Exp 340 Tech Reports.pdf: Link to original PDF

Expedition 340:
Lisbon Dry Dock
Atlantic Massif-Transit
Lesser Antilles
JR Lisbon Dry Dock 2012 JR Lisbon Dry Dock 2012 ….a view from a bar JR Lisbon Dry Dock 2012 ..tight fit JR Lisbon Dry Dock 2012, Techs

Expediton 340 T: Atlantic Massif Crew
Expediton 340 T: Atlantic Massif Techs
Expediton 340 T: Atlantic Massif Scientists

Expediton 340: Lesser Antilles Crew

Expediton 340: Lesser Antilles Techs
Expediton 340: Lesser Antilles Scientists

LO-ALO HAND OVER NOTES

William Mills, Chieh Peng, and Steve Prinz

INTRODUCTION

With the discover of hull integrity issues during the previous expedition, it became necessary to dry dock the Joides Resolution in Lisbon and make repairs. To complete the repairs, a 3-week dry dock and tie-up period (340D) was inserted into the schedule pushing back the start dates for the Atlantic Massif APL (340T) and Lesser Antilles science programs (340). As a result of this schedule change, the planned port call in Antiqua was moved to San Juan, Porto Rico. Exact time and dates of all three periods can be found in the operational reports.

SUMMARY

LISBON PORT CALL ACTIVITIES

Logistic activity and technical cross-over was routine with the exception of our delayed ocean freight that arrived after the ship entered the shipyard. The scheduled 3-days of core off-loading, was completed in just one. During the port call, extensive Public Relation tours were conducted for students, press and VIPs. Representatives from the Shell Oil Company surveyed the ship in anticipation for possible coring work off of Greenland. Additional tours were given to the USIO and ODL insurance underwriters.
Upon the competition of logistic and PR activities, the shipped moved to the Naval Rocha, SA shipyard dry dock facility located on waterfront in Lisbon.

DRY DOCK

The initial scope of work for the dry dock repairs was focused on the plate replacement of the sea chest and surrounding hull plate. Other shipyard work included hull power wash, spot painting and various inspections. However, upon entering the dry dock, the aft end of the sonar dome landed on a block causing extensive structural damage to the hull attachment point, flange and neck of the sonar dome (details of the damage and repair work are covered Underway Geophysical Report).
In addition to the ship's repairs, a number of technical improvement projects were completed. Details of which are covered in the Special Project section of this report. While in dry dock we received and loaded our missing ocean freight and off-loaded hazardous waste.
Just prior to leaving the shipyard, the Atlantic Massif science party and additional technical staff boarded the vessel. Upon completion of dry dock activities, the vessel left the dry dock without incident, took on fuel at the REPSOL bunkering facility across the Rio Tejo. The following morning the vessel departed Lisbon for Site U1309.
Note, while in dry dock, a member of the ship's crew survived a heart attack, was treated locally and returned home for further evaluation and therapy.

ATLANTIC MASSIF SCIENCE ACTIVITY AND TRANSIT

Routine bathymetric and magnetics were collected on all transit to and from the logging site. While on site, a 2-day VSP was conducted during daylight hours with a Protected Species Watch. The GI Gun cluster operated without problems and no protected species were seen. Technical staff continued to work on projects started during the Lisbon Dry-dock.
An attempt was made to core possible hydrothermal deposits seen during one of our re-entry attempts. Only a handful of material was recovered for Hole U1392A.

SAN JUAN PORT CALL ACTIVITIES

Upon arrival in San Juan, the Atlantic Massif science party, Assistant Lab Officers, and ASPP staff departed and the Lesser Antilles science party and replacement technical staff boarded. During the portcall and initial transit, the science party received extensive training on our systems and protocols. A minor amount of freight was handled and there were no PR activities.
Note, due to a family emergency, our photographer returned to College Station and was not replaced. Technical staff filled in as necessary to cover his duties. Etienne was elected to be the photographer, and the responsibilities were spread out between the ALOs, Etienne, Emily, and Rhonda.

LESSER ANTILLES SCIENCE ACTIVITY

Routine bathymetric and magnetic data was only recorded during the initial and last transit. Because of the shallow water and high drilling rates, technical staff was primarily focused on science support. In addition to coring support, VSP operations (with Protected Species watches) were conducted on X sites. On one site, operations were suspended due to the presences of marine mammals.
Due to difficult drilling conditions in very sandy formations, the expected high recovery of 5000m did not happen. After coring 9 sites and 22 holes our total recovery came to 2384m.
Two temporary technicians, Emily Fisher and Carrie Miller, sailed in the core lab. Emily is a great asset to the program, we highly recommend her to be hire for permanent staff.
All, but one, scientists have never sailed on the JR before, including both co-chiefs. The result was that we, the technical staff, had to do quite a lot of explaining and show and tell.

LOGISTICS

• Address list (crew & cruise) sent from shore is not complete. There is quite a bit of missing information, mainly scientists' institution and department. Some were missing street address. Updated lists were received from curator and Yeoperson. An email was sent to Rakesh, but was told that the addresses were exactly as in the crew and cruises.
• This issue requires attention since it affects AMS generated Customs Declaration and Packing List, as well as the printed parcel labels. Parcel labels have been mostly shifted over to Dymo labels due to problems with AMS label function, but the need for extensive edits to the crew and cruise file remain a big and unnecessary time sink.
• Property identifier:
  • Type 03 is NSF property (cost more than $5000), we do not have authority to dispose of onboard
  • Type 01 is TAMRF property (cost less than $5000), we can get permission to dispose onboard, but tag needs to be removed and sent home to Michelle Strickland for record keeping
  • Type ZZ is item transferred to ODL. ODL can decide its course, but tags need to be removed and send home if items are disposed onboard.
• Saw very usage of 11x17 copy paper, all 35-reams were used. We should consider upping the stock levels
• Property items 52290 (Sola Transformer) and 52322 (light curtain were) tagged.

SPECIAL PROJECTS

CORE DECK

ALL LABS

Numerous floor cracks were repaired and repainted throughout the labs.

MAGNETICS LAB

A sound proof cabinet was built and installed around the Cryo Cooler (made a big difference in sound level). Now we need a system to tell us when the unit is off.

PHYSICAL PROPERTIES LAB

SHMSL: A new instrument mounting plate was installed on the X-axis to provide a mounting point the 3D laser profiler. The camera, laser and mounting hardware was installed and initial 3D was collected for analysis. The camera and laser was removed for Expedition 340 and is stored in the cabinet above the LO's desk.

CORE ENTRY

Laser Engraver: Issues with ventilation where resolved by simply turning on the exhaust fan's breaker. Additional baffling was installed under the door's vent slot insure that no reflected laser beam cam make it outside the cabinet. Attempted to install an air flow monitor were curtailed when the unit was damaged during installation.
The engraver was used throughout the expedition and was given a vigorous shakedown by the technical staff. A thorough discussion of technician comments is presented in the Core Lab report. The overall opinion is that the quality of the engraving is good, but the current configuration presents an impediment to efficient core flow. It takes more time and more work to do the job with the laser engraver because of the delays in LIMS to report the section halves ID. Although, if we had to engrave by hand both the Text and Label IDs (as the laser does) the laser engrave would be much faster. The ergonomics is what is hindering tapping and labeling activity. Work is in progress to design a system built into the rack to address these issues.
Changes made to the system during the expedition:

• Replaced the roller tray with the extruded aluminum rack tray (prevents the unbalanced cores from rotating)
• Changed to a more efficient Web Service call and merged the site and hole column on the front panel. These few alterations changed the response time from a few minutes to only seconds. Also, each selection column on the front panel automatically defaults to the most current core.

White Board: Moved the core log white board to the side of the working rack (in front of the door). So everyone likes the new location.
Core Log Station: Installed a wide format monitor so that the techs can keep multiple windows open to monitor data quality. The Zebra Printer was moved under the laser engraver.
Core Images: Without a photographer onboard, the technical staff was assigned to review core images for quality control. The following procedure

• Create a folder on the desktop with the name of the site/hole;
• On the ship web/Science Application/Bulk Data Retrieval, select Review Line-scan images;
• A message box appear asking to open imagegrabber.jnlp, click OK;
• A security warning box appear, just "run" it;
• A "Image Grabber" list appear on the upper left corner, select the site/hole and consumer (jpg), and "get image";
• Browse the folder you have create on desktop and click "open";
• The program will start downloading all the images from selected site/hole;
• Open "core tracking sheet" under Web Tabular: Coring summaries;
• Now you can verify each section image against core log before core is boxed;

CORE RECEIVING PLATFORM

The drain salt water wash-down that was partially installed in Singapore was completed. The Siem crew are looking into installing a timed solenoid that will periodically run water down the trough to prevent a buildup of mud.
The steel deck under the catwalk is starting to rust and blister the paint. Strongly recommend that this area get maintenance. Spoke to the OIM (Wayne) about this. Not sure if it is on Siem's radar.

FO'C'SLE DECK

COLD LAB REPAIR

While in the Lisbon dry dock, the Cold Lab was stripped of all furniture and equipment and a local contractor was brought in to repair the water damaged floors. While the floors were being repaired, staff cleaned up rust and repainted the steel furniture as necessary.
After the floors were repaired and painted, the staff installed a split level drop ceiling to help control noise from the room's fancoil and to improve lighting. Three LED lights were installed and a fourth is on order. The sink cabinet was not installed but this space was left open for access to the floor drain and maintenance. Under the Glove box table we installed only one Vidmar cabinet and built a core rack in the remaining space. The flexible gas lines running in the ceiling were replace with hard piping and service regulators installed on the starboard and port walls.
The installation of the ceiling panels slightly lowered the noise level for staff working directly under the fan coils. Additional acoustic foam has been ordered to line some of the ceiling panels to gain further noise reduction.

HAZARDOUS LOCKER

The brown floor cabinet was removed and replace with unistrut shelving to provide more space for organizing our hazardous response equipment. Equipment stored in the Upper Tween Shop Stores was relocated to the new shelves.

SCIENCE CONFERENCE ROOM

All of the ceiling light fixtures were removed and the black bezels repainted. When re-installing the lights the were rotated to face to correct direction. The white column was repainted.

UPPER & LOWER TWEEN DECK

STAGING AREA AND PALLET STORAGE

The walls, overhead and duct work was repainted in the staging area. The material rack was cleaned out and reorganized. The bins for the core box storage was widen to accommodate the wider core boxes.

MOVIE ROOM

In Lisbon, the staff upgraded the movie room's lighting system to include a programmable color led strip along the walls and black lights on the ceiling. Maple counter tops were installed along the port wall.

IT OFFICE AND MACHINE ROOM

The IT office floor was refinished in Lisbon, so far the floor's surface has held up to the current occupants. In the data center parts of the floor where starting to fail. Repairs were made and the floor repainted. Recommend a second coat of paint in Curacao be applied.

HOLD DECK

REFRIGERATOR CORE STORAGE

At the Lisbon port call we received one of the four fancoils and all of the installation supplies. Overhead mounting frames were fabricated and installed in the ceiling. This required extensive modification to electrical cable trays and insulation. All of this work was completed during the transit to the APL site.
In San Juan the remaining 3 fan coils were delivered and installed by the crew. Because of the high recovery rates expected, the core storage was filled with D-tubes precluding any other additional installation work during the expeditions. As of writing this report, we are in negotiations with a local refrigeration contractor in Curaco.
Prior to loading D-tubes, the floor was cleaned and repainted.

UNDERWAY / FANTAIL

UNDERWAY LAB

• Removed illegal extension cords from overhead;
• Removed old seismic signal cables
• Removed and discarded Gyro repeaters
• Reorganized parts drawers
• Installed new Trimble and retired the Ashtech GPS recievers.

FANTAIL

• Fine-tuned level wind on the port winch, better not perfect.

RECOMMENDED PROJECTS

• The Core Splitter squeaking noise is getting louder and very noticeable. The main body need to be lifted up and the under carriage needs to be cleaned and greased
• Spiral cutting continues to be an issue with core cutters. A solution needs to be found.

VSPs and Protected Species Observation

Vertical Seismic Profiles (VSP) and Protected Species Observations (PSO) were conducted at the following:

Our current Marine Mammal Policy is out of date and does not fully reflect the requirements as stated in the EE reports submitted by LDEO. This was confirmed by Dr. Mitch Malone and I was instructed that the EE super cedes or Marine Mammal Policy. In an effort clarify the situation the following decision tree was created and approved by the LDEO logging staff scientists and IODP Operations manager.
In addition, the new guidelines and PowerPoint were provided to the staff (in T:\IODP_Share\UW\10 VSP and PSO\Exp 340).


To help with locating the Exclusion Zone boundary EZ sticks were made by Randy and Garrick. Anything below the stick is in the boundary and above is out.
Inside the EZ ZoneOutside the EZPlace edge on the horizonHold the end of the stick against your cheek.
…don't poke your eye out!

CURATORIAL REPORT

Gemma Barrett

SUMMARY

Expedition 340: Lesser Antilles Volcanism and Landslides
San Juan, Puerto Rico on March 3rd to Willemstad, Curacao on April 17^th, 2012

SAMPLES:

A total of 4772 samples were taken on Expedition 340. A total of 194 personal samples were taken and 4578 shipboard samples were taken. 2252 shipboard residues were claimed by the science party.
Personal sampling is largely being deferred to a Sample Party at the Gulf Coast Repository from August 13^th to 17^th, 2012. The only personal samples taken on the vessel were for McManus (1343IODP), Palmer (1340IODP), Lafuerza (1316IODP) and Manga (1334IODP). A requested list of samples were acquired by the curator for the Sample Party before the end of the expedition.

Shipments:

18 pallets of374 core boxes were shipped from Willemstad, Curacao. The core pallets were divided into working and archive pallets. Core inventory sheets are attached to one of the pallets, to the pallet holding all residues and will be emailed to the GCR Superintendent. Two core boxes full of split liners were send back on this pallet also for repository use.
There are two special shipment requirements. A frozen shipment of 1 cooler of samples collected by Martin Palmer (being shipped to BK Song) for microbiology. This shipment contains a temperature logger and a list of samples taken since the scientist was not on board the expedition. A refrigerated shipment of 3 boxes of refrigerated samples will be shipped for Sara Lafuerza for tri-axial and geotechnical testing.

Hand Carrying Samples:

Michael Manga has 9 samples that he will be hand carrying. Mohammed Aljahdali will be hand carrying residue nanno & MADC samples. Christoph Breitkreuz will be hand carrying residue MADC samples. They have all been given hand carry letters for customs and immigration.

ResIdues:

Scientists were asked to list the types and volume of residues they are interested in requesting at the end of the cruise. This allowed squeeze cakes, PAL samples, IW porewaters and MBIO scrapings to be divided as the samples were processed. This avoided extra labor at the end of the cruise to divide these samples. Table 1 shows a summary of the splits of these residues.
Table 1.

The remaining residues (MADC, TSB, CARB/XRD, ICP, PMAG) were claimed and divided between scientists during the last site and transit. These residues were reassigned to each scientist's request code and number. 402 FORAMP, 402 FORAMB, 341 NANNO, 400 PAL, 110 PMAG cubes, 246 MADC, 340 CARB, 8 XRD and 3 ICP samples were claimed and reassigned.

THIN Sections:

A total of 43 thin sections (including 9 grain mounts) were made during this expedition by the thin section technician, Gus. Five duplicate slides (TS#12, #14, #15, #16, #28) were also made which were treated as residues and 2 of which (#15 & #16) were claimed by the science party.
Table 2

Site Conversion:

The conversion between pre-site and site identifiers is given below. No sites were drilled within Dominican waters as was originally in the operations plan.
Table 3

ACTION ITEMS

Borrowing Thin Sections:

There were no requests to borrow thin sections or smear slides by the science party following the cruise.

CATWALK SAMPLING

Whole round samples consisted of IW whole rounds for shipboard analysis and personal samples (McManus 1343IODP), microbiology whole rounds (Palmer 1340IODP), geotechnical testing whole rounds (Lafuerza 1316IODP) and rheology testing (Manga 1334IODP). Hole A was preserved in order to keep a full stratigraphic record so whole rounds were taken on the B or C hole. U1401 was the only site with one hole and therefore no whole rounds were taken at this site.
Table 4

Head Space (HS)

Head space samples were taken by the chemistry technician on Hole A in the top of a section roughly in the middle of the core. Head space samples were resumed on later holes at a site if drilling continued deeper than in Hole A.

Geochemistry (IW)

Whole rounds for geochemistry were taken on Hole B and Hole C at U1400. A maximum of 2 10cm whole rounds could be taken by the geochemists on shift if the material was conducive to squeezing. Many cores consisted of large grained volcanic sands which resulted in large gaps in IW sampling. These whole rounds were always taken at the bottom of a section. Inconsistencies in IW lengths (later found out to be due to the ruler on the catwalk with 1.5cm cut off of one end) when the curator was off shift resulted in the ALO or Curator measuring out and cutting the whole rounds for geochemistry.

Microbiology (MBIO)

Whole rounds for microbiology were taken on Hole B at sites U1394, U1395 and U1396. These whole rounds were 10cm and were subsampled for DNA analysis (stored in -80C), bacterial analysis (0C), and geochemistry (room temperature). The DNA and bacterial analysis subsamples will be shipped frozen to BK Song as requested by Martin Palmer.

