LAB OFFICER REPORT

Roy Davis

General Leg Information

Expedition 361 P3, Cape Town Tie up commenced on June 9,2016 at Cape Town, South Africa with the boarding of the marine specialists. Expedition 361 P3 ended and Expedition 362T began with the sailing of the vessel on July 4, 2016 bound for Site 1437A. The Expedition ended at Colombo, Sir Lanka. The vessel arrived in port 3 days early on August 3, 2016. Crossover with the oncoming staff occurred on August 6, 22016.
During the 361 P3 tie-up and 362T transit one of the primary tasks was the creation and implementing the new web services by the software development team. The team during tie up had 6 developers onboard and the vessel sailed with 4 onboard. Extensive testing by the marine specialists was carried out on all tracks, instruments and software. Included in this testing was the KTLF exercise.
The microscopes were serviced and training given by Emile and Lorentz Meylan.
A little over nine days were spent at Site 1473A in a successful attempt to clean the hole out and retrieve 2 cores.

Port Call Activities Overview

Cape Town, South Africa
Loading of

• 1 ea IODP container of D-Tubes and misc. science supplies
• 1 ea operations flat
• 5 ea 40' Flat of Drill Pipe
• Bulk
• Regular air freight

Offloading of

• Trash
• No Surface.
• 1 x RAF (yellow box in chemistry lab).
• Off going cores (4 core boxes plus 'bit case' containing the extra-large diameter core) going to KCC with EXP362 cores.
• A core box of split core liners is in the Hold Reefer – LO requested we not trash good liner but split them for use back in College Station. Requested that this dtube box, once full, be sent to College Station. No end caps placed on them to not use ships supplies.
• VIT Cable Drum is in 362 Pending – to be returned with S/F from Singapore – located on Core Tech Roof.

ASSISTANT LAB OFFICERS REPORT

Heather Barnes

SUMMARY

EXP362T was a transit from Cape Town, South Africa to Colombo, Sri Lanka with two main objectives for the technical staff. 1. To process cores recovered from the re-entry of U1473A (upon successful recovery of the mechanical bit release ring that was lost down hole on EXP360), and 2. To test the new Web Services. The remediation of U1473A was a success, although no metal ring was retrieved. It is believed this ring fell onto the seafloor during the last RCJB attempt during EXP360. Five cores were recovered (92M – extra-large diameter core, and four half cores 93R, 94R, 95R, and 96R). We sailed a skeleton crew of technicians and four programmers. The testing of the new Web Services required continuous testing of all instruments and web applications. There was an ongoing relay between technical staff's testing and reporting of bugs and the programmers. Outcome of new web services was to proceed with the update for the upcoming EXP362.

CORE LAB and OTHER

• A large diameter core, 18.5cm (7.5") was recovered during U1473A_92M. It was decided not to split this core onboard and it will be shipped as is to KCC (with EXP362 cores). The four half cores recovered were run through WRMSL MS and GRA, NGR, SHIL, SHMSL. The Archive sections are being kept in the core lab for Xixi to run in the SRM.
• Saw covers/cases in splitting room were all replaced with new in-house fabricated plexi glass. Complete overhaul of saws was completed during tie-up. They were tested during the splitting of the cores recovered. The super saw also worked very well – we did not notice any skewing.
• Please note: the Supersaw was found to have Aqua-Lube coating all the rails, screws, etc. This material is horrible for the Supersaw (or anything inside the labs) because rock dust is caught in the aqua lube making it very difficult to clean and damaging to the rails, screws etc. Please advise the technical staff of the use of AquaLube (an underwater lubricate) – not to be used on the super saw rails/screws.
• New lights installed in splitting room.
• The Brady Labeler that was returned for repair came back to ship without being fixed. Brad Julson said to keep onboard for spares.
• Large Treadmill is having difficulty keeping incline. Etienne and I are going to do an overhaul.

AMS/INVENTORY

• White Mugs price increase to $12.00.
• 2014 labels for Zebra printer in the sample entry printer was gumming up – may have to clean the metal flap on inside regularly. Since replacing with a new 2014 roll we have not had any gumming.

SHipments

• No Surface.
• 1 x RAF (yellow box in chemistry lab).
• Off going cores (4 core boxes plus 'bit case' containing the extra-large diameter core) going to KCC with EXP362 cores.
• A core box of split core liners is in the Hold Reefer – LO requested we not trash good liner but split them for use back in College Station. Requested that this dtube box, once full, be sent to College Station.
• VIT Cable Drum is in 362 Pending – to be returned with S/F from Singapore – located on Core Tech Roof.

EXP 362P/T Remobilization Activities Final Report

David Houpt

Introduction

The JRSO has implemented maintenance tasks that under normal circumstances curtail or even circumvent the need for a "kick the tires, light the fires" (KTLF) effort following a maintenance period/tie-up. The instruments in the laboratory are exercised during the tie-up and problems are identified and dealt with wherever possible before a return to the operational phase.
The Exp. 362P/T tie-up and transit was significantly different because of the scope of changes planned by the ITDS Department:
Changeover of database servers
Changeover of network servers
Utilization of ORACLE Database Appliance architecture
Rebuild of all Web Service programs
Rebuild of all JRSO software to fit the new architecture and Web Services
JRSO management decided that a more extensive and exhaustive KTLF activity was needed to ensure that the new environment and software would be tested to the degree possible and that as many problems as possible would be identified and corrected prior to Exp. 362 (Sumatra).
The scope of changes was extensive and even within ITDS, opinion was divided whether the systems would be ready for operations; the Web Services project was built with a cutout, at which point the decision could have been made to go back to some of the old architecture and software. (It was not possible to completely go back because of some of the changes made.)

Summary

The majority of systems are fully functional at the time of this report, with only a few continuing problems, only two (possibly one) that resulted from the Web Services and architecture change:
The LIMS2Excel tool is exhibiting a memory leak when images are downloaded and will crash upon second image download and
LIMSPeak will give inconsistent results on the GC3 and NGR hosts; one is Win/XP and the other a 32-bit install, so this particular problem may lie with dependencies involving Silverlight and not Web Services.
The developers are working on resolving the LIMS2Excel problem as well as many of the ones below. The LIMSPeak issue does not have a resolution; users will be instructed not to use LIMSPeak at either of those stations.

IMS-Related Problems

Some of the remaining problems we have are related to IMS changes (or could possibly be old bugs not reported previously):
The Section Half Imaging Logger (SHIL) will not upload files for 360° whole-round imaging,
The SHIL does not respond properly to manually-entered lengths,
The RGB offset error corrected during the last tie-up has recurred, and
The Superconducting Rock Magnetometer (SRM) is not functional.
The developers are in need of assistance from Bill Mills to resolve these without tremendous expenditure of resources, given that their best LabVIEW programmer (Algie Morgan) was not available for Exp. 362T.

Old Problems

Many of the items remaining on the developers' bug list are old bugs and inefficiencies that were noted again by the KTLF team or were already known. Most of these have nothing to do with the Web Services project or the architecture changes. They are:
Drill Report knobby values do not update under certain conditions; have to be manually updated by developer,
Megauploadatron (MUT) will display additional ghost files on the Automated Vane Shear (AVS) when the AVS files are incomplete,
SHIL will crash after some number of scans; this was originally attributed to the 360° capture mode, but that was ruled out through testing,
Image Capture software saves files to the Temp directory no matter where it is told to point; MUT handles this and the system works, just can't be configured properly,
MADMax pycnometer "rerun" button will not work properly; if one accepts the result and then double-clicks "Volume Dry (cm3)" again it will rerun and replace the value as expected, and
DESClogik mass delete function gives unpredictable results.

Environmental Changes

The biggest changes took place behind the scenes, with new servers, new appliances, etc. For the technical and science user, most of these are invisible, except that old servers like KRAKATOA are gone and ones like EIGEN are here. Even that detail is not important to the majority of users. Likewise, the developers' business practices have been better defined—the way they build their applications, publish, and deploy them is under a higher degree of control and deploying a new version is much less fraught with peril. For example, we went through approximately 30 versions of Sample Master as various bugs were dealt with. By the time we got to the latter half of those, the auto-installation of a new version was functioning properly and now it is almost impossible to be working from a "stale" version of Sample Master and many other applications.

One-Click Installation "Feature"

JRSO technicians have been firmly trained always to use Mozilla Firefox to install applications, but at the current time, at least, it is necessary to install them from Microsoft Explorer…but always to run applications through Mozilla Firefox. This will no doubt cause some confusion and will be a topic of Paul Foster's crossover training for the oncoming technicians.
Web applications (e.g., Auther, LIME, LIMSPak, LORE) and Java applications (e.g., Correlation Downloader, LIMS2Excel) are not affected by this, and should be run and for Java, installed from Mozilla Firefox.

Authorization Change

The Auther program that governs user accounts, roles, and privileges has been greatly expanded to control a large number of application privileges (in fact, any application that writes to the database has an Auther privilege), and this includes Sample Master. The Curatorial Specialist is the default user account to grant privileges (including the ability to grant privileges) to other accounts, and we have configured Auther for the upcoming expedition to help the Curatorial Specialist.
Note: the Laboratory Officer is authorized to grant or revoke privileges on any application except those that touch the samples (Sample Master and LIME-Sample), but historically, both LO's have delegated this authority to the Curatorial Specialist. As this has become de rigeur, the Curatorial Specialist account is the only one with any ability to grant privileges. The developers can step in if needed as well, so this is not a single-failure point.

Login Screen Changes

One of the ways a technician can easily see if they're on an old version of software is that the login screen has changed in appearance. If a tech sees the old style login screens, they should uninstall, reinstall, and then continue.
The new login screen also includes an information window in the upper right corner that appears if the version is outdated or if the software is pointed at a database instance incompatible with how it was installed. If one is using an application that is configured to work with the SHORETEST database, for example, pointing it at SHIP will trigger the message, which instructs them to reinstall the software for the version compatible with SHIP. It is much more difficult to be "in" the wrong database now (mostly a problem if one was doing a lot of work in a test DB and then inadvertently did something in the production instance).

Application Page Changes

The developers have built a new application landing page (web.ship.iodp.tamu.edu/apps) that is organized in a different way. Web applications are collected alphabetically together, as are Java and Windows applications, respectively. All of the user-installable and/or Web-based applications can be found here. The organization of the page may not be ideal; the developers can build one divided by type of program (e.g., uploaders, reporting, data collection, etc.) if they are provided with a schema for organization.

Technical Documentation

Technical documentation was somewhat disorganized, including the creation of "convenience" folders in some labs that had copies of the user guides (UG) and/or quick start guides (QSG) from all of that laboratory's systems gathered in one place. These have all been deleted, because orphan directories will eventually lead to orphaned document versions.
We also found many UGs with references to and screen shots of years-old software, while QSGs often dealt with the new version. In some cases, QSGs were updated and revised while the UG remained untouched, many years out of date. Technicians in charge of each lab need to tackle the admittedly big job of updating the full UGs, from screen shots to workflow, not just focus on the simpler (and easier) job of authoring or updating QSGs.
In speaking with the technicians, another technical documentation hiccough appeared. In many cases, a revision to the UG (or just the QSG) was in the directory as a draft, but no copy of that draft made it home to me and Lorri Peters for review and redistribution. In these cases, the technicians told me that they were waiting for input from their counterpart(s) on the other crew before they send it in to me. Unfortunately, based on the draft document dates, this philosophy isn't working.
We will discuss this at the Colombo crossover and I will reiterate that the process should be "write draft, getting approval from ALO or LO if necessary, then send to shore (Houpt) for review." If something is in that draft that I am not familiar with, or that I feel needs discussion, I will distribute it (with deadlines for reply) to the appropriate parties as needed. Otherwise, I will review the document and either send it back to the author for further revision/review, or pass it on to Publications for distribution.

Detailed System Report

This section does not attempt to reproduce the individual laboratory technical reports, but rather to give a detailed overview of the problems and solutions during the cruise.

