were overexposed. To solve the problem we tested various parameters. First we brought down exposure time and current intensity, in both cases the quality of the images were better. As I understand this is because of the less number of photons used. After that we brought down the voltage which provided better contrast. We should improve our understanding how voltage, current and exposure time affects the images.

Software Issues

Parameters used during the expedition are on the table above.

• • X-Ray source stopped ramping up few times (while the warming window was on the screen). To make it work again we ABORT that window. Same issue happened ones during calibration. Connections were checked, after that we get the issue couple more times.
  • When core information is enter using the MANUAL tab entry, X-Ray took a first image, then the error window appears but the X-Rays doesn't turn off. It is possible to select between CONTINUE, QUIT or RETURN TO LOAD POSITION. If CONTINUE is selected it takes the same image, and the error window appears again.

Technical Service

Etienne Claassen installed the Ludlum area monitor and scanners that were sent for calibration at the end of X384. The Emergency red light was not working. Fiber optic cable was loose. See image bellow. ETs fixed it.

Velcro of the X-Ray source box was changed, to allowed the led-neoprene shield to cover the area properly.

NATURAL GAMMA RADIATION (NGR)

QSG and instrument checklist were reviewed and updated in Confluence.

Software Issues

Twice during the expedition, after running the Detector Profiler utility, LabVIEW reported 'Not enough memory space'. After restart the computer the NGR continued to work properly.

THERMAL CONDUCTIVITY (TCON)

• • At the beginning of the expedition, when the label was scanned there was a SPACE after the ID. The scan gun was reset using the curator barcodes, without the code 4 (Send <Space> key). Appropriate barcodes for this situation were put on the TCON box and screen.
  • With the help of Jurie Kotze and Heather Barnes, edges of the three remaining Half Space pucks onboard (H11060, H11038 and H11028) were milled using the CNC. Testing was done before and after the pucks were cut, see below.

Testing

• • Needles, Half-Space and Mini Half-Space probes were tested using the Macor standards. Each probe was tested during 20 rounds. H11040: Reports lower values than expected. It was sent to IODP for recalibration, at the end of the expedition. H11027: Reports a damage probe. It was already labeled as Play-Puck.
  • Remaining sensors report accurate measurements.
  • Data is saved on T:\IODP_Share\PhysProps\Testing and Calibration Notes\TCON\TCON_X390C_ProbesTest

New tests were performed on the Half Space pucks, after the edges were trimmed. Each puck was tested during 40 rounds. We observed the message "No Data" on each of the three pucks, no specific reason why, but the pucks measured correctly before and after this message.
H11028 presents the most erratic measurements, even though the data are still between the vendor limits . This behavior could be seen also before cutting the edges.
Data is saved on T:\IODP_Share\PhysProps\Testing and Calibration Notes\TCON\TCON_X390C_ProbesTest.

AVE VELOCITY BAYONET/ CALIPER GANTRY (PWB/PWC)

• • • Velocity Bayonet/ Caliper Gantry QSG and checklist were reviewed and updated in Confluence.
    • Caliper Gantry springs and square o-rings (PP5023) were moved to drawer PPTRKF7 in order to have all the components of the caliper together.

Technical Service

• • • Caliper VNC cable, that goes from the bottom of the caliper to the pulsar, was changed due to erratic signal. Etienne Claassen machined a transducer lifter that allowed to use the red caps for measuring cores.

SHEAR STRENGTH STATION (AVS)

• • • This station was not used during the expedition.
    • Tests will be performed while in port during next expedition.

SECTION HALF MULTISENSOR LOGGER (SHMSL)

• • • QSG and instrument checklist were reviewed and updated in Confluence.
    • New calibration data sheets and linearity tests of QEpro 90899 and 91126 provided by the vendor were added to the QEPro Inventory page.
    • On X384 it was reported that the laser profile kept measuring far past the end of the section. This was most prominent on short sections and core catchers where the profile records the length to be 125 cm and shows a sloping end to the section in the profile.

After performing several tests, we realized that this issue was divided into three different situations:

• • • The laser profile kept measuring far past the end of the section: Once the laser detects that core liner is not present it will continue for another ± 10 cm to make sure that it is the end of the section. If the laser is set to the incorrect height, it could see the black supports and continue the measurement.
    • The profile shows a sloping end to the section: This feature is due to a process applied to the raw data when the laser finishes taking the profile. The processing applies edge corrections at the top and bottom of the section, values there are smoothed. This also implies that gaps at top and bottom of the section are removed. Another question is that the laser can also reject a measurement for quality reasons (ambient light sources, rough surface, etc.), if the rejection happens over several cm the plot will look like a ramp. For solving that it is possible to measure at a slower speed.
    • The profile records a 125 cm length for short sections and core catchers: 125 cm is the position of the end of the last bracket of the track. If the laser is taking this measurement, it means that it is measuring bellow the range that it is suppose to measure, and is taking the bracket as part of the section. To solve this problem it is necessary to physically move the laser up, in this sense we are looking for a range where we can see the core liner but not the bracket.

The measurement range of the laser is, starting from the laser, from 78.2 mm to 179.9 mm. Greater accuracy is at 129 mm.
At the beginning of the expedition the physical distance from the laser to the benchmark was 118.5 mm, at that distance the laser could see the track and because of that it would confuse the bracket with the core.
After lifting the laser to 134 mm from the benchmark it measured the end of the section correctly. (Note: Now the benchmark distance measured on the Y-Axys Setup is 55.53 mm, that it is close to the default value of 56.99 mm reported in the User Guide).

Technical Service

Halogen bulb replaced.

Testing

Two tests were performed in order to compare the measurements between the QE Pro that it is already installed on the SHMSL (90900) and the two QE Pro that were sent to the vendor (90899, 91126) at the end of X387P/T. They all behave similarly but there are small variations between instruments.

• • • Test 1: Perform the QEPro calibration, continuously, seven times. On QE Pro 90899 and 91126, the calibration was performed again after 1 hour of work. Dark calibration values were collected. Data is saved on T:\IODP_Share\PhysProps\Testing and Calibration Notes\SHMSL\QEPro_Tests\SHMSL_X390C_QEProCalibrationTest. A summary of the results is on the rights part of this page under "QE Pro (90900, 90899, 91126) Calibrations Comparison Data X390C (Nov 2020)".

• • • Test 2: Perform seven continuous Color Standards measurements per each QE Pro. Data is saved on T:\IODP_Share\PhysProps\Testing and Calibration Notes\SHMSL\QEPro_Tests\SHMSL_X390C_QEProColorStandardTest. A summary of the results is on the right part of this page under "QE Pro (90900, 90899, 91126) Color Standards Comparison Data X390C (Nov 2020)".

SECTION HALF IMAGE LOGGER (SHIL)

For more information about the SHIL please review Imaging Technician report.

• • • SHIL QSG and checklist was reviewed and updated in Confluence.
    • New Imaging/Microscopy Laboratory Notebook page is under construction.
    • IMPORTANT: There are different versions of QP cards onboard. Technician should be aware of which version is being used because they could have different Dark Gery, Mid Gray or White values. A label with the version of the QP card in use was set on the SHIL.
    • Issues reported during X384 and 390P (Red and green bands, vertical stripes) were found to be largely related to calibration, since then the occurrence of artifacts has been reduced. A file with the calibration images was saved on IODP_Share\PhysProps\390C SHIL Calibration-Fixed GreenRed streaks.

Technical Service

• • • The light stand was moved across, to better center the illumination over the core.
    • At the beginning of the expedition, the track began to get stuck when moving and displayed the E- Stop window. The M-Drive motor seized, and we ended up replacing it for new one. The worn screw of the track was greased.

Software Issues

• • • CANCEL button was not function properly in (at least) the Image Correction tab. It acted as a save action button. Problem was solved for the Image Correction page.

Testing

Sarah Kachovich and Alexis Armstrong performed several tests during this expedition. Tests were conducted in two ways:

• • • Reviewing RGB values on several QP cards measurements. A drift on the blue spectra was detected in high intensity values. It related with increment of the lights not stabilizing during measurements. The data shown that after approx. 10 mins, the LEDS stabilized, but the heat sink is not efficient enough to run the SHIL at this level. Moreover, the calibration needs to be done for the correct

stabilization (or temperature as proxy) time. This drift in RGBs intensity values could cause problems when imaging really white cores or highly reflective/wet sections. See Imaging Specialist report for more information.

• Measuring real cores. Three types of tests were conducted.

1. Duplicate measured sections were analyzed,
2. measuring the same section continuously during multiple runs, and
3. measuring a complete core, seven sections, continuously during multiple runs.

In all cases, the RGB data produced by the SHIL were compared. A drift on red, green and blue intensities could be seen as the lights stabilized (as a proxy, the temperature of the lights is increasing). A drift in the blue intensity diverges at a faster rate than in red or green intensity over time. After 7–10 minutes, the red, green and blue intensities were observed to reach an equilibrium and should be used as guide when running the SHIL, until we understand this phenomenon more. Overall drift values were small, with the highest value of blue drift corresponding to ~5. Change in RGB values between duplicate sections (sections which were re-run for higher image quality) were on average ~3. We do not know if this drift value of 5 is significant; however, to decrease blue drift, running the instrument before taking your image is shown to have a significant impact, as shown in the figure below. Data related with this experiments could be find on: T:\IODP_Share\PhysProps\Testing and Calibration Notes\SHIL\390C SHIL testin

MOISTURE AND DENSITY (MAD)

• • MAD station was not used during this expedition.
  • Following the recommendation of Alejandro Avila, we have been running the pycnometer every two weeks, in order to keep the lines clean. Data measurements has been reviewed during this time to verify its accuracy.