Paleontology (PAL)

Paleontology samples of 5cm whole rounds from the core catcher were taken on all holes at all sites. These samples were divided for benthic forminifera, planktonic forminifera and nannofossils. The residue PAL samples were split and claimed by Martinez-Colon (MART 1325IODP) and Fraass (FRAS 1318IODP).

Geotechnical Testing (Lafuerza1316IODP)

Following the completion of Hole A, Sara would look at the physical properties measurements taken on the cores and determine at what depths she would like her whole rounds to be taken on Hole B. The whole rounds would not be cut on the catwalk since her measurements require specific intervals in the cores. Sara would put a post-it note the cores that she anticipated wanting whole rounds from while they equilibrated in the core racks. The whole rounds would go through the tracks and after looking at the data, she would determine the specific interval where she wanted her whole rounds. Every effort was made to avoid taking whole rounds from the top or middle of sections but there are a few exceptions that could not be avoided. Before splitting, the Curator or ALO on shift would cut the whole round for her and log it into SampleMaster. If the whole round was taken at the top of a section then a spliced piece of core liner would be patched to the top of the core after splitting to avoid confusion in the labs and later in the repository because the top does now not begin at 0cm. The whole rounds would be capped and sealed with acetone and stored horizontally at all times. They were kept in a 4C refrigerator in the chemistry lab to avoid movement and were shipped refrigerated following the cruise. These samples were sometimes 40cm or 5cm in length depending on the material.

Rheology (Manga 1334IODP)

Rheology 1-2cm whole rounds were taken next to whole rounds taken for geotechnical testing. These were taken by using the hand saw to cut off a 2cm interval which was then capped and sealed with acetone, wrapped in plastic wrap & sealed in a plastic bag. It was important that these samples did not lose their moisture content. The number of sample taken at each site can been see in Table 4.

WORKING HALF SAMPLING

Shipboard analysis included the following measurements done at the following frequencies:
Table 5

The total number of samples taken for each type of analysis is given in Table 6.
Table 6

NEW ITEMS

Core Entry

A large monitor was installed at the core entry station to allow us to check core images before cores were boxed up since an imaging specialist was not onboard. This set-up worked very well and it allowed simultaneous programs to be viewed at the same time which was convenient (SampleMaster, LIMSpeak, Excel template, LIMS Reports).
The zebra label printer at core entry was moved to a sliding shelf underneath the laser engraver to free up valuable desk space. This new location also aids the labeling of cores in the laser engraver.

CURATION NOTES

A number personal samples taken by a scientist for geotechnical testing were necessary to be taken from the top of a section (U1394B 1H-5, U1397B 2H-5, U1398B 9H-4, U1399B 6H-3 & U1399B 13H-1). Every attempt was made to not take whole rounds from the top of sections by the scientist but in some cases this could not be avoided to obtain the material needed for her testing. To avoid confusion with the remaining section starting at a value other than 0cm, a piece of liner patch was used to weld on a piece of core liner the sample length of the sample that was taken. This prevents any confusion about the section starting at a different offset as it moved through the labs and in the repository.
A shattered liner prompted me to rethink the way we identify disturbed or unoriented material on the core liners and the d-tubes. Currently a set of 'Caution' stickers are used that must be written on with the necessary warning which often rubs off and the labels do not stick. Using the Avery labels used for sediment flags, I created a set of caution stickers with the most common problems needing this type of core identification (unoriented, shattered liner, disturbed, etc.). I have printed a number of sheets with these warnings which are located in the 'sticker drawer' at core entry. The template for these stickers can be found in VOL1\Curator\1_Forms_Labels_Signs_Templates\Labels saved as 'CAUTION Shattered Liner'.

SAMPLEMASTER, DATABASE & SOFTWARE

During Sample Table training, a scientist onboard asked why we could not scan the labels of cores at the Sample Table to populate the rows for a sample taken instead of clicking through the hierarchy. I inquired with David Fackler about whether this was possible and an email went out to JR Developer. This feature should not get rid of the hierarchy but simplify the data entry process. Often scientists forget to change the hierarchy between sections since they are often entering samples for an entire core at a time. By scanning the cap of the d-tube for each section, this would eliminate most of this error and speed up sample entry time.
A procedure was created for anyone (myself or the ALO's) who were forced to recalculate depths for a hole. Each time the depths were recalculated, the Staff Scientist, Operations Superintendent and the Core technicians were all emailed when this occurred so that they could edit their recovery values as needed in real time.

Core Lab

Lisa Brandt
Expedition 340 was a sediment expedition with about 2000m of recovery. This cruise was this crew's first expedition using the new Laser Engraver; the reactions and suggestions for improvement are listed in a section below.

MODIFICATIONS TO CORE LAB

• The Zebra Printer at the Core Entry station was relocated to a shelf under the Laser Engraver. This was done to free up space at the Core Entry Station. This new location seems to be working out well. A splash guard might need to be made to protect the printer from drips out of the Laser Engraver.
• A new white board was installed on the port side of the working half D-tube section rack. This was done because people were crowding around the old white board by the NGR and it was causing traffic issues. The new location makes it better visible for scientists.
• This cruise was the first to use the new, slightly larger waxed D-tube boxes. These D-tube boxes were very slightly larger (a few square centimeters) than the old D-tube boxes, which were sometimes extremely difficult to wedge the cores into. The new boxes were very easy to pack the D-tubes into, and caused no problems.

SUGGESTIONS AND FIXES

• The black hoses that connect to the aft water power washer on the catwalk sprung several leaks this cruise. It was repaired using hose clamps and duct tape, but the reason for the leak is that the hose is made out of a material that wears away from being dragged on the rough grating of the catwalk. The ET's out a req (REQ340#2) together for a new hose, but this needs to be followed up on and replaced.
• The large Acetone reservoir on the catwalk is rusty and it is becoming difficult to pull the dispensing handle. It would be nice to get a new one.
• It's been mentioned that the new core liner cutters on the catwalk seem "flimsier" than older models. It's getting harder to turn the latching mechanism that holds them closed. It would be good to have a few spares.

LASER ENGRAVER

As mentioned before, 340 was this crew's first expedition with the Laser Engraver. It was used at all sites to do the engraving on all sections long enough to be scribed with it. We made one change to the system (removing the rollers and installing solid core trays), but still have many concerns that need addressing.
Overall View Pro: The engraver does make pretty engravings, and the speed of the engraving (once you finally get to the point of engraving) is fast.
Overall View Con: You have to wait for the cores to be entered into Sample Master by the drillers and the ALO's/curator. In the time you are waiting, you could have the cores dremel inscribed already. This was infuriating. Overall, this crew feels that the quality of the Laser engraving does not outweigh the speed and efficiency of using the dremel tool.

Problems we fixed:

• At the start of the cruise, the engraver used rollers for the cores to be placed on. We had many sandy, half-filled, and unevenly filled cores to be engraved. On the rollers, this caused the following problems:
• Partially filled cores would roll to the heavy side.
• End caps were catching on the end of the rollers.
• When putting on the barcode labels (section 5 and higher) the labels would get caught in the rollers and get stuck or cause the cores to not rotate as well.
• These problems were solved by installing the solid gray metal core trays in the place of the rollers. This prevented the sections from rolling and becoming stuck.

Problems to be Addresed

• Cores leak water into the machine. The yellow tray under the machine does not catch all of it. The water leaks onto the table by the phys props tracks and NGR. It also runs underneath the Vidmar cabinets. The machine either needs to be water tight, or have a better draining mechanism.
• The exhaust fan needs some kind of screen. We lost a strip of labels going up the vent.
• The location of the engraver in front of the doorway is awkward, and there is always a traffic jam there.
• If the working half is finished being engraved and there is a problem with one or more sections, you cannot go back in the software to remove them and continue on with scribing the archive half of the unaffected cores.
• There is not enough room in front of the "box" to stick hands in to rotate cores and place labels and tape. The clearance is too tight and this led to several cases of skinned knuckles.
• While replacing the rollers with core trays solved several problems, it also created another problem in that it is now much more difficult to rotate the core, especially with so little room to stick your hand in to grab the sections.

CORE DESCRIPTION

Sandra Herrmann

Summary

Expedition 340 is the most diverse expedition (sediments, volcaniclastics, hard rocks) that documents cores with the DescInfo2 schema and Desclogik.
The pre-cruise preparation started beginning of January 2012. Feedback was received from a few lead core describer as well as paleontologists. When the scientists came on board of the JR, they checked the templates based on this input (March 4-5, 2012). We added some more entries for paleontologists (species, events, datums); the templates for the core describers were subject of major changes on board.
All templates were fully prepared before the first core was on deck.
A total number of 8 core describers and 4 paleontologists worked with Desclogik during EXP340. The templates were used for the following scientific disciplines: core description, benthic foraminifers, planktic foraminifers, and nannofossils.

Pre-cruise preparation

The template used for sediment description on EXP339 was send to the core describers, co-chiefs and paleomagnetists via e-mail at the beginning of January 2012. In the following weeks this template was reconfigured; columns and value lists for volcaniclastic sediments were added.
The Paleontologists also got an e-mail with preservation, abundance, datum, zone and species list as well as an example of an occurrence worksheet (exported from a nannofossil template) in early January. They were asked to choose their basic set up. The last feedback to this e-mail was received 3 days before the port call in San Juan.

Preparation during the first two days

The templates, based on the pre-cruise surveys mentioned, were discussed with the core describers and paleontologists. Major changes were made to the core description template:

• Approximately 50% of all columns were hidden (mainly for sedimentological observations),
• The value lists were reduced (e.g principal_lithology_name to only volcaniclastics and general sedimentological terms),
• The template layout was changed from a separation of a drilling disturbance and lithology tab to a general and detailed tab (plus additional 15 tabs for macroscopic structures, smear slide, thin section description, units, age). With this layout change all important observations for volcaniclastic sediments that need to be logged for the VCDs were in one tab.

Changes during the cruise

Paleontologists requested additional species in their templates every day or two, as expected. Several new species and genera were added to the value lists – all approved through references in books and online databases.
The core description template was modified on March 14 and 15, 2012 – the template needed to be reconfigured to log all sedimentological observations. Additional columns for matrix observations and layer grading, as well as value list changes/additions were created/preformed.

Issues

• Server shut down (3/6/2012):
  • A shut down of all server occurred around 0300hr on 3/6/2012. Since no DESClogik work was in progress during this phase no major issues occurred. Another shut down occurred around 1500hr (recognized through DESClogik: no login possible) – David Fackler restarted the server.

• Data entered against hole does not download:

Entering data against the sample "Hole" was uploaded to the server, but could not be retrieved (3/8/2012). Comment from Chris Bennight:

• • All desc requests decompose to a depth range on the hole - so errors in hole depth parameters (x_length is the typical one) will cause problems/inability to download data. No way around this really though - the depth data has to be correct (depth data being all sample length/offset/etc. properties).
  • Result: recalculate depth in SampleMaster helped.

• Launcher error when adding a dynamic column in DL:
  • Adding a dynamic column in the foram template (additional species column) resulted in a Launcher error. The developers are trying to find out why this happens.
  • Result: Tim Blaisdell fixed the bug and released a new DescLogik version (3/28/2012).

• Server slowdown related to SQL backup:
  • DESClogik uploads to LIMS slowed down on 3/15/2012 around 0700hr. Tim Blaisdell could not figure out why this backup was running and what initiated it. We had the same issue on X339 – it is still not solved. The same issue came up several times during the cruise.

Change requests for DESClogik

Several updates to Desclogik were requested and implemented. Please check developer's report for more information.

Other information

The scientists on EXP340 used grain size cards that are very useful for core description. We recommended these cards as new tool in the core lab, as well as more of the hand lenses and some new Munsell color charts.

Changes to DESCINFO

DESCINFO2 within Google sites and the online DESClogik manager works fine on board. One more component was implemented: sub_domain.

MICROSCOPE AND PALEO-PREP LABS

Sandra Herrmann

Micrscopres

Configuration:

The microscopes were configured as per the request of the users. The microscope usage was light with a setup for microfossils (Axioskope, Objectives: 20x, 40x, 63x and 100x oil; Axiophot, Objectives: 5x, 10x, 50x, 63x and 100x oil; Axioplan, Objectives: 10x, 20x, 63x and 100x oil), three binocular for foraminifera analyses (benthic and planktic), and two microscopes for core description investigations (Axioskop, Objectives: 10x, 20x, 50x, 100x; Axioskop, Objectives: 2.5x, 5x, 10x, 20x).

Issues:

On arrival to the ship and preparing scopes the new V8 body was replaced and the optical issues are gone. The part was brand new and shipped to San Juan port call (02/03/2012). The phototube that needs to be send back to Zeiss was wrapped and is ready to be shipped out from Curacao.
The specimen holder on one of the Axioskops was loose. It was fixed by Etienne Claassen (12/03/2012), polished and readjusted and finally rearranged on the microscope.
The image upload at the nanofossil microscope station did not work properly – the image was uploaded but no local copy was saved on the computer. The image also did not show up in the LIMS report. Tim Blaisdell is trying to figure out what the problem is (12/03/2012). The issue was fixed the same day, please refer to the developers report for details.

PALEO-LAB

A total number of 4 paleontologists worked in the Paleontology Lab during EXP340. The expertise was nannofossils (using the UV light, smear slide preparation, etc.) and foraminifera (using sieves, filtration, needles, valves etc.). Smear slides of sediments were also prepared in the Paleontology Lab.
An inventory of the analytical sieves in use was made. This should help/ did help defining the restock levels.

PHYSICAL PROPERTIES LAB

Thomas Gorgas
EXP340 was blessed with a good performance level of all machines, including track systems and instruments for discrete measurements.
As usual, we utilized the WRMSL, NGR, Therm-Con, SHIL, SHMSL, MADMAX (Mettler Balance + Pycnometer), PWave Gantry & Automated Shear Vane (ASV) to their full capacity. In addition we included an onboard Pocket Penetrometer as well as a Fall Cone Penetrometer; the latter was provided by one of the PP scientists.
The performance levels of the individual measurement stations in the lab are described as follows:

WRMSL

Figure 1Overall the system worked quite well, and produced good quality data. The drift was slow and benign over time, and required infrequent recalibrations. We replaced the end caps of water standard with new end caps that allow for easy refilling of the core with distilled water (Figure 1).
Some issues with the WRMSL system can be summarized as follows:

• Figure 2As in the past, we continue to encounter some issues with the Acuity Laser and/or GALIL motor control software (Figure 2). Albeit not extensively frequent, some few re-runs were required due to faulty laser readings and/or issues with the software. How these phenomena might be intertwined, we don't know yet. The action steps to remedy the issue are:
  • Flip sequence and measure shorter core section before long core section
  • Scan/use other label (instead of "W", use "A" label)
  • Close application, shut down PC and restart everything, re-do measurement
• One issue that might be improved upon is that the "pusher system" requires an entire core liner, which is to be measured, be fully pushed through by the "pusher core". Say, we are measuring a "34cm" long rock-filled core (of 150cm length) at the end of a measurement sequence, the pusher system will still force to push the entire core to its full length through the WRMSL system.
• Over a short 24-hour time period the drift of the H2O-Std. data were off by more than 1%; re-newed calibrations did not make a difference, and eventually all values went back to the reproducibility as observed all along the expedition. Go figure!
• WRMSL has displayed at two occasions (during Michael MInga's day shift) first a slow-down in moving forward the core section and eventually skipping every other interval (5cm instead of 2.5cm). First time it was reported we informed Tatsuya-san (Michael's night shift counterpart), but we never experienced that effect during our shift. Must have happened again around 23:00 tonight (April 13th). Fix: close down software and shut down PC, reboot, restart software (per David Fackler's report)

NGR:

The system was calibrated using our Cs/Co standard samples about 24 hours before reaching our first drill site (U1393A); background radiation was measured for 11 hours using an empty core liner according to our standard procedures before expecting "First Core On Deck". Issues:

• While in dry dock it was discovered that we had lost several channels of power, on both power supply cards, for the active shielding. Spares could not be delivered in time for Expedition 340, so we decided not to power the shielding in the doors. This means that detectors 1 and 8 will have higher background counts which should be accounted for by the background correction; although this will reduce the s/n for those detectors. (mills)
• A power-outage on the morning of the first day in the core lab (around 0605 on 3 Mar 2012) was buffered by the UPC Battery Station, which runs the NGR independently from the ship's power for such emergency cases.
• Additional test were performed verify the absolute position from the home switch to the center of each detector's response curve. This distance is critical for correctly applying the background correction as positions 1 and 2 are hard coded into the software (NGR Master). While we see a +/- variation 1.5cm, when measured to the center of a Gaussian fit, the overall fit for all 8 detectors is the best compromise. Because the Home switch position is critical, Margaret scribed the linear actuator to show where to place the home switch id it is ever replaced. (mills)
• Figure 3aOne "goof-up" occurred with uploading data when a User entered a name into the OPERATOR dialog window with more than 10 characters. As a "warning" we ought to educate ourselves and our scientists that this can cause a problem and disruption in the data uploading routine (per Tim Blaisdell). Another upload issue occurred when the cursor was not placed properly into the corresponding TEXT-ID tab of the (SCAN) dialog window; obviously this issue is taken care of by carefully placing your cursor into the right place on the SCAN window.
• The science party noticed that our edge correction process was not fully correcting and requested a number of experimental measurements to verify our process. To facilitate these experiments a quick LabView utility was developed that allows the user to select the following parameters and perform a measurment:
  • Start position(all positions are relative to home)
  • End position
  • Move interval
  • Figure 3bOffset correction (used for the point standard)
  • Measurement time

The current version of the program only records and displays only total counts for each detector without any correction. Nichole has requested that the program be modified to collect the entire spectrum which may be done if time permits. Another known issue is that data detector 5 is not being saved but just duplicating detector 4's data. The issues should be fixed by the end of the expedition. Currently this not part of the NGR executable but is running in a development copy of the code. (mills)

Thermal Conductivity:

Our TeKa probes (both needle and half-space puck) have been behaving quite well. Following Maggie Hasted's final conclusion on this topic (after her extensive studies during EXP340T), we decided to plug in the power of the APC into the "Dirty Power Line" (WHITE-colored socket), which seems to be a better choice than keeping the instrumentation plugged into the "Clean Power Line" ("Blue Socket"). This goes back to EXP327 and our on-going discussions and tests around this topic.
We ended up using the needle probe throughout EXP340 and not the puck because measurements were only performed on sediment material not rock samples.