Chemistry and Microbiology

At the start of the Web Services project, the chemistry laboratory was the focus of a lion's share of developer troubleshooting effort. As Erik Moortgat described it, "More things weren't working than were." By the time we departed South Africa, the reverse was true, with most systems working and only a few bugs remaining (e.g., alkalinity software behaved badly if the up/down arrows in the user interface were used). Erik also stated that he wasn't worried as the largely third-party instrument software was working properly, the instruments (save the SRA) were in good working order, and he (or Lisa and Aaron) could always use the Spreadsheet Uploader if they absolutely had to. In the end, that won't be necessary as JRSO and third-party software is all working now.

Analytical Gas Supply and Monitoring

The helium manifold is leaking since the pycnometer was put on the manifold and it was opened up to the core deck level. The leak was quite severe at the beginning of July, but it has been brought into a more acceptable level by finding and tightening fittings. The loss rate is higher than the base consumption rate, so additional effort to find the leaks would be good, but a bank of eight cylinders will last for more than a month at the current consumption rate.
The gas monitoring system consists of the acquisition sensors, software that gathers the data from the sensors, an uploader to feed that into the database, and the actual gas monitor report. The data gathering software could fail without tripping the uploader, and the uploader could fail without warning the report, and this was corrected. The user at the report level will be warned if a new data point was not collected within a specified period.

CARY Spectrometer (and Autosampler)

The autosampler for the CARY spectrometer has been installed and methods developed by Erik. He has written a brief manual for the autosampler as a supplement to the user guide.
Source Rock Analyzer
The SRA developed a fault where the flame ionization detector (FID) will not remain lit, and wouldn't even light with a butane lighter (usually the "go-to" solution in these cases). The decision was reached to send the unit to shore for repair by Weatherford Laboratories, given that Exp. 362 and Exp. 363 are not expected to need it for gas safety purposes.

Core Description

DESClogik and the Value List Manager

DESClogik was tested against the new Web Services and is functioning well (this is compared to its traditional functionality; we'd still like a speed enhancement). The team discussed Value List Management and a working protocol was hashed out until such time as a project to replace DESClogik and its underpinning assets can be developed. The team felt that it was premature to replace the VLM tool without first determining where DESClogik is headed.

LIMS2Excel

As of the time of this report, LIMS2Excel works for tabular data, and will work the first time for image (and I would assume linked files as well) download. Subsequent attempts to bring down images (even a small data set) will crash the program. This is not resolved at this time.

SEM Uploader

The SEM uploader was modified to have "sticky" data entry fields as well as the already-sticky hierarchy selection fields. The user has a "clear" button which can clear all of the fields, but when uploading multiple images of the same type of material (e.g., at multiple magnification settings), they need only enter a new comment (or edit one or two fields as needed). This should make the workflow much easier for the user.

Curation

Auther

One of the biggest changes in the Curatorial Specialists' toolkit is that Auther now authorizes nearly every program that touches the database, including Sample Master's privileges. It will be necessary to go through this with the oncoming Curatorial Specialist to ensure she understands the tool. (As a backup, however, the developers all have the authorization to make changes to roles and privileges as well.)

Sample Master

Sample Master bugs were corrected along with taking corrective action for Web Service-caused errors, and the new version should function much more smoothly. Some changes in functionality may exist, but for the most part, things now work as we expect them to (e.g., updating fields that are actually TEST table records instead of SAMPLE table records works now, and before those tasks were variable in outcome).

Request Code Manager

The developers did not want to resurrect this limited-functionality program, and we agreed with him. The developers will instead train the Curatorial Specialists on SQL Developer, give them write access to the two tables involved, and let them directly edit (and copy/paste if wanted) into the database. The two tables are the link between requesting scientist and their IODP request number, and the link between IODP request number and the shorthand shipboard code. The curators are more than capable of keeping this directly in SQL Developer and they should find that tool much easier to use.

Downhole Measurements

TPFIT Files

The uploader and LORE reports have been modified to capture and specifically call out the various file formats. Both DAT and WTF (WinTemp Files) are recorded and reported, and the image file reported is in EPS format. (PNG format is available through the extended report.)

General Lab

A guide for precision weighing at sea was created and put in the General Lab folder in the Technical Documentation folder on the network. This describes the process, the importance of matching masses between reference and unknown pan, and the expected limits of precision in various conditions.

Imaging and Microscopy

The cameras and other equipment used by the Imaging Specialist were not tested during the cruise as we did not have a photographer on board.

Image Capture Software

A guide to microscope image scaling was created, and the oncoming Imaging Specialist should familiarize themselves with the concepts and requirements of that guide. Rigorous adherence to the concepts in that guide should keep the scale bar error below an acceptable limit.
Image Capture had a number of bugs to work through, and it was discovered that it had never been recording all of the metadata selected by the user; this has been repaired and some metadata items (e.g., filters) are now stored all together in one field.

Paleomagnetics

All of the paleomagnetics lab equipment is in good order, and all of the software save the SRM and its surrounding applications (MUT, LORE, LIMSpeak template, etc.) is in good order.

Superconducting Rock Magnetometer

We were able to test the functionality of the new IMS version of the software to some degree, but the software has not reached readiness for Exp. 362. Margaret is confident that Bill and his team can work those issues out before they get core, but the paleomagnetics technician and scientists will have to keep a watchful eye on the data produced.
Currently identified problems: SQUID constants being truncated at 2 significant figures, some axes are not correct for working and archive half samples, slow performance (slower and slower the longer the section and the higher the resolution), data not in a format to upload, reports not in formats to download. Maggie wrote more extensive reports of the issues to be corrected.

Physical Properties

Gantry

Automated Vane Shear

Moogy got this working! A bug still exists when uploading data if the Excel file is incomplete, but the system is working.

Pocket Penetrometer and Torvane

The software was updated to directly store the instrument observations, not convert them to N/m2 as before. The data back home should be adjusted the same way: units converted to kg/cm2 and the numeric result divided by 98.065.

MADMax

The water circulation system was found badly clogged (only one cell was circulating) and after experimentation with temperature stability with and without water circulation through the back of the box, it was determined that the water was not needed for good data quality. The plumbing was removed and the pump stored in case the alkalinity pump fails. The MAD manual was rewritten during the transit and should reflect the current workflow.

NGRL

The NGRL user guide was rewritten prior to the transit and should reflect the current workflow. The timing calibration procedure is not documented and it will be necessary to hire either Grigor Chubaryan or Maxim Vasilyev to come to the ship (e.g., at the next tie-up) to walk us through it while being filmed. The timing calibration is sound at this point—if it was not, the active shielding wouldn't be showing the efficiency it does, and the coincidence count would drop—but it's a hole in our procedures that needs to be filled.

SHIL

The SHIL still has the pre-existing error that it will crash after some number of measurements (approximately 20+, but it can happen earlier). This appears to be a memory leak, but the source was not found. In normal section-half mode, everything is working properly.

Whole-Round Imaging

The upload file format and filenames were changed for the whole round imaging process, and currently whole-round images will not upload without hand-editing (as we did for the U1473A cores during 362T). This should be a relatively minor fix.

RGB Offset Error

The RGB offset error has recurred, meaning that we lose the top ~2 cm of RGB data and have a "tail" of RGB data after the section. Unfortunately, the fix for that problem was not documented, so the developers don't know where to look to fix it; Algie or Tim should make sure to document how Bill fixes is to that we can deal with it if it recurs again.

SHMSL

MS2/MS2K Zeroing While Moving

We had only one problem with the software: the MS2/MS2K zeroes while the carriage is moving; we'd like a pause added so that it zeroes while still, then continues to the measurements. Motion has been observed to cause a ±1 instrument unit "flutter" in the zeroing that is small but can be avoided. This has not been changed as the calibration behavior is not a user-configurable item.

MS Measurement Offset

For the point MS measurement, we did find a 10-instrument unit offset that is a combined consequence of the metal around the logger and the distance above track that the MS point zeroing is done; this same offset can be found in recent expedition data (except Exp. 361, see below). We have made physical changes (removed Al ruler, Al mounting plate for the laser) and configuration changes (load and unload height is now ~1 cm above track) to deal with this.
The low load/unload height is necessary to keep the MS2K probe from reacting to the proximity of the 80 mm x 80 mm aluminum frame that the Delrin frame is mounted on. Although the 80 x 80 frame is pretty far away on an inverse-cube sensitivity measurement, it is really massive so it causes a 2-3 instrument unit offset if the MS2K is zeroed at the previous height of 4-5 cm.
Under current conditions, the MS2K zeroes properly for the sections and no offset is observed. The logger also shows no "slanted" results across the section.

Exp. 361 Offset Mystery

There were puzzling results on Exp. 361, where the normally -10 offset was instead +15. We looked at photographs of the logger during Exp. 361 and could find nothing in or around the track that could account for such an offset (25 instrument units compared to the usual offset baseline). The PP tech should keep an eye on the agreement between the whole-round MS2C results and the MS2K.

General Comments on MS2C/MS2K Agreement and Offsets

For 6.6 cm sediment cores, the MS2C 90 mm loop has a correction factor of 1.054 due to the diameter/diameter correction. (This means that the instrument unit result should be divided by 1.054 to obtain SI units.) The WRMSL and STMSL MS data should therefore be within 5.4% of the SHMSL MS data (with additional variability because of the different integration areas of the sensors), and this difference will scale with the magnitude of the MS values. An offset always represents a problem with the zero point of either the whole-round loggers or the SHMSL. The source should always be identified and corrected out. Figure 1 shows the difference between the expected MS2C/MS2K variation without using the 3.45 x (d/D)3 correction for 66 mm cores in a 90 mm loop, compared to a -10 offset (green trace).
Note: When calculating D, the diameter of the loop, it is necessary to add 8 mm for the distance between the inner plastic of the aperture and the actual position of the coil inside the housing.
Figure 1. Effect of a -10 offset on MS data. The normal comparison between MS2C and MS2K on sediment cores should be within ~5.5%.

WRMSL and STMSL

At the beginning of the cruise, we had a lot of problems with the WRMSL, the most egregious being the storage of final-section, final-sensor data with the pusher core. All of these were eventually solved—with thanks to Bill for pointing the developers in the right direction—and the WRMSL is fully functional.
Toward the end of the cruise, we decided not to keep the STMSL on IMS 9.0 any longer (we had done this for contingency) and the system is being upgraded to 9.1 at the time of this report; it will be tested by the KTLF team prior to the port call.

Stratigraphic Correlation

The stratigraphic correlation tools have been tested and are functional. A number of undocumented changes to the Correlator Downloader (extra features) were found and a draft manual was created to at least create placeholders for them. Completing the draft will require input from the developer(s) who made the changes.

Conclusion

The changeover to the new architecture and Web Services went amazingly well, but I will caution the oncoming and future crews that we almost certainly did not find all the bugs, problems, and glitches. We have patched the worst of the problems or outright replaced the bad code in some cases, and the environment runs better than I have seen it, especially given that new versions of programs were being pushed out regularly.
I wish to commend the developers for their hard work and dedication during the entire process. Many long days and a great amount of effort went into this project, and a tremendous amount of patience as we "broke" things within minutes of them patching something.

Curatorial Report

Heather Barnes

SUMMARY

EXP362T was a transit from Cape Town, South Africa to Colombo, Sri Lanka with two main objectives for the technical staff. 1. To process cores recovered from the re-entry of U1473A (upon successful recovery of the mechanical bit release ring that was lost down hole on EXP360), and 2. To test the new Web Services. The remediation of U1473A was a success, although no metal ring was retrieved. It is believed this ring fell onto the seafloor during the last RCJB attempt during EXP360. Five cores were recovered (92M – extra-large diameter core, and four half cores 93R, 94R, 95R, and 96R).
Samples
There were no shipboard/shorebase samples.
Cores
An interval of 19.7m was cored. A total of 16.9m of core was recovered (85% recovery). Cores collected are 92M, 93R, 94R, 95R and 96R. 92M was a 36cm large diameter core drilled during the use of the RCJB. All cores are to be shipped to KCC, Japan from Singapore (with the EXP362 cores).
Residues
No residues.
Thin Sections
No thin sections
Core Preservation
All Working halves were shrink wrapped. The Archive sections were not shrink wrapped and are in the Core Lab for Xixi to run in the SRM. The extra large diameter core recovered from 92M was not split into Archive and Working and will be shipped to KCC for splitting onshore. It is package in an aluminum bit case (in core lab for show and tell).