PALEOMAGNETICS LAB
Alex Roth
SUMMARY
Since Expedition 390C sailed without a science party, the main objectives were to install reentry systems and collect preliminary cores and data for the South Atlantic Transect, with the intent of returning for Expeditions 390 and 393. For the Paleomagnetic Laboratory, this entailed measuring core sections on the Superconducting Rock Magnetometer (SRM) from sites U1556A, U1557A, U1558A, and U1559A with all APC cores magnetically oriented except for U1559A.
All magnetic orientation tools (MOTs) appeared to be functioning properly (Icefield tools deployed – no Flex-IT tools). Both Icefield and Flex-IT Keyed End-Seal Snubbers (KESSes) were properly aligned and documented.
No other magnetic measurements were required during the expedition, but most instruments were calibrated and used solely for characterizing the new Pmag Play Cube standards. The exception was the Kappabridge, which was only tested but for communications and basic functionality, but not calibrated nor properly exercised.
General lab diagnostics and maintenance were carried out at the beginning of the expedition (BOX) and the end of the expedition (EOX). The SRM was routinely monitored throughout the expedition.
The only significant issues were communication problems between instruments and computers after Window updates and initial difficulty with the SRM and the SQUIDs having unstable output. Both are detailed below, but more in depth writes up are available on Confluence under the lab notebooks.

MEASUREMENTS

CORE ORIENTATION

All three Icefield MI5 magnetic orientation tools (MOTs- 2007, 2043, and 2052) were deployed for all APC cores from U1556A, U1557A, U1557B, and U1558A but not for U1559. Log files from RigWatch were used to create standpipe pressure plots with data every 10 seconds to approximate the sampling interval for the MOTs. From these charts the firing time was determined and used to calculate the magnetic tool facing (MTF) for each core. The values chosen to average were focused on the final intervals just before the core was shot as this point should best represent the actual orientation. The picks for the cores that had the ACP- T run proved challenging as the core was shot immediately and then the wait period was 10 minutes after the shot (normally ~5 minutes before the shot). In this case the pick was biased to the values immediately following the shot.

SRM

All split core archive sections were measured on the SRM (0, 5, 10, 20 mT AF demagnetization steps) at 2 cm intervals. Data was collected for all sections regardless of potential disturbances, gaps, etc. Since the sites were reported to have such low sedimentation rates (<10 m/Ma), it wasn't uncommon to see multiple reversals within any given section and thus it was not realistic just use the corrected declination data to verify
that the MOTs were functioning correctly.

CORE LINER SET SCREWS

For all oriented APC cores, the core liner is fixed relative to the core barrel by a set screw on the core barrel which is inserted into a small hole in the liner between the working-half lines. At least 40% of oriented core liners had evidence of significant set screw migrations to a 2nd location (many had multiple locations). As with X384 photos were taken to document most of these core liners and set screws holes. No interpretation is offered but the photos are located in ~\IODP_Share\PMag\Core_Orientation\Set_Screw_Photos .
COMMENTS AND ISSUES

SRM

The SRM field was trapped in port in Kristiansand, and the SRM profile looked acceptable, with values under 20 nT at the SQUIDs, but the background measurements were dominated by extreme drift and the SQUIDs appeared very unstable. A second field trap was attempted, with the shield and SQUIDs reaching higher temperatures, allowing the field to be re-trapped but also releasing any potential trapped flux in the SQUIDs. Again, the profile looked good, with even lower values, but still the drift was extremely large and the SQUIDs remained unstable. After several more attempts at re-trapping/flux release at higher and higher temperatures, it became apparent that the Fluxgate probe itself (cable as well) had acquired a strong magnetization (10^2 A/m2).
The Fluxgate probe and cable were demagnetized according to the instrument manual. Then the field was successfully re-trapped. At this point the SQUIDs were stable and the background drift was no longer an issue. The z axis SQUID still had significant noise (the final field trap was performed during transit) but everything was within acceptable levels of noise and drift.
The field was trapped and re-trapped at least 4 times, and more complete write up can be found in the Confluence Lab Notebooks (along with details on the Fluxgate demagnetization). Some general conclusions are the following:

1. 1. The fluxgate probes and cables can acquire a significant magnetization.
      1. AF demagnetization on the SRM (80 mT) remove most of what is possible to be removed.
      2. AF demagnetization on the D-2000 (up to 200 mT) did not demagnetize the probe and cable any further and the residual moment was still ~10^-2 A/m2.
      3. Fluxgate probes/cables should be stored alone in the mu-metal shield bin and since other components could magnetized them.
      4. The magnetization of the probe and cable are easily measure on the SRM by sending them through as a sample (SHLF) and ideally should be checked before trapping the field.
      5. A newly demagnetized probe will require the Fluxgate unit to have its zero-offset adjusted with the probe in a "zero-field" environment (according to the manual).
      6. The actually fluxgate probe x, y, and z pick up positions are not physically at the same locations and are not properly labeled on the probe (consult manual for actual positions).
   2. A clean SRM profile does not necessary mean that the trapped field is in fact low (in the case that the probe added a significant component to the net field) nor does it necessarily mean that the SQUIDs are stable.
   3. Better null field values can be achieved by:
      1. Positioning the probe in the middle of the tray away from the highly magnetized tray ends

1. 1. 1. Once the field is minimized on the Fluxgate at the 10 mOe continuing to the higher 1 mOe sensitivity is possible and will typically yield better results.
   2. The cold-head gradient currently seems consistently large and, in the future, should probably be adjusted prior to minimizing the individual axes (as stated in the SRM instrument manual for the initial step prior to minimizing the three axes).

After the field was successfully trapped, the X, Y, and Z demagnetization fields were measured with the hall probes. Peak demagnetization field where within reason (X: 2.5%, Y: 0.7%, and Z: 6.8%) with the actual field consistently higher than chosen field.
All COMs were randomly off on 2020-10-10. In order to get the COMs reset properly, all settings had to be completely deleted and then recreated. The formatting of the COMs setting on confluence was changed to make it easier to read and match what a user would actually see on the computer's control panel settings.
MagSpy was not working at the BOX and the developer worked with shore to re-instate a prior version of the IMS that now functions properly again.

MAGNETIC ORIENTATION TOOLS (MOTS)

After discovering the misalignment of one of the Keyed End-Seal Snubbers (KESS) on X384, likely the cause of years of problematic data, a protocol was needed for easy, accurate, and repeatable alignment of the KESSes. After some basic design work, prototype Mule Shoe and T-Bar shoe holders (for both Icefield and Flex-IT MOTs) were 3D printed and attached to an extruded aluminum slot rail to create an alignment jig.
Once satisfied with the functionality of the proto-type jig, the shoes were properly fabricated from aluminum billet on the CNC and then assembled into the final "MOT KESS alignment jig". A SOP was written for aligning both the Icefield and Flex-IT KESSes. Several IODP techs assisted aligning all of the KESSes while also vetting the SOP (located on Confluence under the Lab Notebooks).

A digital logbook was created for the MOTs that tracks basic orientation run data, but also tool type and number, KESS and pressure barrel numbers, and specific monitoring platform (e.g., which Palm Pilot). A separate log should be generated for each expedition and the blank is stored on
~\IODP_Share\Pmag\Core_Orientation. The paper is logbook is still used for quick notes and ease, but all data needs to be entered into the digital logs.

After many hours of tool use, it was noted that the AA batteries very still at 1.7-1.8 V (without load) and thus had many more runs in them. While investigating the Icefield specs for power consumption, it was noted that the tools are only rated to 3,500 m H2O while in the tool's pressure barrel (only 300m without) and we are using these tools at times in 5000 m H2O depth with standpipes exceeding 2800 PSI above that hydrostatic pressure. However, the tool and its pressure barrel are actually in another pressure barrel that is closed at sea level and thus never experience any elevated pressures at all.

KAPPABRIDGE

The Kappabridge was not actually used on this expedition, but was responsive after all computer software updates.

JR-6

The JR-6 was used to characterize Pmag Play Cube standards (see below) and appeared to be properly functioning. Comparisons of the magnetic moments measured on the SRM versus JR-6 were within ~15% of each other, with the JR-6 consistently higher. Differences in volume assumptions for the instruments' internal calculations may account for some or all of this, but since the samples were measured on the SRM as section taped to SHLF tray in various positions, imprecise placement is also likely to cause discrepancies as well.

D-2000 AF DEMAGNETIZER

The AF Demagnetizer was used to demagnetize (up to 200 mT) Pmag Play Cube standards (see below) and was properly functioning.

ACS IMPULSE MAGNETIZER

The IMS-10 and IMS-10-30 were tested to impart IRMs (<80mT) on Pmag Play Cube standards (see below) and were properly functioning.

THERMAL DEMAGNETIZER

The Thermal Demagnetizer was used at 120°C for several hours to dry new Pmag Play Cube standards (see below) and was properly functioning.

HASKRIS

The Haskris water was changed and the reservoir cleaned at BOX and EOX. The previous condensation
EXP 390C Technical Report
catchment system was redesigned to more efficiently capture all water dripping off of the heat exchange coils. Since a significant portion of the water spilling on the floor and evaporating is now being contained, the catchment bin fills
up very quickly and needs emptying around every 2- 3 (depending on relative humidity and ship roll and heave). A basic water sensor and circuit was designed to alert the technician when water needs to be emptied.

STANDARDS

The lab was lacking standards that could be run on both the SRM and the JR-6 for cross calibration, but also standards that could be magnetized and demagnetized. Samples were collected into J-cubes from two different sources of play core mud (Mud A: MA01-04, Mud B: MB-01-02, and a mixture of the two: MC01- 02). These samples were then dried out in the Thermal Demagnetizer at 120°C and the resulting voids were filled in with epoxy. The resulting suite of standards (referred to as Pmag Play Cubes) were then subjected to various IRMs (<80mT to avoid flux jumps on the SRM), measured on the SRM and JR-6, with AF demagnetization steps on the SRM (up to 80 mT) and on the D-2000 (up to 200 mT). The experiment was repeated to show that samples can be demagnetized and then restored to the previous magnetic state.
Obviously long-term alteration may be an issue, but on the shorter times scales the Pmag Play Cubes are standards that can be used repeatedly throughout the lab (including IRMs, ARMs, and AF demagnetization steps).