SHIL

At the beginning of the expedition the SHIL was operated as on past expedition using ImageMagic to apply sharpening and lightening of the consumer jpeg images. As in past expeditions, the science party requested that the images be printed on 11x17 paper with custom description columns. These sheets are used for handwritten notes which are later transcribed into DescLogik. The template and scripts to produce the these sheets was setup by Tim Blasdale for the first half of the expedition before being rolled up into the SHIL LabView Code.

IMAGE CORRECTION

Because the core were so dark the ImageMagic corrections were not enough to keep them printing (or viewing) as dark bands. The science party asked that we do something to correct the problem. Because our photographer left in San Juan for a family emergency and was not replaced, we initial considered assigning someone on the staff to correct each image one-by-one using photoshop. We quickly saw that this was not a practical solution. Instead the SHIL software was modified to include an in-line process to correct and crop the image in one step using the LabView IMAQ tools.
Figure 5The initial version only included Brightness, Contrast, and Gama (BCG) correction which produced a usable image of our dark cores by sacrificing the white end of the image. After some research and recalling discussion with the photographers, I was able to implement a LUT based correction using either a natural log(ln), exponential, or sigma functions. These functions allow selected portions of the RGB space to be enhanced without loss on either the dark or light end. After experimenting we found that setting the BCG values to their neutral positions, adjusting the ln function until we had good color separation on the dark end (using the color standard) and then slightly tweak the BCG values until you had a presentable image on the monitor. While we still had issues with the color on the printed image (11x17 plan paper), the science party was happy with the images because they could identify all of the features on the core in the printout.
We did look for monitor calibration tools but could not find them; also, getting time on the SHIL was difficult because the rate of core recovery. The ImageMagic correction was taken offline and all corrections were made using this inline process. The correction methods and value are recorded in the "roi" load files.
As part of this in-line correction, I also included a feature to insert the image into an Excel spreadsheet template based on the earlier work by Tim Blasdale. This saved a lot of processing steps and file manipulation by the scientist. Once the image is taken the user is presented with a screen that shows the original TIFF on the right and the processed JPEG on the left (Figure 5). At this point the save button is disabled until the user performans a crop operation. The image is then saved as a cropped and un-cropped jpeg, the crop image is loaded into the excel file, printed and saved. And finally the "roi" file is made so that MUT can perform an upload.
In addition, this in-line processing code can be accessed as a utility from the front panel and used to correct existing TIFF images. New JPEG cropped and un-cropped are saved and a new "roi" file is made. When loaded into LIM this will create a duplicate record, so it necessary to remove the initial images. This is handy to have when you need to go back correct mistakes. (mills)

OTHER UPGRADES

As part of implementing the in-line correction, the SHIL code was cleaned up, removing unused cases and renaming cases to reflect their actual functions. The issues of the lights not turning off, was resolved by properly implementing the wait period between commands. As coded the wait could occur before, after or during the command, thus sometimes work or not. (mills)

Figure 4Other ISSUES

Eventually, some images started to suffer from the "Dropped Line" phenomenon (Figure 4), which was mitigated by rubbing some silicon spray with a paper towel along a track rod as part of the mechanical moving mechanism of the system. However, the problem might be also simply related to a software glitch, providing faulty "Error" messages on dropped lines. When zooming into the image to the pixel-size level, no dropped lines were observed or noticed. These "error messages" must be investigated thoroughly, case-by-case because in some cases they had been for real in the past!

SHMSL

Dry Dock Upgrades

While the vessel was in the dry dock shipyards, the following hardware changes were made to support the future deployment of the 3D Camera system.

• The aluminum plate that held the Y-axis actuator was replaced was a large plate so that 3D camera arm could be attached and provide more space on the back for additional support electronics.
• USB control switches were added to control power to the light sources. When IMS starts, the lights are switched on and off when the program closes. A warm-up time notice is shown prompting the user to wait until the 15 minute warm-up period has expired. The user can ignore this and the program does not take into account when the light was turned off. When the lights come on, the timer just starts. Future upgrades will take into account the shut down time; and shut the lights off when idle for than x number of minutes and track the hours on any bulb.
• Encoder splitter was installed. This takes the X-axis encored signal and splits it into two signals, one for the Galil and the other for the 3D camera.
• 3D camera J-box installed but not wired. This will eventually control the laser with a lock out key.

(mills)

3D Camera DEVELOPMENT

After completing the above work the 3D camera was extensively tested and the code refined. Prior to the start of the Lesser Antilles science program it was removed and is stored in the LO's office. Here is what was accomplished:

• A solid set of dependable LabView software code was developed and debugged.
• A utility panel for testing and setting acquisition parameters was developed. This and the code above will be rolled into IMS plug-in for the 3D Camera.
• Test data was collected on a full length section of hard rock core. This data will be used to test the processing code for height (instrument control), sample volume (data correction) and 3D-image (cloud of points).
• We demonstrated that a Class 1 laser is more than sufficient for the 3D-camera. Using a class 1 will avoid the safety issues of using a 3b laser.

The first full test deployment should occur during the Greenland expedition. The SHIL hardware has been setup so that testing can be done without effecting the collection of prime data. (mills)

Lesser Antilles Science

The color-reflectance/MS Point sensor system (Section Half Multi Sensor Logger) operated quite well during EXP340, thanks to Bill Mills' diligence on de-bugging and improving on both the hard-and-software components (Figure 6a & b). Specifically we did:

• Polish the white standard for white-color corrections
• Cleaned the MS standard with a dental toothpick, which enhanced the MS calibration process as well
• Observed closely the track-&-traveling capability of the laser system due to spotty behavior reported from test measurements during EXP340T.
• Instead of using the Blue LED which does little to enhance the spectra, the second Halogen light source was used. Doubling the Halogen light source reduced integration time down to .8 seconds but also improved the blue end of the spectra. On the blue side we often saw correction factors near 100%, with the double light system the correction factor is down near 70%
• Cleaned the "black fur" of the "black color calibration station" due to an increased dirt contamination from previous sand-&-rock measurements. Keeping this clean and ensuring that the integration sphere lands correctly can reduce the Black calibration to just over a 100 counts above the dark pixel mean.
• Continued to record "color tile" data for verification purposes of the system with respect to accuracy and reproducibility of the produced data output.

Figure 7Issues

• The USB plug of the OCEAN OPTICS electronics had to be un-plugged and plugged back in a few times to re-initialize a measurement recording (Figure 6a). This issue might require some attention in the future.
• Again failure to pay attention to the quality calibration can cause data displacement as seen below. It is important to train the scientist to look at the correction graph after the black and white calibrations have been performed (the graph with the red chart). If you see 100% correction valueS, stop. Make sure all of the standards are clean, re-run the calibration and make sure that the integration sphere is setting down correctly over the standard. If you still have problems make sure that the white calibration is not saturating. If it is, change the start point the %saturation values (Set-up Panel) until it stops. Also you may time to change the bulb.

Figure 8

Positive Results

Based on the preliminary data analysis provided by our EXP340 Science Party we observe some strong correspondence between Point-MS & Reflectivity data and scanned core images – a "First" provided in that form by our scientists (Figure 8).

MADMAX Station

Figure 10METTLER Balance & Pycnometer measurement systems and corresponding software (MADMAX) worked well, and were further enhanced throughout EXP340 in terms of "User Convenience" and practical performance levels (Figure 9). (Per Tim Blaisdell; see also: Developer Tech Report). Due the high reproducibility and accuracy of the systems, EXP340 scientists consistently produced good discrete density/porosity data, which further tie into logging and other data sets obtained during EXP340.

Improvements

During the first two weeks of EXP340, Cell-1 produced faulty data, and thus was replaced with a brand-new cell. Ultimately, the original cell was restored (with new o-rings and fittings), tested over a period of time to regain confidence in its output, and then reinstalled. Results were according to the expectations (within 0.5% of the expected values when measuring & verifying the volume of the 10.2cc spheres). More technical details on this process & procedure of cell-installation & testing is summarized in the ET-Tech-Report (per E.Claassen - Figures 10)

Recommendations:

• One scientist proposed to measure the MAD Vial containers with the plastic lid to better retain the moisture loss of a wet sample (or "moisture gain" of a dry sample). Albeit a valid scientific consideration, this is not possible because we need to work with open containers inside the pycnometer cells. The inevitable drift from moisture-loss is unfortunate, but cannot be avoided (Figures 11a & b).
• Furthermore, it was suggested to wipe the rim and lid of the beaker clean to minimize material influx into the measurement cycle from the vial after the wet-mass measurement is complete (per Chris Breitkreuz).
• Last, but not least: The same scientist suggested (and acted upon) to re-moisten sand samples inside the beaker with standard sea water (provided by the Chem-Lab) in order to produce reliable porosity-density results. It turned out that the porosity values were up to 20% higher when following that recommendation, simply due to the fact that w/o performing this extra-step of re-saturating the sample properly, too much water loss causes the porosity calculations to drop porosity values signifcantly (See: EXP340 METHODS, Physical Properties).

NOTES

Etienne brought over a spare PYC cell which is now located inside the bottom drawer (labeled "MAD ELECTRONICS") of the corresponding MADMAX cabinet.

Automated Shear Vane (ASV) & PWave Gantry:

Issues

• The ASV and P-Wave Gantry software is operated from one PC platform, which requires the closing of one application to use the other. This seems to be consistently cause "Master-Slave" (aka: communication) problems between the various COM-ports involved to direct the signals from and to the PC and probes. It would be a great enhancement of the performance level of this station if this inconvenience could be eliminated.
• The P-Wave Gantry still sometimes causes grief and problems, for example when the uninformed user does not pay close attention to the "homing" movement of the transducers pairs, or for (literally) other un-reproducible reasons. One scientist (eventually nick-named "Demolition Man") managed to bury two transducer pairs entirely into the sediment-filled core liner several times; the transducer moves all the way up to the upper shaft of the x-axis transducers, which requires to resetting the two transducer pairs via the E-TRITEX software, and applying commands such as "removing/adding network" for the various com-ports (add some more screen shots of those maneuvers…).

Eventually, we figured out that it is the easiest to open the most recent E-Tritex control file for the corresponding transducer (under "FILE/"- look for "Recent Drive Files" and/or "Recent Application" and find the "Generic.edrv" file and/or "Caliper X.eapp" file) to re-set the system into its proper operational mode. Further, the operator might have to play around with the "Com" port selections and also network occupations to get the correct "Master-Sleeve" combination for the warranted transducer operation in place. The exact pathway to success seems to be still a bit elusive (per Heather Barnes and Maggie Hastedt, who report back similar experiences with the system). If all still fails, simply unplug the (thick, yellow-colored) transducer cable and plug it back into its socket.

• Figure 13We suggest for the PWave Gantry system to replace the currently existing "Save Data and Exit" button with a "Save" button, which allows the User to repeat a manual data reading (not the measurement though), and to upload more than one value. This might be useful for the experimental case where poor signal quality can call for more than one solution. Of course this leaves both the producer and also final user of the data in a state of ambiguity about which data point now is called to be "valid" (Figure 13).
• It would be a positive improvement to implement a dialog window of some-sort for the PWave Gantry laser to reduce and minimize the risk of damaging your eyes when bending into the light beam. Essentially, we like to see a procedure in place that switches on/off the laser upon need of a data recording. Right now the laser is still sometimes active after the measurement is complete. Also: Use a "Post-It" or other sticky paper and put it at the front end of the core liner so that the laser signal is not compromised. It seems to be an easy "fix" to a fault-reading of the offset (where numbers are read as "-" away from the top of the section instead of "+" and increasing).

Improvements:

• Figure 12The ASV system now utilizes a solid "EXCEL template", which is fired up within the application, and respectively collecting and saving data with this utility (Figure 12). Results obtained with ASV BLADE-A were in accordance with expectations for the observed materials, and uploaded via the IODP Standard up loader tool MUT (however, make sure to save your file in "MSDos csv" file format!) Only when the servers were down, data could not be uploaded (which happened a few times at the beginning of the expedition).
• Developer Tim Blaisdell further improved the up loader system (see Developer Tech Report), which now enables the uploading of the ASV-xls files from the same directory of their origin (before this change and upgrade the files needed to be manually moved from their original directory into the IN-director). They are also now showing up properly as ASMAN.id files in the web-tabular working tool (not in LIMS Reports though).
• We adjusted the original position of the ASV blade from a slightly left-of-the-center to a "center-positioned" landing spot. For this purpose the upper brackets were untightened and the entire frame, holding the ASV blade, was pulled toward the user
• The new PWave Gantry system works very well compared to the previous prototype-model; the system now produces good data, which are a lot more reproducible than they were with the old system. This positive result is attributed to the hard and software improvements that have been implemented since the last tie-up period.
• As part of the regular maintenance of the PWave Gantry system, silicon spray was rubbed along the moving parts and rods; we used paper towels to perform this task - mostly to avoid silicon spray to get on the floor (which creates a hazard for people to slip on the greasy liquid).

Figure 14 POCKET & FALL CONE Penetrometer:

These systems were used by two scientists and are not used on a regular base for standard measurements. For completion purposes they are added to the list of instruments that were used during this EXP340 as well (Figure 14).
LE FIN

magnetics Lab

M. Hastedt

Summary

The lab saw moderate use during this normal-recovery expedition. Most of the routine work was done using the SRM, but the Agico JR-6A spinner and D2000 got a workout for discretes. The discrete SRM program was not used. The pulse magnetizer and Kappabridge were used very lightly, and the thermal demagnetizer not at all. The Flexit tools were used extensively for core orientation.

General information

The Molspins and the old Walker Scientific Hall-effect gaussmeter were shipped home at the end of the expedition.
A new manual for picking Flexit data files has been created and is in the initial review stage. A copy has been placed in the T:\TAS\dml\software\labsystems\Flexit folder.
In order to protect moderately lithified sediment cubes from flying apart in the JR-6A, they were cut on the parallel saw then gently wet-sanded on a piece of 240-grit wet/dry sandpaper until they fit into an IODP plastic cube. The excess material was then removed with either a ceramic knife or the cutoff saw.
Preliminary measurements of the extent of the SRM's degaussing fields were performed using the brand-new model 6010 Hall-effect gaussmeter. The ultimate goal will be to automate motion-control and data acquisition into a single application to get a real-time look at what a core experiences as it is demagnetized in the shipboard lab. A similar application (or, one application serving multiple instruments) would be created for the fluxgate magnetometer to facilitate field profiles.

Problems encountered

The D2000 demagnetizer suffered from periodically-frequent error messages complaining "excessive demagnetization field present." This was nearly always at 20 mT. My working theory is that it is a serial-cable related timing issue between the controller and the computer, although why it favors 20 mT over the other levels is a mystery. Reseating the serial cable with null-modem adapter seemed to improve things somewhat, but the problem still occurs. I will put in an order for a real null-modem cable that will fully secure to the unit and hopefully that will solve the problem.
New Flexit data file processing bug in Windows 7/64: after downloading the data you have to tell the program what synchronization file to use. In XP days there would be a pause, and then the filename would be displayed. With Windows 7 you must click Exit on this screen, and then return to it again by clicking the Work with Surveys button on the main screen. The selected synchronization file will be properly displayed and you can continue processing the survey.
We continue to shed pins from SRM boats, only now they can't easily be found. An order has been placed for two new 160 cm boats and some spare pins.

ET report

Expedition DryDock and Altlanitic Massif APL(340T)

Garrick Van Rensburg and Randy Gjesvold.

LO's Office

• Manufactured two shelves to house various equipment in the office.
• Installed a small safe.

Core Lab

• Disassembled the SHMSL and installed a new mounting plate. (Boy is it shiny). Assitied with the installation of the the new 3D camera.
• Tested battery packs for the Tensor Tool.
• Modified the power supply to the new laptop for the spinner magnetometer to work with 120V systems.
• Manufactured a storage shelf for three UPS's outboard of the NGR.
• Modified the lighting on the close up table.
• Modified the door to the Laser Engraver to ensure no Laser Light could escape.