Special CURATION

Curation for 362T U1473A Reverse Circulating Junk Basket
One RCJB (92M, M= Miscellaneous in sample master) was used and produced an 18.5cm (7.5") diameter core, 36cm long. It is too large for our facilities onboard and will be split at the KCC.

Sample MAster

Updating Web Services: Major project for 362T
The updating of web services required relentless testing of sample master to iron out any bugs before EXP362. There were a plethora of issues (discussed in David Houpt's LFKT 362T Report), however with most issues having been addressed, at the time this report is being written, there still remains one major issue. Sample Master is taking a long time to update edits to curated and catwalk length. For example, if an edit is made to a section length and you subsequently click to the sample entry screen to enter catwalk samples the new updated lengths do not appear until several minutes later. The programmers are aware of this issue and are working on it – hopefully all will be sorted before EXP362.
Hard copies of following box info is in ALO Office.
CORE BOX INVENTORY
EXPEDITION 362T - WORKING
First Last
Box NumberHoleCoreSectionHole Core SectionMissing or Added Sections
1WU1473A93R1U1473A95R5
2WU1473A95R6U1473A96R4plus 5 empty Dtubes (space filler)
CORE BOX INVENTORY
EXPEDITION 362T - ARCHIVE
First Last
Box NumberHoleCoreSectionHole Core SectionMissing or Added Sections
1AU1473A93R1U1473A95R5
2AU1473A95R6U1473A96R4plus 5 empty Dtubes (space filler)

Software developers REPORT

Paul Foster, David Fackler, Jon Howell, and Rui Wang

SUMMARY

Transit 362T
Completion of the web services project, creating and implementing new web services. All applications were modified to comply with the new web services. Coordinated with KTLF team for testing of all applications. Correction of reported issues completed on all applications except for the tracks, which were left unchanged.
Project report for web services project appended at the bottom.

PENDING WORK from web project

• Assist curator with handling sample requests and codes for 362
  • Loss of Request Code Manager means the curator needs a means of keeping these up to date.
  • If curator is comfortable with SQL Developer, grant access to insert and delete on the appropriate tables and work with them to get them started editing.
  • If not, assist curator by providing editing of these tables for them.
• Work with curator to design replacement program for Request Code Manager
  • Coordinate with shore curators and develop design for new program to support this activity.
  • Begin development if time allows.

Applications

Windows C#/.NET applications

• Bulk Label Printer –
  • Converted to new web services
• Chlorinity Titrator
  • Converted to new web services
• Coulometer
  • Converted to new web services
• DESCLogik
  • Converted to new web services
  • Fixes applied to allow load and download of extremely large hole information. Slow, but functional.
• Gas Analysis Report / Gas Safety
  • Converted to new web services
  • Non-functional reports for higher gases fixed, except for the comparison of Methane to sum of heavier gases.
• Gas Monitor Uploader
  • Converted to new web services
• ICP Analysis
  • Converted to new web services
  • Modified to use a batch results loader to improve performance
• Image Capture – Microphoto / Thin Section / Closeup
  • Converted to new web services
  • Filter capture in Microphoto modified to put all text in one result
  • Label printer in Closeup fixed
• MADMAX
  • Converted to new web services
• Mettler Toledo
  • Converted to new web services – no changes
• MUT – MegaUploadaTron
  • Converted to new web services
  • Modified to use a batch results loader for tracks to improve performance
  • Modified to load time measured for tracks and SEM
• NGR Master
  • Converted to new web services – no changes
• Samplemaster
  • Converted to new web services
• SpreadSheet Uploader
  • Converted to new web services
• Thermcon
  • Converted to new web services
• Thermcon File Converter
  • Converted to new web services – no changes
• TPFIT temperature file uploader
  • Converted to new web services
• Virtual Photo Table
  • Converted to new web services
• Worklist Generator / Chem Work List
  • Converted to new web services

Web Applications

• Auther
  • Converted to new web services
  • Lots of new privileges and roles added to support new granularity of authorization
• Change password
  • Converted to new web services – no changes
• DESC Value List Manager
  • Converted to new web services
  • Google services fully disconnected
• Drill Report
  • Moved to new server environment unchanged. Not converted.
• Gas Status Monitor
  • Converted to new web services
• Image QAQC Report
  • Converted to new web services
• LIME – LIMS Editor
  • Converted to new web services
• LIMSPeak
  • Converted to new web services
  • This application can ONLY be built on ship build box. Treat gently.
• LORE – LIMS Online Report
  • Converted to new web services
  • Modified to use batch retrievals to improve performance
  • Modified download options to include display capture and remove Java code
  • Download modified to only handle asman based files.
• OLD WTR Summary Report
  • Converted to new web services
• Overview
  • Converted to new web services
• SCORS Uploader and Manager
  • Converted to new web services
• TASAPPS Application assist menu
  • Converted to new web services
  • NOT fully configured for new applications. Links and menu out of date. Needs considerable data base encoding to be production ready, but little interest expressed by users.
• Thin Section Report Builder
  • Converted to new web services

Java Applications – JNLP Launch

• Correlation Downloader
  • Converted to new web services
• Image Grabber
  • Converted to new web services
• LIMS to Excel (L2E)
  • Converted to use the modified data base and the new login service
  • Major modifications made internally to make the program conform.
  • Splice options removed.
• SEM Uploader
  • Converted to new web services
  • Comment moved under other entry options.
  • Most entry options made "sticky" between uploads.
• Splice File Fixer
  • Converted to new web services
• Thin Section Report Writer
  • Converted to new web services

Physical Deployed Applications (require direct installation on target computer)

• Balance 64 / Cahn Balance
  • Converted to use modified data base
  • NOTE – DB location now embedded in .bat file that launches the application
• Java Label Printer
  • Converted to use modified data base
• Penetration Strength Entry
  • Converted to use modified data base

Web services and related libraries

All web services and libraries created and tested during the web services project. Everything is new.

Legacy Web Services

• resteasy-asman
  • currently required to support Drill Report – to be removed as soon as Drill report application is converted for FileGet and the web services converted for FilePut
• resteasy-drillreport
  • converted to build and run on Olympus – no other changes
• resteasy-imagetiling
  • converted to build and run on Olympus – no other changes
  • expected to be removed as soon as the new LIMSpeak application goes production

developer resources

Build Box

• Added libraries to support building GWT applications
• Removed old dependencies on profiles for build process

servers

<ac:structured-macro ac:name="anchor" ac:schema-version="1" ac:macro-id="e3db4b52-7fda-471f-98a6-ff7b1c20a600"><ac:parameter ac:name="">_Toc331834871</ac:parameter></ac:structured-macro>Tomcat servers - normal [ELCAPITAN and MATTERHORN]

Servers were restarted after completion of deployment of build box production build

<ac:structured-macro ac:name="anchor" ac:schema-version="1" ac:macro-id="b9be0c8a-2467-4920-9071-926eb2de2d97"><ac:parameter ac:name="">_Toc331834872</ac:parameter></ac:structured-macro>Tomcat server - file/asman [OLYMPUS]

Servers were restarted after completion of deployment of build box production build

<ac:structured-macro ac:name="anchor" ac:schema-version="1" ac:macro-id="c44ee42d-62a6-4293-8b7a-243d8d031791"><ac:parameter ac:name="">_Toc331834873</ac:parameter></ac:structured-macro>Apache web server / redirector [EIGER]

This box is no longer a primary work area for developers except as needed to fix redirector attributes. No deployments are done at this location and no web pages are maintained by developers on this server.

DATA BASE

SHIP

Added procedure and scheduled job to prune the pitalog.log table to remove all entries over 5 days old and INFO entries over 3 days old.

SHIPTEST

Currently contains expedition 360, 361, and a few pieces of older ODP expeditions for testing. Fairly good copy of 362T cores in TEST-U1437.
Data base column removal tested late in 362T. Data base restored to same configuration as SHIP.

Web services project report

Project Report – 31^nd July
Summary
The KTLF team approved our going forward with the new services. Expedition 362 is expected to successfully use the new services and revised applications. The project is over 95% completed, with all goals met for the portions that are completed. The project will not reach 100% completion. There are two applications running with old services and two applications which could be not converted or moved into the new server structure.
Development activities specific to the new web services project have been finished. Further correction of issues will continue as normal maintenance activities.
The conversion of the shore data base and applications will be accomplished in late August early September. Specific timing to be worked out with the rest of IT and users.
The goals of the project from the charter and scope are:
Primary Goal: Provide implementation of secure authentication for all services which use accounts and passwords (part of meeting an ISAAC requirement)
Secondary Goals:

1. Improve application maintainability
2. Organize services by function instead of by development project
3. Consistent formatting of input arguments
4. Consistent structures for outputs
5. Remove duplicate or similar services, reducing the overall code base
6. Create service deployment packages that can be deployed to any of our web service locations without having to be rebuilt for that location
7. Create test framework for web services

These goals have all been met for the new web services. They were not met for Drill Report and Image Tiling services since they were not converted as discussed above. Those services do not have a need for secure user credential transmission.
Primary goal: All web services and related applications now communicate with encrypted user passwords, providing secure authentication.
Goal 1: The new services were simplified by placing most of their logic into libraries, providing both better reuse and easier testing. Each service is now isolated into a single program file which changes independently of other services. Service files are grouped for deployment into .war files based on how the service needs to interact with the Oracle data base, and each group's data base parameters can be adjusted independently of the services.
Goals 2 and 5: We have reduced down from 19 web service delivery packages (called .war files) containing over 300 services to 9 packages containing about 155 services. The services are grouped based on how they interact with the data base and file system.
Goals 3 and 4: All services use input and outputs based on the JSON (JavaScript Object Notation) data interchange format. This change caused the greatest amount of changes to implement in the applications as the old services used a variety of different formats. Making these changes was very time consuming in the beginning as a lot of software had to be rewritten. As we moved farther into the project, much of that work was re-used repeatedly by other applications, especially our desktop based C# applications.
Goal 6: These new service .war files can be copied to any properly configured tomcat server and run there without need for any changes, unlike the old ones which had to be rebuilt for every environment they worked in. All services for any tomcat server can be reset to use a new data base, account/password, or web redirector in less than 5 minutes.
Goal 7: The test framework for the libraries which support the creation of the services is part of the compile process and runs every time the library is built to ensure nothing was accidentally broken in any module after a change. Each service group has another set of tests that exercises its services after they are deployed to ensure they are functioning normally.
Additional benefits designed into the new services, but not part of the original goals:

• Reduced Oracle logins – implementation of an Oracle pool manager in the services allows multiple service requests to use a common login connection. This reduces Oracle logins by 2 orders of magnitude, down from over a million a day to less than a thousand.
• Output to tomcat logs greatly reduced – removed physical logging references from services and libraries, transferring to log messages stored in Oracle. This provides a single common log lookup location for finding problems instead of searching multiple files across multiple servers. It also reduces chance of server failure due to loss of disk space from excessive logging.
• Integrated service and library documentation – documentation is written into the code, extracted and published via a java utility. Admittedly, the documentation was much better earlier in the project and somewhat lacking towards the end.
• The new design of the web services strives to isolate changes to the smallest effect possible. The purpose was that changes in items like data base location, account/password used to access the systems, Oracle usage settings, and other attributes are isolated from individual services and placed into controlled locations to limit what has to change when changes happens. As an example, changing the primary password for our LIMS data base a few years ago cost 4 days of effort and hours of user service interruption. We can now do it in less than 10 minutes with a 2 minute service downtime. During the test period we changed which data base all the labs were using as a cutover test, in less than 5 minutes.
• Upgraded all tomcat servers and java environments to version 8.
• Moved all developer deployments to tomcat, removing the need to deploy to the Apache web server.
• No functions left on the Solaris servers. (A coordinated effort with a project in Systems to move off the old Solaris servers.)
• Move onto the new Oracle Data Appliances (ODA) (A coordinated effort with a project in Database to upgrade Oracle.)

