X390R Technical Reports (PDF)

Individual Reports

LAB OFFICER’S AND ALO’S CROSS-OVER NOTES

LISA CROWDER AND AARON DE LOACH

IODP Expedition 390R: Cape Town Tie-Up

Expedition 390R was a tie-up maintenance period in Cape Town.

Operational Dates and portcall

• Cape Town, South Africa December 5 2020 – February 4, 2021.
• JRSO Staff arrived in Cape Town staggered over many days and all spent at least 4-5 days isolated in a local hotel and received two COVID-19 tests and results prior to boarding.
• Expedition 390R officially began on December 5, 2020 ending expedition 390C. On the next day, the 5 staff boarded and completed a short crossover with the off-going staff.
• Expedition 390R ended on February 5, 2021 at 0800 and thus began 395P.

STAFFING

• Tie-up staff was reduced. Alejandro Avila Santis was able to return to the ship.  Sarah Kachovich and Eric Moortgat had to return to Cape Town due to travel restrictions to the US and returned to the vessel untill Dec. 22^nd.

LOGISTICS

OFFGOING SHIPMENTS

• F390R_RAF parcel containing Minolta and Fluxgate Magnetometer was picked up from the vessel Jan. 29.  Waiting on AWB to send shipment.
• A Scientist Sample Parcel for Dr. Jin, from 390C was returned to Cape Town, and is on its way back to Tonji University.  Scientist did not answer his phone or e-mail when package was being originally delivered.  Tim Bronk and Emily Estes are coordinating.  Air Way Bill is in 390R shipping folder.  No further action is needed.

Pending Shipments

• MCS HP drive kit to be returned RAF.

ONCOMING SHIPMENTS

Air Freight

• T390R Air freight arrived on Dec. 5^th.
• T395P04A Schlumberger tools in 395P have been received and in Telemetry Lab. T395P05A NGR check sources have been received and placed in lock box.
• T395P01A arrived Jan 31 and the replacement HP drive kit the MCS’ need to swap out with one on board was removed immediately. The remaining items were received and distributed.

FLAT RACKS

• T395P03S flat racks arrived Feb.1. T395P03S is in Cape Town still to be delivered.

AMS/Inventory

• Increased the 3D printer cooling fans RSL to 3. 
• Had John Miller order 6 extra NGR fans (PP5016) to make a complete spare rack, but did not up RSL in AMS.
• We ordered a replacement Gel Coat resin and 2 bottles of hardener (MEKP) from agent.  There are 2 types of Gel Coat on inventory, HW5502 and HW5850.  Not sure if these are different.  One type of resin (HW5502) has 2 quarts in BFLM from 2017, and It takes the same hardener. Maybe Etienne knows which one is good to keep on inventory, and which one should be removed. All gel coats have been moved in AMS to BFLM, and the small repair kits remain on CSPLT checkout.

Special projects

• SCBA Scott Escape packs and hoses were sent to Novamarine for hydrotesting and evaluation and should be returned Feb. 3.
• Repaired cracks and painted worst areas in Core Lab floors. 
• Refinished Down Hole bench top and sampling table.
• Splitting room super saw trough; repaired cracks and resurfaced gel coat.  West Maine sent us the wrong kind of hardener (Dibenzoyl Peroxide).  I put it with other hazardous waste in Chem Lab to be disposed of.
• Cleaned and serviced the super saw.
• Loose Argon bottle racked.
• New fire place is behind the D-Tube caps.
• One of the 3 reaming SCBAs bottles (SCBA #6) leaks and needs to be surplussed next returning SURF.  It's labeled in pallet stores area.

Tasks & Issues

• Gel Coat the upper splitting table. The hardener is attached to the gallon mix in BFLM.
• On the ALO PC, few times the screen went into startup mode and couldn't find the operating system.  Had to hard restart.  Had MCS look at it twice, it happened 3 times after they changed the "boot up order."  May want a backup of your folders.
• Siem received 2 child size immersion suits for individuals <1.5m tall and up to 49kg.

Laboratory Summary

GENERAL

• The COPE Protocol was followed to get all personnel to the vessel safely. Contractors were aboard the vessel almost the whole time so personnel wore masks in all common areas.
• Significant time was dedicated to GEODESC meetings, planning, and testing.
• Catwalk module testing continued at a minimal level and programmatic changes were made as necessary and as part of the ongoing project.
• Individuals worked on their own projects.

Core Deck

Core Lab: 

Track Systems: 

• SHIL: Installed and tested a 45° light angle geometry. Conducted an experiment using various light geometries. Developed methods to quickly extract RGB values from images.
• AVS: Designed and conducted experiments to test the performance of the AVS.
• SRM: Conducted many field measurement experiments and evaluated the Fluxgate magnetometers. One Fluxgate probe and console sent to IODP for calibration.

Other:

• One Minolta spectrophotometer sent to IODP for a shore project.
• Trough under the core splitter repaired and gel coated.
• Refinished Downhole bench and Sample Table.
• Floor crack repair and painting.

Focsle Deck

Chemistry Lab:

• ACID TANK is in line but no limestone is present. No chemicals in the sinks, water only!
• All instruments shut down other than the IC.
• Helium bottles are closed in the Pallet Stores.
• The oxygen monitor once again displayed big cycles in nitrogen quality.

XRD Lab:

• Service call for Malvern PANlytical Aeris XRD performed by two local reps. Entire sample changer was replaced with a new model.  Instrument is functioning as expected with occasional minor errors.
• Aeris User Guides added to Confluence.

Microbiology:

• Lab Notebook page changed to a new format.
• Koach Bench set up with particle counter and ionizer.

LN2 Generator:

• Functional

Underway Geophyics Lab and Fantail

• Jurie Kotze Sr. boarded the ship on Dec. 6 to evaluate the sonar system. After the repairs made on 390C it appears the sonar system is working properly.
• Hull inspection video clip of the sonar dome is in the Lab Notebook Sonar Dome page.
• Electronics module in magnetometer changed.

  Lower decks

Gym:

• Floor repair and painting in the gym entry way.

Core Lab Report

Core Splitter

Trough under the core splitter was repaired and a new coat of Gel Coat applied and sanded smooth.  The MEKP hardener did not come with the can of gel coat like it was supposed to but the hardener that was later ordered and sent out to go with the Gel Coat was the incorrect one.  We borrowed some MEKP from the crew before we realized there is MEKP hardener on inventory to go with a different resin. 

Floor Cracks

Floor cracks were repaired and painted in the microscope lab, by the printer, and in the logging office.

Catwalk

Core Catcher Press and Vise cleaned, lubricated, and covered for storage.

Core description and micropaleontology preparation laboratory

NICOLETTE LAWLER

Summary

390R was a tie-up with no core recovered. The focus of this tie-up was to ensure the Core Description position was well documented in preparation of this technician leaving, training others on DESClogik, and contributing to GEODESC. Instruments and software were used minimally with no issues to report.

Issues and Updates

DESClogik

Current version: 16.2.0.0

No issues or updates to report. DESClogik was used for testing purposes only to familiarize other technicians with the process of creating and editing templates. As a part of the training. several value lists and sublists were updated and uploaded into value list manager. Value lists and sublists from X384 will be uploaded in Value List Manager to replace them as the most current lists. 'Test' expedition folders have been deleted off of IODP_Share. The macro 'Value List Builder' code was updated to account for recent changes in the server directories. 

Thin Section Report Builder

Was not used and no issues or updates to report.

SEM

QAQC images of the reference mesh were taken and put into Confluence. No issues or updates to report. Tif images can no longer be uploaded to Confluence. To upload SEM images to Confluence open and save the images as .jpg. Unclear when this became an issue and is not related to image file size (our .tif images are ~1.3MB).

Paleontology Wet Lab

No issues or updates to report.

User Guides

A new user guide for DESClogik was created that walks technicians through the process of creating and editing templates. The intent is to assist technicians with DESClogik until the replacement description software, GEODESC, is ready to be used. At this time the expected date for GEODESC is the end of 2021. 

GEODESC

Development and testing are both underway, with the primary focus being Template Manager. Data Capture is a secondary focus at the moment. Over the winter break, shipboard technicians had panel reviews to gather new user feedback on applications and developed a list of suggestions for improvements. There are now TM and DC Change Request sheets on Zoho, where users can request a change, the request is discussed by the group and assigned a priority level. These requests will stay in the document to serve as a historical record of requests and decisions so moving forward the group can have an easier time moving forward. The group is hoping to start gathering external user feedback around June/July 2021, although details are still being worked out. It was requested to extend to project deadline from April 2021 to December 2021.

Screen Resolution and size for Core Description and Microscope computers given to James and Algie to aid in optimizing screen layout for larger monitors.

Template Manager

Latest release date and version: 28 January 2021, v.0.0.16.

The last month was focused mostly on bug fixes, re-design due to change requests, and prepping specs for Edit Entry Validation List and Adding Values to Entry List. The latter two will likely be the first new features focused on.

All communication in slack was done using the message groups that included both description technicians. Specification and behavior changes have been recorded in Slack by Peter Blum.

It is recommended to look at the TM Change Request Spreadsheet in Zoho and slack communication between James and James/Peter to get a thorough grasp on all changes. Test plan was updated to reflect specification changes and application behavior. 

Updates

Template additions:

• Taxa and Taxa-like columns with entry types of numeric, formula and text were created and added to the template 'microscopic_micropaleontology_Ostracods_TAXA and TAXA like template'
• Validation lists for some taxa columns were created and are in two templates 'microscopic_micropaleontology_Ostracods_TAXA and TAXA like template' and 'microscopic_micropaleontology_Ebridians_TAXA template for testing'.

Notable specification changes include:

• 'Keep Changes' and 'Return' buttons changed to 'Save' and 'Cancel'. Selecting 'Save' will take user back to the previous page, in at least most instances.
• Button changes on Edit Template screen: The Edit Attributes button that changes with radio button is now 'Edit' and moved to the top of the table with the radio buttons. Edit Header moved to the top of the table. 'Edit General Template Settings' is now
• The addition of another radio button 'Column Display' which shows the attributes that apply to the column. Selecting 'Edit' for the three display buttons take you to the same page. The Display Attributes page now has three areas: column, header, and data.
• Double clicking on a project template will open the Edit Template page.
• Add Values to Entry Validation List, the first, second, and third order filters will now be a nested dropdown list. A pitch was made to make it look and work more like the Add General Observables Page, but, due to some programmatic difficulties, and group preferences we will be sticking with the current layout in the mockup.
• 'Please' should be taken out of all messages. Spreadsheet made to try to more easily nail this down.