Conference Room

• Cleaned up the wiring and worked on cable management around the computer system.

Chem Lab

• Assisted in ripping up the floor in the cold room.
• Manufactured unistrut mounts for the ceiling.
• SRA glow plug ceased to function. Voltage checked OK. Found Amperage too low. Informed IODP. We were directed not to jury rig a repair. Parts being researched at IODP.

Sonar Dome

• The Sonar Dome came to rest on the blocks in the Drydock before the ship settled. This caused the dome to shift up on the aft end which broke, bent or ripped out several of the mounting bolts. The mounting collar was also bent and had to be replaced.
• The cable to the Bridge Fathometer was damaged during removal. This was repaired.
• The Sonar Dome was removed and a new flange and upper pipe fabricated by the shipyard. A new O-Ring was installed on the Sonar Dome Mounting Flange and the dome was re installed.
• Air was leaking bye the O'Brien bulkhead connectors and the pressure test failed. Replaced two of the O-Rings on the O'Brian connectors. Pressure test passed.
• A water tank was assembled around the Sonar Dome for testing. All three arrays were tested. The 3.5Khz, 12Khz and the 50Khz array for the Bridge Navigation system all passed a functional test.
• Inspected and cleaned the transducer faces.
• Recommend a new cable set from the bulkhead connector to the junction box be purchased in case of emergency.

Gym

• Re inflated the speed bag.
• Changed new running machine power from 120 V to 208 Volts for more durability. Packaged up and sent 120 Volt equipment back to IODP.
• Older Treadmill: Changed out the brushes. They showed about 25% wear. Re tensioned the running belts on both running machines.
• Cleaned out the dust and dirt from all the machines.

Movie Room

• Manufactured LED light strips and wall mounts and installed them.
• Disassembled old Entertainment Center and removed it.
• Manufactured three table tops. These were mounted on the port side and on top of the Audio Visual rack.

Underway Lab

• Removed Ashtech GPS and installed a new Trimble GPS.
• Removed the old Digital heading repeater.
• High graded equipment found in the lab and disposed of useless equipment.

Fantail

• Assisted in deploying the magnetometer.
• Applied Dry Slide lubricant to the guide bars.
• Assisted in setting up and testing the two air gun cluster.
• Conducted a VSP.

Expedition DryDock and Altlanitic Massif APL(340T)

Jurie Kotze and Etienne Claassan.

Core lab

• Pycnometer:
• Pycnometer cell 1 kept on getting calibration values marginally out of spec at times. It seemed to be unstable. We replaced everything that could possibly cause it but the error kept on pitching up. Only after installing a brand new cell dis we realized that it is not the cell itself but rather its position on the nitrogen feed line. Any other good cell will do the same in the no.1 position and work well in any other position.
• Etienne found that a small movement on the gas line will make a difference in calibration values while filling. In theory it does not need happening but seeing that it's at the end of the very thin feed line it does have enough influence to cause a pressure fluctuation that shows up while filling causing the "out of spec" values.
• The solution to this is to build a manifold; in doing this we have more capacitance to act as buffer and have a regulator on each gas line, it can be regulated before entry into each cell with enough head pressure.
• We still plan to replace all the plungers (with the new seats/seals) as soon as we have the instrument available for a couple of hrs. Hopefully during transit to Curacao. This will be part of a yearly maintenance schedule for the instrument that we are planning for several instruments as well.

• Cellophane Bag Sealer was repaired for the sample table; the hot wire broke, removed and repaired.

Down hole lab

• APCT3:
• Temperature tools were deployed on all the sites and loaded onto the network. One set of fresh batteries were replaced on the running APCT 3 tool.
• All heat flow measurements (except one with faulty capacitor) were very good as long as the formation allowed it. We however lost two APCT3 tools, the first one died while standing idle to be deployed, no reason or indication of why this happened. It was ready and after a attempt to startup and log it lost communication to the PC and stayed in that mode. The second APCT3 failed while in the hole, it came back with failed comms as well. After opening it we found a ceramic capacitor cracked around the upper half. Most probably it broke with all the mechanical handling through the process, both will be sent back for repairs.
• A new APCT3 battery pack was found between the spare batteries that we have with one loose lithium cell, it looks as if the spot-weld on the cell did not make a good fused contact. Instead of sending it back we might get the cells as loose units from Dean F. and do the cell replacements here instead of all the travelling to C/S and back again for such a minor job.

• Set Tool:
• The SET tool was deployed after some re-engineering in C/S. All started up well and was sent to the rigfloor where all joints were torqued and sent down the hole. On opening up the water was almost everywhere and the logger itself was dead and the battery collapsed under the water pressure. At the thermistor tip we found the seal (O -ring) to be sliced around the outer circumference as shown on the image. The same signs were visible on the hex screw plug closing the communications port as well.

This can only happen if the seal does not slide in position upon assembly of the tip. After some inspection we found that instead of having a little bit of chamfer on the entry part it was rectangular and caused the seal to be cut. The seal will in most instances go in okay but you never know what the situation is before the tool returns. The same happened to the communication port outlet plug on the side of the tool, its seal did exactly the same. Mike M. asked us to return the tool for a closer look and rework at C/S. A set of images of the damaged seals were sent off to Mike for their attention. It must be noted that this is not a new event and is a historic concern, we are just fortunate that it does not happen very often. We need to keep a set of spare seals on board for both plug and tip and change them with every run. At the moment we do not have any spares seals and we will arrange for some.

• We will return the complete tool as requested. The SET electronics will be shipped with the faulty APCT3's that will be sent back as well.

Underway

• The slip-ring contact was fitted to the old seismic winch drum that is now in use for the Magnetometer. Two pigtail connectors were fitted on both sides of the slip ring enabling a slip-ring bypass if it fails or if its contacts become suspect. Doing this we could prevent the original Magnetometer cable connector so be severed to fit the slip-ring which has amphenol connectors. By removing the rubber coupling between the drum and slip-ring the cable connector will be exposed and can be connected a bit further down the line for the other connector feeding the slip-ring, effectively bypassing it.
• Gus did do some mechanical re-fitment and adjustments to the mechanical level wind fleet angle mechanism and we still have to fine tune the electrical limits and run it on our transit to Curacao.
• VSP Guns were deployed on the three sites, all successful without any problems. Fitted two new 12V lead acid batteries into the external firing box as well.

Movie room

• The movie room UPS is showing signs that it does not like the regulated power, we have found that it helps to switch the power feeding it, this way it works until it get to a point that it have to be reset again. This is not a problem on the UPS side but on the regulated power, we have seen this before in the core lab, all we can do is to keep our eyes on it.

Rigwatch

• Rigwatch ran smoothly with no problems.
• Although the software ran smoothly we had a failure of the draworks encoder. The shaft seal started to leak and water came into the electronics, supposedly water mixed with some ospho-acid as well seeing that there were signs of pretty bad interaction with the aluminum case inside .It was replaced and back to normal again. A new one was ordered by Mike M. together with some buffer modules for use with it in the data box in sub-sea as we do not have any spare units if needed.
• The load pin data transmitter box fitted on the blocks on the Derrick was removed for some refurbishments as well. The box was cleaned and rewired and fitted with a solar panel and two Lithium battery packs. A high intensity flashing white led indicator was installed onto the underside of the transmitter box to indicate the supply availability to the unit. Thus relieving the ET to exchange the lead acid battery before every expedition. Hopefully we will have the blocks available soon to replace the box in its position after the drilling is done. New antennas we fitted to the transmitters as well.
• Discussed the options with L.O. (Bill M.) for the installation of a bigger ship system time synchronized display for the driller. Sometimes we need to know what the exact time events happened during heat flow measurements. The drillers shack clock is running separately and normally not in sync with ships time. The system time is available on the PC there but during coring and measurements it's not possible for the driller to have his attention away finding the right time on the small pc clock, he needs to have a proper display without distracting him from the operation to note down on the run sheet as things happen.

General

• Numerous smaller odd jobs were done as we went through the expedition and Etienne helped with close-up digital imaging table repositioning to the new spot.
• Constant lubrication and cleaning on battery operated drills used on Catwalk were done to keep it from corrosion as it was a high core recovery expedition. We might have to purchase a bunch of extra 3 to 4 mm drill bits as we use them at a high rate while core liners are vented. Some gets blunt from the abrasive mud or gets broken.
• Some spare parts were ordered and probably a component order will follow a stock take soon.

Photos of Flooded SET tool

Expedition 340 XRD Report

Heather Barnes

Summary

Expedition 340 was a sedimentary expedition. The XRD lab ran bulk samples on every core from the 'sampled cores'. No problems were encountered with any of the XRD equipment.
Total XRD samples: 369

Equipment and Software

The Bruker Diffractometer ran without any problems. The parameters for the scans were:

• 35 kV, 40 mA
• Scan angles: 4 – 70° 2 ¿
• Step Size: 0.0174
• Scan Speed: 1 s/step
• Div Slit: 0.3° = 0.6 mm

Freeze Dryer vacuum pump oil was changed. I suggest changing the oil again during the tie-up in preparation for EXP 342.
The new XRD software licenses that were purchased are useful for the Evaluation software. The instruction for uploading the mineral database to the software is saved in IODP_Share/XRD/DIFFRAC_EVA and MINERAL DATABASE UPLOADING.pdf. I would suggest installing the new DIFFRAC.EVA on the computer in the MBIO Lab, and 3 more in the CORE lab. Save one dongle as a 'floater'. Do not uninstall the old EVA software on the computers. It is convenient to keep both programs available. Curacao tie up may be a good time to install and test the new software. In addition, a new quick user guide needs to be written (a version has been started and saved in T:\IODP_Share\XRD\DIFFRAC.EVA QUG, and 3 screen shots are in the same XRD folder as well. Bruker sent a great quick user guide that we should follow, see the file: IODP_Share/XRD/DIFFRAC_EVA and MINERAL DATABASE UPLOADING.pdf.
The oven in the XRD lab was brought to the lounge for baking and a new oven was installed in the XRD lab.
Currently, the MEGAuploadatron for XRD does not accept the format 'PWDR3334567 U1399 23H4 23 24'. I name/save all files in this format for easier sample identification for the scientists, but subsequently have to rename all the files to contain TXT_ID only before uploading into the database. David Fackler said he will change the uploader so that it grabs the TXT_ID info only so that it will upload directly with the longer file name. It is on the programmer's 'to do' list.

Publication Specialist Technical Report

Rhonda Kappler

Summary

Performed duties Publications Specialist for 340 dry dock/340T/340. Collected 340T Preliminary Report content and delivered to shore and prepped for Expedition 340.
In addition to seeing to 340T needs, I also used time on the transit expedition to prepare the graphic log drawing template and associated scanning instructions that would be needed for Expedition 340.
The scientists boarding for 340 were a very "green" group as related to sailing knowledge and the requirements for core description. They had trouble with timeliness and expressed feeling pressed to describe complex layers of material as a mass of entries within a mass of columns and cells to provide details in an assembly line (quoted) manner. They struggled with the learning curve necessary for DESClogik and dealt with the frustrations that occurred over the processes involved plus had no fellow scientists with prior experience to help guide them.
The VCD template had changes with the arrival of the scientist and then another change to a column before additional significant changes were made. On the third site and after multiple holes, the template being utilized with its previous alterations was abandoned and columns restructured resulting in two new and separate templates. The current and previous holes would use one of the new templates and all subsequent holes would require the second new VCD template.
I spent a lot of time working with the scientists on their entries within DESC through the VCDs and trying to teach them how to proof themselves for "gaps" by scrolling through the data itself with little success. VCD notebooks have been marked with corrections often multiple times and returned to them. Those that holes were in the first, second and finally third templates changes were reviewed around four to five times due to different data plotted. Currently, there are approximately 2110 VCDs (for this less than 32 planned coring days expedition) that have been reviewed several times with last hole count still undetermined.
This was especially true of for the graphic logs creation and electronic capture as it was slow learning process as well. The scientists and I have found that samples taken can create drawing depth issues and cropping problems. This is especially true if samples taken from the bottom or top of a section were not included within the drawing itself then subsequently the scan and crop was incorrect and loaded into Starter centered within the image column creating top and bottom blank space and not lining up with the data.
In addition to other duties, I was delivered instructions to create Preliminary Report/Summary figures for all holes drilled (18). I was unaware until several weeks in that this would be a need for this particular expedition on behalf of the Staff Scientist and Science Party from the Publications Specialist. I have individually seen to the needs of this project from gathering all the data to developing the figures. See additional duties explanation.
As the expedition wraps up, I will continue with duties of creating the VCDs, finalizing summary figures for the Preliminary Report, and collecting volume content in preparation to transfer all the materials to shore by FTP for the PR or by DVD and paperwork by shipping.

Equipment and software performance summary

Issues regarding the hard disk space and slowness of processing speed of the Yeop PC computer were reported. I have found these same or similar issues pointed out in previous tech reports and recommendations made as far back as Expedition 334. On Expedition 330, I experienced the same slowness, but not the hard disk problem.
The computer does better if it is kept above 10GB remaining which basically means that's 10GB of useless work space because if it goes below then it does not want to work. I made sure all previous expedition and nonessential 340 files were saved to the server and removed. MCS Mike Hodge found 5-6 GB of operating files that could be removed which helped gain space and I utilized the server for storage and nonworking files. Since most of the 80GB computer space is taken up by the operating system, software, and associated files, that leaves approximately 20 GB actual working space to actually have available to utilize. While I had many VCDs and other to produce on the PC, I did not have large amounts lithology or such graphic related data. Problems were reported to and followed up with MSC Mike Hodge, and provided in detail to shore via email.

• Strater performance was good with exception of one crash and loading large amounts of data, especially lithologies, due to the slowness of the PC.
• The Yeop PC issues created problems using DESClogik and Lims2Excel as well as reported to jr_developer and Programmers, David Fackler and Tim Blasidell.

Database, entries and data upload or download related

Helpful was the addition of lightened core images. While images have been previously available, the change allowed a better reference for the scientists on their work and resource for proofing VCDs against the data and graphic logs being produced.
Issues were reported to Programmers David Fackler and Tim Blasidell, as well as jr_developer, Debbie Partain and others as needed. There were multiple versions of DESClogik released during Expedition 340 and new versions of Lims2Excel for test and/or release.

• The decision was made not to utilize the change to a newer versions of L2E L2E 7.1.2.3 or 7.1.3.0 and stay with L2E 7.1.1.3 for two reasons – the current version was working for VCD and Pubs related needs so why mess with that and to keep consistency since the change in versions would have altered the format of the Title-Section header found at the top of all remaining VCDs and corrections to be produced.
• L2E underscore changes to hyphen issue resolved with L2E 7.1.1.3
• L2E analysis depth data problems plotting until discovery was made that columns to pull data from into Strater had changed, previously used CSF-A and now need to use "Depth in Hole" column to plot.
• L2E export of Title_Section – VCD header title displays by core and did shows section number issue was resolved with L2E 7.1.1.3
• L2E image overwrite not working properly for downloads, but did not directly affect work so to replace old images with new, I simply trashed previous and downloaded new. Replacing was necessary for several core images as well as updated graphic logs produced for this particular expedition.
• L2E had issues with freezing, slowness and long "lag" time for the "Select Core/Hole" process and in downloading, but once the realization that hard disk space was a problem and the computer was kept above 10GB remaining this subsided to a more normal level.
• DESClogik issue related to PC computer hard disk space and processor speed caused the programs to "hang up" during performance. At one point, I timed how long it was taking to download to view data using all tabs for a Hole and it was 22-25 minutes minimum for that particular one (it was not the deepest) and not including time to load the template or export to an Excel file. With a template utilized as much as 340_core_description and tab General, downloads will typically be slower, but I was told no one on the ship reported having the "lag" time that I was having causing the belief that the computer itself is a factor.
• DESClogik duplicate description export issue was an artifact of incorrect entry in DESC resolved after scientists were provided with instructions for proper entry.
• DESClogik Launcher messages and Autosave began with the release of version switch from version 3.23.4.73 to 3.23.4.79 and persisted through 3.23.4.80, 3.23.4.81, 3.23.4.83 and until the current 3.23.4.85 version. I received this message regardless of using download "All Tabs" vs individual tabs as needed to download and entire hole or typing in sample entries vs using the "Select Sample" process. The temporary solution was to disabled the Autosave feature. However, I had to remember to do this each time I reopened DESC.
• DESClogik "upload or lose changes" messages received upon trying to close DESC and asterisks in the corner tabs of a template indicating changes made have been received for downloads where no changes or any entries were made.
• DESClogik multiple intervals occurred causing problems with plotting within Strater columns. Most of the time it is only one or two lines additional and generally does not affect most plot columns, but "stacked" type bar log this require that all columns total 100% and there must be 0s in the cells were needed. I have had to manually adjust to "fill in the blanks" with the appropriate number and ensure all entries are one row to get Strater to plot. For one instance reported, the additional lines for the same interval are on both the General tab and the Detail tab, but Detail is only 11 lines deep (vs 37). The extra interval lines were oddly stairstepped in DESC.
• In addition, there were issues pertaining to depths discrepancies between core images and DESC entered data. The cropped core images have often been 1-2 cm short or long and in quite a few instances more cm than that. I consulted with both Curator Gemma Barrett and Programmer David Fackler multiple times to try to distinguish whether it was curation related, such as a recalculation, or problems with entries coming from DESC. There were a few rebuilds of depths to account for re-curation. However after referring many of these inconsistencies to David Fackler, the majority of issues appear to have stemmed from scanning in core images and cropping incorrectly or incorrect measurements related to samples taken (PAL, IW, WR).