Unexpected benefits from the project.

• It was a goal to make the services agnostic (able to be run anywhere without rebuilding). Additionally, new techniques adopted during development have allowed the SAME benefit for the applications. Almost all of the applications can now be distributed without rebuilding, getting the necessary information from their environment.
• We developed highly improved Oracle test environments, both on ship and shore. Use of the ODA to establish, reset, and remove special purpose test environments allowed testing of scripts and processes at a pace and level we have never had before.
• While it was stated that correction of old issues with the applications was outside the scope of this project, many old problems have been resolved by the new development. Additionally we found and corrected several "discovered" issues that were masked by coding contained in the old web services. Example: while many of the LORE reports stated they were reporting the date-time a measurement was made, it turned out they were actually reporting the date-time the data was uploaded. The measurement date-time used to be auto-populated when not provided and when that changed we discovered it was never uploaded. MUT, SEM, and TCON now report that information correctly. Other instruments can be added to the process as needed.
• The ability to control data base assignment from tomcat servers instead of code allows developers to debug production code against test or production data bases on their laptops with no code changes. Our ability to use debugging tools in production like environments without disrupting actual production is highly increased, improving the speed at which we can find and fix issues.

Unexpected issues from the project:

• The new service architecture and development process allow changes to be made at a speed that is almost out of control. It quickly became impossible to tell which versions of which library were in use in any set of services. We had to set a process in place during the development to enable us to work together, and even then there were occasional issues. This process will need continued refinement over time to create products we can trust and rely on.
• The new error reporting from the libraries and services contains much more information but it is not well integrated back into the applications. Simply having the information is not enough, it must be properly provided. This will be a continuing effort for some time to improve the error reporting by the application when a service error occurs.

From the original list of 89 applications:

• 2 were unable to be converted
• 2 were changed only enough to move to new servers
• 7 were identified as obsolete and removed
• 16 were checked and moved to new servers
• 64 were converted and moved to new servers

Two applications were found which we are unable to convert or move over to the new servers.

• Request Code Manager is written in Silverlight and has been semi-functional for several years, requiring each sampling code and request number to be typed in by a curator. We have an alternative method for entering and editing request codes and numbers that should support the curator during 362 as well as the old program did. I recommend that Curation meet with the developers and determine what they actually need this application to do and what information should be captured. I expect that cut and paste from a spreadsheet list of request numbers would be preferable to retyping them, for example.
• LimsBarCoder was once a label printing routine used in Chemistry to create labels for IW Splits. The source code we have is for a much older version than what was being used. The author, who is no longer with IODP, apparently never checked in the final version. In discussion with Chemistry, the primary use is for getting a set of sample text_ids for the IW splits, which were then copied into the BatchLabelPrinter application for actual printing. We recommend implementing a better means of selecting IW split samples for the BatchLabelPrinter. This interface to be worked out with chemistry.

Two applications remain unconverted, Drill Report and Image Tiling.

• Drill Report was upgraded, moved to the new server environment, is currently meeting user requirements, and the user community is resistant to change. This system has no interaction with the LIMS data base or applications. I recommend that converting this system be left to a separate initiative, if this is actually required.
• Image Tiling provides images for display in LIMSpeak. It is already clear from the new LIMSpeak specifications under development that we will not be using image tiling with the new application. Therefore the current services have a short expected life span and are not worth the effort to convert. They have been upgraded sufficient for deployment to the new server environment.

All tracks were modified during May by Bill Mills to bring them to the same level of IMS as the new SRM development. Algie modified the track sample entry screens to use the new web services in June. Issues found with the tracks were not counted towards the web service project's bug reports nor repaired counts when they were corrected. Our thanks to Bill Mills for helping out from shore with some of these issues.

During the first 3 weeks of July the TAS test team logged just over 145 bug reports (not including track issues). These included bugs introduced by new services, application conversion, same old bugs that were there before, and discovered bugs (old bugs which were not known but were exposed by the changes). In the same period, the developers corrected 114 of them, leaving no critical or major bugs regardless of how long the bug had been around. These counts do not include repeat offenders (bugs which are pronounced fixed and then show back up.) Most of the remaining bugs are old or discovered and are queued for continued remediation as normal maintenance.
While the scope of the project never changed, the target environment continued to evolve over the year of the project. The project coincided with two other projects in IT; to transfer Oracle to a new computing platform and to retire the Solaris server cluster.
The resulting system on the ship consists of all new servers running updated tomcat and java software, completely new web services, and rebuilt applications created by a new development and deployment process and delivered via new techniques.
I credit the fact that this new creation is actually working to the intense hard work and dedication of our systems people, MCS, data base support, TAS test team, and our developers.

PHYSICAL PROPERTIES

Z. Mateo, M. Hastedt, D. Houpt, E. Moortgat and Exp362T Technical Staff

Summary

Expedition 362T involved a KTLF assessment of newly revised web services and logger modifications, and the remediation operation for Hole U1473A atop the Atlantis Bank. The remediation operation required coring a ~20 m interval to prove the viability for future expeditions in extending this hole. Four half-advanced RCB cores with 15 sections were ran through the WRMSL, NGR, SHIL and SHMSL. Although only these four loggers were utilized, all PP loggers and stations were extensively tested as part of the KTLF exercise. A major modification to the MAD-Pycnometer system was implemented with the removal of the water circulating temperature control. Most user and quick guides are also updated by X362 Technical Staff to reflect changes implemented during this expedition.

Individual Measurement Systems

velocity gantry

The Velocity Gantry was not used to measure samples from this expedition, but was tested several times for the KTLF. No problems were encountered during the testing process: correct data were acquired and uploaded to LIMS.
The only minor issue is at the beginning of the expedition when the PWAVE caliper was found to be stuck in the closed or home position. As the limit switch was triggered, the manual control buttons to the left were inoperable. To solve this issue, the limit had to be unscrewed loose and the Exlar software used to open the actuator.

Moisture and Density (MAD)

No samples from this expedition were analyzed at the MAD station. However, it was significantly tested for the KTLF exercise, in light of the new web services deployed. Routine calibration of the pycnometer was included in the testing routine.
Several bugs were reported, but were all addressed as of the writing of this report, with the latest MADMax version being 2.2.0.19

Issues

1. The Tygon water circulation tubing for the pycnometers are badly clogged! Despite the regular addition of Zymit enzyme cleaner to the water bath, organic residue has built up in all of the internal tubes (see photo below). In an attempt to dissolve the residue, the circulating water was heated up to 55°C and more of the cleaning solution was added. This revealed the gravity of the problem when water was only able to circulate through cell #3; flow to the remaining five cells are impeded (see FLIR image below). However, the situation barely improved and the circulation remained blocked after 3 days. Continued use with the blockage into the upcoming expeditions can eventually clog the only open cell and potentially cause pressure build-up that can disconnect any of the tubes, thereby seriously damaging the electronic circuity of the pycnometers. In addition, with stable laboratory conditions, this temperature control system has minimal or no contribution to the accuracy and precision of the pycnometer cells. Therefore, it was decided that the water circulation system, including the dirty tubes, be removed. During the cleaning process of each cell, compressed air was injected to the inlet or outlet tube in order to remove most of the residue inside of the pycnometer. In some, as much as 35psi of air was required, demonstrating how badly clogged these tubes were.

The cells will now run at ambient room temperature. Pre- and post-modification calibration and verification measurements of the cell and standard sphere volume indicate differences that are less than 1% compared to legacy data (cf. file:///:\{color:#548dd4}IODP_Share_362T_test_folder\Physical Properties\MAD (see subfolders)\MAD Pycnometer\Pycnom CalibVerif_EXP362T.xlsx). Cell volume is higher across the board by 0.6%, but the ratio of cell to expansion cell volumes are on the average only 0.03% higher for the current set-up. Normalized volume of standard spheres also indicate a higher estimate but by only about 0.1%.
However, despite this initial demonstration of comparable and still accurate volume estimates with this new pycnometer set up, it is highly recommended that the upcoming expeditions regularly perform, closely monitor, and document the calibration and verification measurements, taking note of any temperature-related effects on the values.


Close-up photo of the Tygon circulation tubing of pycnometer #4, clogged with organic growth that is preventing water from circulation through the cell.

FLIR image of the pycnometer cells with warm (55°C) water pumped through the series, showing that the water is only able to circulate through cell #3 because all other cells have clogged tubing.

1. The combined volume of the 200 and 300-series of standard precision balls used in calibrating the pycnometers is changed from the 10.2 cc to the more accurate value of 10.255 cc indicated in the actual calibration certificates (cf. IODP_Share\PhysProps\ Certificates\MADMAX\Precision Ball calib certs.pdf and IODP_Share\PhysProps\MADMax stuff\Precision ball calib cert.xlsx).

Table 1: Comparison of parameters estimated using pycnometers with or without circulating water temperature control.

Shear Strength Station (avs)

IT'S ALIIIIIVE!!!
Thanks to Erik Moortgat, the AVS is now working again! Below is the narrative of the troubleshooting process that he underwent.
"It was reported to me that the AVS Giesa system had not been working for a couple of Expeditions and since I had worked on it before I was asked to take a look. Sure enough, the Giesa application would not start at all.
I sent some information to Giesa mbH, primarily about concerns about the environment (Windows/Office), but they said it should work fine as such. So I decided to do a complete clean install of the software. The Giesa application could now run!
The next issue was the inability of the FL2 to talk to the Excel spreadsheet required to record the data. None of the templates we had on the PC would work. The FL2 was working, blade was turning and there were bits of data going into the sheet, but we were not getting the updates at the frequency specified. Another e-mail was sent to Giesa mbH and what we learned is that the tab order in the template was critical. Since our FL2 is running on COM2 of the PC, the main tab, Flügelversuch, has to be in the second tab position. So the template's tab order has to look like this:
Tabelle1, Flügelversuch, Tabelle2, Tabelle3, …
When you save the sheet as a csv, for upload via MUT, the main tab, Flügelversuch, has to go back in the first order position. Also, the file name has to end as …avs.csv (e.g. TextID_avs.csv). I think that everything else from the QSG stayed the same."
Additional notes about uploading data: To identify the sample in the Excel file, enter the TextID right of the cell labeled barcode. Otherwise, use the scanner, but make sure to cut out everything right of the Text ID and paste it to the adjacent cell to the right (2^nd cell to the right of the barcode). Remember to enter the offset in the appropriate cell below, not necessarily in the filename after the textID.
The Penetrometers and Torvanes were also found to be in good condition during the KTLF assessment.

Special Track Multisensor Logger (STMSL)

No data from the STMSL was collected during this expedition. However, test runs for the KTLF showed no problems with the instruments, data capture, upload and reporting process. As of the writing of this report, the STMSL is running with IMS v. 9.0

Whole Round Multisensor Logger (WRMSL)

The WRMSL was upgraded to IMS v 9.1 during 362P2. Two code-related issues were encountered and resolved. Other than these, the WRMSL is running well, even with the new web services.

Issues

1. IMS failed to write a separate file for the last instrument in the array, for the last section in a sequence. Instead, the data was getting included in the file for the standard water core pusher of that analysis.

Solution: Hard code the first PUSHER measurement to set FIRST IN SECTION = TRUE, which was omitted in the update. Bill Mills sent a replacement VI to solve this - C:\IMS\PLUG-INS\DAQ_PI_WRMSL\WRMSL ACTION CALC PUSH Filter.vi. However, LabVIEW still needed to be "repointed" to these component VIs. In a nutshell, open the lvlib (LabVIEW library) and its top-level VI. Even though we dragged and dropped the replacement VI into the exact location of the old version (and it had exactly the same name too) it still needed reminding if you will. Save when quitting LabVIEW at this point should do the trick.

1. The analysis name and file extension was not being properly transcribed from the configuration file. In the case of the PWAVE_L (underscore) analysis, it is converted to PWAVE-L (dash) which prevented MUT from uploading it to LIMS.