LAB COMPUTERS

Monthly software updates for all Pmag computers were completed on 21-10-2020 and again on 16-11-2020. Both times all COMs correctly mapped on SRM and functioned properly. The Kappabridge responded and appeared to be functioning proper, though a calibration was not attempted. JR-6 had COM issues initially both times but went away after the second computer restart. JR-6 calibration and empty sample holder corrections were both successful.

MUT UPLOADS

All SRM data was routinely uploaded to LIMS via MUT. Core Orientation data was more of a challenge due to matching the exact header and data format. The previous example file on confluence was not really helpful as it was just basic text with white space characters within header elements, between headers, and after lines, instead of comma separated values with carriage returns. A file from X384 was used as an example to get the exact format and is now link in the SRM user guide for future use.

DATA

All X390C data was backed up to Data1 and removed from local storage. All X384 SRM data was verifying to have been properly uploaded and then removed locally as well. Diagnostic data for all instruments (background measurements etc.) were organized in ~\Diagnostic_Data folders for SRM and Core orientation and further organized by expedition on local storage. The intent being to keep the instrument diagnostic data locally (non-sample/non-moratorium data) in case of future issues with data and or instrumentation.
CHEMISTRY LAB
Johanna Suhonen and Vincent Percuoco
SUMMARY

AMPULATOR
The ampulator was not used this expedition. It was turned on once to verify it is working properly.
BALANCES
There were no issues with the Cahn or Mettler balances.
A work light was installed at the Cahn balance station. A retractable arm was built for it to enable the light to be pushed completely out of the way if desired. More lighting was desperately needed, as the Cahn balance corner is very dark, and the light in question happened to be available onboard. It had recently been removed from the paleo lab. We have no spare bulbs for the light. Spare bulbs can also not be purchased, as they do not seem to exist, so a replacement light fixture will eventually become necessary. The replacement light can be installed on the existing retractable arm.
CARVER PRESSES
Due to the reoccurring oil leaks that seem to be caused by the unnecessary turning of the valve handles, the said handles were removed from all the AutoPak-operated presses. The handles were placed in a sample bag that is taped to the wall next to AutoPak #3. The valve handles can be put back in anytime should the desire arise to do so - use Loctite on the threads. The cap screws were also replaced with set screws to even further lessen the temptation to open these valves. The Carver presses are operated by the AutoPak hydraulic units under the counter. Other than placing the squeezer assembly onto the press, no further "above-counter" actions are ever required. The AutoPaks do all the work. To release pressure, press the red center button on the AutoPak.

CARY SPECTROPHOTOMETER
Upon starting up the software, an error code was received: E9329 Fatal chopper failure. The start button in
the software also had no green light. When "fill" was pressed on the spectrophotometer during a pre-run rinse cycle, the peristaltic pump did not start up. According to the software the instrument was offline. After opening up the instrument, a broken chopper motor belt was discovered inside. We did not have a spare belt, but a suitable o-ring was found, and the belt was replaced with the o-ring. Spare belts were ordered. CM9032 belt, chopper motor was added to AMS. See images of the procedure in the Chemistry Lab Notebook on Confluence.
While running the autosampler during both the first ammonium and phosphate analyses the A/S probe would collide with the edges of several vials, causing the analysis to hang up and requiring the autosampler to be restarted. We started new analyses using duplicates of running blanks for the instrument to zero to. After analysis we corrected the data by de-normalizing from the respective blanks and normalizing to the raw instrument baseline before analysis. This caused the intercepts of the calibration curves to be higher than normal, but ensured the data was not biased from using different blank corrections.
Long story short: make sure to use the numbered autosampler rack faceplates to hold the vials in position before starting an analysis. The racks themselves give too much leeway for the vials to slant.
COULOMETER
There were no issues to report with the Coulometer.
ELEMENTAL ANALYZER
The CHNS is working properly.
At the beginning of the expedition the active furnace was switched from the right to the left-hand furnace because its inner glass annulus is more intact than the right-hand furnace. The glass insert for the furnace thermocouple was checked and found to be fractured. It has not affected the furnaces heating or temperature setpoint stabilization. Changing furnaces did not change the 0.006 uV noise we have been seeing in the detector baseline for the past several expeditions. We will continue to use the left-hand furnace in the future, but the right-hand configuration can also be used.
We used glass inserts for the reactor tubes when doing our sample analysis. We found that the insert needs to be changed out when the sample count approaches ~90 samples. The sample residue stacks and keeps samples from entering the furnace hot zone, and biases subsequent check standards towards lower concentrations. After removing the glass insert, and performing a leak test, subsequent check standards were within tolerance. The reactor was used as is afterwards. We were able to run a total of 140 samples (~15 mg each) on one reactor tube this way and likely could have extended the run since the reactor copper metal was not totally oxidized.
FREEZE-DRYER
There are no issues to report with the freeze-dryer. It was turned on once and is working properly.
FUME HOODS
There were no issues with the fume hoods. Light bulbs were replaced in hoods #1 and #3 by taking the covers off from outside, atop the fume hood. The flow monitors were cleaned using compressed air to remove lint from the resistors.
GAS LINES/MANIFOLD
There were no issues with the gas lines/manifold.
NGA1/NGA2
Both NGA1 and NGA2 worked well.
Helium and nitrogen lines were reconfigured and a 3-way valve was installed for both NGA1 and NGA2. The valve enables us to run nitrogen through the columns instead of helium while the instrument is idle. This would save us a lot of helium when we have a layup or a long transit and the GCs are not being used. More investigation is required on the potential effects of the nitrogen generator N2 flow on the columns before implementing the procedure. For now, the valve should stay in the helium position.
We also experimented with running generator nitrogen as FID makeup gas instead of helium. The experiment was conducted on both NGAs. This resulted in a fluctuating unstable baseline > 100 pA with continuous approx. 1-minute-long "bumps" that could be caused by the cyclic nature of the nitrogen generation process. At the time of the experiment, the oxygen sensor was measuring a steady 4 ppm of oxygen in the generator nitrogen. UHP nitrogen from a bottle was also tested as FID makeup, and the baseline was perfectly flat, around 15 pA and looked just like the helium baseline (approx. 14 pA on both GCs). See screen captures of the different baselines in the Chemistry Lab Notebook under the NGAs on Confluence. The makeup gas flow was reverted back to helium.
HYDROGEN GENERATORS
There were no issues with the hydrogen generators.
IC
We had issues with contamination of the suppressor module on the IC during the first run. We are unsure if this was strictly due to the sample matrix or something else. The calibration curves generated from the first set of standards in the first run were linear and their slopes matched the slopes of calibrations from previous expeditions. The check standards gave really good reproducibility (+/- 2%) but the samples in this run were biased high by ~10%.
After the run, we replaced the ultrafiltration membrane and several inline filters, and switched out the MCS H2O air scrubber. We also cleaned out the suppressor with a cocktail of sulfuric acid, methanol, and acetone in water as specified in the Metrohm troubleshooting manual. The subsequent calibration was good and so we reran samples from U1556-U1557. All analytes behaved properly in the check standards except bromide, which decreased gradually from 100% to 85% recovery. We could not identify the cause of the low bromide so we rejected bromide values from those samples during upload. The rest of the cations and sulfur (as sulfate) accurately matched ICP values.
After this duplicate run we replaced the anions guard column, switched out the inline-filters, used new cation and anion solutions and ran samples from U1558 and U1559. Bromide values from U1559 were again poor.
We performed another deep clean on the suppressor and noticed that the pump pressure on the anions column was approaching 12 MPa when it usually is 8 MPa. We tracked it down to the anions guard column (which was only installed a week prior). We changed out the anions and cations guard columns, eluent inline
58
filters, the MSM inline filters and the air scrubber. We reran a calibration and several check standards at the end of the U1559 run. The calibration came out fine, 7 subsequent check standards gave good reproducibility for all analytes.
Metrohm mentions that the suppressor unit has a 7-8 year lifespan, so we will look into ordering a new one.
ICP
There were no issues to report with the ICP. Some peristaltic pump tubing was replaced before the first run.
MICROBIOLOGY
Under-cabinet lighting was installed in the microbiology area. The cold room door was fixed. It now closes on its own.
SALINITY
The calibration screws in the optical refractometers were replaced. They had started rusting and becoming stripped.
SRA
The previous tie-up crew had trouble with the FID igniting and staying lit. We experienced the same issues when PMing the instrument at the beginning of the expedition.
When the pedestal goes into purge position or into the sample inject position the SRA lights the FID glow plug. This added energy sink changes the total voltage supplied from the onboard power supply module located within the main SRA chassis. This voltage typically is 5.40 V DC (exactly) and if it sinks below that number the SRA's main control board will reset and cut communication with the PC. We would see a voltage reading of 5.37 V DC before the command to light the FID was sent. The glow plug would ignite, falter and then the system would reset.
We used a multimeter to read two power supply terminals on the main board and adjusted a single potentiometer on the power supply to get the voltage to 5.4 (turning a screw). The FID was working properly afterwards and we were able to get a stable calibration for the instrument.

Some additional indicators of this problem:

-If you keep the computer's Device Manager open, where the COM ports are listed, you will see the screen flash and refresh itself if the SRA communication is lost and reestablished. This coincides with the loss in gas flow.
-The FID hydrogen gas flow is set at 100 ml/min and verified with our Agilent flow meter. When the FID is correctly lit, the hydrogen generator display will usually list a gas flowrate of ~90-100 mL/min. If the instrument quickly resets itself, it cuts the hydrogen flow and the generator display will read about 35 ml/min.
PIPETTORS
There were no issues with pipettors.
TITRATIONS

ALKALINITY

There are no issues to report with the Alkalinity Titrator. A note has been made in the confluence lab notebook about unplugging the probe's gray side-hole plug (near the top of the probe where the cable attaches) so that the inner reference electrolyte is exposed to atmosphere during measurements. This allows the electrolyte hydrostatic pressure to equilibrate and ensures proper flow of fluid through the probe tip side- hole. With the plug unplugged the pH equilibration takes ~30 sec, when the plug is in it can take several minutes.