Volume content and materials

There were some minor issues with the submission procedure of volume material. I asked for a few brief minutes during the initial meetings to do a quick explanation, but this did not occur as the staff scientist was to address this. I made the science party aware of the publication processes and procedures for submitting material were sent via several emails. Folders were created for putting finished and approved files on UserVol in preparation for transfer to shore plus asked to provide printouts. Needs for editable/workable figures, text, tables, addressing call outs, proper caption needs, and labeling, etc. were also relayed. In looking at my sent mail to see how many had opened emails. I found that typically around 10 less than the number of recipients remained unopened throughout the expedition. In addition, they had confusion so I re-sorted asking individuals as needed with verbal explanations of the process and reminders were also given.

General duties performed for 340D (end), 340T and 340

• Provided administrative, graphics and publication support throughout the expeditions.
• Distributed and completed necessary expedition paperwork (including cabin deficiencies, communication policy, photo release, manuscript and photo copyright forms).
• Provided support for visual core descriptions, methods figure and core recovery summary figures.
• Created the Publication directory, tracked/ collected materials and prepped for transfer of volume to shore.
• Modified initial shore-created Strater templates and Methods figure during the start of the expedition to display specific plots requested by science party. Continue to update Methods figure as needed for the expedition.
• Assisted in coordinating social events (including birthdays, expedition t-shirt design contest and other).
• Communicated with shore based IODP travel administrator to verify hotel arrangements for end of expedition.
• Check in/out lists, helping with passports, customs and immigration requirements and other associated

Additional duties

• During 340T, I completed preparations for the graphic log drawing templates in Adobe Illustrator for use in creating hand drawn logs for scanning in and import into an image column within Strater and produced within all VCDs. I customized the cyan drawing grid to match for printouts specifically from the core-color printer as the F-deck copier/printer made them too dark and did not the same quality to allow the grid to "drop out" automatically as scanned.
• In addition, I worked on creating scanning instructions for the VCD graphic logs using the F-deck copier and took pictures with my camera insert in the document. In addition, I created information for cropping the scanned images and saving the files using Photoshop. I combined the scanning and cropping instructions and inserted the pictures to create a how to guide for the scientists. Once the scientists arrived to begin working, I walked them through the process and encouraged coming to ask questions.
• Summary/PR figure information is being produced for each hole drilled. A marked example up from what was done on Exp 334 was provided. I have created a Strater template to produce the figures and personally gathered data from needed sources (Desc, analysis data, and scientists) to make this happen. I have consulted the scientists as needed and multiple times to collect and ensure that I am utilizing the correct materials. These will all have some standard columns (depth, core recovery, lith unit, lithology, etc) whereas others will vary by hole (for example, not all will have logging data). A pdf is being made Strater and brought into Adobe Illustrator then placement of one additional column as needed. The original estimate for columns all inclusive at a figures maximum had the potential to reach a count of 22+ columns including those "standard" and some that would overlap. This was subsequently reduced by meeting with a contact or multiple contacts each discipline group and discovering that a particular data set was either not usable or not the same available as it was on Expedition334.
• Collected photo release forms from IODP staff who still had completed theirs for delivery to IODP Employee Services.
• Printed and posted new bulletin board notices for the IODP Employee Services Office.
• Helping with the Imaging Specialist duties and coordinating tasks with Etienne Claassen to cover Expedition 340 needs (absence by the Imaging Specialist due to a family emergency).

SUGGESTIONS

• Cover and coordinate with the EPM Staff Scientist all needs for an expedition delivered to work on within a timely manner on shore and on ship
• Try to find an efficient way to better determine VCD structure needs and prevent the VCD templates from changing multiple times and greatly within an expedition. The VCD template had changes with the arrival of the scientist and then another change to a column before additional significant changes were made. See also summary section comments on VCD template changes. With proper time to prepare on shore and a more accurate gauge for needs would be of significant help to the Publications Specialist in meeting expedition work needs.
• Being required to do the summary figures all holes drilled was an unknown factor that required creation of a new Strater template, gathering of cleaned up or filtered data, coordination from all sources, and time. It would be helpful to have some way to be aware of this need sooner and try to make the figures along the way throughout the expedition; possibly even to know was going to happen in advance and with time on shore to prep.
• To help the above suggestions, prepare for the data that you know you will always encounter and want to graphically relay (in VCDS and/or summary figures) on an expedition. In addition, create some kind of networking among the scientists to try to figure out expectations for what they may discover to help determine what may be plotted or produced. Try to plan meetings for the Staff Scientist, Co-chiefs and key scientists that can cover this for DESClogik templates and graphics, similar to that done for Exp 339 yet more inclusive of needs.
• Investigate electronic media alternatives to creating graphic log type drawings.

Chemistry lab

Mike Bertoli & Erik Moortgat

Sample Summary as of April 12, 2012

More details to be provided in lab notebook (\\JR1\TAS\Lab Notebooks\Chemistry\Chem 340\Open Notebook.onetoc2)

Equipment STATUS

Ampulator

• The ampulator was used to seal 5mL vials, from the IWS residue, for storage in the repository.
• The belt was changed.

Balances

• No problems were encountered with either the Cahn or Mettler balances.

Carver Presses

• There still appears to be a source of leakage in the left and center pump units. The situation is being monitored.

Cary Spectrophotometer

• The Cary was used to analyze ammonium concentrations.
• A 10% Tween^®80 solution was run through the flowcell at the end of the Expedition.

CHNS

• The CHNS was used heavily this Expedition – primarily as a component of the C/N ratio.
• Replaced the separation column (CM1009) because of poor peak separation. Additionally, the prepacked reactor columns are a welcome addition; the quartz insert no longer needs to be adjusted before installing the reactor column.

Calibration standard

• We used the Thermo CN standard (P/N 338 40025) which is ~ 0.2% nitrogen and 2.1% carbon – this gave a close matrix to our samples.

Coulometer

• The coulometer was used heavily this Expedition.
• Gas was observed leaking around the pre-scrubber bushing and was sealed with silicon/Teflon tape.

Discrete Analyzer

• No samples were analyzed on the DA.

Freeze-drier

• No issues to report. Samples for COUL/CHNS analysis were dried in the XRD prep lab.

Gas lines/manifold

• Issue with the argon pressure transducer. The Analytical Gas Status application has the pressure basically fluctuating as noise as not representing actual manifold pressure. Info was sent to the appropriate parties on March 14 but no responses have been received as of yet.

GC3/NGA

• All headspace samples were analyzed on the GC3. No issues were observed with the instrument itself.
• A few times the MUT appeared to not be processing results, for no apparent reason we could determine. Results CSV files were placed back in the queue and the MUT processed w/out errors.

Hydrogen generators

• No issues to report.

IC

• Removed the Luer locks from the helium line connecting to the eluent refill bottles due to numerous gas leaks.
• Receiving warnings that the "Sample Syringe Cycles has exceeded its limit. Service is now due". This will be a task for the transit from Bermuda. The maintenance kit (CM1030 p/n 060581) has already been checked out so a new one can arrive to replace the one to be installed.
• Added two dilutions to the calibration curve per Scientist's request (1:300 & 1:400).
• At the end of the Expedition, DI was run through the system for twelve hours, with the eluent generator off. The suppressors were capped and the guard/columns removed. The guard/columns will be replaced during the transit from Bermuda. The reservoirs were rinsed with a 5% methanol solution.

ICP

• ICP sample prep and data analysis was handled by the scientists and alignment/instrument preparation by the techs. Significant sample drift (both concentration and signal) was eventually reported in the last week of the cruise, but additional sample analysis pointed the finger at a sample preparation problem (not following the ICP User's Guide) and not an instrumental issue. Independent of this, values will still be reported but the main geochemistry contingency did not really value the shipboard ICP analyses.

salinity

• Two new optical refractometers (Fisher Model S66366) arrived and were used instead of the digital refractometer.

SRA

• Lisa Brandt worked on the SRA during the transit from Lisbon to San Juan. Her findings are outlined here and more detailed information can be found in OneNote.

Replicated problems that Erik had in the past with the SRA. Checked/adjusted all gas flows prior to the run starting. FID will not light on its own. The FID will light if you use a lighter. Glow plug does not seem to actually "glow" at all. I removed the small washer from the outside of the glow plug so that the plug would be seated further into the opening, and this did not help. I had Garrick, the ET, come and help me measure volts and currents. Voltage between the glow plug and the chip on the board was 2.5 volts. Current between the two was only 1.6 amps. Garrick and I examined the FID on the GC3, and also took a spare glow plug up to the ET shop for examination. In both instances, the glow plug required 2.3 to 2.6 amps in order to glow.

• I sent an email to Clarence Kuhnel (Clarence.Kuhnel@weatherfordlabs.com) detailing our problems. They wanted three more specific voltages from the following locations as shown in the pictures:

• • Location 1 voltage is supposed to be .6 to .9 V; ours was .518V
  • Location 2 voltage is supposed to be 1.5 to 1.8 V; ours was 1.811V
  • Location 3 voltage is supposed to be 2.5 V; ours was 2.46 V

They also sent the following picture of what the glow plug should look like, and it turns out that they really need the coil from the glow plug pulled out and extended into the FID gas stream.
I took a pair of tweezers, cleaned the tips with methanol, and gently pulled the coil from the glow plug, out into the gas stream. I then did a test analysis, and watched the FID with the little mirror on a stick. With the glow plug coil extended, it does, very slightly, glow. Not nearly as much glow as on the FID on one of the GCs, where the glow seems as bright as the end of a cigarette, but it does glow. This was enough to ignite the gas stream.
I performed a test sequence run with one blank, one calibrator (STD 99986), and then ten more 99986's run as unknowns. I wanted to do a long run unattended to check and see if it would light every time, and it did. My results for S1 look slightly strange, however. The calibrator and first 8 or so "samples" came in very low. S1 should be .08 to .24, and my values were all about zero.
Sent another email to Clarence, asking for assistance:
Lisa,
The third STD is the only one with a normal S1 peak. I do not understand the jump in FID signal at the beginning of the S2 peak. The low values could be due to a small leak during the purge. Check the internal pedestal seal for scratches or replace it.
I took the pedestal apart to check the conditions of the O-rings and seals. Instructions for taking the pedestal apart are in the SRA manuals binder. The pedestal middle O-ring did seem to be extremely flattened and crimped. I replaced the pedestal top O-ring, the pedestal seal, and the pedestal middle O-ring. I then did a run of one calibration 99986 standard, a blank, and ten standards run as unknowns.
The run from last night looks better for S1, but the S2 and the S3 values look strange. Adjusted the pedestal height, using the software. I ended up setting the pedestal run position to 0852, and the pedestal purge position to 4260.
Calibrated the IR detector using the CO and CO2 gas standards. Performed another run of one blank, one calibration standard, and ten standards as unknowns. The S2 and S3 values look good. I also tried to run some blanks as unknowns. The software will not let you enter a mass of zero, so I just put in 1 mg. The results look strange for the blanks run as unknowns. Also the S1 values still look a little high. Sent an email to Clarence Kuhnel for help.
Lisa,
Your data looks good. The S1 is not too high. Had the crucibles been unused for awhile? Have they been somewhere that they could have picked up some oil, finger prints, setting on vinyl or plastic? The blanks run as a TPH is the normal way to run as an unknown. The blank data makes more since to run with a weight similar to your samples. This is good progress.
I fully cleaned all of the crucible, crucible tops, and crucible holders by sonicating for one hour in methanol. I also cleaned the sample holder tray by spraying it down and wiping with methanol. I then did another test run of one calibration standard, one blank, ten standards as unknowns, and three blanks as unknowns. I entered 60 mg for the mass of the blanks, as per Clarence's suggestion.
 Results from last night look good. Using a mass of 60 mg for the blanks gave S1, S2, and S3 values of about zero. A few times over the last week of dealing with the SRA, I've had small problems with the alignment of the autosampler tray. I have found the following settings to work well:

• left/right:1438
• front/back:133
• up/down:220

Pipettors

• The Eppendorf Research pro pipettor was very popular this Expedition. It would be very nice if we could acquire another single channel (100 – 5000 µL) pipettor (21-378-79 / No. 022461346).
• Most pipettors are significantly out of calibration. A few pipettors are especially bad, and one was broken by scientists who did not use it properly. It is recommended to have oncoming technicians confirm pipettors are in calibration; calibration confirmation methodology will be developed and sent to appropriate management.

alkalinity

• Metrohm electrode (6.0253.100) shattered and replaced with 6.0234.100 model. Plastic sheathing had to be replaced with an o-ring to facilitate the diaphragm being submerged into the liquid. Calibrated and a new standard ratio calculated (340_0234probe). The 339.RATS dispensing rate was used the entire Expedition.

Chloride

Incorrect AgNO₃ solution (0.014N instead of 0.14N) ordered for the Expedition. Hopefully mistake will be rectified for future Expeditions.

Water system

• Replaced both RO membranes and all three filters (prefilter, MPS cartridge, and carbon cartridge).

Misc

IW prep

• We used shipboard nitrogen plumbed into a glove bag to 'prep' our IW whole rounds for the squeezers.

lighting

• The requested lighting for above the IW prep area/titrators has yet to be installed.

Shipping equipment

• Hand pipettors (12) – to be cleaned/calibrated

THIN SECTION

Gus

Summary

There were a total of 43 thin section requests of volcanic rocks and tephra.

Special projects

Trained "temp tech"

Problems encountered

None

Miscellaneous

• Routine equipment maintenance as needed.
• Repaired VS-2 glass vacuum flask drain spout.

DEVELOPERS

For IODP Expedition 340 — Lesser Antilles Volcanism and Landslides3 March – 17 April 2012 Tim Blaisdell, David Fackler, Bill Mills, et al.
For IODP Transit 340T — Atlantis Massif Oceanic Core Complex APL17 February – 3 March 2012 David Fackler, Paul Foster, Bill Mills

Overview

This document highlights changes to the JOIDES Resolution laboratory data management environment on this expedition and transit. No features and issue list is provided this time. Instead, see the Pending pages of the developer site: https://sites.google.com/site/iodpdeveloperwork/projects [its Google, just search].

Curation and Core Handling

SampleMaster 2.2.3.6

SampleMaster was updated with more comprehensive handling of errors and messages from the back-end web-services [Blaisdell]. Release 2.2.3.6 was applied for a week for evaluation at the Core Entry station, then reverted to 2.2.3.3 in use since expedition 339. Will move forward on shore when other bug fixes and feature changes get queued.
The most frequently reported issue for SampleMaster: "it's slow". But the root causes on examination lie outside of the SampleMaster code:

• In one case, the Image Grabber software was left running in the background on the Core Entry station. Examining Task Manager showed that it was in an unusual state consuming excessive CPU time and memory, therefore competing with SampleMaster for workstation resource.
• In most other reports, the report is attributed to unquantified "slow" web-service responsiveness. Point measurements can be taken with Fiddler (an HTTP proxy tool), but are not sufficient to provide longitudinal comparison.

Routine monitoring of web-service response times and error responses are required to best determine where optimization effort should be spent.
Outstanding feature request. Drillers requested that SampleMaster core entry support these additional fields:

• 3 columns for core-catchers, instead of just one whose content changes every expedition just a little bit.
• Enable the drop-down lists for types of core-catchers to adapt to XCB or APC/RCB coring. The XCB tooling can have up to three core-catcher mechanisms applied. APC tooling supports two CCs. RCB tooling supports 3 CCs.
• An additional check-box requested for tracking "core jams". Very important information when re-visiting a site or in formations expected to be similar to a previous site.

LaserEngraver aka LazerKatjie 2.1.0.2

[Remove if covered elsewhere.] The engraver is an accepted part of the Core Entry workflow. The engraver is a temporary but limited (4 in, 4 out) core storage point. Engraving is fast, but is offset by being an extra stopping point for core in it travel from catwalk to equilibration rack. Labeling and taping the sections is a bit more ergonomic for some technicians at the equilibration rack rather than at the engraver.

• Work station was updated with the LabVIEW 2011 environment during 340T; then again updated to SP1 (11.0.1) during 340.

• The engraver software was given a facelift, now fully usable by touch panel only. [Mills]

• More efficient calls to back-end web-services were implemented [Mills]. Significantly reduced reports of "its running slow". Nearly always in conjunction with reports of SampleMaster being "slow".

• Watch for this issue: Sample comments containing the special characters "&", "<", ">" will cause the LaserEngraver to fail to display holes, cores, sections properly. Work-around at the moment is to remove these special characters from core and section comments via SampleMaster. The fault is not in the LaserEngraver software, but in how the web-services encode data. These special characters are supposed to be specially encoded for transmission.
• Fixed: At one point the LaserEngraver stopped working because it only accepted 22000 characters of a longer document encoding a list of holes. With release 2.1.0.2, documents up to 65000 characters are accepted and processed. Ideally a more efficient set of hierarchical browsing services should be provided in the web-services back end.
• Requested software upgrades:
  • Engrave only Archive or Working
  • At the ability to engrave user entered text.