Points still stalled

• Creating a formula was not discussed and no progress made on those specifications.

Test Plan Edits

• Changes were made in the following tabs: Project Template, Copy Catalog Template, Create New Template, Delete Project Template, Edit Template, General Template Settings, Add General Observable, Reorder Observables, Delete Observables, Entry Controls, Edit Header, Edit Entry Validation List, Numeric, Formula, Display Attributes, and Comment.
• Most changes reflected button name changes, changes in messaging, and missing steps. New tests were added on to General Template Settings, Copy Catalog Template, Project Template and either added as additional rows to existing tests or brand new test at the bottom.

Reported Issues

• Not all issues reported in Zoho and listed in the Test Plan on 'Testing Status' come from 'fails' reported by users in the test plan.
• One issue was 're-opened' in Zoho and will affect testers testing v.0.0.16.

IMAGING & MICROSCOPES

SARAH KACHOVICH

Summary

Sarah Kachovich performed basic beginning of expedition activities after returning to the vessel.  Worked with technical staff on SHIL calibration procedures and installed a 45 degree angle mount for the SHIL.  Performed many tests and provided a report of activities described in the Physical Properties report.

Projects

• Generated the headshot posters, holiday edition.
• Technical staff group photo.
• SHIL - See Physical Properties report.
• Gave hands on training sessions on microscopes and smear slide making.
• Gave a presentation on the new SEM.
• Hosted a line scanning workshop with JAI camera rep, Ole K. Jørgensen.

PALEOMAGNETICS LAB

MARK HIGLEY

Summary

Expedition 390R was a tie-up and no scientific data was collected. All systems were exercised to ensure proper functioning condition. The only significant issue noted was with regards to one of the fluxgate magnetometers. Extensive testing was conducted which resulted in fluxgate magnetometer probe A and control unit N2300 being sent to Applied Physics for calibration.

COMMENTS AND ISSUES

General Lab

• On 12/26/2020 the ship lost power and the chill water supply was interrupted while the technical staff was off shift. The SRM null field was lost during this time so a new field was trapped.
• The SRM cryomech compressor hours are approaching 18,000 hrs. The adsorber must be replaced every 20,000 hrs. When it comes time to replace the adsorber, the spare cryomech compressor should be connected to the SRM and the new adsorber (when it arrives) installed into the compressor which was just taken offline. This way, both compressors get exercised. We still have some time but keep this on the radar.
• Began migrating the Pmag lab notebook over to a new format which is more consistent with other labs. The old layout is still the active page. The new page is linked at the top of the pmag laboratory notebook.
• The cabinet under the Kappabridge was jacked up and screwed to the wood counter top. This was in an effort reduce the amount of flex in the counter which has large effects on the kappabridge readings. The counter still flexes a little if you lean on it but not as much as it used to which was ~.5 cm.
• The cryomech cooling water heat exchanger was put online and the ships cooling water flow increased.  This increased the temperature of the ships chill water going into the cryomech compressor by ~17°F  but the flow was increased to keep cryomech parameters the same. This set up works well when the ships chill water is around 45°F as it was for this expedition. If the ships chill water increases much in temperature, the heat exchanger will likely need to be taken offline since the flow rate is already maximized. Condensation on the heat exchange coil was reduced. Condensation on the pipes still occurs but the catchment system does an excellent job containing it.
• The haskris was turned on to flush the lines at the end of the expedition. The reservoir was drained, cleaned, then refilled with tap water. The float switch was on upside down so the haskris was giving a low fluid warning and not starting even though the reservoir was full. Once the float was taken off and put on top, the haskris turned on.

SRM

When attempting to zero the fluxgate probe, it was observed that there was a +.2 to +.4 mOe shift on the X and Y axis of control unit N2300 when changing from the 10 mOe range setting to the 100 mOe range setting. The shift was specific to the control unit because it was present with either probe connected. Control unit 90348 also had a shift when switching ranges but  it was much smaller (~.1 mOe) and could more easily be attributed to rounding or noise. The shifting values are documented in the excel workbook here: fluxgate_range_shifts.xlsx. At first, I suspected the cables might be the cause. The cables were swapped with no improvement. The probes were zeroed inside the smaller mu metal shield which was nested inside the larger mu metal shield (Figure 1 and Figure 2). This nested arrangement is probably not necessary but it provided a convenient means for stabilizing and rotating the fluxgate probe while zeroing. It was also observed that probe B was much more stable than Probe A, regardless of which control unit it was connected to.

Figure 1.

Figure 2.

SRM field profile data was collected to document the fluxgate probe behavior. All of this data was collected with probe A connected to control unit N2300 (acquired in 2018 from Brad Clement's lab) and probe B connected to control unit 90348. Over 60 profiles were collected so to save time, they were only measured from 250 cm to 350 cm to focus on the SQUID measurement region.

• January 16th: Both control unit/probe setups were zeroed inside the nested mu-metal shields. Probe B was zeroed using the 1 mOe setting since it was stable enough. Probe A was not stable enough to zero on 1 mOe so the 10 mOe setting was used. This setting shouldn't make a large difference if the field is within range but since there seems to be an offset when switching between certain ranges I have been careful to note which range was used for what. The probe was zeroed according to the vendor manual although on the ranges used, the amplitude was near zero (probe still read zero on the selected axis when rotated 180 degrees). The probe was rotated inside the shield for each axis so that each axis was aligned in the same direction (up) when it was zeroed. After both probes were zeroed,  a new null field was trapped in the SRM using probe B. This field is referred to as the B-Field. This null field was trapped with the control unit set to the 1 mOe range since it was very stable on this range.
• January 17th: Field profiles were measured using each probe setup on the 1, 10, and 100 mOe ranges. These profiles are in the excel workbook 20210117 B-Field combined range tests.xlsx located in T:\IODP_Share\PMag\PMag_Documents\SRM\Field Profiles . A new null field was then trapped using the A probe setup. This null field is referred to as the A-field. The A-Field was also trapped using the 1 mOe setting for consistency. It was difficult to use this setting due to the noise although I monitored the 10 mOe setting periodically and I dont think I could have done any better with that setting (still had fluctuations on the order of .02 mOe but it was easier on the eyes when watching).
• January 18th: Field profiles were measured using each probe set up on the 1, 10, and 100 mOe ranges. I also repeated all the field profiles with the fluxgate probe rotated 90 degrees to starboard such that the Z axis corresponds to the -Y axis. After applying the rotation corrections, I wanted to see if the X and Y axis would read the same (or similar) values as they should. Although the field was trapped using the A probe, the profiles measured by the A probe had intensities close to 40 nT in some cases (in the measuring region). The profiles measured by the B probe on the other hand were pretty good. I checked the zero reading of both probes inside the mu metal shielding. Probe B was still zero on all axis, Probe A was reading ~.3 mOe on both the Y and Z axis. The X axis was still at zero. I re zeroed the A probe and collected all the profiles again, including the YZ rotated profiles. Profiles collected from the A-Field are saved in the excel workbook 20210117 B-Field combined range tests.xlsx. This workbook only includes the A-probe readings after it was re-zeroed. 

Some PDFs of some key plots are located here: 20210118_Field Charts.pdf. The data is probably be more clear in the workbooks though where you can sort and filter the data. I found it most helpful to click in the upper right of the chart sheet. There are three buttons, the bottom of which will allow you to filter which series to display. The series naming follows the convention of Axis range_setting Probe (i.e. X 1mOe A is the X axis, measured with the 1 mOe setting on Probe A). If the probe was rotated, this is noted by the text YZrotate.

A couple things that stand out:

• Probe A is much noisier than Probe B. This is very apparent at this scale. On a typical profile measured along the length of the SRM, this noise is not apparent until you zoom in.  I did a quick scan through a few previous field profiles. Around mid 2019 the profiles have similar noise to probe A. Prior to that, it is much quieter.
• Probe B has good agreement between the YZ axis when rotated (within 2 nT). The Z axis on probe A has a difference of ~9 nT when rotated (Z becomes Y axis). The Y axis records a similar value when rotated (Y becomes Z).  See charts A-Field: Probe B 10 mOe Range with YZ rotation vs  A-Field: Probe A 10 mOe Range with YZ rotation. THis is a very interesting point because the idea for this came from the fact that in the ambient ship environment, on the 100 mOe setting, probe A reads ~138.2 mOe on all axis while Probe B reads ~138.2 on the X and Z axis and 127.8 mOe on the Y axis.
• The two null fields have a different shape on the x axis (corresponds to SRM Z axis). Perhaps adjusting the gradient could fix this?
• Probe B has good agreement on intensities measured by each range setting whereas probe A is all over the place. See chart A-Field: Probe A all Ranges vs  A-Field: Probe B all Ranges.
• Not sure how probe A became so offset from zero so quickly. It was handled in the same manner/locations as probe B.
• Both Probes look pretty good on the 10 mOe range which is the most useful for the SRM.

It was decided to send control unit N2300 and probe A back to Applied Physics for calibration. Prior to sending the unit back, a new label for probe A was made (Figure 3).

Figure 3.

JR-6A Spinner

The JR-6 had an issue communicating with Rema6. Usually when initializing the instrument, communication is through comport 1. Rema6 could not find the JR6 on any of the ports. The issue was resolved by shutting down both the JR6 and the computer. Upon restarting, everything worked normally.

D-2000 AF Demagnetizer

No Issues

ASC Impulse Magnetizer

No Issues

Thermal Demagnetizer

No Issues

Kappabridge

No issues

Magnetic Orientation Tools

Not used

PHYSICAL PROPERTIES LAB

Alejandro Avila Santis AND Sarah Kachovich (SHIL)

Summary

Expedition 390R was a tie-up and no scientific data was collected. The systems were tested for correct functioning. Several tests were performed with the AVS to determinate the accuracy and precision of the instrument, results and methods is available and linked to this report.  A 45-degree angle light configuration was installed on the SHIL and tested and the calibration procedure reviewed in detail.