Solution: Bill Mills sent instructions on how to fix this behavior. The VI that caused the transformation from underscores to dashes was removed. It is nested very deeply in the section of the code that writes the data files. Since it was actively converting underscores to dashes in the (wrong) spot during data file creation you would never have found it by searching for "PWAVE-L" strings in the static code itself. That's why the config file edit attempts weren't working either.

Section half image logger (shil)

The SHIL was used for both archive section half and whole round line scan imaging.

Issues

1. During the whole round scanning, three images were generated (jpg, trim_jpg, and tiff) and named similar to those when scanning section halves, instead of just the two jpg and tiff files for WRLS analysis, named by the quadrant/angle of the image. As such, MUT was not used to upload the individual line scans of the whole round core, but were rather manually uploaded to LIMS by David Fackler.
2. In scanning the section halves for 362T, the consumer JPG images appeared way too dark.  Maggie took a look at the config file in use and confirmed that it is the one that is created by default when there isn't one available to load at launch.  Presumably the last one in use on X361 got stepped on or otherwise trashed during various forays into the software during tie-up.  Therefore, the default RGB lookup tables and brightness, contrast and gamma were nowhere near where they should be to make acceptable corrected JPGs.

Solution: To fix this, Maggie hand-edited the I_PI_aJAI-CV-107VL.ini file and substituted in the lookup tables and the latter 3 corrections from those in use on Exp 360.  No change was made on any of the actual camera settings.  Cores 93-96 archive halves were reimaged, deemed acceptable by the EPM and uploaded to LIMS.
 

1. Unfortunately, the RGB offset issue from Exp 355 has made a reappearance. This issue is best described as the RGB data being recorded starting at offsets about 3.5 cm from the top of the section, and running past the end by about the same amount. This was fixed by Bill Mills during the pre-Exp 356 tie up but we could not lay our hands on the solution to date. Awaiting Bill's return for this problem.

Section Half Multisensor Logger (SHMSL)

The SHMSL was used to scan all section halves collected during 362T.

Issues

1. During the KTLF testing, it was noticed that the zeroing point of the MS2K is about -10 units off compared to a blank measurement at the level of the section half surface. This was attributed to the significant distance between the zero point and the section half surface relative to the 2x2 extruded aluminum bar frame below. As such, David Houpt changed the zero point from 3 to 1 (in Motion>Setup >Fixed Positions> Load and Unload). This allows the MS2K probe to zero at a level similar to the section half surface and at similar relative distance to the extruded aluminum frame. Though the frame still has an influence on the measurement, at least it is low enough and constant throughout the track.
2. It also appears that the zeroing step occurs about the same time as the gantry moves to the first measurement point, akin to an old behavior that was rectified, but is now back. In order to minimize or eliminate all possible sources of error, a time short delay should be placed after the zeroing step, prior to moving to the first measurement point.
3. Aluminum, although paramagnetic, is displayed by the Bartington meter as if it is quite diamagnetic (gives high negative susceptibilities when aluminum is placed close to the probe). As such, the aluminum mount for the laser and the hefty aluminum ruler were replaced with Plexiglas versions. Many thanks to Etienne for his craftsmanship on both pieces.

Natural Gamma Radiation (NGR)

The NGR and NGR Master operated without problems under the new set of web services. Instead of the normal 300 s per position, data for Exp. 362T were collected at 900 s for each of the 15 sections in order to be consistent and comparable with those acquired during Exp. 360.

Notes

1. A new NIM crate and spare electronic modules were ordered and stored in the drawers and spaces underneath the Correlation table. To date, the following spare parts for the NGR electronic control are available:

The following are active parts that are in the surface freight for the Exp. 363 surface freight:

1. Discussions about the NGR legacy data mining exercise continued, particularly on the use of only the 1^st position of the background measurement when doing data reduction. One quick validation experiment was made on 31-7-2016 to collect background data with the data reduction engaged. Result indicates counts of less than 1 per second for detectors 2 to 7, whereas the outermost detectors 1 and 8 were about 1.2 counts per second. This close to null background value demonstrates the importance of NOT REDUCING the data when doing background measurements. More discussion will have to be made on a more efficient and way of collecting and applying the background data.

Thermal conductivity

No thermal conductivity measurements were made on the newly acquired cores. However, KTLF testing showed that the system is functioning. Moreover, a long-time file re-naming "bug" has finally been understood and corrected!

ISSUES

The bug associated with incorrectly named replicate files is now fixed by rebuilding the ThermCon Uploader as a 32-bit program (previously a 64-bit program). Apparently, the ThermCon Uploader, on upload, automatically renames the files to correspond to the core- type-section-run number, but often fails to rename all files, resulting in failed or partial upload. The reason behind is that the renaming process invokes a 32-bit Microsoft database (MS Access 97). However, because of the incompatibility of the previous program with this MS database, it throws the loop out after the first set of files are renamed, and therefore fail to rename the remaining run files.

Paleomagnetics

M.Hastedt

Summary

The SRM and assorted support equipment were exercised to test functionality, with the exception of the Flexits which were ground-truthed during the previous tie-up period. A great deal of time was spent assessing the performance of the new software and motion control for the SRM.

SRM

The IMS-SRM software debugging reports submitted to the developers are in separate email documents and will not be discussed further here. Just be wary of starting the new SRM software with a default M-drive INI file. The (lack of appropriate) parameters in that file makes the boat fly back and forth down the track and smack the limit switch hard.
The SRM was fine early in the transit but by July 15^th began exhibiting all the classic signs of coldhead trouble: falling IVC voltages (= rising temperatures) and coldhead noisiness. The noise from the coldhead did not quite reach "ratcheting" but it was markedly louder and more labored than normal. However, the boiloff rates never rose outside of regular weather-related bounds nor did the dewar pressure ever rise. After about 3 more weeks and a lot of monitoring it looks like these IVC voltages are the "new normal." Occasionally they do rise but never reach traditional levels and tend to fall back again. I'd suggest checking the vitals every other day for the next expedition with He level checks once a week per usual.
Quick note for future reference - How to convert LabVIEW timestamps in the SRM data files to Excel equivalents: use the following equation, making sure the new column containing it is changed to Date format (mm/dd/yy hh:mm:ss) or Time format (hh:mm:ss.0) if you are looking for time differences between events.
Excel time = (Labview timestamp/86400) + 1462
Notes for measuring the X362T cores from U1473: please confirm with the 360 Pmag Methods report found in IODP_Share\360_methods. The gist is to cull all pieces less than 8 cm long from the split section, track velocity of 2 cm/s to avoid saturating the SQUIDs, measure at 2 cm intervals, and the demag sequence is NRM-5-10-15-20-25-30-35-40-50. Leader/trailer of 15 cm, 25 ms settling time, and no averaging. Double check the report! Email any queries to Peter Blum.

JR-6 spinner magnetometer(s)

Both magnetometers were calibrated, holder-corrected, and used to measure the same samples. The data compared well between the two spinners (see table below). The current desktop spinner tag #91063 got some extra TLC polishing to remove deep salt staining on the base of the sample enclosure. If there is extra time remaining during the transit the other unit will get its share as well.
Unit #90769 had its shaft decouple with the belt drive AGAIN. The ETs repaired it and made sure the set screws were locktited. Hopefully it won't happen in future.
Note that the shield cap is especially tight on #90769. Take care that it is fully seated before measuring the holder. The "tell" that it is not well-seated is suspiciously high holder moments (into the E-4 range).
Spinner comparison data

Data uploads using the latest MUT were also verified operational. Initially I was unable to find the user guide for spinner uploads on our servers, but eventually a paper copy was located in the Pmag file drawer. My biggest takeaway with spinner uploads in general is to always use the barcode gun to scan samples, even if they show up in the drop-down sample menu as abbreviated names. Using those short names causes trouble with the upload process as it is clunky enough right now due to limitations of the REMA6 acquisition software (limited numbers of characters allowed for sample naming). Another thing I learned is to be sure you are on the DAQ tab in REMA6 before you export your sample data. If you happen to be looking at the Specimen tab all you will export is the one you are examining at the time.

Dtech discrete sample demagnetizer

No issues seen with this relatively new instrument. The axial Hall probe was used to verify the AF fields produced by the unit as seen in the below table and graph.

Kappabridge

The Kappabridge performed well and exhibited no issues. The Kappaeigen utility program was tested and still runs; it is also still sensitive to the space between the sample's name and the first data column. Be sure the space is there so that you get the correct values back.

Thermal Demagnetizer

The thermal demagger was tested on 7/24/16. The tray contained no samples. The oven was heated from 100C to 700C for up to 50 minutes and then allowed to cool down with the fan running until the middle thermocouple was within 2-3C of room temperature after which the next run was started. The following table contains observations of the temperatures seen after the central section reached its peak stabilized temperature. The worst overshoots for samples seem to be concentrated at the lower temperatures, but I don't know what effect an empty sample chamber has on the outcome.
Keys: EZ = end zone; program = automatic temp based on selected; measured = thermocouple values from the zones.

IM-10 impulse magnetizer

ASC IM-10 Pulse Magnetizer
This unit (tag #52142) was tested in conjunction with the spinner testing. It was used to impart anhysteretic IRMs to 9 hard rock cubes. Fields imparted were 400, 200 and 100 mT. The unit charged and discharged as expected and the trim button also worked well to fine-tune the field strength. No overheating or other issues were observed during this period.
Axial Hall probe check (DC Fast Peak mode) of IM-10 calibration performed on 7/25/16:

Hall probe

Both axial and transverse probes were utilized during the testing of the SRM, IM-10 and Dtech coils. The unit performed well. The only odd thing I saw right very late in the transit is that the console inexplicably shut itself down twice during testing for no reason I could see. We'll just have to monitor it for the foreseeable future.

X-RAY DIFFRACTION, ICP PREPARATION AND MICROBIOLOGY

Seth Frank

Summary

The transit from Cape Town to Colombo went smoothly with no problems experienced in the Xray lab. The XRD and software worked per program, and the water in the Haskris tank was siphoned out and replaced. Updates to the PC's went out during the transit and nothing on either of them was negatively affected.

Total Samples

XRD: 0
ICP: 0
MBIO: 0

X-ray Diffractometer

A full QAQC at the beginning of the expedition showed no need for adjustment. Subsequent runs of the NIST1976 throughout the expedition also showed no need for any adjustment. Water flow rate from the Haskris began at 6.40 l/min and at the end of the expedition was 6.34 L/min.
X-ray tube conditioning should still be recorded and monitored for any changes.

ICP Prep

THIN SECTION LAB

Seth Frank

Summary

1. 30 Thin Sections were made as practice over the course of the transit. Routine maintenance was preformed

special Projects

None

problems encountered

The connection cables for the Plate Flatness Monitor were damaged, upon removing the metal housing at both ends one of the five wires had a broken lead. After soldering the lead back together the connection was restored and the Monitor worked properly.
The WG2 on the PM5 was not responding properly to commands. This only occurred once and no cause could be determined, the problem didn't present itself again. This will be mentioned in port call to find out if there is anything that can be done.

Miscellaneous

Being my first thin section lab trip, some rearrangement was done in order to make things more orderly. Some rearrangement was done in my absence during the tie up and all the changes are fine with me.

ELECTRONIC TECHNICIANS REPORT

Jurie Kotze, Etienne Claassen

The transit was a software developer's extravaganza and we did some outstanding equipment maintenance. Etienne did some major work on the parallel and small rocks saws over the whole tie up period, the units itself were stripped down and rebuilt, painted and new Plexiglas shields were built for them. The plumbing and valves were refitted and renewed.

WRMSL

Replaced silicone hose on the P-wave rotary water pump, it was leaking at the joints strapped with cable ties. It's better to use a sealant if necessary and a tight fitting tube. The cable ties has a tendency to pull the pipe skew and causes dripping.

Chem lab

SRA

We spend some time on the SRA, again the glow plug worked on of and we did get some information from the vender, he asked us to check the voltage on the board that drive the glow plug, we did found a deference as of 0.3V and did set the voltage as vender suggested. The glow plug did work but like usual only for a while until the same problems were detected, a decision was made to send the instrument back to be check and repaired by vender.