30" monitor now in place at Core Entry. Laser printer moved underneath LaserEngraver station. Whiteboard now faces the stairwell (reduces congestion around the laser engraver). [Mills, Peng] Engraving became a cottage industry at one of the longer coring breaks.

Geology

DESCLogik 3.23.4.85

The above version is deployed for production use on ship and shore. An alpha version, Numerous bug-fixes and enhancements [Blaisdell]. Follow the link above to see the release notes.
Deferring to Herrmann and Hastedt to elucidate the best practices and pain-points of managing the descriptive data process. From an outside-the-process perspective:

• Template development remains an exercise for the experienced. A template manager can create templates that are actually invalid for data entry use.
• Value list management is an exercise for the experienced. The structure of the spreadsheet to be imported and the relationship of the values and parameters are both important. If not structured just so, the sheet won't upload. Messages are terse. Errors cryptic.
• Pre-cruise training of participants is believed to be helpful in DESC ramp-up for expeditions with short lead-time to first core. Without it, plan for a week of learning, plus another week of re-writing templates and value lists as the lights come on.

"A good tool guides you through a complex process. A better tool not only guides you, but makes the complex task easy." [paraphrase Blaisdell].
A new version, 3.23.5.0, contains a feature that allows the user to "collapse" or "merge" several rows of description on the same sample into one row. It has been in alpha testing for several days as of this writing, with Sandra Herrmann being the primary (only) tester. She has reported a defect in the handling of file data columns, so this is still under development.

Barrel sheet production and Visual Core Description

Lims to Excel (L2E) 7.1.1.3

Several fixes were implemented to address Publications needs [Hornbacher]. 7.1.1.3 is the present production release. An alpha version 7.1.3.0 is linked on the USIO Applications page for review and evaluation [Fackler]. Both versions are quite stable for retrieving analytical data and files. Neither are of any production value for retrieving DESC data by template or via Format 3. Follow the link above to see the release notes.
The primary consumer of the tool remains the Publications Specialist. Barrel sheet title lines, scales, ripped-down images are successfully and routinely retrieved via this tool. The more specialized DESC variants require significant development review, debugging, and testing. Where DESC data was required, DescLogik direct exports were used.

Barrel sheet production

Remains an excellent tool for data quality assurance. Images are constantly reviewed. Multiple data retrieval methods are applied daily and repetitively. Depth scales, images, and data tracks from multiple sources usually align with each other. When they don't, each source dataset can be examined to determine the root cause. Variances of these kind are typical:

• A foam spacer is placed in line-scan images to denote removed material. When the material is removed at the top or bottom of the core, the operator often fails to check the total curated length of the material, and will crop the image too short or too long. When the cropped image is scaled into the barrel sheet display, then it does not align with the rest of the data.
• Sometimes re-curation happens. Core changed with time, or a cataloging error was corrected. The barrel sheet scales may have been downloaded before re-curation and re-computation of depth. Depending on timing of downloading source data, one dataset may have been acquired before the change, and another after. These show up as discrepancies in the reports.

• A few reports still rely on the legacy depth fields in the sample table [Core Summary, Section Summary]. It is possible for the depth scales to be out of sync—but only if the developer runs the recalculate depth services directly. SampleMaster presently kicks off a recomputed of both sets of depth scales.

Outstanding issues? See jr_developer traffic and archives [Lab Help], and Pending pages on the development site for applications used in barrel sheet production [L2E, DescLogik, WTR, LIMS Reports].

• Fix DESC Format 3 support for L2E.
• Download speed optimizations—every little bit helps when multiplied by 2000 barrel sheets.
• Holes U1393A, U1394A need to be lightened to match the other cores.
• A number of images do not align with the data. Most of these will need to be re-cropped.

L2E release 2.1.3.0 contains several speed improvements for analysis data and file download, but remains excruciatingly slow for pulling DESC data by template (4+ hours for an entire hole of data), and has not been evaluated or approved for production use other than by development staff.

Virtual core composite generation

The Virtual Photo Table compositer is installed and in routine operation on the Publications Specialist workstation.
Seen once. Unknown cause, but the VPT software did get into a state where it was spamming the error logging web-service to the point that other web-services were slowed down. 2000 sessions had been accepted by the error logging mechanism and were gradually being processed. Stopping and re-starting the VPT tool enabled the Tomcat server to catch up and recover normal operation.

Correlator

The participants tasked with stratigraphic correlation were familiar with AnalySeries and applied that instead as sufficient for expedition needs.

Closeup, Microphoto, Thinsection Capture 2.0.0.8

Original plans were to vet a revised version of this package. But these plans were scrapped due to extenuating circumstance. The tools existing tools were applied without issue to thin section photos, about a dozen microphotos. Closeup photography was very little utilized. Participants were for the most part happy with the line-scan images, or snapshots from their own cameras. [Bill we miss you!]
Binaries for evaluation of the next version are available in tasapps/imagecapture2 since expedition 339. Code for the new version is forked to NET/CloseupCapture2.

Geophysics

Whole core systems

Whole-round logger (WRMSL)

Running binary release 2.0.4.2. System upgraded to LabVIEW 2011 service pack one—additional upgrade notes here. Revised local configuration file and backup configuration files to reflect that magnetic susceptibility loop serial number 477 is in use on this track. Modified database records to reflect this; did not recode the internals of the raw files already captured. Revised local configuration to reflect that the photo-multiplier base on this detector should be driven at 900V (not 650V).

Special task logger (STMSL)

Running binary release 3.0.0.0. System upgraded to LabVIEW 2011 service pack one—see additional upgrade notes here. Confirmed that magnetic susceptibility loop serial number 476 is in use on this track and so configured in the local file. Confirmed that configuration for this photo-multiplier base is set to drive the detector at 650V, and that the sensor is tagged as "GRA2".
19520, 19540 amplifier swap. The 4-axis 19540 motion control power amplifier was swapped for a 19520. The 4-axis amp was borrowed for motion control failure isolation testing on SHMSL. When restoring the STMSL system to full functionality, took time to try out the other spare amplifiers on-board. Only the one installed actually works with the STMSL configuration—and on that one, only the X-axis. Failure behavior: when commanded, the motor will not servo here—as if the amplifier is never enabled, though all the control signaling is good. Tested the same amp and motor with the controller in the pending NGR Win7 station and it worked fine. The hardware is not "plug and play". Proper configuration is required.
All spare amplifiers have been consolidated to the Galil parts drawer under STMSL. One amplifier is being shipped home for repair (the controller power light does not come on).
STMSL, WRMSL A reminder to development staff to leave production systems in production readiness when done. When development occurs at the production track systems, settings are modified for the purposes of development testing and verification. These settings are often at variance with the equipment on a given track, and often are not appropriate for operational science support—varies depending on the development and testing intent. Care is required to restore the stations to last known good operational configuration—even the small metadata details.

Natural gamma (NGR)

Failed high voltage power supplies. Replacements expected to arrive and be installed in Curacao. Failed boards will be shipped to the manufacturer for replacement or refurbishment. Noted during 340T maintenance in Lisbon, following a second announced power outage, while bringing the system back into operation. Two high-voltage power supply boards, 8 channels each, are used to drive photo-multiplier tube bases for anti-coincidence plastic scintillators.

• Board one (EHQ00) channels (CH) 2-5 failed to drive to target 1300V. CH2,5 reached 1.1V; CH3 reached 985; CH4 reached 948V.
• Board two (EHQ01) channel 7 failed to drive to target 1100V. CH7 reached 1.0V. CH6 was consider operational, though it only ramped up to 1268V of the targeted 1300V.

Decision was made to operate NGR by only powering the anti-coincidence scintillators over the body of the system. The elements in the doors were left unpowered for the duration of transit 340T and expedition 340. [Fackler]
Edge correction. The edge correction being applied to adjust for the estimated volume of core material over a detector does not work for the material collected on expedition 340. Anecdotes and limited documentation of the same behavior is available for previous expeditions. The cause is unknown. Significant experimentation required to solve this. See traffic in Lab Help.
Several experiments were conducted at centimeter and half centimeter scales to assess the response curves for each detector as a collimated Cesium-137 source was moved through the detector barrel. The experiment providing for an independent verification of sample placement has not been conducted. The current data reduction math has been reviewed.
Detector response region assessment. A one off program was written to automate the detector response region assessment, as the experiment is time-consumer and error-prone to conduct manually. A placeholder for the code is here: https://build/svn/hq/LabVIEW/ngr_assessment/trunk. Otherwise, contact [Mills].
Replacement host computer. Not done. The goal was to upgrade the system to Windows 7, LabVIEW 2011sp1, current Galil motion control drivers, current ORTEC multi-channel buffer card drivers, and re-build a fresh copy of the NGRMaster data reduction DLL. Code changes are committed to trunk for the LabVIEW 2011 upgrade, Galil motion control upgrade and ORTEC multi-channel buffer card driver update. The code is NOT end-to-end tested against the production equipment. Nor has a clean and vetted build of the NGRMaster data reduction DLL been applied to the updated code. New code is here: https://build/svn/hq/LabVIEW/ngr/trunk. An image of the new system has been snapshot to the development travel drives. The current drives have been set aside to ease the resumption of the effort at a later time.
Existing host computer. The existing Windows XP instrument host has been updated with the LabVIEW 2011 sp1 development and runtime environments. This was installed to support the one-off code for detector response region assessment. The existing NGR_TRACK software is a binary and runs under the LabVIEW 2009 run-time environment [unaffected by the operational update]. Code for the production system is here: https://build/svn/hq/LabVIEW/ngr/release/jr-2.0.0.0.

Split core systems

Section half image logger (SHIL)

LabVIEW Updates. Operational instrument host (DIS1) is updated to LabVIEW 2011sp1. All the necessary drivers and development environment components are present on this workstation.
Core lightening workflow. Re-written and replaced. A snapshot of the new screen is visible at the development notes page linked in the header above. Tagged for code management as release 2.5.0.6—may show something different on the startup screen, available here: https://build/svn/hq/LabVIEW/il/release/2.5.0.6. The revised code was deployed in the gap between 340-U1394A and B. [Mills]
The lightening controls are presently exposed to operator control. This has not been an issue this expedition. The material has been consistent, and the operators of this station not inclined to twiddle or tweak. The settings applied are recorded with each image uploaded.
It is expected that this same code can run as-is on the imager in the ODASES lab. There is no need to fork the code.
Image printing for core description workflow. Is now implemented and integrated into the LabVIEW code-base. A dependency on the LabVIEW Report Generation Tool is introduced (32-bit only). The workflow is dependent on visual core description artwork laid out in an Excel template. The template for 340 is found in c:\data\shil or in the code repository: https://build/svn/hq/LabVIEW/il/release/2.5.0.6/config/VCD-S Templates. Note the scaling and printing variables are hardcoded. While capable of working with other Excel templates the user must take care not to resize the Excel document from the Expedition 340 template. A new version (see below) provides for an image editor to resize the image to a specific templates.[Mills]
ImageMagick is no longer used for image generation in either of the above processes. The former command-line ImagePrintPrep scripts are retired. Ability to scan whole round images was vetted, but should be re-tested before it is needed on a full-blown hard-rock expedition.
This version of the SHIL uses IMS common Vis which must be loaded into the user library folder.
The Spare. Is NOT a mirror drop-in image. DIS2 is presently a Windows 7 64-bit box. It was updated with LabVIEW 2011sp1 in both 32-bit and 64-bit flavors. An existing goal is to move operation of the SHIL to the 64-bit platform. There are no technical impediments to doing so. Only equipment swap, Imager software update, and testing time are required.
If the spare is required for operational replacement, restore from the SHIL Windows 7 32-bit image in the Acronis backups. There is no need to preserve the 64-bit system image, as it has already been captured to peg that effort. [Fackler, Hodge]
Pending SHIL code upgrade. A tested but not released version of the code will be reviewed on shore with the Photographers and Houpt. This code has the following features:

• Password protected access to the image correction values;
• Major code clean-up and reduction;
• Image buffers are private to a single VI significantly cutting own on memory allocation activity;
• Improved lighting control with set-up panels;

• Camera Focus routine moves the image camera away from monitor for easy access to lens.[Hastedt]

• All processing, correction values etc are managed by configuration files, with editors accessible from the SHIL front panel;
• Utility for scaling images for the core description print out (VCD Scratch), title change, page size etc.. With support for working/archive and whole round image support.

[Mills]

Sonic velocity (GANTRY)

Binary release 2.0.0.2 is still in production use under the LabVIEW 2009 runtime. The code associated with this release has been tagged in the code management system, so as to make way for new developments: https://build/svn/hq/LabVIEW/gantry/release/2.0.0.2. Raw signal files were not uploading for this system. The component configuration was updated to accommodate, and the content reloaded to ASMAN. [Blaisdell]
A development evaluation of the next release was vetted during the 340T transit, but not put into operational production. The development evaluation codebase is checked into the code management system: https://build/svn/hq/LabVIEW/gantry/trunk. Express Vis have been flattened. Codebase is converted to LabVIEW 2011. [Fackler].
LabVIEW Updates. This instrument host was upgraded to carry LabVIEW 2011sp1 and updated driver sets. Carries both 32-bit and 64-bit version of the development and runtime environment.

Reflectance and susceptibility (SHMSL)

Changes. User interface made more touch screen friendly. The lighting systems for the reflectance module is now directly computer controlled via a set of power relays. Development work with the 3D camera was done during 340T. The 3D camera work was rolled back on this station for production 340 work. Snapshot of the current production SHMSL code is here: https://build.iodp.tamu.edu/svn/hq/LabVIEW/shmsl/trunk. [Mills]
Motion control fail. Isolation testing indicated a failure in the motor power wiring on the X-axis: one power pin of the 4-node, 3-wire connector was recessed to the point of being a failed connection. ETs reset the pin. All good. [Mills, Fackler, Jurie]
LabVIEW upgrade. This system was upgraded with LabVIEW 2011sp1. Full development environment, run-time environment and current driver sets applied for both 32-bit and 64-bit architecture. Details noted on the development Google site. Search for "NI 2011 upgrades". The progress matrix provides a detailed overview of the software updated.

Discrete sample systems

Thermal conductivity (TCON) 1.2.0.3

Release 1.2.0.3 now correctly imports specified offsets as centimeters. [Foster]

Moisture and density (MAD) 2.0.0.0

MadMax software upgrades. On 14 April, a new version (2.0.0.0) of this application was officially deployed, after it had been in test for several weeks off and on. The new version includes what amounts to a complete re-write of the LabVIEW portion, which interfaces with the pycnometer. Also included are many bug fixes and improvements to the C# portion (the main program).
Perhaps the most interesting thing about the new version is a new "PycDriver" interface, which allows the user to monitor all six cells simultaneously, and control each of their valves directly. Within minutes of deployment of this tool, Etienne, Erik and Tim were able to quickly find and fix two leaks in the system. The tool also highlights the interaction between cells dramatically. It is Tim's opinion that until this interaction problem is fixed, cell #1 should not be used for measurement unless it is the only one being used. Etienne has a good plan to fix this problem, which he has said he intends to implement while in port at Curacao.
Because this new version includes so many changes, and was only released officially at the start of the last week of this expedition, it should probably be watched closely for a while. The previous version (1.0.0.7) is still deployed on the workstation in case we need to revert to it in a hurry.
It also should be noted that as of this writing there is still a fairly annoying defect of sorts in the application – the LabVIEW portion will only work on the MAD station if it was built on the MAD station. It cannot be built on the build machine, or on a programmer's laptop (except for testing on those machines). Tim is investigating this, but it may not be fixed before he leaves.
LabVIEW upgrade. This system was upgraded with LabVIEW 2011sp1. Full development environment, run-time environment and current driver sets applied for both 32-bit and 64-bit architecture. Details noted on the development site.

MadMax

Bugs fixed in this version of MadMax.

• Register new sample feature and workflow is streamlined. The Text ID field is cleared and becomes the focus again after each new sample is specified.
• Registering a new sample while the pycnometer is performing a measurement no longer causes the application to crash or hang.
• Accepting or rejecting measurements on one cell before some other cells are finished is now Ok to do. The system properly handles multiple cells operating at once without crashing.

Paleomagnetics

The paleomagnetics report supersedes content here.

Point susceptibility

Not used. No modifications this expedition. [This is applied on some expeditions as an adjunct measurement providing a quality check.]

Kappa Bridge KLY-4S

Not used. No modifications this expedition.

Superconducting magnetometer (SRM section)

Routine operations. No modifications to the deployed software system.
LabVIEW upgrade. This system was upgraded with LabVIEW 2011sp1. Full development environment, run-time environment and current driver sets applied for both 32-bit and 64-bit architecture. Details noted on the development Google site. The existing binary deployments are unaffected as they run in the LabVIEW 2009 run-time environment. The next time the code is touched, it should be converted to LabVIEW 2011.

Superconducting magnetometer (SRM discrete)

Not used this expedition. No modifications.

Fluxgate Field Survey

Defer to Paleomagnetics report.

Underway

Content here adjunct to Underway report.