General tasks

A pdf version of log sheets has added to confluence for to quick print of the files.

Laboratory notebook page were reviewed and no structural changes added (like it so much!!).

Instrument review

MAD

• Tested each cell with standard balls and results is in the historical spreadsheet.
• Quick Start Guide were reviewed and formatted.

No Issues

Multisensor loggers (WRMSL and STMSL)

• Both was tested and calibrated.
• New chocks were made in the 3D printer for the GRA.

No Issues

NGR

• During tie-up time, power outage occurred and NGR was shut down, after that, a partial restart procedure was applied to restore PL detectors (they were showing 0 value on panel).
• NGR User guide were updated in section shut down to better clarify procedures.
• Power bank (UPS) was replaced temporally with the MAD oven power bank while the batteries of NGR power bank was replaced, after that with the original power bank was tested and reinstalled. Bias voltage adjustments and calibration was performed to compare with previous values.  No issues.
• Fans of the ventilation panel s/n 170067 on the left was replaced, but still failing so the panel was replaced by s/n 060448. Panel s/n 170067 is repaired and stored under the counter as spare.

• I recommend to keep the extra external fans just in case of ventilation panel fail again and no people on shift.

• Along with the arrival of the new sources, an organizer is designed for the sources metal box so that a better order and selection of the sources that are in use is obtained and the old ones have a compartment on one side.

P-Wave Velocity Bayonet/Caliper Gantry (PWB/PWC)

Not used

Section Half Imaging Logger (SHIL) 

• Two RGB extractions methods were written in R software (Lisa C. method) and MATLAB (Alejandro A. method) both permits the extraction the RGB values and plots, this is two alternatives to brute force RGB extraction using magic, notepad, and excel. See more in  RGB extraction methods in the Lab Notebook.

• Many tests were carried out with light angle variation and light distance to core, more details in Image and Microscope There are 2 configurations now available onboard, the old 70-degree setup and a new 45-degree setup.  The brackets, baffle, and light shields for the 45-degree setup are kept together in PP2B drawer.

• No decision has been made on which configuration is “best” therefore the SHIL was restored to the configuration it has been used in since installation with the 70-degree light angle.

instalation of 45° Light geometry

A 45° mounting plate with a baffle insert, to prevent direct illumination of the lens, was made on shore and sent to the ship at the start of expedition 390R.  The angle of the lighting system was changed to 45° to the scanning plane (Fig. 1).  Firstly, the sockets for the main screws, were the wrong size and needed to be carefully milled out (Fig. 2) to fit on the system. Also, the inside screws had to be omitted from the set-up as there was no space for all the plates and bolts to sit flush (Fig. 3). Even with the missing bolts, the system was able to mount firmly.

Figure 1. New 45° illumination. Left, Solidworks mounting plate with a baffle insert by Bill Mills. Right, mounting plate with a baffle insert installed on expedition 390R.


Figure 2. The new mounting plate next to the old plate, before it was milled to allow the screws to fit.

Figure 3. View from above of the heat sink, new mounting plate with a baffle insert, showing the two removed mounting screws.
Due to the angle of the copper rods at the new geometry, the protective shield no longer fits and new sides would need to be made (see figure 4). New light shields were later printed with the 3D printer.

Figure 4. Only the front panel of the illumination shield was mounted onto the SHIL. The angle of the copper rods at 45° prevents the side plates of the illumination shield from sliding on and had to be removed.

Testing

1. Decreased illumination: due to the 45° setup of the lighting system, illumination reaching the lens was less. With this configuration, you need to either open your aperture (decrease the f-stop) and/or increase the sensor sensitivity (but this is likely to introduce noise to your images). Easy solutions.
2. The idea of the new lighting geometry was to exclude the specular component of reflection (glare). However, the light's pattern was still detected (Fig. 5). The reflectance pattern does appear to be slightly decreased, and the new orientation is preferred over the previous direct reflective lighting. In direct reflective lighting the light is reflected directly off the subject into the lens.

Figure 5. Reflectance pattern of the new lighting configuration. Left, the metal scraper (used by the core describers) was placed at an angle towards the front lights. This showed the intense reflection of the light's pattern, if something on the core is at this angle. This will be rare, but will sometimes occur in our samples. Right, is the metal scraper flat, perpendicular to the camera. This test represents the majority of our cores. As you can notice, the circle lights pattern can still be distinguished.

A second reflection test was done to show the two methods (Sarah's and Bill's) of reflection testing, together. Water on the core, scraper and a QP card was also tested to mimic other requested tests.
Firstly, the lights were lowered from 6 cm to 2.5 cm above the core, as per Bill's instructions (Fig. 5). In figure 6, you can notice the reflection pattern to be worse in the metal scraper that is slightly raised and perpendicular to the cores. The height of the metal scraper is 1.2 mm and sit right at the core liner height. It is my opinion that these tests mimic situations we will see in our cores, mainly with any expanding cores. Moreover, it is my opinion that the perpendicular scrapers are more level than the scrapers resting on the concrete cores. Hence why they are brighter, as the other scrapers are likely to be at a slight angle to either side and reflects more light away. Lastly, in my tests, the scrapers were placed at an angle to try and capture the total reflection of the width of the core better.

Figure 5. The lights were lowered to be 2.5 cm above the core. Without a shield that fits (techs on expedition 390R are 3D printing a temporary shield) the wires from the lights are too close to the core surface and will scrape.

In figure 6, notice that, even though you don't see the circle lights in all of scrapers, they all have different shades. This is demonstrating the reflectance issue with scrapers at different angles. In scan 3, I am not sure why the overall scan was darker. Scan 5 was done after the lights had been off for ~30 mins and could have destabilized the LEDs.

Reflection tests with the scraper on the core were done before expedition 384 and 390C, but yet, when we got around to scanning real cores, the scans showed unacceptable reflection artefacts of the circle light, meaning that the tests wer not adequate. I have asked the crew on expedition 390R to design a 3D reflection standard that will more accurately test and monitor this artefact to help us move forward. A 3D reflection standard has not yet been fabricated yet.  A variety of gray silicone mat material was ordered for 395P and further discussion will be needed to design the correct kind of standard.


Figure 6. Reflectance pattern in multiple scans. Scans 1-4 are done of the concrete core, where it's height is lower than the core liner. Scan 5 is done on the concrete core which is level with the core liner.

Recommendation

The new orientation is preferred over the previous direct reflective lighting. In direct reflective lighting the light is reflected directly off the subject into the lens. If an object has a specular component of reflection (glare), it will be excluded by 45°/0° illumination automatically. Why? Light that is reflected specularly will be reflected at the same angle as it strikes the object. With 45°/0° illumination optics, light that is reflected away at 45 degrees will not be "viewed" by the spectrophotometer.

A line scan camera application eventually only requires a thin line of light as illumination, as only a 1-pixel wide line is detected by the sensor at once. However, it is important for all line scan camera applications that the light is as bright as possible and has an extremely high frequency in order to avoid flickering.

The light source may need to be diffused to prevent hot spots. Diffused lighting is usually used for photographing evidence with shiny or reflective surfaces.

A Note on Imaging Scrapers

The metal scrapers used to scrape and clean up the core sections appear to have a consistent wear pattern from the user cleaning them the long direction with paper towels.  The worn scrappers have a predominant scratch direction in the long direction and when they are placed perpendicular to the scan direction they reflect a lot of light back to the camera.  After core sections are scraped they also often end up with scratch marks across the core.  When the core is wet this may contribute to the reflections.

Lighting Configuration Experiments

After examining the images produced with the 45° light angle and consulting with shore we were requested to lower the lights as much as possible and send images.  In order to be a bit more systematic we came up with a plan to image the same core section at the two light angles and different heights.  The diagram below describes the geometry of the lights and the two variable we changed, angle and height.

The procedure was to change the configuration, calibrate, then scan a freshly cut core section and the cement core with the gray mat and scrapers.  The core section is a 384 play core from the top of hole so fairly moist. The table below is the key to the five configurations used.  No forward and aft light shields were used since the original shields only fit configuration 2. Images were sent to shore as configurations 1-5 without knowledge of the the geometry in order to eliminate bias.

All of the SHIL images captured on 390R are in the following location on the servers for reference. T:\IODP_Share\PhysProps\Testing and Calibration Notes\SHIL\390R SHIL. Images from this experiment are in the January 10 folder.

The height listed in the table refers to the height of the lowest edge of the LED light holders above the bench.

Notes on configurations:

Configurations 1 and 5 have the lights very close to the bench thus making it extremely hard to calibrate because the lights produce so much heat on the card and media.  The lights cannot be this low and allow for 360 degree whole round imaging.

Configurations 2 and 4 have the lights at 70° (or 20° as noted in the table) where config 2 is the geometry originally installed and config 4 is at the optimal height to produce the most light as the incident light produced at the center of each LED intersects at bench height.

Configuration 4 has the lights at 45° and the height of the whole light carriage was set at the same height as configuration 2.

Observations

Here are crops from the top of an image from configurations 1-5 in order.

• Configurations 1 and 5 show the least reflection of the individual lights in the black strip above the QP Card and on the red bar, however, these configurations are not practical for imaging.
• Configuration 2 then 4 show the most reflection in the black strip above the QP Card and on the red bar with configuration 4 a little less.
• Configuration 3 shows less reflection than 2 and 4. 

Note that in all locations where the core material is wet that there are reflections regardless of the height or angle.  The fact that core sections are scrapped across the core surface also induces scratches across the core that tend to reflect more light. See note on imaging the metal scrapers.

The following graphs are of RGB values extracted from cropped sections of the QP card and a cropped core section.

Note how the values for configurations 2 and 4 are overall higher.  This may be due to more reflections back to the camera.  We also thought that the light over the ruler may also have an influence, especially when the core is wet. 

It was noted that calibrating for configuration 5 was challenging, however the QP card looks okay.

Conclusions:

Based on observations from this experiment and comments from the initial analysis of the 45° light angle by Sarah early in the tie-up, the 45° light angle at the original height of the light carriage (Config 3) may be the best configuration at this time.

The SHIL was left in the light configuration used on 390C (Config 2) in the event the same light configuration wanted to be used on 395P collecting core from the same project.  The lights can be easily reconfigured with to 45° with the kit left in the PP2B drawer.