CHLORIDE

A new program to perform chloride titrations was developed during the expedition. The program is based off the Alkalinity Titrator program using Labview and the dynamics are similar to the previous ClTitrator program in that it specifies the instrument parameters, measurement type and endpoint type to the Metrohm 875 DMP Titrino using serial commands. The Titrino performs the titration autonomously and uses its onboard algorithms to determine the equivalence point at which all chloride has been titrated. The program constantly pings the Titrino for its equivalence endpoint, once it is populated the program collects the endpoint and determines the chlorinity of the samples using the endpoint, silver nitrate titrant molarity, and sample volume. The data is exported as a csv file to a directory.
There are a few items to correct in the program before deploying it for use:

1. There are a few libraries it is referencing from the Alkalinity Directory which need to be moved the chloride directory.
2. The audio file which plays when the measurement finishes does not play correctly. This is likely due to some incompatibility with the Labview environment used for development (Labview 2014) and audio drivers.
3. A MUT module should be created to upload the data exported in csv format. The datafile is similar to the data fields in the alkalinity data export, so the capabilities of the MUT Alkalinity module may able to be scavenged and employed for chlorinity.

TOC
The TOC was not used.
WATER SYSTEM
There were no issues with the water system until the end of the expedition. A crackling sound was coming from the line that leaves the pump and enters Feed1 of the first RO Membrane cartridge. Jurie found there to be a kink in the tubing, which caused it to rattle against the water system housing and against the pump. The tubing was replaced and the pump mounting screws were tightened.
We also noticed air bubbles going through several of the system lines. We traced these down to the base connection of the pretreatment prefilter cartridge. The water feed to this connection was clear of bubbles but the water out, which goes to the MPS cartridge, had steady streams of air. We removed the base snap adaptor and cleaned it out with compressed air. After reconnecting the adaptor and the cartridge, we allowed the
system to flush. It does not have air flow through the lines now.
During the tie-up the system should be flushed once a week by running water from the DI tank and both nanopure outlets for 5 minutes. Also, flush faucets (both hot and cold) that aren't frequently used, especially the one in the cold room. The cold room sink only has cold water plumbed to it.
AMI NITROGEN GAS O2 SENSOR
At the beginning of the expedition we monitored shipboard nitrogen values for oxygen concentrations. We found that the over the course of three days oxygen would sporadically increase from 40 to 500 ppm. We passed UHP nitrogen through the sensor to verify the sensor was working properly. The values were less than 5 ppm. When we reconnected the shipboard nitrogen values stabilized below 50 ppm for several days, and were below 25 ppm for the majority of the expedition.


We attempted to port in the O2 sensor readings to the current Labview gas monitoring software using a NI DAQ Chassis and DAQ ethernet module, however NI-Max did not recognize the setup as valid and couldn't communicate through it. We are ordering a different DAQ module before continuing.
MISC
The Confluence Chemistry Lab Notebook was redesigned. Each instrument was separated onto its own page. The new design is clear and easy to navigate. No information from the old notebook was omitted in the redesign. The old notebook page does still exist and can be accessed through the search feature on Confluence. It is called "OLD Chemistry Laboratory Notebook". No edits should be made to the old notebook.
Zebra Designer software was installed onto the chem tech computer. We currently only have the 30-day free trial, but the purchase of Zebra Designer Pro has been requested. It is an excellent tool for printing custom
labels on Zebra printers. Label formats and databases were created for fast and efficient printing of clear
easy-to-read labels for IC, ICP and spectrophotometer calibration and check standards. These can be found in "LABELS" folder on desktop. To print, open one of the label files, for instance "ICP IAPSO label.nlbl" and hit Ctrl-P for printing. Please do not modify the label format. Should different standard concentrations become necessary to add, the Excel database files can be modified. See chem lab notebook on Confluence for what these labels look like.
A magnet was installed to hold the chemical fridge door open.
The MBIO incubators were defrosted. All the chemicals were loaded into the AFT incubator, and the other two were turned off. This will lessen the time and effort continuously spent defrosting them. The two FWD incubators should be able to stay off until we actually have a real MBIO expedition.
A Chemistry Lab PMS Checklist was created on Confluence. It can be found under "Info for Chemistry Technicians" in the Chemistry Laboratory Notebook on Confluence. It should be used to log any maintenance activities.
GEOCHEMISTS
There were no sailing geochemists.
MICROBIOLOGISTS
There were no sailing microbiologists.
XRAY LAB
Jenna Patten
SUMMARY

• Reentry cones – no science party
• All the instruments restarted
• Aeries sample arm errors continued. Temporary fix was connected to laptop and switched into manual mode until a service call in port.
• New Haskris installed
• Key might have start to fail
• New MM400 grinder
• 133 Carb samples prepped in MM400 grinder
• One agate jar chipped, sent off for repair

TOTAL SAMPLES: 659
XRD: 659
ICP: Processed 0
pXRF: 0

XRD: MALVERN AND BRUKER
Malvern AERIS Benchtop

• Aeris ran fine for the first few weeks during transit, about 150 samples.
• Motion control arm error occurred the first 24-hour period when no samples were analyzed. The Aeris was turned on/off, the error cleared and ran for a about 3 days without further issue.

Again, motion control error occurred when samples had not been analyzed in 18+ hour window. The Aeris needed to be restarted 2-3 times to clear error. Motion control error happened again 2 days later and, became a daily error for about 4 more days. By the end of the week the sample arm would only initialize and move down the track to sample position 1. When the sample arm reached the sample one location the arm would abruptly stop, while making a large clunk sound. The sample arm would go up and down but would no longer move back to the home position after. I VERY gently manually pushed the sample handler back to it's home position, turned the Aeris on/off and the error cleared.
The sample arm started to work properly and had no further issues that day. The next day again, sample arm error, on/off and manually moved the arm same as the previous day but, the problem persisted and the error did not clear. I removed the front cover of the sample arm to ensure there were no abstractions on the track.

• We Contacted Malvern's service team. Working with our MCSs we were able to connect the Aeris to a laptop and through it connect the Aeris online. Once online the Malvern service team was able to remote in and change the Aeris to a manual setting. The Aeris can now run one sample at time, by- passing the sample arm. I have run about 130 samples in the manual mode and have not had any other problems with the Aeris.
• A service call is currently being set up for Cape Town port call to replace the sample arm. The service call is tentatively planned for the 1st or 2nd week of January 2021 pending end of year production of sample arms. the point of contact for the South Africa branch is Johan Lubbe email:

johan.lubbe@panalytical.com. The USA service manager that is overseeing our case is Eric Fleury
+1 (971)338-7700 email: eric.fleury@malvernpanalytical.com
*Note: The sample arm errors only occur when the Aeris is idle. I have a feeling that the problem might be a relay or circuit board issue rather than a simple mechanical failure.

• Cooling water was "low" after approximately 100 samples, It will probably need to be filled in the middle and end of expeditions.
• All new zero background disc for Aeris were scanned for base background. The scans are in XRD data QAQC file. All zero back ground disc produced essentially identical scans (See scan below). All new zero back ground disc for the Aeris were scanned 5-120 2 Theta. All of the disc had almost identical to the scan above.

Figure 1. All new zero back ground disc for the Aeris were scanned 5-120 2 Theta. All of the disc had almost identical to the scan above.
BRUKER D4
Bruker started up and ran well after new Haskris was installed. No Zinc correction was needed. Bruker ran well and X-Rays stayed on through the expedition. X-ray tube conditionings were done when the x-rays were off more than 24 hours. I created a maintenance log in confluence to help keep track of the X-ray tubes wear. Bruker X-Ray Tube Conditioning Log Bruker sample holders were moved to drawer labeled "Sample holders and Mettler Toledo"
Box was made to hold all of Aeris sample holders and disc etc. See Figure 2

Figure 2. Box for all Aeris sample holders and preparation tools



HASKRIS
New Haskirs was installed with the help of the ET October 6th. The new Haskris is wider than the older one, so new holes were drilled into the metal floor mount in order to secure the Haskris to the floor. The sound box does not fit over the new Haskris, but the new haskris is much quitter. We may want to make another sound box in the future just to help lower ambient noise in the small lab. Temperature is set to 69 degrees and has held consistent while the D4 is actively running or not. The flow rate shown on D4 tools is 6.53 (L/min). I have created maintenance logs in confluence to help keep track of chill water flow rate Bruker Water Flow Log and, Haskris Maintenance Log for all other maintenance.
In the last 2 weeks of the exp the Haskris started making a louder noise. ET thinks the key may have started to fail already.
Haskris was drained and chill water lines closed for anticipated tie up.
MM400 GRINDER
New Retsch MM400 grinder arrived. There are 4 agate lined 10mL vials and 4 agate agitation balls. Filled requisition for 4 additional 12mm agate grinding balls as replacements.
While grinding the last samples from U1559A one of the grinding jars agate was broken inside upon opening (Figure 5). The sediment was soft, freeze dried and primarily carbonates. The grinder was run for 12 min at
28Hz/min with one agate milling ball just as all the previous samples. None of the grinding jars have been dropped. All jars have been cleaned with DI water and isopropyl alcohol. It is unknown what cause the agate to break. I suspect it was just a weak point in the stone. The jar and lid are being shipped back for repair. The grinding ball is staying onboard with the remaining jars and milling balls. See Figure 3 and 4 below.

Figure 3. New MM400 Ball grinder by Retsch

Figure 4. Four 10 mL agate grinding jars and agate grinding balls
.