Navigation, bathymetry feed

NAVloader is installed and configured on both Winfrog1 and Winfrog2. It will not be run anywhere else at this time.
On 340T found copies of the NAVloader utility running on Krakatoa, the Development BUILD box, and an installed copy [not running] back in Underway.

• The version on Krakatoa was removed. FireDaemon was also removed. Developers are not welcome on this box except to assist Operations with Coreline/Camera winch video overlay feed issues.
• The version on the BUILD box was run for the transits during 340T. Then retired on transition to expedition 340 in Lisbon.

The version of the code running in each case was different. Releasing and versioning on the source code repository didn't help me, so I picked the first version that worked for me and made sure it was properly configured and operational on Winfrog1 and Winfrog2. went from there. A copy is snapshot on the USIO Software Distribution volume [tasapps/nav/1.0.0.0]. If you decide to work on the code—read the notes there first.

Winfrog1, Winfrog2

LabVIEW upgrade. Both systems were upgraded with LabVIEW 2011sp1. Full development environment, run-time environment and current driver sets applied for both 32-bit and 64-bit architecture. Details noted on the development Google site.

New LabView Application

JNRAV-Google Earth: Issues with memory management and application responsive have been resolved and a new code bas is under testing. Completion of testing, user documents need to be written before general release expected during the Greenland espedition(??).
Site Fix: Based on the JRNav code a new utility that captures data calculates the mean vessel position and generates an operational report was released towards the end of the expedition. See Underway Report [mills]

Geochemistry

Adjuncts to the Chemistry and X-ray reports. Defer to the respective reports for more detail.

Alkalinity 3.0.0.0

LabVIEW upgrade. Both systems were upgraded with LabVIEW 2011sp1. Full development environment, run-time environment and current driver sets applied for both 32-bit and 64-bit architecture. Details noted on the development Google site. During 340T the application was rebuilt under LabVIEW 2011, and after test and approval, deployed.
The source is tagged for release: https://build/svn/hq/LabVIEW/alkalinity/release/3.0.0.0. The build is distributed from the USIO Software Distribution volume [tasapps/alkalinity/3.0.0.0].

CHNS

The pending samples list needs to be cleaned out occasionally. Lims-on-Line is available to cancel the tests which are never completed. Lims-on-Line is not specifically tailored to the task: it's a bit onerous and requires careful cross-checking to avoid cancelling validly completed tests.

Gas bottle monitoring

No change this expedition.

ICPAnalyzer

Noted, but not changed as of this writing: the standards management facility of this application depends on Bennight's LIMS account to function. It does not currently support the login screen.

X-ray fluorescence

Device not used this expedition.

X-ray diffraction

Outstanding bug: The MUT uploader module does not move the PDF or UXD file when the RAW files are loaded.
Outstanding feature request: At present the XRD files are labeled with just a text_id [e.g. PWDR1234.pdf]. For human browsing and readability it is requested that the uploader support file names of this pattern: 340-U1400C-1H-2-W 43-44 pwdr1234.pdf—where the text_id will always be the trailing portion of the file name.

Operations

Core/VIT winch counter video overlay

Continues to be problematic: issue presents as randomly rolling numbers that do not correspond to the actual state of the winch drums. The "random" numbers are because the Video Overlay Transmitter (VOT) software is forwarding partial data records from the Veeder Root. The record received by VOT is mediated through a software port splitter and the RigWatch Veeder Root polling mechanism. The precise failure mechanism is unknown. The work-around is to stop and restart VOT. If that is not sufficient. The stop VOT, stop the serial port splitter, and stop the RigWatch Veeder Root poller [avoid shutting down RigWatch, please]; and then restart them all again.

RigWatch

Spent a merry hour or two chasing failed RigWatch connectivity. When all was said and done: the network connectivity path between the Master (Krakatoa) and the subsea shop concentrator [instrumentation feeds from the rig floor] was interrupted. The line from the subsea shop to the network switch in the Core Tech shop had been unplugged at some point, but then not firmly re-seated.

Other

Reporting Systems

Lims-On-Line

Was requested and used by multiple technical staff for management of data in their purview. Yayy. Now we have data managers who are close to the data [Chemistry, Paleomagnetics, Curation].

WebTabular reports 3.0.0.4

No change this expedition. Noted issues [follow the link to the Pending page]:

• Auto-update of Expedition, Site, Hole lists fails under Internet Explorer. Configuration in the component table was adjusted so that science reports would show manual velocity pick columns for GANTRY data.
• Core Tracking Sheet does not properly display depth intervals for whole rounds (only show tops).

LIMS Reports 3.0.6

Deployed for evaluation to address data retrieval issues for SRM. Will be pushed into production post 340 after merging additional changes from both ship and shore developments. Issues noted on the development web-site as linked.

LIMSPeak 1.7.7

Was ubiquitously used throughout the labstack. At Core Entry, this display is always on. At the description station near Physical Properties (SHMSL), the display was always on for reference and quality control checking.
Release revised for a separate template display showing STMSL instead of WRMSL. Already deployed on shore, per request of Paleomagnetists.
Outstanding request from paleomag: change the display to help distinguish demagnetization levels, show all plots.

Web Services

IODPUtils. Added a new ErrorReporter system for use with the C# apps. The main benefit of this system is that it allows error messages reported by the web services to bubble up and be reported in error dialogs to the user. This is being used in SampleMaster and DESClogik now. [Blaisdell]
lims-webservices-java-3.1.1.6.jar No changes this expedition, but judging by the server logs, there are several more getter and setter errors to fix. Or a number of web-service WAR files need to be redeployed built against the current library.
resteasy-desclogik-services-1.6.8.5. Unchanged since 339.
resteasy-image-tiling-2.0.0.1. Unchanged this expedition.
resteasy-lims-webservices-4.4.6.3. Unchanged this expedition.

• getLIMSdata service XML output overload method needs to be modified to properly escape characters reserved by the XML specifications. Bug fix: extraneous text "file" removed from first column of file.
• Surveyed the codebase for references to x_sca_depth, x_scale, x_scale_instance. Theres a few bits that still need to be updated to use the x_sample_depth tables and current x_scale table.

resteasy-monitor-1.0.0.1 No changes this expedition.
resteasy-reports-3.0.3 Code changes made, but not yet committed, vetted, or deployed. Still running 3.0.3.

• The field x_curr_len is not a substitute for curated length. The SRM report was using this field to cull returned data, in a couple of circumstances erroneously. If data outside the range of section material is to be culled, the x_length field should be used.

resteasy-affinesplice-webservices No change this expedition
ops-2.0.1.0 No change this expedition.
Lambda Probe Undeployed from all production servers.
Hyperic Undeployed the WAR file from all production OES servers [except Solaris web:8080].
Preferred to use top, prstat, multi-screen log monitoring, and the Tomcat Complete Server Status pages to conduct monitoring.

Laboratory System Services

MegaUploadaTron

The GANTRY software presently embeds the name for an uploadable file in the <RAW> section of the file. MUT was modified to enable finding and uploading these files, until such time as the LabVIEW software is modified. [Blaisdell]
MUT fixed so GIESA vane shear raw files are submitted to ASMAN and cataloged. [Blaisdell]
Observed, worked-around: MUT silently fails when an operator name in an upload file is longer than 10 characters. The web-services throw an error [which is not clearly reported by MUT]. The database only allows 10 characters in the various name fields.
Developer note: MUT needs some lead time to be rebuilt and thoroughly tested before the next expedition. The next time MUT is rebuilt, it will inherit a default use of the new error handling mechanisms. MUT however is intended to run mostly unattended, so some careful coding will need to be done to manage reported errors and their presentation. Bulk data load should proceed regardless of error, on the probability that most of the files queued are good for upload.
Feature request: MUTs convention for creating directories stuctures is mis-matched with what we actually do. First installs of MUT litter our systems with unused "upload", "archive", and "log" directories because the built-in conventions don't match the depth of our actual data management trees.
Feature request: Encourage users to login. Prompt for a login every startup. Don't autologin. Don't remember logins for people from 3 expeditions ago. Perhaps even add an auto-logout timer so re-login operator metadata can be better captured across shift change.

Oracle

LIMS_EXPEDITION_DELETE Beginning of expedition method for cleaning out data, owned by the TRANSFER schema. Rewritten to:

• Delete samples one at a time in reverse order of entry. Progress is committed after each sample. All tests and results for that sample are removed with it. Progress may be monitored by a simple select count from sample. Archive log space usage must still be monitored.
• Runs a task to defragment ("shrink space cascade") the allocations for tables and indexes so that the free space can be efficiently re-used.

SOFTWARECONFIG DescLogik auto-save records older than 2012-01-01 were removed.
Component Changes PWAVE_B, PWAVE_C component definitions revised (reportable) so that the manual velocity picks were visible for all axes displayed in the Web Tabular Reports.

Developer Resources

Desktops

PC51446 is once again a fully functional development stations. Installed these bits:

• TortoiseSVN
• LabVIEW 2011sp1, Measurement Studio
• Visual Studio 10 sp1
• Eclipse 3.7.1 (Indigo) and Netbeans 7.1
• Full Oracle client 11.2.0.3
• SQLDeveloper 3.1.06-44
• Maven-2.2.1, and 3.0.3; and Ant-1.8.2.

Mac51933 Installed:

• CORD, an alternative Remote Desktop Protocol client for Macs. Useful for doing laptop development and BUILD box work side by side on big monitors.
• Synergy+ to enable keyboard/mouse sharing from PC51446 to Mac51993—seamlessly switch between desktops without punching KVM buttons.

Servers

Load Balancer Only Ararat and Rainier are in the load balancer pool. Shasta in all service instances has been disabled. Allow lead time to turn on and test before next expedition.
Actually recommend leaving it out of the pool for contingency purposes until we implement a variant that is resilient against single-node points of failure. Two systems in the pool are sufficient for full laboratory operations. We've run the entire expedition that way.
BUILD box Lots of software upgrades. Similar changes were replicated on shore.

• TortoiseSVN
• LabVIEW 2011sp1, Measurement Studio
• Eclipse 3.7.1 (Indigo) and Netbeans 7.1
• Full Oracle client 11.2.0.3
• SQLDeveloper 3.1.06-44
• Maven-2.2.1, and 3.0.3; and Ant-1.8.2.
• VisualSVN 2.5.2

Maven Common profiles (profiles.xml) are deprecated for version 3+ of Maven.

• All common profiles have moved to settings.xml.
• Settings.xml lives in your maven configs directory: c:\Program Files\Apache Software Foundation\apache-maven-2.2.1\conf\settings.xml. If you haven't done so yet. Get a fresh copy and put it there.
• Whenever new properties or profile environments are added to the common set, the changes and the updated file must be communicated to ALL developers. And the changed file implemented on all BUILD boxes and development laptops. Otherwise the code we build will not be the same resulting product.

Krakatoa Removed all traces of FireDaemon and the NAVloader from this system—only RigWatch and the necessary components for Video Overlay Transmission remain. If you are servicing RigWatch, go up to the Ops office, make your intent known, and use the Ops account.
Subversion code repositories. The firewalling mechanism that prevented the code repository synchronization is once again open. Synchronization is only one-way: from shore to ship. Only the HQ repository is mirrored.
Presently all LabVIEW and Java code reside in the HQ repository. All major .NET applications (SampleMaster, DescLogik, MUT, and underlying libraries) have been moved. A host of chemistry and one-off applications remain to be moved.
Please note that the JR repository on ship is DIFFERENT and out of date with respect to code movement than the one on shore. If you are updating a .NET application that hasn't been moved yet, for comparison, see the JR repository on shore, NOT the one on ship.
Repository replication mechanism. The repository replication mechanism is now implemented in a much more efficient fashion than previously. When a code commit transaction is completed, the HQ repository fires a post-commit hook script. The script asynchronously launches the RSYNC file replication mechanism, causing the shipboard mirror of the HQ repository to be updated. The lag time between check-in and update of the shipboard mirror is totally dependent on the size of the commit transaction and the state of the satellite link.
In general, there is not much value in using the shipboard HQ mirror, other than for quick reference purposes. It is and will remain a read-only replicate. It provides backup for those small corner case periods where ship and shore cannot communicate.

Data Statistics

Method Reference

1. select count "Routine Samples" from sample;
2. select count "Exp Samples" from sample where x_expedition in ('340') and standard='F' and instr('ICPAR', status) > 0;
3. select count "Std Ref Materials" from sample where x_expedition='QAQC' and standard='T' and instr('ICPAR', status) > 0 and sample_name not like 'CONT%';
4. select count "Exp Canceled Samples" from sample where x_expedition in ('340') and standard='F' and instr('X', status) > 0;
5. select count "Samples Fulfilling Requests" from sample where x_expedition in ('340') and (x_req_code is not null or x_requestor is not null) and instr('ICPA', status) > 0;
6. select count "Routine Shipboard Samples" from sample where x_expedition in ('340') and (x_req_code is null and x_requestor is null) and instr('ICPA', status) > 0;
7. select sample_type, count from sample where x_expedition in ('340') and instr('ICPA', status) > 0 and sample_type in ('HOLE', 'CORE', 'SECT', 'SHLF', 'PC', 'TS', 'SS') group by sample_type;

Test Method Reference

1. select count "Total Tests" from test;
2. select count "Exp Tests Conducted" from test where sample_number in (select sample_number from sample where x_expedition in ('340') and instr('ICPAR', status) > 0) and instr('ICPAR', status) > 0;
3. select count "Exp Tests Canceled" from test where sample_number in (select sample_number from sample where x_expedition in ('340') and instr('ICPAR', status) > 0) and instr('X', status) > 0;
4. select count "Ext QAQC" from test where sample_number in (select sample_number from sample where standard='T' and instr('ICPAR', status) > 0) and instr('ICPAR', status) > 0 and date_received > to_date('2012-02-14 00:00:00', 'yyyy-mm-dd hh24:mi:ss') and date_received < to_date('2012-04-18 23:59:59', 'yyyy-mm-dd hh24:mi:ss');

Result Method Reference

1. select count "Total Results" from result;
2. select count "Exp Results" from result where sample_number in (select sample_number from sample where x_expedition in ('340') and instr('ICPAR', status) > 0) and instr('EMAR', status) > 0;
3. select count "Exp Results Canceled" from result where sample_number in (select sample_number from sample where x_expedition in ('340') and instr('ICPAR', status) > 0) and instr('X', status) > 0;
4. select count "QAQC Results" from result where sample_number in (select sample_number from sample where standard='T' and instr('ICPAR', status) > 0) and instr('EMAR', status) > 0 and entered_on > to_date('2012-02-14 00:00:00', 'yyyy-mm-dd hh24:mi:ss') and entered_on < to_date('2012-04-18 23:59:59', 'yyyy-mm-dd hh24:mi:ss');

Data Acquired

Breakdowns of samples analyzed, tests conducted, results collected: organized by analytical tests. See Addendum B: Data Acquired Method for query method.

Sample Column Query

select analysis, count(distinct sample_number) from test where sample_number in (select sample_number from sample where x_expedition in ('340') and instr('ICPAR', status) > 0) and instr('ICPAR', status) > 0 group by analysis order by analysis;

Test Column Query

select analysis, count from test where sample_number in (select sample_number from sample where x_expedition in ('340') and instr('ICPAR', status) > 0) and instr('ICPAR', status) > 0 group by analysis order by analysis;

Result Column Query

select analysis, count from result where sample_number in (select sample_number from sample where x_expedition in ('340') and instr('ICPAR', status) > 0) and instr('EMAR', status) > 0 group by analysis order by analysis;

System Manager's Report

Michael Hodge and Andrew Trefethen

Summary:

During Expedition 340 the IT infrastructure performed as intended with minimal impact to operations.

Servers (Microsoft):

• On three occasions the McAfee Anti-Virus repository failed to update, initiated manual upgrade of the repository and it would update.
• While initiating a backup with Acronis Backup & Recovery (AB&R) tool discovered that the software had hung on Mauna-loa and Spurr. Required a reboot of the servers to return AB&R functional. Also discovered during this process that one of the archive raid disks had failed. Replacement unit has been order.
• Server St Helens encountered a power supply failure. Replaced with spare unit and order a replacement.

Servers (Novell):

• Web mail continues to occasionally drop offline requiring a restart of the service to restore functionality.
• Encountered issues where host instruments were logging errors when uploading data via the Tomcat web interface applications on Shasta. Took Shasta out of the load balancer group and errors ceased occurring. Problem identified to the load balancer configuration and Shasta. Attempts to remedy the problem would impact operations so decision was made to investigate it further after the expedition.
• Observed problems with Shasta syncing with the other nodes when creating Samba accounts. Password assignments would not pass between all nodes. Further investigating to occur after the expedition.

Servers (Solaris):

• Encountered one incident where the Oracle archive log folder filled up and ran out of disk space. This caused data flow to stop from host instruments to Oracle until the archive log folder was resolved.
• Cumulus continues to consume disk space in the logging directory requiring an occasional restart of the Cumulus service to free it up. This is an issue with Cumulus itself and should be fixed in the next update of the product.

EVA4000 Storage:

• No problems were encountered with the EVA, it performed as expected.