Maintenance: Heat Sink Cleaned

When the mounting plate for the light's geometry was changed, the copper rods were taken out to avoid damage. The rods were cleaned with isopropanol and fresh thermal stuff was reapplied before they were reinstalled.

Figure 7. Left, taking the copper rods out for cleaning before changing the angle of the lights. Right, the cleaned and straitened rods, with freshly applied thermal joint compound and new light orientation.

Lateral Chromatic Aberrations

We need to maintain the same edge sharpness and color fidelity at the edges of our field of view as in the center. Currently, we are noticing a faint, but persistent green aberration in our scans. I looked through old scans and could notice this aberration (though fainter) with our older cameras too. Typical chromatic aberrations, see at high contrast areas, a red fringe shifted on one side and a blue fringe mirrored on the other side. However, in our scans, the blue and red wavelengths appear to be shifted (behaving the same) towards the center of the lens compared to the central wavelength (green; Fig. 8 and 9). In Figure 8 and 9, the green (spherichromatism) aberration's offset worsens towards the edge of the lens. This might be caused by optical dispersion of the lens, a green secondary spectrum produced by the lens, focusing error, or a behavior of the camera's prism system.

Each lens will have some degree of lateral chromatic aberration – defined as an inability to focus all color wavelengths to the same convergence point(s) along the sensor plane. In other words, the red, green and blue waves associated with a given point on the target image may be focused to different pixels on the camera's imager. The result of this is typically soft edges with color fringes on objects in the field of view. In a line scan camera, this will be most prominent on edges that are perpendicular to the sensor's plane as we can see in figure 8 and 9.

Although the sensors for each channel are precisely aligned with respect to the optical path through the prism, the characteristics of the lens causes the actual focal point of each channel to shift slightly relative to each other. As was the case with shading, this shift is greatest at the outer edges of the sensor.

The JAI rep, recommended trying a 50 mm lens, but also set up and execute a 'Lateral Chromatic Aberration Compensation' in Lab View. He explained, in our JAI workshop (see section 4 of this SHIL report), that the green aberration is always there as a fixed pattern, but only noticeable when you have areas of high contrast. This conversation is still ongoing, but currently, he thinks this correction will easily fix this issue.

The 'Lateral Chromatic Aberration Compensation' process utilizes the line profile graphs to visualize the pixel shifts and to confirm the effects of our compensation adjustments. Need to do more research about the process.

Things to continue to research: How do you for compensate lateral chromatic aberration in the lens, and f-stop? How to execute Lateral Chromatic Aberration Compensation In the JAI SW-2001T cameras, as this is an automatic function in their other cameras?


Figure 8. Green color fringes caused by lateral/spherical chromatic aberration. Left, is a series of QP cards 101 in different lateral positions to one another. If you look closely, you can see the lighter, green aberration. Middle, is the green aberration enhanced in Photoshop to demonstrate the geometry/offset of the green wavelength in relation to the corresponding, high contrast locations. Right, is the location of the aberration to the high contrast areas, demonstrating the increasing offset between the two, towards the outer edge of the lens.

 Figure 9. Green color fringes caused by lateral/spherical chromatic aberration. This test is a repeat of the one in figure 8, but with the QP cards 101 at an angle, because why not. Left, is a series of QP cards 101 in different lateral positions to one another. If you look closely, you can see the lighter, green aberration. Middle, is the green aberration enhanced in Photoshop to demonstrate the geometry/offset of the green wavelength in relation to the corresponding, high contrast locations. Right, is the location of the aberration to the high contrast areas, demonstrating the increasing offset between the two, towards the outer edge of the lens.

Notes From the JAI Workshop

The tech party gathered around the Christmas fireplace in the conference room and had a lovely line scanning workshop by the JAI rep, Ole K. Jørgensen. The focus of the workshop was to learn the best practices for calibrating their cameras. We identified that our methods do not follow what is recommended and we wish make amendments to the current method in confluence, post the second half of expedition 390C (to ensure consistency in the scans between sites).

To sum up the recommendations for calibration: Should be performed with the camera configured at the operating point of the scan (gain, temperature, exposure time, iris).

• DSNU calibration: Should be performed first, lens cap on.
• White balance: perform on a white/gray target, either by adjusting individual exposure time or individual gain settings for red/blue. Green is the master channel for the automatic functions (AH=0, white balance by exposure or AW=0, white balance by gain). Green channel values around 220 in 3x8 bit.
• Shading calibration: Should be performed on a white/gray test sheet, lens (slightly) de-focused. Image values around 220, 3x8 bit. This function works on groups of pixels averaged, so it is the first rough calibration to correct the effects of lens vignetting and uneven illumination.

PRNU/pixel gain calibration: This works on individual pixels. It compares the pixel value with the average value of the line and sets a correction factor per pixel. This calibration is done best on white/light gray sheet (use a uniform target that is close, but provides a light intensity below saturation), while moving the camera. The movement while calibrating causes any grains or dust on the standard to be averaged, to achieve the best PRNU correction. After this, the image should be very close to flat.

Ole also made comments on our light set up. The key point was to make sure the light source should be flat and uniform! The JAI rep gave us the contact for his colleague, David Richards in the UK, who specializes on the physics of optical light and might help us understand how to be stabilize LED illumination, color and temperature. I will contact him when I am back at work to organize a second workshop to better understand optical physics and LEDs. Please express your interest to Sarah if you are interested in joining.

The changed calibration method will be entered into Confluence upon approval from shore team.

Shear Strength Gantry with Automated Vane Shear (AVS)

• Quick Start Guide were reviewed and formatted.
• On Expedition 390R we carried out tests where the sensitivity of the instrument is measured in response to different known loads, arranged in various configurations, explained in the Automated Vane Shear (AVS) Test  Report (*.pdf).

The experiment is designed around a pulley system, where a weight is suspended from a thin cable, over a single or double pulley, then attached to special vane fixed to the AVS.  Using this setup, a torque is measured and compared to calculated theoretical values.

Fig1 support of pulley system and vane to perform torque test

The result of test applied is divided in five groups, one for each distance in the vane using the same weight, the last experiment was using an additional weight (50g) using single and double pulley.

In the configuration n.5 we use 161g of weight (0.06Nm) with good results in accuracy and precision, and this correspond near to half torque of an average of the torque measured in an historic data (X353 to X375), corresponding to 0.19016Nm.

Report is under review by David Houpt, Gary Acton and others on shore.  The plan is to have the Lab Working Group review the report and make recommendations on keeping the current setup and using the pulley method to calibrate, or getting a new AVS, or just using the hand held Torvane.

TeKa TK-04 Thermal Conductivity Meter

Not used

X-Ray Imaging Logger (XMSL)

Not used

• Source door holes were repaired with hard rock epoxy mix and all screws put back (I did not find any more screws of the same type).
• Coolant of source were refilled and upload a manual of pump (Koolance RPM ALX-400) for future reference.

Section Half Multisensor Logger (SHMSL)

Not used

Items Received:

• NGR: 10 NGR coaxial cable. (Mouser electronics) p/n 736-MSB00250LTE150. Stored in NGR drawer NGR1. These are replacements if the PL cables under the system fail, like building too much static charge making the PL counts high.
• NGR: New source for Cesium, Cobalt, Uranium and Thorium
• SHMSL: Spare parts arrived: 3ft of high-temperature silicon o-ring cord stock for the SHMSL sensors (PN 96505K24). Stored at SHMSL drawer PPTRKF3

Items Sent: 

• One Minolta spectrophotometer sent to IODP for a shore project.

CHEMISTRY LAB TECHNICIANS REPORT

SUSAN BOEHM

Gas Lines/manifold

Helium was still flowing to the GC's at the start of 390R.  The tanks were switched when psi reached close to 200psi but the pressure in the new tanks was dropping very quickly in the first two days (losing ~10psi per hour) and no major leaks were found with snoop except for the end green-handle purge valve.  We replaced the valve with a different one and it felt like it was leaking less, although the gas monitored showed it was actually leaking more.  Switched the gas lines to the ones used on the previous tanks and the pressure held more steady (still some loss of about 20psi over 12 hours).  Inspection of the port side octopus, with blue tape on the end, one of the o-rings was missing however this is the case on the "good" starboard side octopus as well.  I replaced the green handle purge valve again and tightened any and all connections and tested the pressure and there was no loss after a few hours.  Both "octopi" should be in working order. 

Lab Officers decided to just save our helium supply since no instruments need to be running.  The tanks are now turned off and the gas line shut off valve is closed.  The bottles with the octopus still attached have about 1400psi.  All helium valves in the chemistry lab are also closed to hopefully avoid any contamination in the lines.

Additional Swagelock valves HW5715 have been ordered by ALO. I think the small o-rings inside the valves don't seal well after time and it does not appear we have any brand new ones, only a few used ones in the swagelock drawers.

NGA1/NGA2

 When it was decided to turn off the helium supply I shut down all the GC's.  All detectors were already off so all I did was press the main power switch on the front of the unit and close the helium valves.

IC

Followed instructions for chem lab maintenance during a tie up and ran the IC once per week for about 2 hours.  The pressures seemed slightly high (8.2 for anion pump pressure) and I took screen shots of them.  Once, the instrument must have lost communication with the PC because I was getting a lot of other instrument errors.  I turned off and turned back on the IC and after it initialized all errors were cleared and it worked fine after that. Anion and Cation fluids topped off on Jan 20.  Anion pump pressure stabilizing around 8.5. 

CHNS

When it was decided to turn off the helium supply I shut down the CHNS according to the instructions in confluence and closed the gas valves.

Water system

Followed instructions for chem lab maintenance during a tie up and 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.

Oxygen Analyzer

The oxygen content of the nitrogen generated by the N2 generator started to climb over 50 ppm once again and more recently is cycling up and down on roughly a daily cycle.  The oxygen content seemed to stay below 50ppm while the ship was at sea during 390C and only started to rise once the ship was tied up in Cape Town.  This was seen in Norway as well.  It is still unclear what is causing this cycling and poor nitrogen quality.  Production of LN2 does not seem to effect the quality nor does bleeding the line continuously.  Nitrogen from a bottle was measured on the oxygen monitor and an air calibration was done, the monitor seems to be working properly.  I would be curious to see what happens when the ship goes back out to sea.  Please save periodic images of the graph and save the data to the AMI/Export folder on the desktop.