Figure 5. Agate grinding jar that broke.
BEADMAKER
The beadmaker was not used. ICP preparation beakers were cleaned overnight in nitric bath.
FREEZE DRYER
Ran for all XRD and CARB samples. No issues, re-lubricated the bell O-ring. Motor oil still looked good, so it was not replaced. I created a maintenance log in confluence to help keep track of oil changes Freeze Dryer Oil Change Log.
XRD SAFE
Safe kept flashing "b-Lock" when code was entered to lock the safe. Batteries were replaced but, that was not the problem. The back of the door to the safe was removed. The code was entered and the mechanism that moves the bolts was manually pushed into the lock position (while the door was opened). The bolts began to work after that. The code was entered several times moving the locking device back and forth between lock - unlock. I have had no problems with it since.
THIN SECTION LAB
Luan Heywood
SUMMARY
42 thin sections for practice, small format. 7 polished grain mounts. 0 requests.
LOGITECH LP-50
Generally ran well, with the exception that the retaining ring and PLJ2 jig did not generally spin even when slides/billets had been polished for a long period of time. Maintenance was performed on the PLJ2 jigs and the abrasive auto-feed cylinders. A new front panel was placed on order, since the LP-50 backlight has been dead for a few expeditions now. This should be swapped out with more specific instructions from Logitech when the part arrives.
During end of expedition cleaning, water overflowed the drip tray and got into the internal cavity. The casing was removed briefly and upon inspection the internal cavity was found to be dry but a little bit dusty. It was reassembled without trouble. Deep cleaning the internal cavity was not completed at this time, under the thought that this could occur during the more extensive disassembly process that will occur when the front panel is replaced.

PLJ2 JIGS

During this expedition, Luan Heywood (Thin Section technician) and Jurie Kotze (ET) performed extensive maintenance and preventative maintenance on the PLJ2 jigs. At the beginning of the expedition, two of the three jigs were found with pistons frozen in the piston sleeve (jigs with serial number 64 and 322). This was extracted via ultrasonicating the two frozen parts in warm water for a period of hours (4-8 hours) before squirting WD40 into the mating surface and applying pressure. PLJ2 jig serial number 64 had red chip seal filling gouges in the metal on the internal surface. Upon cleaning and reassembly, the jigs were found to have good parallelism indicating that the pistons are not overly worn.
Both of the frozen jigs (serial number 64 and 322) had significant unevenness on the chuckface, and PLJ2 Jig 64 had this corrected by lapping the chuckface on the LP-50 using SiC slurry for a period of hours. Upon reconditioning, one of the jigs (serial number 322) was not able to hold a vacuum which will be troubleshooted at a later time.
Logitech informed us that all three of our jigs are over thirty years old and made with imperial units, and no longer serviceable by Logitech (which has since switched to metric units). Jason Jex, North America sales representative, gave a quote for a new PLJ2 jig as follows: 1PLJ2: PLJ2c Precision Lapping Jig to accept 6 slides 28 x 48mm or 2 slides 25 x 75mm plus 3 slides 28 x 48mm or 1 slide 50 x 75mm plus 3 slides 28 x 48mm - $24,946.00. Although we currently have two functioning jigs (Jig 64 and 287), Jig 64 is in significant disrepair (rust in the internal cavity, broken plastic parts) and Luan and Susan Boehm (Thin Section technicians) recommend that a new one should be considered for purchase.

ABRASIVE CYLINDER MAINTENANCE

At the beginning of the expedition, abrasive cylinders were disassembled and cleaned. Using a bottle brush bent into a J-shape, internal discoloration (mold?) was able to be cleaned. Susan (Thin Section technician) and John McCrossan, Logitech Process Engineer, sent helpful illustrated instructions for how to correctly screw the end-cap unit onto the cylinder, which solved a problem where the cylinder was not able to be adjusted down to lower drip rates.
This expedition one of the abrasive cylinders was used with 600 grit Al slurry, while the other one was used with 600 grit SiC slurry. SiC slurry is the preferred slurry for harder materials (including lapping down the uneven PLJ2 chuckface), since SiC has a Mohs hardness of 9 while Al has a Mohs hardness of 2.75.
LOGITECH PM-5
This was only used briefly for a few thin sections and for maintenance on the polishing shoes. On Expedition 384 it was reported that the shoes were leaving scratches on the bottom of slides. Slide shoes were disassembled and ultrasonicated, then the bottom surface of the shoes were polished (with sides removed).
Jason Jex gave a quote for new PM-5 shoes: WG20-1700: Slide Holder Assembly to suit 26 x 46mm and 28 x 48mm slides (WG2) (each) - $83.00.
BUEHLER PETROTHIN
Partway through the expedition, the Welch pump started spitting oil out of the filter due to water in the oil, so pump was disassembled by ET Jurie and Luan, scrubbed of rust, oil replaced, and reassembled. Light misting of oil from the filter persisted afterwards, especially for the first few minutes after power cycling. However, since the internal cavity was observed to be clean and dry, further action was not taken. New clear Tygone tubing was used to replace the black tubing in between the Buehler PetroThin, Logitech VS-2 water trap, and Welch vacuum pump. The new tubing should allow easier visual observation of water in the vacuum system. Some incursion of water into the VS-2 water trap is considered a necessary hazard of regular PetroThin usage, so if the problem persists and the vacuum pump is further damaged, in the future a new water-trap set- up should be considered. If the problem is identified to be the older VS-2 model and a new VS-2 model is desired, Jason Jex gave the following quotes: 1VS22: VS2 Vacuum Unit (free standing or wall mounted) for use with PM5 and GTS1 Saws (110v / 50-60Hz) - $9,511.00; 1VS22 (no pump): $3,969.00.
Prior to this expedition, the PetroThin ventilation system was removed in order to ventilate the Beadmaker, so ventilation and/or PPE for the PetroThin when using ethylene glycol needs to be reconsidered. This is especially important on expeditions where many samples are being prepared using sprayed ethylene glycol as a PetroThin lubricant. Aerosolized ethylene glycol typically will only cause irritation to the mucous membranes, throat and upper respiratory system, and it is unlikely that a toxic dose could be incurred via inhalation (see Hodgman et al., 1997, Journal of Toxicology: Clinical Toxicology). If used frequently, it is recommended that the Thin Section tech wear gloves, safety goggles and consider wearing a respirator to avoid skin exposure, eye exposure or inhalation.
GRAIN MOUNT PROCEDURE
Equipment was purchased for the preparation of grain mounts, since grain mounts will likely become a commonplace method of sample preparation for the SEM-EDS. Grain mounts should be prepared using low
EXP 390C Technical Report
temperature heat-cured Epotek epoxy in the blue silicone Buehler molds, with an initial grinding/polishing performed on the Buehler lap wheel using the coarse and 600 grit polishing pads, then a polishing process using 6 um, 3 um and 1 um diamond paste/powder polishing steps, using figure 8 hand-polishing on separate Buehler microcloth polishing pads and ultrasonicating the grain mounts in DI water in between steps. On a future expedition, an illustrated guide will be created.
Note on ordering: if the Buehler microcloth polishing pads for grain mount polishing are reordered (TS1020; this is separate from Buehler Carbimet abrasive disks and Kempad polishing pads), they should be ordered in 8" instead of 12"; however the same polishing pads can be used repeatedly for e.g. 6 um diamond paste polishing until visibly worn or contaminated. For method development, MetaDi diamond paste (TS1021, TS1022) was ordered from Buehler, however some of these products are duplicative of other diamond abrasives that are regularly ordered for the thin section lab. This should be assessed at a future time, to inform which products should be regularly ordered for the Thin Section lab.
SOFT SEDIMENT THIN SECTION PROCEDURE
Extensive method testing was performed during this expedition in order to develop a procedure for preparing sediment thin sections, since full acetone-water replacement procedures are not feasible for shipboard sample preparation. The full procedure is available on the Confluence Thin Section lab notebook page for review by Susan (Thin Section technician) before finalization, however the short version is as follows: wet sediment is freeze dried, then fully impregnated with Petropoxy 54 epoxy for 12-24 hours in a non-plastic mold. Billet is high temperature heat-cured, before surface to be sectioned is dry sanded using sandpaper. This surface is low temperature heat-bonded to a frosted slide using abundant Epotek epoxy, before careful sectioning as a normal, albeit delicate, thin section. It is difficult to get a perfectly parallel bond, so scientists should be encouraged to accept thin sections that are thicker than 30 um to avoid patchiness.
LAB CONSUMABLES
A very old container of Logitech-branded degreaser 1,1,1 trichloroethane was found in the Thin Section lab chemical cabinet. This chemical has been banned for decades for its human and environmental toxicity. The situation was referred to LO/ALOs for proper chemical disposal, which may occur at the X390R portcall or later. This serves as a reminder to thin section technicians to check chemicals and compounds within the lab before use, especially things that appear be old.
During the expedition, the IODP Business Coordinator John Miller emailed that Buehler/NCI (the authorized dealer for Texas) no longer supplies 5 lb containers of 600 grit aluminum oxide (TS1004). Logitech 9 micron calcinated aluminum oxide powder was identified as a replacement, however this abrasive comes in 5 kg containers, rather than 5 lbs. Reorder/Restock level in AMS was updated from Reorder at 4 (total 10 kg) and Restock to 5 (total 12.5 kg), to reflect the larger container size. AMS currently has Reorder/Restock levels set at Reorder at 2 (total 10 kg) and Restock to 3 (total 15 kg). As of X390C, the lab contains two 5 lb containers of the Buehler branded abrasive, which should be counted as PC=1 to reflect the new size in AMS. 1-2 additional containers of Logitech abrasive are on order.
Meanwhile, if the lab runs low on aluminum oxide abrasive before the restock, 600 grit SiC abrasive (not in AMS, however the lab has about 12 kg currently in storage) can be used on medium to hard rocks. In the future, we should consider stocking SiC abrasive as a regular item in AMS, as SiC abrasive is the
recommended abrasive for standard geological thin sectioning on Logitech instruments (aluminum oxide is recommended for softer materials).
All Epotek 301 epoxy in lab is currently expired, but will be ordered in time for the upcoming hard-rock expedition X395 (June 6, 2020 portcall). A new epoxy (Petropoxy 54), was tested for use with soft-sediment and hard rock thin sections. Petropoxy was found to be a great alternative for Epotek 301 for some purposes due to its quick bond time and long pot time (bonding billets to slides, bonding coverslips onto slides, impregnating sediment), however it exhibits a high degree of thermal expansion, so should be used sparingly so that slides do not break upon cooling.
A few items on the Check-Out sheet were not able to be located by Luan: Apex Diamond Grinding Disks TS1007, TS1008, TS1009, and Lakeside Thermoplastic Cement TS0096, and it was requested that Susan help with locating them.
CROSS-TRAINING
Jenna Patten (XRD Technician) was briefly cross-trained on LP-50 operation and maintenance. This builds on cross-training she has done on X379T and X384.
DOWNHOLE LOGGING (AKA THE CTD REPORT)
Eric Moortgat
SUMMARY
This was the inaugural Expedition for CTD deployments.
The instrument is easy to setup, attach to the VIT frame and download data from. The SeaCast software is very intuitive with minimal interaction needed to setup and export data.
SYSTEM STATUS
CTD