Network:

• The networking equipment performed as expected with no issues to report.
• When installing the NAC agent on a Windows 8 computer, the installation responded with an error message reading "This operating system is not supported by Enterasys". Enterasys has indicated they will release a new version of the NAC Agent this coming summer.
• Installed TAMU-Campus' 4 X-Lite VoIP software and worked with campus personnel to test functional on our network.
• Worked with TAS personnel to resolve rsync connectivity problems with shore. TAS repositories are syncing between ship and shore.

PC Workstations:

• Sample Master Software was causing the Driller's PC to slow down to the point of distraction from work. Pulled memory module from spare Driller's PC and installed in operational unit. This effectively doubled installed memory and dramatically improved performance.
• Userroom PC51166 encountered a failed Ethernet port, replaced motherboard resolved the matter.
• Corelab Microscopy PC51539 has a failed motherboard. Replacements ordered.
• Bathymetry PC encountered some boot-up issues during Lisbon portcall. Request was made for more memory and received during Puerto Rico portcall. The added memory appears to have remedied boot problems because no further boot-up issues have been encountered.
• Received three Dell D630 laptops in Lisbon, reimaged all and made ship operational.

Apple Workstations:

• Optical drive in Mac51938 failed and was replaced by unit from Mac51943 (spare system).

Printers:

• On the Canon printer the black, yellow and magenta toner cartridges where replaced.
• Training took place on the use of the scanner on the Canon copier.
• Black, Magenta & Cyan toner cartridges were replaced on the Core Color printer.

Satellite/Internet/Phones:

• The bow Codan Transceiver encountered a fuse failure. Replacement fuse resolved the matter and the bow dome came back online.
• No further incidents with VSAT equipment. No outages this expedition.
• Worked with Rignet and modified our web portal to reflect corporate change from Transocean to Siem with relevant content.

Other Equipment:

• One VBrick set top box failed, unit return to shore.
• RigWatch was not being distributed on the Siem CCTV network because a video converter failure. Two replacement converters were delivered to Puerto Rico portcall and failed unit replaced.

Special Projects:

• Researched Drill Shack PC replacement, discussed options with ship personnel, packaged and sent to shore for purchase.
• On the core deck's close up photo station network cabling was run for the workstation. A Zebra printer was placed with the appropriate network access.
• Created AMS inventory bin location assignments and labeled all bin locations for the lower tween deck.
• Installed TAMU-Campus VoIP software on a test station and verified functional.
• Implemented data center and MCS office flooring repairs. Done during Lisbon portcall.
• Implemented MGE Comet UPS battery exchange during Lisbon portcall.
• Located equipment on the ship not having export control information and reported to shore.
• Setup Skype software on Userroom PC51536 and announced public availability. Was well received and utilized.

Equipment Repairs:

• Ordered 2 spare video cards and 3 motherboards for replacement of failed units.
• Replaced power supply in Userroom PC51538 and requested replacement units from shore.
• Replaced the DVD drive in PC51444 (Open office, Teacher-at-sea's PC). Ordered replacements.
• Ordered replacement server power supply for failed unit out of St Helens server, HP spares P/N: 403781-001.

Underway GeophysiCS

William Mills

NAVIGATION

FOLDER CLEAN-UP AND REORGANIZATION

!worddav23528321d9ba56be343590b59882f4ef.png|height=144,width=221!The file directories on WinFrog 1 and 2 where cleaned up. All of the previous expedition data files where deleted after making a DVD for Don Sims, plus all of these files have been backed up on Data1 after each expedition. Just no reason to keep them on the hard drive and it makes system back-ups maintenance difficult.
In the expedition folder I created two new permanent folders.

• "Default Config and Vehicle" this folder contains the following WinFrog configuration files:
• JR Rev2.veh: this file contains the graphical information that defines our ship's outline in the WinFrog graphic display window.
• WF# Default Config date.cfg: This file holds the configuration data that WinFrog uses to define the data I/O, navigational displays and various other settings.
• "Copy Me Expedition Folder" contains the empty data folders used by WinFrog during an expedition, along with a copy of the two files described above. Select this folder and create a copy and then rename it "exp nnnn" (i.e. Exp 340 or exp 340t) or whatever is the offical designation of your current Expediton, Transit or APL.

Note: each WinFrog's has a unique configuration file because I/O devices, that use TCP, must use the local machine's IP address. This is all that is different.
I partially cleanned up the UW folder in IODPshare. Over time, past tecnicans have nested copies of the same folders over and over. I went through and created one copy of each file and reorganized the folders. This job is only partially done. The next step is to seperate relevant data from historical data and make it clear what is what.

VIRTUAL SCREENS

As part of the default configuration, I've created two virtual screens (that's what those numbered buttons at the top of the screen are for …. I didn't know). Screen 1 is a basic setup for while the ship is underway. Screen 2 is setup for onsite operations. Use the buttons to flip back and forth. You can setup more virtual screens as necessary.

I/O DEVICES

The I/O Device for the Astech GPS receivers were removed and replaced with a new I/O device for the Aft Trimble GPS receiver installed this expedition. In addition, three other IO devices were setup to output GPS data for the applications Site Fix (2) and HDG(1) programs (see following section).

SHIP'S OUTLINE

On the vessel's outline are two small circles that indicate where the forward and aft GPS antennas are located relative to the moonpool. If the device offsets are correct and the positions of the circles are correct, then the position of the antennas should plot in the center of the circle. When I initially did this on North Pond, the positions where close but not exact. While in dry dock, I took advantage of the ship being stationary and made fine adjustments to both offset and drawing until the antennas plot in the center of the circles. During the transit across the Atlantic, I noticed that the ship no longer jumps (inch-wormed) with each fix; which I take a good sign that I have the positions and offsets dialed in correctly. The new outline and device offsets are part of the default configurations.

HARDWARE

• The obsolete Gyros mounted on the wall were scrapped (now part of Jurie's scrap yard).
• The two Astech GPS Receivers and antennas were removed and returned to ODL (most likely scrapped).
• The Time Clock was removed and returned to College Station for disposal.
• A new Trimble SPS351 GPS receiver and antenna was installed replacing the older Trimble which is now our spare unit. As with the Trimble installed in the LO's office, this receiver is connected to WinFrog via our network. It has been assigned a fix IP: 165.91.72.118. Type this value into any web browser to access the setup screen (admin/password or guest/guest). In the configuration the antenna height is set to zero and WinFrog device offset we enter the actual elevation (per Steve Prinz)
• Changing out the GPS receivers freed up a serial port on the RS232 "Octopus" connection so we no longer need a USB to serial port converter. These converters were problematic and sometimes required a full reboot to get them connect to the correct port, so it is nice not have to use them. Also, now when you switch between WinFrog 1 and 2 you just have to move the "Octopus"

NAV LOAD

This is the code that transfers navigation data to LIMS and used to run on the developer's box. It now resides on each of the WinFrog PCs and is part of the SOP to lunch Nav Load when we start WinFrog. There is a shortcut on the desk top.

MAGNETOMETER

The magnetometer operated on the Atlantic transit without incident. Because of ship traffic and short transits, the magnetometer was not towed during the Lesser Antilles.

• We now have a slip ring connection to the drum which was tested on our transit to Curacao, no problems
• Jurie and Gus have worked on the fleet arm sensor. This was tested on the way into Curacao and is working as designed. Good job Gus and Jurie!
• The GPS signal loss error showed up again for a few days but then went away. Still a mystery, just have watch for this around midnight zulu.

BATHYMETRY

The Bathy 2010 system was very unstable. The application would often crash when you attempted to start data recording. Also, the system was very difficult to boot-up, often taking a dozen attempts or so. While researching a replacement we discovered literature on the computer built into the Bathy2010 and discover it could run on 2 Gb of memory, we were just operating on just 1 GB. Additional memory was order and installed in San Juan and the system has been we'll behaved so far.
We attempted to test the spare computer board but it will not complete the boot cycle. On the transit into Curacao we loaded the Bathy2010 software onto WinFrog 1 and Jurie made some serial cables that allowed us to completely by-pass the Bathy 2010 Sing Board Computer (SBC) control. The test was successful, not only does this provide a working spare but I strongly recommend that acquire a dedicated instrument host and discard the Bathy 2010's very expensive SBC ASAP.
In regard to the rest of the electronics that make up the bathy 2010 system, we have no onboard spares! Steve Prinz priced out the $32K worth of spares. No action from shore has been taken.
Other maintenance:

• Pulled all of the boards, clean and reinstalled;
• The computer is unplugged from the transceivers' auxiliary 110V power and into the UPS. This allows you to power down the transducers without killing the PC.
• Re-bundled cables;

COMMAND AND CONTROL

In the LO's office I've created short cuts on the Command Center's PC that allow you to "remote desktop" into either Winfrog, Magnetometer, and Bathy2010 computers at the same time. All aspects of control and data acquisition can be managed from the LO's office. This is convenient for keeping an eye on the systems during long transits and allows the operations superintendent to make depth checks any time while on site. This was extensive used by the co-chiefs and operations while we camera surveyed the Atlantic Massif.

DEPTH CHECK

!worddav5bcc0db376e3bbc64ddaedaafe987352.png|height=463,width=388!Enter the appropriate valuesDetermine from the Matthew Table mapsTodays dateValue from the PDR, uncorrected @ 1500 m/secCopy this digit to "B"Values from the Matthew tablesValues should never changeCheck with matesThe worksheets has been replaced with an excel spreadsheet kept in an expedition folder on IODP Share. I have my operations superintendent trained to fill in the blanks and the spreadsheet completes the calculations. The formulas for extrapolation are based on the examples in the Matthew Table. A copy of the excel file can be Found in Vol 1:\IODP_Share\UW\2 Bathy\Depth Corrections. A copy of the paper form can be found in the same location if you are too old to try something new.

SITE FIXES

Ok ..I'm lazy! Using the WinFrog Position utility is a pain. Well, the utility is ok but the steps you need to go through to make a report to the ops manager is a pain.
Therefore, in an effort to avoid much pain as possible I whipped out my trusty LabView tools I resurrected SITE FIX! The goal was to make a program so easy to use that even an ops manager could us it!
Well, maybe not that easy. A User' Manual is in progress and give the on-coming crew a quick lesson.

JRNAV

I've final got an application together that works without a lot of hand holding. This program was just completed before arriving in Curaco so a User's Guide is in progress. I'll provide training for the on-coming crew.

SONAR DOME REPAIRS

Figure 1: Damaged Sonar Dome Looking Aft !worddavc0dd0930d9debc5016df026a6510305e.png|height=218,width=341!INCIDENT AND AFTERMATH

While settling onto the blocks in the Naval Rocha, SA shipyard, the JR moved aft ~ 18 inches and the aft end of the sonar dome struck a support block. As the ship settled onto the bock the sonar dome was force to rotate as it was pinched between the block and the ship's hull (Figures 1 and 2). Fortunately the wood block topping the support was crushed instead of the dome's hull.
Figure 2: Damaged Sonar Looking PortOffending BlockThe rotating force pulled apart or deformed all of the hull attachment studs, bent the aft edge of the flange and deformed the upper 100 mm of the stem (Figure 3). A visual and electrical inspection showed that there was no damage to the transducers or electrical cabling.
Figure 4: Preparations for moving the dome of the block. Figure 3: Damaged Flange and Studs
Figure 5: Cut away sketch of repair.The first order of business was to safely secure the dome to the hull. As you can see in the photos, the dome was only attached by a few studs and pinched between the block and hull. The lifting eyes were given to the shipyard and after welding pad eyes to the hull, the dome was secured and blocking cut away to free the dome which was leveled and safely supported on blocking.
Note: the port forward lifting eye was pulled out of the threads while lifting damaging them. This and all of the female threads in the dome where re-tapped, cleaned and lubricated with Aqua Lube before re-installing the brass plugs.

New Hull FlangeNew Dome FlangeStem Replacement SectionFigure 6: RepairsREPAIRS

After a assessing the damage, a repair plan was devised and sent to shore for review by Bill Reinhart and Steve Midgley. The drawings are attached to this report.
Because of the extensive damaged to the threads, it was decided (in consultation with Siem staff) to make a new flange plate and weld it to the hull and fabricate an exact duplicate for the sonar dome (Figures 5 and 6). Both flange plates have an index slot milled into their forward facing sides (Figure 7). This slot will allow diver's in low visibility conditions to feel the alignment positions. Also, the dome flange was machined with tapered holes to help with stud alignment. Unlike the previous situation where the flanges would only mate in only one position, these flanges can easily mate in any of the 12 positions. Divers must always insure that the grooves are aligned.
Figure 7: Index and orientation marks.Index Marks
Figure 8: Dome safely blocked, stem trimmed and cable protection installed.Why is he glowing? Figure 9: Prepping cables prior to weld up.Protection of the cables was a major concern throughout the repair process. To protect the cables they were threaded thru a steel pipe and the inside of the stem was flooded with water. Copious fire blanks were used to protect any exposed cables. Figure 8 and 9 show Garrick, Randy and John installing the cable protection. All excess cable was pulled back into the ship.

FINAL FIT-UP

Figure 10: Final fit up.Before any welding began, the dome was lifted into place with flanges and new stem section loose. The shipyard fitters took great care in aligning and leveling the dome to the hull (Figure 10). Once everyone had signed off on the fit-up, the pieces were lightly tacked into place (Figure 11). The dome was lowered and all pieces fully welded out. All root welds were first TIG welded and the followed by stick welding. All ASTM procedures were followed.
All welds were inspected by MPI and past without problems.
Figure 11 Tacking fit-up into positionThe matting surfaces of the flange and o-ring slot were given a heavy coating of aqua lube and the o-ring installed. The studs were torqued into the hull flange and the whole assembly bolted up to the specified torque values. Double nuts were installed on all studs for security and thread protection.
Figure 12: Weld-out completed.

Figure 13: Connecting trunk in the forward thyrig room.TESTING AND PAINT-OUT

Electrical: Once the dome was bolted up we conducted an electrical conductivity test and a low powered ping and confirmed that the transducers were operational. Because the ODL transducer operates at 50MHz you cannot hear it, so a water testing tank was built around the dome for live ping test. All transducers past the ping test.
Pressure: Per our testing specification, 5 psi of pressure were applied to the trunk and immediately failed. Leaks were found in the test manifold attached to the cover plate. The parts were stripped off and new manifold fabricated.
The test was repeated and immediately failed again. This time we found that all of the O'Brien electrical penetrations were leaking at the o-rings. We pulled the O-ring specs from the web page and notice that all of the o-rings were undersized. Found the correct size in our collection of o-rings and remade the connections. This time the test was successful and held pressure until we got tired of testing and stopped 48 hours later. Testing was witness by the first-mate and signed off. No leaks were detected when the dry dock was flooded.
Figure 14: Final paint-out of the dome. Painting: Upon completion of successful testing, the shipyard repaired paint damage, primed and applied one coat of anti-fouling paint. A request to paint the entire dome was denied by owner. Technical staff applied the white orientation marks for divers.

OTHER ISSUES

Cables Damaged: While attempting to disconnect the O'Brien connector from inside the stem, the pipe nipple threaded into the cover plate spun, damaging the wire's above the cover plate to ODL's 50 MHz transducer. The wires were repaired and swapped with our 12-Khz system. The nipple was improperly assembled using Aqua lube as a thread sealant instead of a Teflon thread sealer.
Missing Acoustic Tiles: One tile is missing from the top of the sonar dome.

FUTURE MAINTENANCE

In the upcoming 2014 Drydock the following work is recommended:

• Remove the sonar dome and strip out all of the transducers, j-boxes and wiring;
• Remove the 3.5 transducers from their mounting plate;
• Clean/repair all transducers as necessary;
• Strip out all of the acoustical tile, both inside and out;
• Replace the electrical pass thru connection with O'Brien bulkhead connectors. This will allow us to replace the spliced cable with factory made jumpers and eliminate the need to cut the cable when removing the transducers.
• Add a 1/2' SS flat bar frame to the top of the dome boarding the recessed acoustic tile location. This will be used to install a double thickness of acoustic tiles to help reduce the transmission of sound into the lower sleeping spaces.
• Sandblast to white metal all surface (including the interior), apply inorganic zinc and build up the paint according to the ship's painting schedule for the hull below waterline;
• Reinstall new acoustic tile;
• Reinstall transducers, j-boxes and wiring;
• Inspect the trunk area and replace steel as necessary;
• Remove all unused electrical pipe penetrations;
• Prep steel and paint;
• Install new cover gaskets;

SONAR REPAIR DRAWINGS

Dimensions of the flanges pieces, hole and thread sizes are as built. Dimension of the new stem section are approximate and all dimensions should be verified.

FANTAIL

Gus

SUMMARY

V.S.P. was conducted at several site locations. Guns operated without failure.

SPECIAL PROJECTS

• Magnetometer signal cable was adapted to winch slip rings.
• Preliminary mechanical adjustments were made to the leveler fleet angle arm. On the transit into Curacao further adjustments were made on the end-of-travel sensor. The level wind was thoroughly tested and working well in both directions.

PROBLEMS ENCOUNTERED

None

MISCELLANEOUS

• Benthos AQ-11 general purpose hydrophone was repaired.
• G-gun array was not servicedand is presently secured to the starboard railing adjacent to the gun line winch.
• Crane boom was acid cleaned with "ospho" and bare spots painted with cold zinc.