Misc

Washed and rinsed dirty glassware in the store room drawers.  They looked like they had that fine dust all over from the sandblasting in a previous portcall.  The acid tanks are still not online so no acid bath was made. 

MICROBIOLOGY

LISA CROWDER

Lab notebook

Microbiology Lab Notebook converted to the style used by Chemistry.  New content was added and all existing content was moved to the new page.

KOACH BENCH

Set up Koach clean bench with ionizer and tested with the particle counter.  KOACH significantly reduces the number of particles between the push hoods but the number of particles varies with position between the push hoods.

XRD & ICP SAMPLE PREP LABS

SUSAN BOEHM

Summary

Expedition 390R was a tie-up maintenance period in Cape Town, SA.  A service call was performed by two Malvern Panalytical service technicians to replace the sample handler.  The lab was prepared for the service call and monitored throughout the tie-up.

XRD

Malvern Aeris XRD

Service Call

PANalytical Aeris XRD service call Jan 12, 2021 EXP390R
Location: Cape Town, SA
Service Engineers: Johan Lubbe, Anant Morar
Report by: Susan Boehm

Service call was scheduled because of continuing issues with the sample changer: An intermittent and frequent motion control error which results in having to restart the instrument multiple times. And ultimately the sample arm no longer working at all and making a loud clunk sound when trying to move. (Issues reported on 390C). Instrument was remotely placed in manual mode which bypasses the sample changer and one sample could be run at a time.

Inspecting old sample changer

Service reps attempted to reinitialize the sample changer with the outer cover off to be able to see components moving. They were able to communicate with it and make it move. It was recreating that clunk sound reported previously- the sample gripper has an optical switch so it can detect when the gripper is moved up and down, however they believe the ribbon cable telling the gripper to stop is not working. They seemed to have seen this problem before and feel that the ribbon cable is a known weak point. Although no visible signs of wear, they are known to be very delicate and easily damaged by rubbing against the other inner components of the sample changer. Confirmed and confident that replacing the entire sample changer is the solution.

Removed old sample changer

The entire sample changer is removed in one piece and the large ribbon cable connecting it to the rest of the unit is disconnected.

Unpacking and installing new sample changer

Some difficulty unpacking the new sample changer and I think that's where a couple small scratches around the sample cups came from. The cups are a tiny bit loose, normal, but just gently press on them to make sure they are seated securely.

Attached large ribbon cable and placed sample changer on the three pins that hold it to the rest of the unit. There was a lot of trouble with feeding the length of the large ribbon cable into the instrument so that it is out of the way of the sample changer moving parts. They took some time on this because they were very concerned about the possibility of it coming out of place and getting damaged on the moving parts. Ultimately, they folded it up into the instrument and placed an extra piece of plastic in between the cable and the housing. I expressed concern about the movement and the vibration of the ship shifting the piece of plastic and the large ribbon cable out of place and stated that I did not like that that was the solution. They felt confident the ribbon cable is being held in place securely and will not pop out. *Note: the outer cover of the sample changer is easy to take on and off with star wrenches, in case anyone suspects there is something wrong in the future.

The new sample changer has a built-in guard covering the small ribbon cable that moves with the sample gripper arm.

Initializing new sample changer

Service techs restarted the instrument with the outer cover off to be able to view the sample changer moving parts. In IMS client they updated the sample changer serial # and reestablished connection. If the boards had not been changed and upgraded during the service call in October (390P) they would have had to replaced them now. But since we already have the latest ones there was no need to change the boards again.
New sample changer initialized right away and they "enabled" the sample changer so that it is no longer in manual mode. Instrument was restarted again and initialized correctly on its own. Ran at least 6 samples. I created a super short program that takes less than 1 min to run so that we could observe it loading and unloading quickly and continuously without having to abort each run.
There was no need for realignment of the sample changer, everything was perfectly aligned already. Service techs were very happy and impressed with the new sample changer. This was the first of the new type they have installed.

Clearing an error

Service tech purposely moved the sample arm by hand and this triggered the motion control error. While they are able to reinitialize the sample changer in the software using their service dongle, it is confirmed that we do not and will not ever have that access. He did this to show that the only way for us to clear the error is to power off and back on the instrument. There is no need to toggle the x-ray key, highly recommended we just leave it where it is or even take it out. I only pressed the power button and let it shut down, and then pressed it again to start up and the error was cleared.

Factory Acceptance Test and radiation survey

Service techs performed factory acceptance test and everything passed. To run the FAT they needed to change the divergent slit and remove the large Ni filter on the detector side.
They pointed out the large Ni filter was placed in backwards, as well as the mask, and the divergent slit was inserted too far. The beam knife is confusing and even the technician has trouble remembering which way is correct because it is counterintuitive the way it is supposed to be placed for lo and hi. They took the time to instruct on how each part needs to be inserted and removed. I pointed out corrosion on the small Ni filter on the tube side but service techs not concerned and our standard runs shouldn't require it anyway. No damage to any components and they were satisfied with the factory acceptance test.
Standard practice for service techs to perform a radiation leak survey after any maintenance and there were no leaks found.

Maintenance and Cleaning

Service techs topped off cooling water and cleaned off the spinner wheels inside the instrument that spin the sample after I asked about seeing a residue on the edges of the sample holders. They just need to be cleaned off with isopropyl when they get dirty.

General Recommendations

Leave the instrument on always. Front unit, x-ray key, everything ON. If restarting is necessary to clear an error there is no need to toggle the key switch. Obviously for dry dock or when it's totally necessary we can shut everything down, but it's not good to be turned off and on often.

Backup the instrument system files and copy to a USB at least once per expedition. This is done through IMS client.

No need to have so many programs uploaded to the instrument. We really only need two or three programs and should not have a need to be switching the hardware often.

The instrument is designed to not have issues with peak alignment (not like on the Bruker where occasionally we correct the goniometer axis to align theoretical and actual peak angles). If in HighScore we ever do see any peak alignment issues the advice was to just use the x-axis correction in the software and not worry about hardware alignment.

Peak intensities will slowly diminish over time, but when to replace the x-ray tube is at our discretion. We can keep an eye on this by simply running the corundum standard on one designated program and run that periodically to track any changes. As far as I know we do not have a certificate for the corundum standard ( ? ).  

Tube conditioning is not a concern because this tube runs at lower voltages than on the Bruker. I pointed out that while the Service Manual says tube conditioning is not necessary, there are instructions for it in the booklet we received with the tube. Still recommended not to worry about tube conditioning and to leave the instrument powered on. Pressing the power button on the side (and NOT turning the key) already ramps down the tube, and then pressing the power button on ramps up the tube.

Post service call

The Aeris was run regularly for a few days to test it thoroughly.  After sitting idle for two days on 1/24/21 when not in use a Motion control error displayed and could not run sample. Pressed green power button, waited, and turned back on.  Error was cleared and able to run samples.

Remote Service Call

Over the next few days various errors occurred when the instrument was not in use and sometimes the errors clear on their own without needing a restart.  Since the Malvern technicians had asked how the Aeris was doing we let them know about the errors.  They requested a remote session using their Team Viewer application.  The PC workstation next to the Aeris was set up to host the remote session and on January 29 a technician logged in with Team Viewer and used their IMS Client to drive the machine.  The instrument checked out okay and there was no indication of why the instrument is throwing errors.  The technician asked if we could record when the errors occurred but they happen randomly and when the instrument is not in use so that is impossible.  The technician thinks this could be a software issue.  The instrument will need to be tested in full operation at sea to determine how serious this issue is.

Error Log showing errors from 1/24 through 1/27 prior to remote service call.

The instrument is currently set up to run "Fast Test" but that may not necessarily be the correct configuration of the instrument, I just overrode it in Advanced Mode.  Double Check the hardware configurations before running a different program.

Standards and QAQC

After service techs replaced sample changer and performed factory acceptance test during service call I created a measurement file C:/> PANalytical > XRDMP Creator > Corundum Standard Scan 5-120 deg.25 div SB.xrdmp and saved that file in C:/ > XRD Data > QAQC

Original File backups are in Vol 1 > IODP Share > XRD > QAQC > Aeris

Opened this file on top of a qaqc run from the bruker and peaks line up but counts are much lower, don't know if that matters or is just a fact of using a different instrument and different xray tube. Maybe my qaqc measurement file isn't ideal and steps need to be smaller or something else changed? I think it should be fine if we are only concerned about relative changes.  Green line is bruker scan. 

Bruker D4

Bruker D4 and Haskris chiller untouched.  D4 system remains on and high voltage ready.  There was an unexpected power outage to the vessel for about 15 minutes but the instrument seemed to recover with no issues.

Spare sample gripper received and in the lab.  As far as I know there is nothing wrong with the current one, it was just ordered to have as a spare.

pXRF

Attended zoom sessions with vendor on basic instrument operation.  Google Drive dedicated to Tracer 5G documentation here https://drive.google.com/drive/u/1/folders/0ALD3dx7KcxT4Uk9PVA

If you do not have a scientific ocean drilling google account you can request one here https://sites.google.com/a/scientific-ocean-drilling.org/www/new-account

Any new documentation regarding the Tracer 5G will need to be downloaded to the ship. 

I added the current pXRF user guides for the Olympus into the google drive so that shore based staff can create a new user guide for the 5G.  It will be used on shore by Denise and Aaron Mechler until April when it will be sent to the ship.

Documentation

Created a Quick Start Guide and Advanced User Guide for the Aeris instrument in the Lab Manuals space in Confluence.  The advanced user guide is a work in progress and any red text indicates that I am uncertain and need more information or confirmation from the XRD techs.  No user guides or standard QAQC protocol existed so I created one based on my best judgment but would like review and approval by managers/lab working group on the accuracy of my recommendations.

Created a page in the Lab Notebook/XRay space about setting up a remote service session with a Malvern technician via their TeamViewer and IMS Client software.

A suggestion for the documentation of XRD procedures is to pull out all of the general sample preparation procedures from the instrument guides and make a separate sample preparation guide.  The instrument manuals would only include procedures specific to that instrument.