ITEMS RECEIVED
390P

• Locknuts, super-corrosion resistant, 316 SS, nylon-insert. 1/2" - 13 thread (DH0004). 2 each - 10/bag.
• Locknuts, super-corrosion resistant, 316 SS, nylon-insert. 3/8" - 13 thread. 1 each - 25/bag. 90715A165.
• Safety-pin shackle, 316 SS. 1/4" thick. 2 each.

• CT-Xchange o-ring (OD2116) ; PC = 0.
• P-Xchange o-ring (OD2015) ; PC = 0.
• Micro 8 male black shorting plug with red power indicator cap ; 2 each in REQ # 6.
• Locking sleeve ; 3 each in REQ # 6.

METHODS AND MANUAL CHANGES

• CTD SOP was updated with photos and relevant information after the first deployment was made. The SOP will still be a work in progress as we become familiar with the instrument and streamline the process/protocols.
• Raw data/logsheets were copied to DATA1\31.0 CTD for backup to the shore.
• The first two casts were done at 1 Hz and the last one at 2 Hz.

Eric Moortgat
SUMMARY
Unfortunately, this Expedition was highlighted by the continued troubles with our bathymetric 3.5 kHz SyQwest array. Fortunately, the 12 kHz transducer worked flawlessly.
We were able to deploy the magnetics towfish in international waters and acquire a good data set.

SYSTEM STATUS:

NAVIGATION

WinFrog1 was used as the primary WinFrog navigation computer. WinFrog 2 was briefly used for navigation during the rebuild of WinFrog1 (see below).

• The newly acquired Trimble GPS (SPS356) was not immediately installed in the place of the older/troublesome SPS351. I wanted to attempt to troubleshoot the SPS351's loss of connection to WinFrog (also see bullet below). After leaving Kristiansand, WinFrog did not loose connection with the SPS351 for approximately two weeks. Then it completely lost connection. The SPS356 was installed (19 Oct 2020) and configured using the old Trimble's network configuration. There have been no issues with the new GPS. The new antenna was not installed on the helideck.
• (15 Oct 2020) WinFrog software crashed after an event was stopped. The software would not restart. After many attempts to troubleshoot, the PC was restored from a backup (two days prior). However, WinFrog would not load any saved configurations so all of the devices had to be manually re-entered.
• WinFrog would occasionally display chaotic values for COG and speed. The software was re-started and everything appeared to be fine until the next random occurrence. No solution has been found and the occurrence is very random and intermittent.
• Upon boarding the vessel, I was planning to update the Trimble SPS351's firmware, per the suggestion of Allterra, our Trimble vendor in Houston. This was an attempt to troubleshoot its intermittent loss of connection to WinFrog. The old firmware was 4.17 8/6/2010 and the new one is

48.01. However, the firmware would not update unless we purchased a warranty reinstatement plan ($600) for the unit. It was decided to not waste the money.

BATHYMETRY

WinFrog2 was used as the primary system for acquiring bathymetry data.

See the LO's sonar dome report for all the goings on with the sonar dome (3.5 kHz array).

• (03 Dec 2020) The 3.5 kHz array is functioning as it should.
• (01 Nov 2020) SEGY files not being automatically created by BATHY software. Creating from ODC files.
• SyQwest still has horrible customer service.

MAGNETICS

WinFrog2 was used as the primary system for acquiring towfish magnetics data.

• (03 Dec 2020) All indicators show that the SeaSpy magnetometer is working perfectly.
• (28 Nov 2020) Towfish magnetomer was deployed (L6T). Constant errors that SYNC was lost and there was a loss of communications with the towfish. (29 Nov 2020) We decided to bring in the cable/towfish around 04h00. The cable was still twisted near the end but the last 50 m or so, the cable became limp in the water. We were sure that the towfish was gone. But it appeared in our view and was successfully brought onboard. The last 50 - 60 m appears to have completely lost tensile strength with its protective shielding. We are pretty sure that if left out in the water it would have snapped and the towfish would have been lost. We cut off 72.54 m of cable and are in the process of re-

terminating. After re-termination and two deployments, the signal remains very steady, voltage in steady @ 47.9 V. First deployment, 12 wraps (~ 23 m) were left on the drum which will give a length of ~ 404 m deployed. The second deployment, 6 wraps (~ 12 m) were left on the drum which gives a length of ~ 415 m deployed. I would not leave less than six wraps on the drum.

• (27 Oct 2020) Upon bringing in the towfish (at the end of L3T), the last 100-150 m of tow-cable appeared to wind upon itself. See figure 1. Might have been the result of another vessel approaching the towfish (IODP staff observed a large container ship passing on starboard side). The top of the towfish/cone could have been hit by the vessel and dragged, forcing the fish to spin, which would hence cause the tow cable to spin as well (see figures 2/3). During L5T, there was no degradation in the signal during this occurrence and it did not appear to affect the towfish in any perceivable way.

Figure 1 : Damage to the tow cable

Figure 2 : Damage to the bend restrictorFigure 3 : Damage to the bend restrictor

• • 238 ft = 72.5 m of towed cable was cut off. New termination was installed. We now leave about 6 wraps of cable on the drum, which measure to be 3.3m (130") per wrap = 19.8 m on the drum
  • The total wraps are 132 = 435.6m (total cable length)

¿ The payout is 435.6 – 19.8 = 415.8 m

• • The winch's level-wind is not correctly operating w/out manual assistance. Please see the ET's Tech report for the details. A new hall effect sensor is on order and will be installed during 395P.

ITEMS RECEIVED:
390P

• Trimble SPS356. IODP tag # 53935. Installed in UWGL as AFT Trimble GPS. Replaces SPS351 that is being sent back to shore. The new antennae was not installed and is in a drawer in the lab.

ITEMS ORDERED :

• UW0002 : SeaSpy cable termination kit.
• Hall effect sensor (1 each) for level-wind. Forum Energy Technologies P/N 0000282-02, Dynacon P/N DY97001-072-04.
• McMaster-Carr oil-resistant Buna-N o-ring for sonar dome flange. P/N 9452K449, dash # 455, width 0.275", ID 12.975", OD 13.525", durometer 70A (medium). Five packs of 2 each.
• Knudsen Engineering EchoSIM signal simulator, D229-05819-Rev1.00.
• Trimble SPS356. IODP tag # 53949. This unit will replace the SPS351 in BLO. The SPS351 will act as the spare.

CRITICAL MAINTENANCE :

• SyQwest boards/NetBurner being sent back for repair/troubleshooting/trash

• A00107-2 (S/N 5920)
• A00108-1 (S/N 5921)

• Level-wind (hall effect) sensor has been purchased and when arrives on the vessel the troubleshooting will continue.

METHODS AND MANUAL CHANGES :

• After WinFrog1 was restored from a backup, the UW inter-computer cabling diagram had to be redone (see figure 2).

Figure 4 : UW inter-computer cabling



SONAR DOME
Chieh Peng and Etieene Claassen
REPORT_1 IN PORT_KRISTIANSAND
After I boarded the ship on October 2, I had a meeting with the SIEM crew to determine what they had done with Beth and Lisa.
The acting Electrical Supervisor (Nico) gave me more knowledge of what they thought and what they did so far, with Beth. To my surprise, Nico informed me that the problem that we are seeing with our transducers, they are seeing on their sonar as well; a weak return signal. This made me believe that there is more to our problem that original I thought.
We know from what Nico told me is that we have some signal, but it is weak, and that they have a similar problem.
I worked with the Captain and the Chief Engineer to open the hatch and to first hand check the connectors and take measurements. At first, we had bad weather and the Captain was concerned that if we opened the hatch and the weather got worse, what then. So for the first two days we waited.
On October 4 we pressurized the hatch and it held pressure. As I climbed down below, I noticed that one of the cables had been stepped on. This most likely occurred when they painted the inside. We opened the hatch to look at the connector. At first, we thought that the reason they had a similar problem is that the space could be flooded, and that the connectors are submerged in salt water. Although they are designed to work in water, they are old and that could cause a problem. But the hatch was dry and the connectors were moisture free. No connectors were loose, and the inside had some oil in it. That was from being sprayed, before it was reconnected, in Subic.
I removed the connectors one by one and took some measurements. Nothing appeared to be out of the ordinary. The measurement they got at the junction box and the measurement that I got at the connectors going down to the dome, were similar:

1. 1. kHz 3.7 ohm 12 kHz 4.1 ohm

and the bride had 1.1 ohm
All the cables have been tested from aft to forward. No cables were damage or have a loose connector.
What we should be doing in the future is to remove the sonar dome and inspect the junction box in the inside. If all the connectors and cables are in good order it must be in the sonar dome.
We recommend that when we have a tie-up, the sonar dome is removed for inspection. At the same time, replace the hatch. The hatch is rusted and the last time we worked on it in Victoria we had problems with the tread on the plate for the connectors and on the photos, you can clearly see rust accumulating around the treads.
We also must build some form of protection over the connectors to insure cables are not damaged in the future.