Fantail

Spooled back the Maggie cable on the drum after welding work above it was completed. Used an electric drill to drive the cross travel worm gear.
The DC drive board that got the polar output transistor and fuse replaced was tested on the workbench with just the 220V power applied, the outputs both for left and right motion was in balance and in idling position with 0.4V on both terminals.
The boards were installed back for a test and it seemed good for a moment but once the input from the cable pulley's motion detector comes available on the DC drive it would just race to one side again without being able to stop it, fortunately we had the drive chain removed for the test.(the chain is in a plastic zip bag above the work bench inside the underway, it was cleaned and stored there) It was found that the input circuit for the motion detector was faulty, It stays at a high once it is activated. It is still using the old TTL type control circuit IC's. We don't have spare TTL IC's anymore and seeing that a new DC drive should arrive in Colombo we left it as is for now.
The spring holding the two parallel cable guides was rusted and totally stretched out. It was replaced with a new spring. We must always be aware to check the mechanical parts holding the T-Bar is in sound condition, otherwise it makes no sense in trying to do an electric Zero as the hanging bars will constantly swing around freely sending erratic signals to the control card making all the efforts fruitless. The analogue input board is in good working order.

Core lab

Core splitter room

New in closures was manufactured for the rock saws all thee boxes were replaced by new boxes. We did change the wiring and water connection, making it easier to remove the saws for repairs and to remove it to clean.
We also planned ahead for the new parallel saw that will be sent out to the ship soon.

New in closers for rock saws

We also made five trays for the boxes that the boxes will not be use as a self and no scratch will later on dim the light in the box, these trays are for packing rocks on when in the proses of cutting.
Five florescent lights were remove in splitter room and replace by nine LED lights making it much lighter in the splitter room especially at the rock saws and supper saw.

Pygnometer

We attempted to do some water flow maintenance on the pipework supplying warm water (36 deg C) to the Pygnometer cells. The pipes were pretty blocked again with the ever-growing algae like white fluff. The small water channels through the cells were so blocked that it seems almost impossible to clean properly. The channels are very narrow and blocks easily. David H. suggested the techs do an open and closed lid test run to see if makes any difference. The test results were the same and he decided we take the water lines out altogether and run them without water as the older models of Pygnometer was always used. So it was removed and tested again. All looks normal.

Agico spinners

One Agico spinner's motor drive coupling became dislodged above the belt drive at the bottom, it was stripped and fixed again.

Movie room

The movie room overhead projectors lamp failed, the light source filament popped. It was replaced with a new lamp. Okay again.

Gym.

The treadmill level setting the up and down motion stop working and we open it and found that the power plug for the motor was loos we clean it and it seems to be running again

Radvan

After a gas change in Cape Town on the smaller A/C unit we kept an eye to see if it operates smoothly and so far it is in good working order, no foreseen problems further. The unit had to get a gas change due to the later industry standard Ozone friendly gas.

General

Four new 2Kva Minuteman UPS's were ordered and 10 new serial control cards as well, all 10 (eventual number) Minuteman UPS's will be on the network and accessed from a single point to do maintenance and various parameters that will be monitored. The six in service at the moment proved very reliable with power problems that we encountered during the Tie-up in Cape Town. It kept the instruments running without any problems.
The 4 new UPS's will be fitted on the WRMSL, STMSL, SRM and Coulomb meter.
A planning list and layout are saved in the ET document.../UPS Locations folder, named "List of Instrument vs UPS's planned.docx"

M-Drive operation training

We did a training and information course with Mike M. on the operations of the new M-drive circuits and related equipment, he was involved in the development and building it, we could ask for training as he was available during the transit period.

ENGINEERING

Mike Meiring

ENGINEERING

VIT System:

Seaview multiplexer SYSTEM

The pod retrofit, Surface multiplexer, FORJ, Optical cable and Labview control software were installed and confirmed serviceable during the Cape-Town tie-up 361 P1/P2/P3.

• At the start of Exp 362T transit, the system was tested and confirmed operational. Minor changes were made to the DVR-Setup.
• HD resolution was changed from 720p to 1080i, both in the HD-cameras and DVR .
• 10 successful deployments were made, nine to ~700m at U1473A and one at the VIT Test site to ~3850m.
• Took delivery of VIT Maintenance laptop. RF 53042.
• Updated "As Built" drawings and handed copy to Siem

CABLE LOADING TEST

The primary goal was to confirm that fibers were not affected by the stress and crushing forces on the cable when loaded close to its SWL of 14000lbf.

• The seafloor was at 3850m. Heave at the time peaked at 2m and loading was calculated to be ~11800lbf.
• A secondary goal was to calibrate the Tensiometer depth against the Siem Veeder meter. This was abandoned when the Veeder meter was found unserviceable.
• It was also an opportunity to log cable tension data to establish the dynamic loading added as a result of drag at different retrieval rates. RIS Livecap was setup to log TENSION, DEPTH, HEAVE and RATE for this exercise. Unfortunately these measurements became useless when the tensiometer came into contact with the fixed roller bar on the deck for most of the deployment. This was an oversight in the design of support bar with initial installation and only manifested at about 2000m down. The Tensiometer support bar was later shortened, which should solve the problem. .
• The VIT was lowered to seafloor where the operators experimented with light/camera settings and then retrieved to deck.
• OTDR measurements were made prior, during and post deployment. Analysis of measurements showed no evidence of a change in optical attenuation during the deployment. This is an indication that strain and crushing forces in and on the cable are not transferred to the fibers and concluded that the cable-build was healthy.
• Report on test at: P:\2-Engineering Files\VIT\6 UMBILICAL\CORTLAND CABLE\Cable loading\Exp 362T CABLE TEST DATA\TEST REPORT 362T.docx

TRAINING

User training topics for OPERATORS:

• Launching Sonar and Labview control applications on the VIT PC
• Initial set-up of Gyro
• Controlling, Lights, Zoom, Pan and Tilt devices.
• Setting-up of the DVR recorder and applying file naming convention.
• Transferring files to IODP server, post deployment.

Attendees:

• Capt Terry Skinner
• Thomas Hartt
• Rudell

Technical training topics for MAINTENANCE PERSONNEL:

• Topics above for Operators.
• System technical overview
• Schematic diagrams
• Course Wavelength Division Multiplexing.(CWDM) techniques.
• Optical Measurement techniques.

Attendees:

• Callie Calitz
• Eugene Griessel
• Ike Sacudit

TENSIOMETER

• Installed 8 pin connectors on LCi-90 box and Subsea end of tensiometer cable. This will simplify moving the box around when calibrating tensiometers.
• Replaced the 8 pin connector on the cable, moonpool side. This connector was badly corroded, even with dustcap screwed on. Used a female connector as dustcap which will better protect pins from environment.
• Waterproofed both tensiometer junction boxes and confirmed units serviceable.
• Noted a smoked component in LCi-90 S/N 1121. Replaced unit with spare and returned faulty unit to College Station, BobA, for repair.
• Calibrated both tensiometers and placed documentation on server.
• Entered calibration values in LCi-90 look-up tables for both tensiometers, S/N 354A and 355B.
• Prepared tensiometer S/N 454A for VIT Test deployment.
• System is operational and performed reasonably until the tensiometer came into contact with deck roller bar. The support bar had since been shortened. Pay-out should be calibrated against the VIT Veeder instrument at next deployment opportunity.

DOWNHOLE TOOLS

ERS

• Optimized operation of "Tool Present" switch.
• Modified wiring of both ERS Pressure housings to accommodate new "Tool Present" Switch.
• Confirmed both systems functional
• Updated documentation.
• Worked with shore updating the ERS User Manual

RIGWATCH

MRU

• MRU S/N 578 was returned to JR after repair. Installed unit and configured lever arm values and outputs.
• Downloaded latest software (v.3.55) to spare MRU S/N 503 and configured. Stored in a container in Subsea, ready to go.
• Updated documentation in Engineering/Rigwatch server.

Job Files

• Converted two job files to ASCII and burnt CD's.

SYSTEM MANAGERS REPORT

Michael Cannon and Steven Thomas

Servers (Microsoft):

• Updated all servers with SPP firmware and driver updates where applicable. Applied Windows updates were required.
• Upgraded Commvault backup software to version 11 and rolled out new backup agents to include our virtual environment in the backup rotation.
• Finalized Maunaloa and Spurr to take over media agent duties from our Solaris servers.
• Installed a virtual server agent on Maunaloa and Spurr. Exported all volumes for virtual servers to Maunaloa and Spurr to allow them to back up virtual machines directly over fiber channel instead of transferring via the network.
• Upgraded Acronis backup software on Maunaloa and Spurr to version 11.7.

Servers (Linux):

• Installed new web server, Eiger, to take over web server duties from Etna and Pico which are being retired. Configured services for load balancer and other misc. software to support web services.
• Installed new DHCP/DNS server, Netsrvc, to take over DHCP and DNS duties from Etna and Pico which are being retired.
• Created a server to test syslog services for centralizing log collection from the various systems we have on board.
• Permanently shut down Rainier, Shasta and Ararat and removed the cabling for those servers. Because there will be no shipment from Colombo we will wait until the Singapore port call to remove the shelves and send them back.
• Upgraded Novarupta, Cleveland, Netsrvc and Mail to OES2015. These servers remain on SLES11 SP3 as that is approved for OES2015. Updated with all patches after upgrade.
• Upgraded all standalone (Non-OES) SLES11 servers to SP4. Updated with all patches after upgrade.
• Upgraded Mail to GroupWise 2014 R2. The R2 client is available to the science party on the ship software web page.
• Upgraded Webmail to GroupWise 2014 R2 web services.
• Upgraded Sync to GroupWise 2014 Mobility services.
• Worked with developers to stand up the new production tomcat servers for web services.

Servers (Solaris):

• Permanently shut down Etna and Pico and removed the cabling for those servers. Because there will be no shipment from Colombo we will wait until the Singapore port call to remove the shelves and send them back.

Servers (ODA):

• Patched ODA up to v. 12.1.2.7.0

Servers (VMware):

• Upgraded vSphere to version 6.0 on all ESXi hosts.
• Updated HP service pack for ProLiant firmware for all ESXi hosts.
• Added an additional 10GB network card to all ESXi hosts and configured teaming for redundancy and capacity. Ran an additional cable to each server to the newly installed NIC.
• Added an additional cable run to each server to configure a new network interface for virtual machines. Adds a new network with no authentication and internet access.

EVA4000 SAN:

• Permanently shut down the EVA and removed the cabling for the shelves. Because there will be no shipment from Colombo we will wait until the Singapore port call to remove the shelves and send them back.

3PAR SAN:

• Received and installed additional hard drives into each of the shelves increasing the total capacity to just under 40 TB.
• Upgraded the SAN operating system and the service processor operating system to coincide with the additional drives. The operating system was outdated and needed updates to recognize the new drives.
• Added capacity to all of the virtual volumes for VMware virtual machine storage.

Network:

• Fixed a communication issue with the switch in the VSAT locker. Changed the management IP and interface to VLAN 10. Switch can now be managed remotely more reliably.

PC Workstations:

• Deployed ZENworks Adaptive Agent to all HP Z420 Workstations and Instrument Hosts on the ship
• Updated the BIOS on all Z420 PC's to version 3.88
• Updated Java to version 8u91 on all Z420 PC's on the ship, and removed outdated Java as appropriate
• Updated McAfee VirusScan Enterprise 8.8 to patch level 7
• Updated to Powershell 5 on all Z420 PC's
• Updated Mozilla Firefox to 45.2.0 ESR
• Installed Google Chrome v 51
• Updated Flash plug-ins to Flash 21
• Pushed out iPrint 6.04 to make sure that PC's that didn't have it yet, have it.
• Updated to Novell Netware Client to the Microfocus Client 2 SP4 IR3 version (latest)
• Updated GroupWise to version 2014 R2 on all PC's that had GroupWise
• Replaced the old HPxw4400 PC in Core Tech Ship with a HP Z420 PC running 64-bit Windows 7 so that they could meet the requirements to run AutoCad LT

MAC Workstations:

• Nothing to report

Printers:

• Installed new color printers on Bridge, Core and Lower Tween decks.
• Updated printer firmware for the new printers.
• We have an issue with the Sharp copier where it is unable to scan to the network folder. As of this report the issue is still unresolved.
• De-commissioned the HP 5200 series printer in Core Tech Shop and replaced it with an HP 4250 printer.