THIN SECTION LAB

SUSAN BOEHM

Kemet Kemvac Vacuum chamber

Initially suspected the start/stop valve was failing, but I think it fails to create a vacuum when the chamber is not seated fully.  The chamber has two large gaskets that need to be pushed in really firmly and also seated on the unit really firmly.  Readjusting these has resulted in being able to consistently create a vacuum.  It also helps to push down hard on the lid when opening the start valve to get all the pieces to stick together.  If having trouble in the future, Kemet recommends putting some silicone sealant around the gaskets and lid o-ring and making sure they are clean.

Inventory

• Apex Diamond Grinding Disks TS1007, TS1008, TS1009, and Lakeside Thermoplastic Cement TS0096, - Luan mentioned she couldn't find these on 390C.  I found 3 of the 70 micron discs TS1007 but none of the others.  I recommend changing these to "inactive" in AMS if Luan and ALO's agree.  I thought I remembered seeing the Lakeside Cement in the past but I can't find it either.  Also maybe change to "inactive" if it's not something either of us see using in the future. 

Found them on the starboard side shelf in the ICP prep area.

UNDERWAY GEOPHYSICS LAB

DAN MARONE  

Summary

• Lots of testing conducted on the 3.5kHz array using the new EchoSIM tool.
• Magnetometer towfish maintenance conducted and it is ready to go.
• No scientific data collected from any instruments. 

System Status

Bathymetry 

• Jurie Kotze Sr. came aboard during the beginning of the tie-up to assist with the testing of the sonar dome. Lots of testing was conducted on the cabling and connections leading to the dome, with many utilizing the EchoSIM. A full detailed sonar dome testing report is in the next section and can be found on the 390R Sonar System Evaluation page.
• While we have yet to test in deep water, everything seems to be working properly with the bathy/sonar dome.
• Knudsen EchoSIM software was installed on both winfrog computers in Underway. 

Magnetics

• Removed magnetometer from its towfish housing to check for any damage to the internals and also the integrity of the housing. There was a missing screw causing one of the weights to be loose and able to move around along with many other loose screws that needed to be tightened. Using spares found in the magnetometer drawer the weight was secured and a few other stripped screws were replaced. The housing was deemed to be secure, both the one in use and the spare have deep lacerations but the fiberglass underneath are not compromised. I do not think we need a new spare.
• Wanted to swap the electronics module (EM) out with our spare to deck test and see if our depth reading issue was with the EM or the sensor itself. I noticed that the spare does not have a capacitor (fig 1.) so I contacted marine magnetics to ensure this would not damage anything if swapped. They responded quickly confirming that it was just a newer EM that does not use the capacitor and will work fine.
• Upon swapping the EM and running some tests the instrument began returning depth readings as opposed to always reading 0.0m which had been an issue since 378T. It seems the issue was not with the sensor but with the EM itself. 
• EM 13553 is now our working spare should we need it, however it does not record depth readings. There is a note attached to it explaining this.
• Cleaned and serviced all of the o-rings, as well as the eight brass screws that secure the internals into the housing which are exposed to the seawater.

Figure 1: Difference between electronics modules

Navigation

• While we did not collect any navigation data with WinFrog we did keep the program running to monitor the connection to both Trimble units.
• No loss of connection occurred with the new SP356 unit.
• The SP351 in BLO did drop connection a few times, but overall will work great as a spare when the new unit arrives.

Items Ordered

• Marine Magnetics SeaSPY1 tow cable, 500 m.

Items Received

• Knudsen Engineering EchoSIM signal simulator, D229-05819-Rev1.00. Stored in Underway down below winfrog monitors next to the LPT.
• Hall effect sensor 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.
• Decade-Ranger Resistance Box, Tag ID: 2349

Critical Maintenance

• Everything is now onboard to continue repairs to the level-wind system. Unit was covered to protect from the elements but otherwise left as it was.

Methods and Manual Changes

• Changed the re-order point for UW0002 SeaSPY cable termination kit in AMS from 0 to 1 so that it will automatically re-order when the spare is used. I noticed that it was not on order even though it was mentioned in 390C report. If this was set to 0 intentionally just let me know.
• Did some reorganizing to the Sonar Dome confluence page and added in lots of old scanned documents and anything I could find that looked like it could be useful to have saved online for the future.
• Attached Knudsen EchoSIM manual and user guide into confluence on Knudsen page and sonar dome page.

Sonar System Evaluation

JURIE KOTZE Sr. AND LISA CROWDER

History

The JRSO staff discovered problems with the Bathy2010 sonar system during X384 in July 2020.  The 3.5 kHz sonar would not perform well at high power outputs of -6 and -0 dB output power.  Staff contacted SyQwest multiple times for troubleshooting assistance with very little success.  Since the problem was specifically with high power outputs our current and former ETs thought there was possibly leakage or damage to the cabling somewhere.  During the 390P/390C crossover, the hatches to the sonar dome were opened and the cables measured and inspected by the oncoming ET to make sure there was no problems in that section of the cables.  It was still unclear where the problem was but there was no appearance of damage in the cabling above the sonar dome. 

390C (see 390C Tech Report)

During the transit to the South Atlantic during 390C the 3.5 kHz sonar behaved as it did on 384 then failed completely where no 3.5 kHz chirp was produced by the transducers so the 12 kHz sonar was used for site depth.  Meanwhile, on shore, staff discovered that Knudsen Engineering makes a sonar testing box for their echosounders, called the Echosim.  This tool would allow the JRSO to test the status of the 3.5 kHz transducer array without removal of the sonar dome.  The Echosim was ordered and sent to Cape Town.  Meanwhile, preparations were made to remove the sonar dome in the event that it did have to be removed.

Towards the end of 390C after consulting with Knudsen Engineering about using the Echosim, the ETs thought to examine the J2 connector on the back of the LPT unit, the connector on the DSS-3 cable that goes to the J-Box in the Fwd Thyrig Room.  The ETs found the jackets on the wires inside of the connector to have pulled back thus exposing the wires.  The exposed wires likely caused arcing at the higher output power.  The wires were insulated temporarily with electrical tape and the cable reconnected to the LPT.  The 3.5 kHz sonar fired up immediately with good output and input signal.  Once in calmer seas the sonar was tested from low to high powers behaving as expected, not as it did on 384.

390R  Cape Town

On December 6th Jurie Kotze Sr. joined the JRSO technical staff for crossover with the off going staff.  The off going ETs demonstrated the use of the Echosim in the Fwd Thyrig room at the junction box.  Over the following days, Jurie performed additional tests of both the LPT output and the transducers.  From all appearances, the sonar system is functional and should perform as expected.  Jurie provided two documents describing the tests performed and the equipment set ups for future use, see attachments below.  For clarity and search capability in Confluence, the procedures and tests are described here.

With the ship docked in port of Cape Town it was the ideal opportunity to make an assessment of the Echosounder as a whole and integrity of the system, that included the integrity of the Sonar dome as well and I was called to come and work through the system and locate the problem. If the dome had a problem it was the ideal opportunity to be removed and repaired.

The 3.5 kHz system initially presented with varying levels of intermittency and at times failed completely. This as far I can remember started from the around the ships anchorage in Panama with the total Covid lockdown. It might have been earlier as well.

I tried to give advice troubleshooting via email and although I was totally convinced that the most likely culprit was the LPT (SyQuest Echosounder) electronics, I started to doubt, some problems with   the Dome as a unit could have failed as we weren’t sure about the very low dc resistance readings of the transducer coils, the  transducer wires were disconnected at the last terminal block in the Thyric bay J-box. That is about 3 meters above the transducer array with nothing in between except for the feed-through O’Brien connector on the ship’s bottom leading into the Dome cavity through a gooseneck to the Txducer array. At that point we accepted it that a low dc resistance of around 2.5 to 4.5 Ohms could be okay but I was looking more towards something like 9 to 10 ohm.

On the ships transit towards Cape Town Etienne and Erik found the problem, the J2 power outlet cable connector on the LPT had a short circuit. The wire strands soldered onto the connector had its wire sleeves pulled back and the copper strands inside the connector was

bare and shorted each other. The type of cable that is used there is very soft and pliable and so is the sleeve material, it doesn’t bind tightly over the wires itself but gives the cable a very pliable property. The danger there is that hard pulling on the cable causes the sleeve to pull back. I think this is exactly what happened. All the cables are lying on the ground gets trampled on and in constant motion as things gets handled in the area as well regularly and I accept that I might have contributed to it over the years that I worked there as well. If you step on a cables edge touching the floor it pulls directly on the connector and the stretch pulls back the sleeves covering the wire. The cables urgently needs to be tied back in the area away from traffic and boots.

As I planned a whole system check, it did not make a difference as we wanted to test the transducers with the new Knudsen Echosim that IODP purchased as well to see if the dome with the transducers is in good shape and give the cable fittings a good inspection. We replaced the two cable lugs in the Thyric J-box.

Knudsen EchoSim

Information on the Knudsen EchoSim page.

Time had come to connect the Knudsen Echosim. The instrument worked as instructed by both the manual and internet conversation with Knudsen personnel via internet conference which I unfortunately missed.

We could get the instrument to send its signals as supposed to, but could only get a curved incremental graph from 1.5 kHz with 500 Hz incremental steps rising till you get to 6.5 kHz. Most of the multiple curves plotted shows a soft kneejerk around 3.5 kHz as it is supposed to do. The dots should initially incrementally rise and around 3 kHz it should start forming a notch downwards as you move towards the

3.5 kHz point where it should show a very definite dip and climbing up again as you move away from the 3.5 to 4 and onward. We could hear relays click inside the instrument, sometimes double clicks and sometimes single clicking. That went with definite range selection of some kind. It would measure around a value of hundred ohms and after some clicking it switches to around 50 ohm. It was not more pertinent at U/W or at the thyrig bay but definitely at intermittent times.

My only conclusion was that the electrical fields that we experience almost all over the ship around high tension cables and with signal cables running on the same trays and pretty much interlaced with 33 Kv cables and thousands of amperes flowing as motors and heavy devices starts and stops with constant variation of loading. The electrical fields playing around the signal cables and inducing the noise products generated by this heavy currents is just too overwhelming for the Echosim. I think it finds it difficult to read his received signal out of the dust. In the thyrig bay with the closest cable run to the dome the thyrig cabinets sits within a meter from the dome connection and the ships 33kv power station and UPS just below it in the Koomey room area as well. In the U/W you have to use the cable that runs to the Thyric bay all the way on the cable trays as explained. This makes a long antenna picking up all the induced noise.