Cables going through the plate, top cable damage.



SUMMARY OF ISSUE ENCOUNTERED

• • • During EXP384, 3.5kHz was ran with no issues at power levels below -6 dB. When output power levels are increased to -6 or 0 dB the signal becomes extremely faint and erratic or lost altogether.
    • During EXP390C transit, 3.5 kHz was turned on with no issue initially at full power (0 dB). Within 24 hours, the signal received got weaker and weaker. Gain was increased from 6 to 48 dB to finally nothing was received. No chirp was heard with full power on. Various power setting, -6, -12, and -18 was tried with same result, no chirp and no signal.

TROUBLE SHOOTING PERFORMED

SUMMARIZED BETWEEN EXP384 AND 390C

• Chirp coming from the amplifier unit in UW sounds as loud as usual and scales with the power setting properly.
• Cables from the unit in UW to junction box in Fwd Thyrig room tested for continuity and passed. Megger test was also completed and passed on each cable.
• When testing the cables from the junction box down to the transducers the tests failed indicating that there is an issue and possible short. The values for these tests can be found in EXP384 tech report
• These cables were tested again after opening the floor and top hatch. Tests were conducted from the dry side of the O'brien connections up to the junction box with the same poor results.
• LPA-10kV A Power Module was removed, cleaned, and re-seated with no improvement. The spare module was also cleaned and tested with seemingly no difference.
• The cover of the lower unit was removed to inspect the internals. Everything was clean and dust free. The spare boards were exchanged with the existing boards with no change.

• Existing Syqwest A/D boards are A00107 (S/N 6209) & A00108 (S/N 6210). We do not know with 100% confidence that these boards are correctly working.
• The spare SyQwest A/D boards were installed and are not working : A00107 (S/N 5920) & A00108 (S/N 5921)
• Forward Thyrig room hatch was opened during 390P tieup, after Etienne came onboard. He removed the connectors, inspected, and tested each one to received similar results 3.5 kHz 3.7 ohm, 12 kHz 4.1 ohm, and the bride had 1.1 ohm.
• The cable going into the top plate of the lower hatch looks as if it's been stepped on and the plates itself is rusty around the connection port on the dome side.
• After consulting with Knudsen on Dec 1 regarding the connection and usage of the tool ECHOSIM, the connector on J-2 cable was checked. The connector on the cable side is suspected of being open and arcing. Etienne insulated the 3 wires together with electrical tape, once it is re-connected back to LPT, we received 3.5kHz signal, and have been consistent for over 36 hours in deep water.
• The wires in J-2 connector will be soldered and re-test before arriving Cape Town.
• A Knudsen ECHOSIM tool is purchased and sent to Cape Town. Once we received this tool, we will perform the transducer test as planned

DOME REMOVAL PREPARATION

• Workscope for removing the dome under wet condition is written up and submitted to shore for review.
• It is also uploaded in Confluence under Lab Notebook/Underway/Sonar Dome
• All necessary parts and equipment are inventoried and located, except the dome neck o-ring, which is coming in the air freight
• A tugger is located on the Poop deck from Engine room. Arrangement has been made to borrow this tugger for wet removal, and can be re-located to the Core deck under the life boats

ELECTRONIC INSTRUMENTATION SPECIALISTS

Jurie Kotze & Etienne Claassen

SUMMARY
Sonar Dome Repair & Service scheduled for Cape Town Tie-Up. No return signal from 3.5KHz Transducer Array - Junction Box flooded or possible Transducer faults.
Replaced all the small 22" Tv's throughout the labs, Schlumberger Office, Upper Tween & User room with new Samsung 32" units with swivel brackets. 17 units in Total.
Hall effect sensor on levelwind causing issues, so replacement sensors has been ordered for a replacement. Unit currently operating on hand controls only.
All CREE Emergency Light batteries are due for 2-yearly replacement. Batteries have been ordered. Assisted with handling and processing cores.
Ran APCT-3 Temp measurements at all sites. Tool #1858002C's Temp probe broke off inside the shoe and will be sent for repairs, along with the shoe.



ITEMS RECEIVED
3 x APCT-3 Tools Returned from repairs - #1858031C, #1858032C, #1858041C.
ITEMS ORDERED
2 x Levelwind Hall effect Sensor.
1 x Ultra-Machinable 360 Brass Rod, 3" Diameter - 1ft length. (UTS Material Stock) 23 x Battery pack for CREE Emergency lights.

1. x Gallon bottle of CNC Mist lubricant.

1. x Heater elements for broken hand roller sealer. 1 x 18V Cordless Impact Driver Kit for ET Shop. Gym Entertainment System Upgrade:

1 x Samsung - 55" Class Q70T Series LED 4K UHD Smart Tizen TV
1 x Sony - 725W 5.2-Ch. Hi-Res 4K Ultra HD A/V Home Theater Receiver - Black
1 x Sony - Streaming Audio Wi-Fi Built-In Blu-ray Player - Black
1 x Rocketfish™ - Tilting TV Wall Mount for Most 32"-70" TVs - Black
1 x Rocketfish™ - 2-Output HDMI Splitter with 4K and HDR Pass-Through - Black 1 x Rocketfish™ - 8' 4K UltraHD/HDR In-Wall Rated HDMI Cable - Black
1 x Rocketfish™ - 24' 4K UltraHD/HDR In-Wall Rated HDMI Cable - Black
ITEMS TO BE SENT BACK
1 x APCT-3 Tools for repairs of broken Probe, and Battery replacement - #1858002C. 1 x APCT-3 Shoe for removal of broken off Temp Probe inside.
CORE DEC K

ET SHOP

Busy with porting info from ET Index Server to ET Shop Notebook in Confluence.
Installed 17 x Samsung 32" new tv's as a replacement for all the small tv's in the Labs, Schlumberger Office, Upper Tween & User room. Small tv's has been assigned to state rooms by the MCS's.
Milled off the edges of 3 x TCON Half-Space Probes on the CNC.
CREE Emergency lights are due for their 2-yearly battery replacement. Batteries has been ordered for installation.
Roller Hand Sealer has a worn/burned out heater element, and parts have been sourced for replacement. Assisted with handling and processing cores and ran APCT-3 Temp measurements at all sites. Used Tools
#1858002C, #1858031C.
Tool #1858002C sent back for repairs and battery replacements. Temp Probe broke off inside shoe. The Shoe is also being sent along with the Tool for the stuck probe leg to be removed from the slot.
Lost signal from 3.5KHz Transducer Array in Sonar Dome. Did tests and troubleshooting on Bathy and LPT in Underway lab, but everything points to the Sonar Dome itself. The Junction Box seems to be flooded most likelly, but we are receiving a Knudsen EcoSounder simulator in order for us to test the transducers for a more accurate answer. Scope of work in the link Below.
2020-Sonar Dome Workscope_11102020.docx

PALEO LAB

Installed 2 x new faucets.
Replaced 7-Segment displays and Display driver for old Temperature bath, but the Temp display is still scrambled. Tested the unit with a thermometer and it is still accurate in relation to the setpoint.

GANTRY

Fabricated larger spacer for new P-Wave Transducers.

SHIL

Track system keeps stopping after start or upon return to home. A lot of resistance on the Mdrive and even with it disabled, the light and camera assembly is difficult to move by hand, so we opened up the track system to check if spiral rod is lubricated and clear of any objects, and that was all good. Removed the Mdrive Motor and found that it is close to seizing, so we replaced it with one of the new units we received in September 2019, and system is running smoothly and can be moved by hand easily with Mdrive disabled.
Some minor adjustments were made to get the camera image correct.

CORE DESCRIPTION

Removed Middle table Countertop for modifications as requested. Cut off one side of the sitting area for standing station so end cap labels better can be seen better.
Made a drawer for the new desk attached to the FWD Description table.

Corner cut off for easier access to cores Added Drawer

WRMSL

Opened P-wave calipers to do thorough cleaning of the shafts since the closing action was very sticky. A more expansive service is needed during tie-up, i.e take it all apart to clean the moving parts, since it stays a bit sticky during the first initial measurements after few days of standing still, and a lot of black grease\dirt comes loose when lubricated and cleaned with WD40.
FO CSL E DEC

UNDERWAY LAB

Towfish was deployed, and upon retrieval, the cable insulation had spiraled for about a 100m starting from the connector. (see photo below)
We suspect the towfish started spinning and only the yellow insulation was twisted off the internal structure. May not have been as tightly compacted upon manufacturing, but we don't know.
The Towfish was set out again after the transit to Cape Town started, but it was later on discovered that the signal keeps dropping, so the Towfish was brought back in, and the twisted cable was cut, of which the length was about 75m.
A new connector was installed and the towfish was set out again without any issues.
The off-cut cable along with the connector, will be sent to the supplier for them to investigate.




Spiral tow cable

FANTAIL

The levelwind is currently down again. When we deployed the Towfish, the levelwind was moving STB side as it should, but when it came to the end for it to switch and move PORT side, it failed, and so the rest of the cable was deployed with the hand controls. Towfish was also retrieved by using the hand controls, which proves to be just as easy as with a functional levelwind.
We spend a lot of time troubleshooting the unit by swopping out the boards, checking and testing the components on the boards and all were functioning as they should since we though maybe a relay had blown as it sometimes does.
After that we performed a "zero" calibration on the Hall Effect Sensor, and still the levelwind would only move to STB side, so we suspected it might be the sensor, as we also swopped out the old and rusted magnet and calibrated it with the new one.
We performed calibration on the spare Hall Effect Sensor in the U/W lab drawer, but it is behaving the exact same. We performed calibration with different magnets, since the sensor is pole sensitive, and we have done tests on the bench in the ET shop, but we are not getting the correct voltages in order for the sensor to distinguish between moving left or right. According to Dynacon manuals, the sensor operated between 0.5V and 5.0V, with the center "zero" voltage being whatever value is in the middle of that range. The voltages we are receiving are symmetrical on either side of the "zero" line, which proves that the levelwind is only moving in one direction since both sides give the same voltage output when the magnet is moved to either side. We also tested the End of Travel Sensors on both sides, so see if a faulty one are perhaps causing the levelwind to only move in one direction, but they both tested fine.
Beth and Garrick has ordered 2 new Sensors from a company that took over Dynacon, so we will see when we get the new ones, what output voltages we measure and how the sensor behave.