Satellite/Internet/Phones:

• Nothing to report

Other Equipment/Projects:

• Replaced all Startech serial servers with BlackBox industrial serial servers.
• Began replacing some older Trendnet unmanaged desktop switches with new NetGear managed desktop switches that allow the use of VLANs.

CHEMISTRY LAB

Erik Moortgat
The primary focus during this tie-up maintenance period and transit was to test the functionality/communication of our equipment with the new web-services installed by the development group.

Ampulator

The Adelphi ampoule sealer was turned on and is functioning fine.

Balances

During 361P1 I noticed some intermittent strange behavior with the Cahn balance (Cahn 29, RF51470) like masses increasing or decreasing with no opposite behavior so I decided to replace it with a spare unit from the shelf. This unit (Cahn 31, RF52427) appears to be working much better.
The Cahn software had some very minor "updates" done by developer Rui and functionality with the new web services seems good.
The UNKNOWN Mettler balance became inoperable due to its faulty display unit. It is being sent home for repair and when the new one arrives (Exp362 freight) it can be installed. One of the other displays coming is for the balance above the IC and the third can be kept as a spare.

Carver Presses

Turned on and tested.
I installed the old motor-pack/press in the reefer for Exp362 use. There is a poop-sheet beside the motor-pack on how to use it.
Auto operation

1. Set to required pressure
2. Switch ON mains switch
3. Press two start buttons simultaneously
4. To stop : switch OFF mains or press emergency button
5. Open hydraulic valve lever

Jog operation

1. Switch ON mains (no start buttons)
2. Press and hold jog switch as necessary (remember to hold on for timer to run down before it will start (5 sec)
3. Jog function will not allow pressure above dial set pressure.

Cary Spectrophotometer

Continued testing of the new auto sampler and functionality with the new web services. I ran a phosphate test and the auto sampler performed excellently.
Note: put DI water in vial #1 to perform a zero at the wavelength of interest, before the sequence is run. This is before the 'blank' of the analyte being run.
When copying the sequence results (TextID, concentration) to your spreadsheet for the Spreadsheet Uploader application, Advanced Reads puts extra spaces after the TextID and this carries over into subsequent 'copy/pastes' so when it gets to SU, it doesn't like the TextIDs. So you have to take out those extra eleven spaces in the cell. Use the formula "=LEFT(cell#,10)" and then do a paste special to copy to a new cell. This leaves you with just the TextID in a format that SU will accept. The results were uploaded to LIMS with no other issues.
Put together a QSG for the autosampler and it is in IODP_Share/IODP Official/_IODP_Technical_Manual/Chemistry/CarySPS3_QSG_Exp361P_draft.docx
Have at it.

CHNS

Worklist Generator was tested and a sequence ran on the CHNS. Both were successful. The results were uploaded to LIMS, also with success.

Coulometer

The unit was tested, ran fine and results were uploaded to LIMS.
However, there is a discrepancy in what LORE reports and what the Coulometer application saves. Maybe this is a LORE Report calculation issue?
Ex. (first one is not-acceptable but the first sample/calibration is always bad due to air in the HCl line). Just a reference point. Doesn't appear to be rounding difference either.
1H3COUL13.991 mg sample
11.47 % IC
1604.11 ug C
95.537 % CaCO3
LORE13.991 mg sample
11.46 % IC
1604.15 ug C
95.540 % CaCO3
2H3COUL11.181 mg sample
11.94 % IC
1335.15 ug C
99.506 % CaCO3
LORE11.181 mg sample
11.94 % IC
1335.16 ug C
95.507 % CaCO3

Freeze-drier

The unit was not turned on.

Fume hoods

No issues to report. They were re-calibrated by LO Roy Davis.

Gas Lines/manifold

The new monitoring application appears to be more stable. There is a new feature to be able to set a time window for 'time-out' that the data capture is not populating. An error will appear on the webpage stating this and it is time to check the data capture application.
Due to the fact that the pycnometer system is now connected to the helium manifold gas system, I made a request to increase our helium stock level by one rack (eight bottles). The Techs on Exp362 can keep us informed how the loads looked since it will be the first time in production with that new scenario.

GC3/NGA1

GC3 and NGA1 were tested, files uploaded with the new MUTS and LORE and Gas Safety Report shows all relevant results.

Hydrogen generators

No issues with the hydrogen generators.

IC

The IC was routinely turned on and a sequence was run during the web services testing. No issues to report. Results uploaded fine but the pdf chromatogram reports are not being recognized by the new MUTS. But since we are not routinely uploading these result files it was deemed to be put way back on the burner.

ICP

An IW minors sequence was run on the ICP and everything ran fine, uploaded and is viewable in LORE.

OI TOC

The unit was not turned on.

salinity

The optical refractometer was tested and results uploaded via Spreadsheet Uploader.

SRA

The SRA was turned on to test its functionality. The desiccants were checked/changed, the flows were checked and the CO/CO₂ detectors calibrated, all looked good to go. Upon initial testing, the FID glow plug would not light, so it was replaced. Then the acquisition software kept crashing once the pedestal moved to do its 120 sec purge. Sometimes the software would 'return' after 10 - 15 seconds, sometimes it would completely hang-up. The FID appeared to light, in the pedestal purge position, as you could hear it 'pop' but once the pedestal moved to the run position, the FID glow plug would not light nor would the FID be still on. Questions were sent to Bruno Leroux at Weatherford Labs and he said to check our voltages, especially the power supply for the FID and to confirm it is exactly 5.4V as deviations (as small as for a millisecond) could cause the software to crash. It was changed to 5.4V (from 5.35V) and another sequence tested. This sequence had the initial blank and calibration standard work fine but on the first standard check, the FID would not light, the glow plug would just sputter lightly and we couldn't even light the FID manually with a lighter. The occurred on the second standard check as well. So it was immediately decided upon to send the unit back home for careful attention by Weatherford Labs. About time.
Bruno also mentioned that they 'know' about these issues: "We do have a fix for the glow plug power supply (using the 12Vdc instead of the 5Vdc to power the glow plug but it does require to send us the SRA main board for update)". So, when it comes back…glory.

GC2-pft

The unit was not turned on.

Pipettors

The three left on board were sufficient for the testing sessions. The 5000µL pipettor is not functioning properly but all three are being sent back anyway for re-calibrations. They are being sent home in the yellow-box with the SRA and Mettler displays.

The new Eppendorf Repeater arrived. Looks like it is going to be a somewhat useful tool. A bunch of 25 mL Combitips arrived and are located in the UTS drawer 26D-6. There is also a bag in the lab with the other tips.

titrations

alkalinity

The unit was tested and results uploaded.
Note: When starting up the application, make sure you first change the volume of sample (3mL), either by using the up/down arrows or manually typing it in. If you select your sample and then use the up/down arrows to get to 3mL, this also changes the sample selection and you will not be able to go back to your IWS sample selection. People have been notified.

Chloride

The unit was tested and results were being saved properly and viewable in LORE.

Water system

The three filters for the RO unit and final filters for the DI unit were replaced.

Misc

The new flow meter arrived and is living in the cabinet above our desk. Don't let it walk!

Work on the AVS system in the Physical Properties lab

Info given to Z. Mateo for the PP tech report.

Microscope and MICROPALEONTOLOGY Laboratories

Zenon Mateo and Rachael Gray

Summary

Regular maintenance servicing from June 27 to 29 was conducted by Emile and Lorentz Meylan on all 13 microscopes on board the JR. ImageCapture has been converted to be compatible with the new web services, and the configuration file standardized and amended for more accurate image scaling. Minor workflow protocols are also suggested to minimize potential errors.
New sieves are supplied for the Paleo-prep Lab, in response to recent suggestions from expedition scientists.

ISSUES AND SUGGESTIONS

1. Microscope maintenance findings

1. Custom-made brass counter-weights were installed in the Axiophot ("Kiwi") and Axio Scope.A1 ("Strawberry").
2. The Axioplan ("Grape") microscope had considerable amount of aluminum fillings from the analyzer slider and accumulated on the reflectance filter module. As a temporary remedy, a glossy sticker was placed inside the slot in order to prevent the slider from grinding against the module housing. No damage was found on the adjoining lenses, especially the objectives below.
3. The SteREO Discovery V8 ("Margarita") in the Sedimentology Lab has a zoom knob that turns beyond the limit (of 1x and 8x). The gear/pinion attached to the shaft had to be re-aligned with the vertical plastic rack. Though there is a hard-limit defined by the length of the rack, there is now an uncertainty in the accuracy of the pre-set zoom levels. Also, pre-set zoom level clicks is not working anymore.

The zoom knob might have been forced beyond its set limit in the past, and can be prevented in the future by reminding them to be gentle in using these instruments. This stereoscope may have to be sent to the vendor for servicing, during which the third stereoscope of the same model at the Microscope Lab or a Zeiss SV-11 in the Imaging Office are available replacements.

Photo 1: Detail of the gear/pinion and rack system for the zoom knob in the SteREO Discovery.V8

1. The reflector module for the new Axio Scope.A1are now labeled as to what filter cubes are placed in each position.

1. The Zeiss Standard 04 Pol Student Microscope in the thin section lab has a loose reflected light module. The threaded hole for a set screw is worn out and Emile was not able to repair it. If a similar microscope is still available back at the IODP office, a replacement can be sent to the ship.

2. Microscope image scale bar

Microscopists from recent expeditions raised the question about the inaccuracy of the scale bar generated by ImageCapture. A document detailing our findings is attached to this report.

1. In summary, several causes are identified, particularly the use of an intermediate lens (Optovar) or partial CCD/CMOS imaging. Emphasis on these matters should be continued when users are introduced to the laboratory equipment and software at the beginning of the expedition.
2. On the software side, the values, equations and code routines needed to generate more accurate metadata results are improved, especially in calculating the scale bar and field of view. There is no more need to manually or visually adjust the adapterFOV for individual microscopes, as it is now equated to the CCD/CMOS horizontal dimension. Virtual objectives are now also added to the drop-down list to accommodate the Optovar lenses for the upright binocular microscopes and the zoom and adapter tube magnification in the stereoscopes. An adapterFOV value of 15.16 mm is given for all microscopes with SPOT Flex camera. For the SPOT Idea camera that are attached only to the stereoscopes, the sensor dimension should be 5.7 mm. However, values are more variable because the continuous zoom nature of the stereoscope, and possibly, due to differences in the 0.5x adapter tubes used. For the stereoscopes, the value for the adapterFOV are empirically determined as follows:

The error between the computed scale bar and the imaged micrometer for each zoom and magnification level are shown in the table below. The highest error of ±2% for the Margarita is attributed to a possibly mis-aligned zoom knob that is not able to indicate the click-stop for each zoom level.

1. Microscope configuration file are now standardized for all upright binocular and stereo microscopes. As with other program-specific files with the new web services upgrade, the ImageCapture configuration file (ws_config.xml) now resides in C:\ProgramData\IODP\ImageCapture\. The most recent and more readable format is followed.
2. A proposal has been submitted to David Houpt and Paul Foster to create microscope standard image references. This would involve individual users to image a micrometer using all the objectives and virtual objectives available in the microscope that they will use during an expedition. Users can then have the option to use these visual dimensional references, as an alternative to using the calculated scale bar. The merit (or lack thereof) and implementation details of this proposal may be discussed in the next Geology LWG meeting.

Data Backups

No microscope samples and images were taken during this expedition.

Image Capture: Scale Bar Calculation

I. Sources of Error

Several microscope users have flagged the accuracy of the scale bar generated using IODP's ImageCapture application. This is despite the regular calibration of microscopes using a micrometer in order to derive an accurate factor for calculating the scale bar. Potential sources of more obvious errors include the following:

1. The objective used is different from what is selected in the ImageCapture program.
2. The newest microscopes in the JR, the Axio Scope.A1 and the Axiophot, are equipped with a tube lens turret (Optovar) with magnification lenses of 1x, 1.25x, 1.6x and 2x. A setting other than 1x would previously have resulted in a scale bar shorter than what it should be.
3. The ImageCapture program invokes a vendor-supplied module (SPOT software) to set and control the CCD/CMOS camera and capture an image. One of the many functionalities of this module is the ability to define a region of interest, thereby using only part of the sensor/chip area (Fig. 1). If this is selected, the result is a variably underestimated scale bar (Fig. 2) that is a function of the area selected.