After hours of running up and down between U/W and thyric room making different measurements at different times and spots no different results could be logged. I have no doubt that the noise level is overwhelming and the signal/noise ratio is too high at both our measuring spots. No doubt though that in dry-dock it will be a very handy instrument if you have the transducers separated from the dome you will be able to make excellent frequency response curves of any single transducer or the multiple transducers fitted in arrays.

Results from 390R Echosim tests (Excel File)

Transducer Audio Sweep

At this point I told Lisa it’s time to do the transducer tests using the plain injection with a signal/function generator over the 1.5khz to 6.5khz band in 500hz steps as with the Echosim and look at the signal amplitude on an oscilloscope as the signal generator gets loaded, getting closer you will see the amplitude decreasing the closer you get to 3.5khz as you reach the resonant point at 3.5 kHz and max power will be drawn from the generator showing the amplitude should be at a minimum. As you move further toward the higher part towards 6.5 kHz the amplitude will gradually rise again as the generator will be relieved from the peak load. We only did the 500 Hz steps as required to minimise the time period as echosounding in port is unwanted and we could hear the transducers screaming in the thyric room clearly although the instrument BK Precision generator is way less powerful than the LPT but in port you are close to the bottom.

This worked excellent and at 3.5 kHz the amplitude on the scope dipped as well and turned around right on the millivolt as you move over it to the higher freq. half. We took readings from the scope’s digital display on the screen and plotted the 11 points on excel.

Once in open ocean the ET’s should do a similar run but slice the steps at 100 kHz steps and plot a nice and smooth graph as a reference to keep on the ET docs file. On the one we did in 500 Hz steps shows the dip on the graph but not as impressive as with following the voltage display on the scope but it will be very clear if you can slice the plot points, say at 100 Hz increments or finer for a good graph print.

See Jurie's hands on report below for details on the instruments and apparatus required to perform the transducer audio sweep.

To understand the basic function of the transducers and its coils it will be handy to read the section below about the coils and how they function and be the transmitters and receivers of the Echosounder signals. It is both Tx and Rx. As described below.

Transducers general description.

To start off we need to know how transducers of this kind works. The transducers are widely printed as Txducers as a driven element pushing the power or can be an Rxducer if it’s in receiving mode in the echo sounding field. Sometimes just called Tx and Rx. The printed term Tx would generally refer to a transmitter of a signal of any application, radio, TV, instrumentation etc. and received by a tuned receiver of that frequency, a receiver or Rx somewhere further away, again radio, TV or instrument etc. That just a bit of info as we are dealing with a hybrid situation on the ship, our transducers acts as both Tx and Rx on exactly the same set of equipment, this is important to understand as it causes confusion. Both LPT and Transducers are acting as Tx and Rx in echosounding alternatively.

Various vendors was asked for their opinion and came up with various values for dc resistance and ac impedance of their transducers and equipment. That brought up questions that we might have a problem in the dome, it looked like moisture in the wrong places entered causing problems with very different values

that we got from the vendor’s values, although theirs were given in

both dc resistance and ac impedance which are both valid.

An instrument bought from Knudsen is an instrument that can simulate the LPT and test the transducers to see if they resonate at

3.5 and 12 kHz respectively (or any freq. transducer for that matter) the instrument was received in port.

Basic physical property of an Echosounder transducer

We are using transducers that acts as a single loose standing coil with a particular value in dc, or ac impedance in its active running mode. Dc resistance measurement is measured with a multi meter and is measured as you would measure a normal carbon resistor. There is no activity of any kind, just the flow of a very small dc current through the coil from the multi meter, that is always much smaller than the impedance value.

Measuring impedance is applying a frequency signal over the coil and its normally the mains freq. of 60 Hz because mains ac is always available, the measuring instrument always will be plugged into a mains wall outlet but can be a portable instrument and generates its own frequencies as required for different applications, the signal cycles as sinusoidal changing voltage going positive and negative at a rate of 60 Hz then. The coil will build up a magnetic field as the voltage rises, as the cycle goes negative again the coils field will collapse but now the collapsing field will generate an opposing voltage, it will be opposing the forward current flow. The resistance that it creates towards the applied ac voltage is called impedance, a capacitor will do the same in a bit different way but similar effect. It should be clear now that this be the reason for the ac resistance (called impedance) will be of much higher value than that of dc resistance.

Another property of a coil is that it has a resonant frequency, this is where the coil’s speed of building and collapsing his magnetic field is exactly in sync with the applied frequency. This is when it acts as a “superconductor” and will allow the maximum ac current to flow through and has the least value of impedance, but just at that specific frequency that’s applied, we call it the coil’s resonant point or resonant frequency.

In a circuit that you know the operating Frequency of, 3.5khz in our case, the coils in the Txducers are turned and manufactured to resonate at exactly 3.5 and 12 kHz for the two systems we use and the 3.5 had the problem.

The LPT sends a FM style frequency signal, meaning the signal amplitude (signal voltage) stays at the same amplitude during the pulse bundle, it starts with a low 2 kHz running to a high pitched 7 kHz or so bundle. That’s the audible chirp that you can hear. This pulse is very strong and is capable of up to 500 Watts of energy with a voltage of up to 50 volts amplitude with very high current flow because the coil is exactly at resonant freq. of 3.5 kHz. The pulse intervals are decided by the operator of the Echosounder and its signal intensity will be decided and set by the operator as well.

At this point the coil will turn all the energy that ran through it in a huge magnetic field and shoot it forward into the depth of the ocean, the magnetic field will bounce back off the sea floor and eventually reacts with the same coil that sent it. It is called the Echo. This bounced back field around and over it will cause the same coil to generate an emf (electro-magnetic force but I prefer electromagnetic voltage because it’s the voltage that’s generating the force). This signal that the coil generated now as the Rx or receiver of the bounced back field, will be send back the line to the LPT where it’s electronics will receive the signal and get processed. It measures the time the LPT fired the pulse till the time it received the bounced back

signal and calculates the depth of the seafloor from the ship and makes a dot or marking on a display. It will receive various echoes from various parts of the seafloor under the ship’s surrounding and plot points for each pulse’s residual echoes from different higher and lower surfaces on the seabed. The LPT will send signals constantly and will constantly plot the points. As the ship moves on a good representation of the seafloor will form on the display.

Another interesting thing about the coil is that they can shape the footprint of the magnetic field by stretching the coil, the coil gets divided in 3 parts (as ours are). They manufacture it in a way that the first third part is turned and has a short interconnection with the second part of the coil and then to the third part of the coil, all acting as one single coil but looks like 3 coils. Now the magnetic footprint will be in a longer but slightly narrower footprint. Now you can stack more transducers to add to the shape you want to cover/see at the sea floor. That’s why the individual transducers needs to be correctly installed in the array and orientated to face forward that the collective footprint can cover your desired area to be scanned with every pulse that’s sent.

Sonar Signal Generation

A quick inspection of the SyQuest LPT with a 50 ohm/ 50 watt load on the J2 power output connector on slots A and B we could see and measure the signal very clearly. With the cable short circuit on the LPT output it goes into an idle mode, (as it was) with the short cct removed and repaired it could start sending his signal again. A blue flashing LED flashes in rhythm with the signal pulse. It sits on top of its electronics and can be seen through the air slots of the enclosure. If something goes wrong like the short it had it starts flashing faster indicating a problem and shuts the power amp down. A physical inspection of the amp showed a good and healthy instrument, no signs of hot connections and frying components.

See Jurie's hands on report below for details on the instruments and apparatus required to view the signal generated by the LPT.

Conclusion

To conclude, after testing the LPT and transducers I can confirm that both are in good shape and so is all the cable connections in- between. The ship’s 3.5 kHz sonar should be in good working order once it sails again.

Jurie Kotze sr.

Jurie's Original Reports

390R Echosounder ET Report

390R Hands on Echosounder Tests

Downhole Report

Dan Marone

Summary

• No instruments were run or tested during the tie-up.
• A program named CTD Plotter was made to quickly turn the exported cast data into plots for each of the four main measurements (temperature, conductivity, salinity, sound velocity). 
• DHML PC along with its communication cables were removed in order to resurface the port side DHML workbench. Everything was connected back with the same configuration and communication with tools should not be affected.

System Status

• No changes were made to any of the instrument systems.
• CTD was not serviced as it stayed in its case for the duration of the tie-up.

Methods and Manual Changes

Created a page/user guide for CTD Plotter and linked it to the CTD section of the Downhole Logging Laboratory Notebook. This is a project that I will hopefully be adding to and improving, but it completes its basic function well. It was designed with a processing step in mind but the exact method has yet to be determined. Please visit the CTD Plotter page for more information. 

ET REPORT

RANDY GJESVOLD

CORE DECK

DHML

• Conducted training and familiarization on the CTD Instrument. (Conductivity, Temperature, Depth)
• Set up the Mini Lathe to manufacture parts for the AVS.
• Conducted safety training on the Drill Press and the Mini Mill.
• Reviewed Kuster Tool.
• Used as a workshop. Worked on “NewYears” electronics. Assisted in re finishing the large workbench.

Core receiving platform

• Preserved and covered the Press and Vice so they don’t rust during the stand down.

Microscope lab

• Assisted with floor repair.

Laser Engraver

• Held training.
• Cleaned Filters.

SHIL

• Machined the mounting bracket screw holes in the SHIL light mount so they would fit correctly. Remounted it on the track. Assisted with the alignment of the Light Source.

Core splitting room

• Assisted disassembling and reassembling the Super Saw. Cleaned and preserved the saw motor. Removed the connectors to the actuator and sealed the connectors so dust and dirt will not get in them. Repairs were made to the fiberglass tub. Re attached wiring to the actuator. Tested Sat. Re attached the cable bundles running under the Tub.

NGR

• NGR UPS failed to hold charge during the blackout. Installed new 12V 8Ah batteries in Minuteman UPS IODP # RF 52990. These were all tested and conditioned prior to installation. Battery P/N 522-1023ND.
• Have 5 failed fans on Infra Cool IP Unit S/N 170067 installed on the outboard side. Replaced 6 fans.
• Infra Cool Fan Remote Unit S/N S1521470715157 is installed on the inboard side and has 1 fan failure.
• On Jan 18 Infra Cool IP Unit S/N 170067 failed completely. Had no indications or fans running. Replaced with Infra Cool Remote Unit S/N 060448 to reestablished NGR cooling.
• While Troubleshooting S/N 170067 found that one of the power wires had com un soldered. This was re attached. Currently stored under the counter as a spare.