RAD VAN

Removed old incubator fridge and secured it in Lower tween.

HALLWAY

Secured new -86 Freezer with Unistrut brackets

LN2 GENERATOR

Received Pressure valve with Gauge, along with the filter, all for chillwater installation. Will complete during Tie-Up.

THIN SECTION LAB

Serviced 2 x Logitech PLJ2 Precision Lapping Jig. Pistons was stuck on both, so we took the units apart, cleaned and regreased all the parts and they are as good as new.
Serviced 1 Vacuum pump. Had some rust and oil was very milky. Also replaced the old black vacuum tubing with new clear ones.

RAY LAB

Removed and installed new Haskris unit. Old Haskris unit was tested with in-house machined keys and the unit is working good. To be stored as a backup.
Made a wooden box with sliding lid, to serve as XRD/XRF samples holder.

CHEM LAB

Agilent Cary 100 Spectrophotometer had a broken chopper belt, so we replaced it with a O-Ring that fits and works as a good replacement. New Spares has been ordered which can be installed when there is down time during Tie-up.
Below Link is for more info from Chemists. SPECTROPHOTOMETER - Agilent Cary 100

L O W E R DEC K S

GYM

Replaced batteries of exercise bicycle console.
New entertainment upgrade is needed to switch everything from Analog to Digital components and connections. The current setup also is not compatible with the new Aries system.
The new system connection layout will be as shown in the diagram below:

Gym Entertainment Upgrade Connections
SYSTEM MANAGERS
Mike Cannon and Kerry Mullins
SERVERS (MICROSOFT):

• • Updated security protocols to meet TAMU IT requirements on all servers.
  • Applied monthly updates to servers as required by TAMU IT security protocols.
  • Built three new Windows 2019 servers for TAMU Division of IT to replace their aging email server and domain controllers.
  • Uploaded new Cumulus exports to Nebo.
  • Updated Commvault to service pack 20 hot fix pack 9.

SERVERS (LINUX):

• • Updated security protocols to meet TAMU IT requirements on all servers with exceptions to appliances.
  • Confluence would occasionally stop serving content and the service would have to be restarted. We started a support case with Atlassian but so far all efforts to collect logs and find a cause for this issue have been fruitless.
  • Built replacements for the following servers with Suse Linux Enterprise Server 15 Service Pack 2 to replace servers with aging operating systems no longer supported: Eiger, Elcapitan, Matterhorn, Olympus, Uluru.
  • Upgraded the following servers with Suse Linux Enterprise Server 12 Service Pack 5 to bring them up-to-date with current supported operating systems: OEMJR, Teton and Yellowstone.
  • Upgraded the following servers with Suse Linux Enterprise Server 12 Service Pack 5 and Open Enterprise Server 2018 Service Pack 2 to bring them up-to-date with current supported operating systems: Cleveland, Netsrvc and Novarupta.
  • Patched iPrint server to version 4.1.2.

SERVERS (ODA):

• • Updated security protocols to meet TAMU IT requirements on all servers.

SERVERS (VMWARE):

• • Updated security protocols to meet TAMU IT requirements on all servers.
  • Updated Thunderhead vRealize server to version 8.1.

3PAR SAN:

• • No issues or changes to report.

NETWORK:

• • No Issues or changes to report.

PC WORKSTATIONS:

• • Updated security protocols to meet TAMU IT requirements on all workstations and instrument hosts
  • Applied monthly updates to all workstations and instrument hosts as required by TAMU IT security protocols.
  • Restored a SRM backup to a spare computer to allow developer and PMAG tech to recover some missing files needed for instrument operation. Performed the same operation for the SHMSL as well. Both successful.
  • Installed Zebra Zdesigner print software on core entry and chemistry lab PC's to allow custom label printing.
  • Setup a third NIC in the XRD computer connected directly to the Aeris XRD instrument to allow control of the instrument from the instrument host.
  • Tested Crowdstrike AV software for use in future deployments as a replacement for McAfee AV.
  • Started a support case with Extreme Networks to address an issue with NAC agent not detecting Catalina's firewall. Extreme networks issued a new version of NAC agent to test, v.1.22.1.0. We tested and confirmed it fixed the issue and have deployed to our download page.

MAC WORKSTATIONS:

• • Installed a new VDU and TV in the publications office.
  • Upgraded Mac workstations to Mac OS 10.14.6 Mojave.
  • Upgraded VDU's to Mac OS 10.15.7 Catalina.

PRINTERS:

• • No major issues or changes to report.

SATELLITE/INTERNET/PHONES:

• • We experienced several outages during expedition 390C including some that were several hours long but our providers, Siem and Marlink were able to restore service.

OTHER EQUIPMENT/PROJECTS:

• • Installed replacement 50" TV in EPM office in place of the old 42" TV.
  • Installed old 42" monitor removed from EPM office in the MCS office for use as a system monitor display.
  • Replaced all 22" TV's used with VDU's and other locations with 32" TV's and articulating mounts.
  • Deployed old 22" TV's to the IODP state rooms to be used with SnapTV system. There are still three rooms on the upper tween accommodations without TV's.
  • Installed a new O2 sensor in the chemistry lab that will be used to monitor oxygen content in the nitrogen gas line.
  • Our SnapTV boxes stopped connecting to the server caused by an upgrade Siem made to switches on their network. Siem IT support was able to find and fix the cause.
  • Created a LO and ALO groups in Confluence and set permissions to allow those groups to delete content in Lab Notebooks and Lab Manuals spaces.

• Specified new monitors and mounts for the description tables.
• Hard mounted all monitors in the science office.
• Conducted a test audit with TAMU Division of IT representative, examining our workstations.

APPLICATION DEVELOPER
James Brattin
SUMMARY
This document highlights changes to the JOIDES Resolution laboratory data management environment during Expedition 390C.
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://banff.iodp.tamu.edu/display/DEV/Developer+Home+Page+ The activity log specific to this expedition will be placed here:
{+}http://banff.iodp.tamu.edu/display/DEV/Ship+Activity+Log+

SPECIAL PROJECTS
During Expedition 390C the developer worked on the following projects:

• • Catwalk: worked with ship and shore personnel to fix bugs and test those fixes.
  • GEODESC: worked with ship and shore personnel to design and implement GEODESC applications. Primary focus was on implementing Template Manager application.
  • Servers: worked with MCS to test OS upgrades to all ship servers

GENERAL DUTIES PERFORMED

• • During Expedition 390C the developer participated in: Routine expedition support.
  • Maintenance of software applications (as detailed in the sections below).
  • Assist with data management in cases where LIME and other software tools do not suffice. Other duties as assigned.

CHANGE SUMMARY

Outstanding Issues

• • Server communication is spotty (as detailed in the section below).
  • LimsW on older version due to new version probably the reason why some Hole data was not able to upload. Catwalk is also on older version after updates caused app to crash on startup.
  • SampleMaster was not able to parse some Hole data back into its table cells.
  • Tech reported an error on the CahnBalance; went over error logs and sent them to shore developer. The error was not critical.

SPECIAL PROJECTS / ISSUES

• • Issue with the SRM not showing plotted data after sample measurement was complete and MagSpy not showing any data at all. After troubleshooting, SRM stopped working entirely. Then, the MCS restored a PC using an image he had taken of the SRM PC a few days prior to the issue. The entire IMS-10 directory from the PC using the restored image was copied back over to SRM PC and the original issue was mostly fixed. The UI for the SRM was still not showing plotted data after the sample measurement was complete, but the MagSpy was showing the plotted data correctly.
  • Adjusted the image crop values for the SHIL. The tech from the previous expedition had adjusted the start and end values for the image crop in one of the VIs. I set it back to the original values and a tech later tested and verified it worked correctly.
  • Built and deployed new version of the resteasy-drillreport web service to fix an error that was preventing approved reports from being sent to asman.
  • Reprogrammed the label scanner for the XRD tech. It now parses the label into the same format required by the software running the XRD.
  • Deployed a small fix to the OldSummary app to get some dropdowns populated; per the Ops request. Web call was failing due to no url encoding. Tech found a bug where the Cancel button in several of the LabView UIs was functioning as a Save action. Bill Mills emailed how to fix and the ALO and tech applied the fix in several places and verified it worked correctly.

DEVELOPMENT TOOLING AND INFRASTRUCTURE CHANGES

• • Copied the printers from the ship production database into ship test to allow Catwalk testing of printers from ship test.
  • Removed the ServiceUser account from ship production and ship test databases, along with the password safe. Account is no longer used; and should be replaced with the Writer account as

EXP 390C Technical Report



HARDWARE AND SERVER

• • All ship servers had OS upgrades applied to them.
  • The firewalls had to be disabled due to the way communication with printers is not constrained to specific known ports. Server communication is currently unreliable:
  • Matterhorn tomcat was hanging after receiving a call to a web service, and eventually retuned 502 (Bad Request) error.
  • Possibly one error was the unpacking at least one war file since deploying the same war files from El Capitan to Matterhorn seems to have temporarily fixed one issue.
  • Tomcat logs have errors related to establishing a connection to the oracle connection pool
  • Still troubleshooting the issue. Possibly related to the servers' memory allocation and the tomcat configuration.