Figure 1: Screenshot of the SPOT module configured to image a subset of the full chip view

Figure 2: Screenshot of the ImageCapture window showing the erroneous scale bar for an image captured using only part of the CCD chip. Longest tick mark interval is 1 mm, making the image almost three times bigger than for a full-chip image.

Also, previous calibration methods involved imaging a micrometer using the various objectives attached to a particular microscope. The image width or "field of view" is then measured. The values are then extrapolated to a magnification of 1x to derive a factor used in calculating the number of pixels per mm. However, the micrometer has an accuracy of only 0.02 mm and the imaged tick marks may vary in thickness depending on user settings in acquiring the image.

II. Corrections Implemented

Factor Accuracy

Given the fact that the scale bar is calculated from a baseline of 1x, the factor, the adapterFOV in the ImageCapture code should then be theoretically equivalent to the sensor width of the camera. To date, there are only two types of SPOT digital cameras used with the following specifications:

At 1x (e.g. camera without any lens in front of it), the image should be the same dimension as the sensor. Therefore, to calculate the scale bar for any given total magnification:
pixels/mm = total magnification (image dimension in pixels / sensor dimension in mm)
For the upright binocular microscopes, the adapterFOV is equivalent to the dimension of the sensor, which is 15.16.
*For the stereo microscopes that use only the CMOS camera, there is a slight distortion of 0.12% between the vertical and horizontal scale. Another element to consider is that the fixed adapter tube has a 0.5x lens and that the zoom level is determined by the level of the intermediate lens. With all of these considered for the stereo microscopes, the adapterFOV are specific to the microscope set-up, and are empirically determined as:

The highest error of ±2% for the Margarita is attributed to a possibly mis-aligned zoom knob that is not able to indicate the click-stop for each zoom level.

Total Magnification

The total magnification value of a microscope-camera set-up is a product of the objective magnification and other intermediate lens accessories in the ray path to the camera. The new Axio Scope.A1 has a lens turret (Optovar) with magnification lenses of 1x, 1.25x and 1.6x (Fig. 3 top photo). The SteREO Discovery.V8 stereoscopes have a more variable magnification anywhere between 1x and 8x, and a camera connector tube with a magnification of 0.5x. At present, Image Capture v. 4.0.0.1 is not set up to capture these intermediate magnification values. As such, "virtual objectives" are now inserted in the configuration file (see Appendix A and B):
Figure 3: Photograph of the intermediate lens turret module (Optovar) for the Axio Scope.A1 (top) and (bottom) the zoom knob of the SteREO Discovery.V8 with preset zoom values and the screw on the side of the knob for adjusting between continuous and discrete zooming

For the Axio Scope.A1, these "virtual objectives" should be modified when a new objective of different magnification is added to the nosepiece. For the SteREO Discovery.V8 stereoscopes, the "virtual objective" magnifications are calculated for only the discrete zoom values set in the control knob (Fig. 3 bottom photo). Anything between these pre-set values would create an inaccurate scale bar. To aid the user, the zoom knob should be set to click on these pre-set values by turning the side screw to the recessed position. Nonetheless, the ability of continuous zoom for any stereoscope is always an ever-present source of error in calculating the scale bar.

III. Recommendations

Applying the above-described steps to improve the accuracy of drawing a scale bar for photomicrographs, ImageCapture now has an accuracy of about 0.5%. This can be attributed to other sources of error such as line thickness and picking points to measure within an image. Despite these, a note of caution is given in SPOT's user manual:
"Calculated Calibrations are, in reality, mathematical estimates based upon the accuracy of the values input by the user. Because there may be tolerances to consider on any optical element in the system, or simply inaccuracies between "nominal" and actual values, the resulting calibration should be close, but is not a true calibration. For exacting work, it is best to manually calibrate your optical system..."
In light of these, the following are recommended:

1. When objectives are added, removed or swapped for any given microscope, the usual practice of updating the configuration file should be continued. The file now resides in C:\ProgramData\IODP\ImageCapture\ws_config.xml.

1. The use of the intermediate lenses for the Axio Scope. A1 is often deliberate, and most users assume the default of 1x. It would be a good practice to make sure that this is the default setting at the beginning of an expedition.

1. At the start of an expedition, when ImageCapture is introduced to the scientists, emphasis should also be given on factors that are critical in drawing the scale bar:
   1. the selection of all lenses and magnification used in the capture of images, making them aware of intermediate lenses and pre-set zoom levels
   2. the use of the full chip of the camera instead of defining an ROI. Users can either use a higher magnification objective to zoom in to a particular specimen, or use other software to edit the photo later.

1. Prior to receiving the first sample or taking the first microscope image for the expedition, it is highly recommended that scientists image the micrometer using all of the objectives installed in the microscope that they will be using. This should also be done whenever a new objective is used. More importantly, a copy of these set of images should go with the set of images that they have taken with that microscope, or be uploaded to the database as a set of standard applicable to that particular expedition, microscope and user. This dataset would represent a graphical check on the scale bar calculated and drawn by Image Capture, especially given the difference of as much as 2% for the stereoscopes.

Appendix A

Example of a configuration file (ws_config.xml) for the JOIDES Resolution upright binocular microscopes.
<workstation_config>
<microscope>
<!-- This field populates TEST.INSTRUMENT on upload. -->
<option><text>Axiophot MICROLAB Kiwi USG90257</text></option>
</microscope>
<camera>
<option><text>SPOT FLEX USG90819 sn242233</text></option>
</camera>
<adapter_tube>
<option>
<name>1001</name>
<text>HRD100-CMT</text>
<value qual="magnification">1</value>
<field_of_view>15.16</field_of_view>
</option>
</adapter_tube>
<!-- Objectives available for the various Zeiss scopes. -->
<objective>
<!-- A basic set. -->
<!-- ImageCapture parses the numeric here. -->
<option><text>202-PlanNeoPh2 40x</text></option>
<option><text>218-ECEpiNeo 50x</text></option>
<option><text>38-PlanNeo 63x</text></option>
<option><text>196-PlanNeoPh3 63x</text></option>
<option><text>177-PlanNeo 100x</text></option>
<option><text>198-PlanNeoPh3 100x</text></option>
<option><text>1.25Optovar40x 50x</text></option>
<option><text>1.25Optovar50x 62.5x</text></option>
<option><text>1.25Optovar63x 78.75x</text></option>
<option><text>1.25Optovar100x 125x</text></option>
<option><text>1.60Optovar40x 64x</text></option>
<option><text>1.6Optovar50x 80x</text></option>
<option><text>1.6Optovar63x 100.8x</text></option>
<option><text>1.6Optovar100x 160x</text></option>
<option><text>2.00Optovar40x 80x</text></option>
<option><text>2.0Optovar50x 100x</text></option>
<option><text>2.0Optovar63x 126x</text></option>
<option><text>2.0Optovar100x 200x</text></option>
</objective>
<!-- Illumination methods available on this microscope. -->
<illumination_type>
<option><text>Transmitted</text></option>
<option><text>Reflected</text></option>
<option><text>Other: see comments</text></option>
</illumination_type>
<!-- Light sources available with this microscope -->
<light_source>
<option><text>Halogen bulb 12V 100W</text></option>
<option><text>VisiLED MC 1000</text></option>
<option><text>Other: see comments</text></option>
</light_source>
<!-- Contrast methods available with this microscope -->
<contrasting_method>
<option><text>Brightfield</text></option>
<option><text>Darkfield</text></option>
<option><text>Uncrossed polarization</text></option>
<option><text>Crossed polarization</text></option>
<option><text>DIC (Differential Interference Contrast)</text></option>
<option><text>Fluorescence</text></option>
<option><text>Other: see comments</text></option>
</contrasting_method>
<!-- Filters available with this microscope -->
<filter>
<option><text>polarizer</text></option>
<option><text>analyzer</text></option>
<option><text>Green: broad-band interference filter</text></option>
<option><text>Blue: conversion filter 3200/5500 K</text></option>
<option><text>Light Gray: neutral density filter 0.25</text></option>
<option><text>Dark Gray: 32mm dia. neutral density filter 0.06</text></option>
<option><text>Acridine Orange</text></option>
<option><text>FITC</text></option>
<option><text>Rhodamine</text></option>
<option><text>Texas Red</text></option>
</filter>
</workstation_config>

Appendix B

Example of a configuration file (ws_config.xml) for the JOIDES Resolution stereo microscopes.
<workstation_config>
<microscope>
<!-- This field populates TEST.INSTRUMENT on upload. -->
<option><text>SteREO MICROLAB BEER USG90812</text></option>
</microscope>
<camera>
<option><text>SPOT idea RF52676 sn257778</text></option>
</camera>
<adapter_tube>
<option>
<name>1001</name>
<text>DD50ZNC</text>
<value qual="magnification">0.5</value>
<field_of_view>6.25</field_of_view>
</option>
</adapter_tube>
<!-- Objectives available for the various Zeiss scopes. -->
<objective>
<!-- A basic set. -->
<!-- ImageCapture parses the numeric value here. -->
<option><text>1-zoom 0.5x</text></option>
<option><text>1.25-zoom 0.625x</text></option>
<option><text>1.6-zoom 0.8x</text></option>
<option><text>2-zoom 1x</text></option>
<option><text>2.5-zoom 1.25x</text></option>
<option><text>3.2-zoom 1.6x</text></option>
<option><text>4-zoom 2x</text></option>
<option><text>5-zoom 2.5x</text></option>
<option><text>6.3-zoom 3.15x</text></option>
<option><text>8-zoom 4x</text></option>
</objective>
<!-- Illumination methods available on this microscope. -->
<illumination_type>
<option><text>Reflected</text></option>
<option><text>Transmitted</text></option>
<option><text>Other: see comments</text></option>
</illumination_type>
<!-- Light sources that are available with this microscope -->
<light_source>
<option><text>VisiLED MC 1000</text></option>
<option><text>KL2500 LCD</text></option>
<option><text>KL2500 LCD + VisiLED MC 1000</text></option>
<option><text>Halogen bulb 12V 100W</text></option>
<option><text>Other: see comments</text></option>
</light_source>
<!-- Contrast methods available with this microscope -->
<contrasting_method>
<option><text>Brightfield-stereo</text></option>
<option><text>Uncrossed polarization-stereo</text></option>
<option><text>Crossed polarization-stereo</text></option>
<option><text>Other: see comments</text></option>
</contrasting_method>
<!-- Filters available with this microscope -->
<filter>
<option><text>polarizer</text></option>
</filter>
</workstation_config>

DOWNHOLE TOOLS AND LOGGING

Zenon Mateo

Summary

One logging run was scheduled upon re-entry into Hole U1473A with just the temperature (from LEH-MT logging head) and gamma ray (HNGS) tools. The aim was to collect temperature data to compare with previous data from Exp. 360; the gamma ray log is for marking the seafloor to enable appropriate depth matching and correlation.
Logging started on 12 July 2016 at around 2200H. However, a bridge was encountered at about 997-998 mbrf and the operation was aborted after logging only 273 m of the borehole.
Raw DLIS and LAS data sent via Yellowstone to Lamont-BRG were processed into DLIS and DAT files , which are all archived to :\data1\27.1 Logging and :\Uservol\362T-U1473A_ Logging. Petrel plots from Exp. 360 were updated to include latest data and prints were made available to the OIM and Toolpusher to aid in the cementing process.
For the downhole temperature measurements (APCT-3 and others), the database components is revised in order to more accurately reflect the data file format uploaded. For the raw data, both .dat and.wtf files are uploaded to their respective components, and so does the .eps and png files, although only the eps file will be reported in LORE. See table below for list of new LIMS components.