ET Shop

• Conducted 3-D printer training. Printed several small projects to gain familiarity with the printer.
• Solid works training is ongoing.
• Continue familiarization with Confluence.
• Working on familiarization with the CNC machine.
• Ship suffered a blackout on Dec 26. Re set all the equipment in the labs and cleared the alarms.
• Prepared the “NewYears” ball for deployment.
• Ran a load test on UPS RF 53096. Re installed by MAD Oven.

Focsle Deck

    -80 Freezer on F-Deck

• Cleaned Filters.

    LN2 Gen

• Ran from Dec 16 to Dec 17 in auto. Ran from Dec 26 to Dec 27 in auto. Ran from Jan 07 to Jan 08 in auto. Ran from Jan 19 to Jan 20 in auto.

Other

Upper Tween Stores

• Fully charged the Pallet Stacker Dec 15 2020 and Jan 21 2021.
• Cleaned the -80 Freezer Filters.

Gym

• Found the Speedbag laying on top of its stand. Eye Bolt was missing. This was replaced. Added Air and placed back in service. S Hook is showing significant wear. Sourcing a new one. Found the Speedbag laying on top of its stand again Jan 10. Re installed.
• Tightened the screws on the manual treadmill. They keep unscrewing due to ships vibration.
• Trotter 750 Treadmill left rear cover broke off. Epoxied parts back together on and re installed.
• Cleaned and oiled the Chain on the Rower.

Movie Room notes

• New Video System ran with no problems.

Underway

• Bathy 2010. Resistance checked the cable from the U/W lab to the Fwd Thyrig Room and it tested good. Resistance checked the Cables from the Junction Box to the Sonar Dome and they tested good.

Fantail

• Level wind was covered. New parts received.

3D printer

• Machine was calibrated and it ran well.
• Several small test patterns were made for training.
• 3D Printer Extruder Front Cooling Fan failed. It was replaced. AMS P/N GE0086. Fan Number DA 03510S12M. Entered use on the inventory sheet. Recommended bringing the Qty up to 3.

MISC

• The Pipe Counter Sensors were removed for metal replacement, painting and preservation of the surrounding area. The Aluminum 2 X 4 box was damaged during removal. Found a Replacement 2 X 4 Aluminum Junction Box. Looking into finding back up Pepperl + Fuchs Through Beam Optical Sensors and Connector Cables. Manufactured a Cover for the Sensors.

SYSTEM MANAGER’S REPORT

MICHAEL HODGE and STEVE THOMAS

Servers (Microsoft):

• Incident occurred on Expedition 390C where EOL Backups were occurring during daily Base Backups (incremental and weekly full backups). Suspect this occurred during the Commvault software update from Service Pack v16 to v20 on prior expedition.  Worked with Commvault and identified where the EOL Backup policy had become part of daily backups.  Modified backup policy stopped EOL Backups from occurring daily. 
  • Commvault Incident #: 201202-227.
• At BOX, encounter issues where shipboard emails were not being delivered to shore. After several weeks of troubleshooting issue with TAMU support, they identified the problem to incorrect IP address assignment in ship’s Exchange server.  Corrected IP address resolved matter and email started flowing correctly.
• Shipboard Microsoft Update Server (WSUS) encountered full disk and stopped downloading updates. Prior OS and Server updates were removed and WSUS setup to target more current OSes.  Over 500GB recovered in disk space.  New and current updates resumed downloading and made available to shipboard systems.
• New Acronis license for instrument host backups registered and secured with our other software licenses.
• AdRem Netcrunch software license expired. Received new license from shore and activated software.
• McAfee Anti-virus software is being depreciated on all shipboard workstations and servers. TAMU supports CrowdStrike Endpoint Security software and was implemented in ship environment this expedition.

Servers (Linux):

• Evaluated Confluence for hung states as experienced on Expedition 390C. Heavy usage on Expedition 390R but did not experience any hung states.  Recommended to vendor to close open support ticket and vendor indicated that same support ticket could be reopened if issue returns.
• All Linux servers played nicely without any issues.

Servers (ODA):

• Ship Oracle ODAs K1 & K2 and Oracle database version on both ODAs were updated to version 19c successfully. Oracle Java Database Connectivity ojdbc files were updated current on Confluence and Tomcat servers successfully.  Confluence, JR webpages, LIMS and JANUSJR databases are all operational.
• Modified Apache/Tomcat configuration file on server Eiger for JANUSWEB queries to function. This required pointing to correct version 19c libraries verses prior version 11.2.0.

Servers (VMware):

• VMware servers performed as expected without any issues.
• In association with shore efforts upgraded ship servers HP iLO systems on all physical servers.
  • HP iLO 5 v2.33 and ROM/BIOS v2.40 successfully installed on ESXi servers Kilauea, Tambora and Vesuvius.

3PAR SAN:

• HP 3PAR SAN performed as expected without any issues.

Network:

• TAMU not able to remote access into new Exchange server EX19 along with new domain controllers. Discovered EX19 and the Domain Controllers were not in Server Group on SonicWALL firewall.  Placed new servers in SonicWALL Server Group remediated shore access issues.
• Discovered ports C42-054 & C42-055 in CPMAG lab were connected to wrong ports on switch. Further investigating showed premise wiring was connected to wrong port in ISO ductwork.  Switched cables to proper ports remediated mass confusion.
• Obtained Extreme Network annual contract renewal. Located it with our other software licenses.

PC Workstations:

• Installed EchoSIM software on WinFrog1 PC53317 and WinFrog2 PC53312 per Dan Malone’s request.
• Discovered Microsoft Office 2019 will no longer receive software updates from our JR WSUS (Windows Software Update Services) server on Cannon. Office 2019 embracing Office 365 method where updates are pushed by cloud Microsoft CDN directly to Office 2019 installations.  Discussions underway about alternative solutions.
• Userroom PC’s and Zoom PC station have been updated current by JR WSUS Windows Update server. Userroom PCs have also been updated to Windows 10 v2004.  McAfee anti-virus has been uninstalled and replaced with CrowdStrike.
• Downloaded LabVIEW 2019 SP1 Runtime 64-bit from NI and installed on ChemLab PC53243 and Core Entry PC53257 for new Oxygen sensor instrument.
• Due to various media corruptions, staged LabVIEW 2017, 2018 and 2019 onto external USB hard drive for future installation. Media labeled for identification.
• Installed software R and Rstudio on PC53268 in Bridge Tech Office per LO’s request.

MAC Workstations:

• Applied Security Update 2020-007 to ALL Mojave Macs on the ship.
• McAfee uninstalled and replaced with CrowdStrike on all shipboard Mac workstations.

Printers:

• Downloaded and installed Zebra Designer software on Chemlab PC53242 and Core Entry PC53257 for custom label printing by Curator and Chemists. Software license stowed with other software licenses.

Satellite/Internet/Phones:

• Jan 5^th, internet service outage at ~5PM. Outage lasted about ~20 minutes.
• Jan 14^th, internet outage at ~2:40PM JR time per email notification from Marlink for planned maintenance. However, Marlink incurred satellite issues causing internet services to be down until Jan 15^th ~4:30 AM.
• Jan 21^st, 7:06PM internet outage. Duration ~10 minutes.

Other Equipment/Projects:

• Shore has decided to not renew WSFTP software license and let expire due to vendor depreciation of software. Substitution recommendation is to use FileZilla for internet transfers (has a resume feature) and WinSCP for shipboard usage.
• JR_BPnas logged error “Activation Key Expired”. Contacted vendor and received current license key.  Stowed license key with other software licenses.
• Adobe ended support for Flash software December 31, 2020. All newer versions of browsers uninstall Flash with update.  Our AVTech environment monitor requires updating due to Flash based software.  Shore working on purchasing new software.
• Received directive from shore to proceed with CrowdStrike Endpoint Security installation aboard JR.
  • Created credentials to CrowdStrike cloud services and got dashboard operational.
  • Installed software on all physical and virtual servers.
  • Deployed CrowdStrike to all Mac workstations.
  • Deployed CrowdStrike to all PC workstations.
  • Setup Proxy server for non-internet workstations for access to CrowdStrike cloud service.
  • Uninstalling McAfee anti-virus software as deploying CrowdStrike.
• Dec 26^th ~6AM ship lost power and data center switched to UPS power. Ship power was restored about 20 minutes later. 
• Siem Electricians installed electrical box on Orange Damper power cord E1-F-02 in LTDAT data center due to un-terminated disconnected wiring.
• Jan 23^rd, Siem planned power outage at 1PM to service main breaker between ship power and MGE UPS. Power outage was ~15 minutes and MGEUPS maintained power without incident. 
• Discovered warning light on HP MSL6480 Tape Library. Error indicated tape drive failure.  Initiated a tape drive reboot then a tape library reboot but error condition persisted.  Opened case with HP support and reviewed error logs and tape drive condition.  Vendor confirmed tape drive failure and issued a replacement unit.  Replacement unit in Air Freight to Expedition 395P.
  • Return freight setup for failed unit’s return to shore by EXP390R ALO. On-coming MCSs to expedite replacement before departure from Cape Town.
• HP MSL6480 Tape Library firmware updated to rev 6.0. Tape drives updated to latest firmware version M571.  This in response to shore updating their HP MSL6480 tape library and drives.
• Tracercam in Mud Room ceased functioning. After various troubleshooting efforts discovered Ethernet network cables to webcam failed.  Replaced NIC cables, power cycled Tracercam and switch restored functionality.  Also, discovered LED lighting failing.  Replaced with spare LED light.  Replacement parts ordered.
• In association with shore efforts upgraded ship servers HP iLO systems on all physical servers.
  • HP iLO 4 v2.77 and ROM/BIOS v2.80 successfully installed on Maunaloa and Spurr.
  • HP iLO 5 v2.33 and ROM/BIOS v2.40 successfully installed on Erebus & Fuji.
  • HP iLO 5 v2.33 and ROM/BIOS v2.40 successfully installed on ESXi servers Kilauea, Tambora and Vesuvius.