TECHNICAL REPORTS
EXPEDITION 345
HESS DEEP

LO – ALO Handover notes

William Mills, Lisa Crowder & Tim Bronk

Objectives:

Expedition 345 is the second drilling program at the Hess Deep Rift to study crustal accretion processes at the fast-spreading East Pacific Rise (EPR). The expedition will take advantage of well-surveyed crustal exposures to recover the first cores of young, primitive plutonic rocks that comprise the lowermost ocean crust.

Operational Dates:

START

• Port: Puntarenas, Costa Rico, Commercial Wharf #4
• Arrived: 11 December 2012 @ 0502
• Departed: 17 December 2012 @ 1715

END

• Port: Balboa, Panama
• Estimated Arrived: 12 February 2013

General Port CALL information

• IODP logistics was routine and without incident with the majority of the work occurring in the evening due to daytime work restrictions because of the Cruise Liners along the opposite dock.
• IODP safety presentation and Hazardous communication tours were conducted as normal.

AMS/STORE ROOMS

• Images of many property items were attached to their AMS records for reference. The project is ongoing.
• Quantities of bulk supplies were verified in preparation for upcoming high recovery expeditions.

Shipment

All surface and air shipments will be sent from Victoria, Canada after 341T and include the following. A few items will be hand carried from Panama.

• Cores and residues from 334, 344, 147 and 345 will be sent to the GCR.
• The hand held XRF scanner will be returned for storage.
• Old Bead Maker
• Gas bottle racks and other normal surface items.
• Hartley Hoskins' pinger, to be returned to WHOI
• The JAMSTEC ASR that was used on 344 will be sent to Japan

AREA-BY-AREA SUMMARY (issues not covered IN THE INDIVIDUAL TECH REPORTS)

Bridge Deck

Nothing to report;

Core Deck

Core Entry
A fold-away table was constructed in from of the two core racks for additional hard rock sampling space. When not in use the legs fold up and the countertop is stored between the racks
Splitting Room:
Both single-bladed bench saws were fitted with stabilizing brackets on the right hand side of the saws.
Core Lab:
CryoMag:
Paleo Lab:

Fo'c'sle Deck

Chemistry Lab:
Science Lounge: A new cabinet was installed to support the AV equipment.
X-Ray Lab:

• A sound proof box was installed around the Haskris water chiller;

LOWER TWEEN DECK

Lounge and Movie Room:

• LED Lights repaired in moive room

Poop Deck

Underway Geophysics:

• The remaining cabinets were installed and ET supplies transferred to the UW lab. Still waiting for countertops to arrive in Victoria.
• WinFrog 2 PC was replaced with a new instrument host (HP Z420). This instrument is fully setup to run all Underway Lab applications except for SB_Logger. On the transit in to Panama we ran both the Bathy 2010 and Sea Spy (Maggie) software at the same time, without issue.
• The 3.5 kHz acoustic pinger (Hartley Hoskins at Woods Hole) was used to collect sub-bottom profiles from the VIT frame using our Sonar in passive mode. After fixing numerous problems we were able to collect some very good records.
• Bathymetric and magnetic data were collected on all transits.

CORE LAB

CRUZ ST.PETER AND TIM BRONK

Summary

Given the low amount of core recovery on this expedition, there was plenty of time to complete a few projects in the core lab. Upon receiving core from the rig floor, all available technicians worked together to efficiently process and curate the core sections. All equipment worked as expected, and there were no known hardware failures during the cruise. The bench saws were used to split most of the rock pieces, while the "super saw" was used occasionally for the longer pieces.

Maintenance & Projects

• A scientist requested to sample the saw cooling water produced while cutting rock sections. To satisfy this request, the drainage pipe for the saw water was diverted and collected in appropriately labeled carboys (Fig. 1).
• Both single-bladed bench saws were fitted with stabilizing brackets on the right hand side of the saws. Also, to facilitate efficient water collection (see above), the two single-bladed saws were switched regarding their position on the bench in the splitting room.
• The blades for the parallel bench saw were replaced. Also, the two brass flat-head screws that hold the blade protector to the saw unit were replaced with steel allen-head screws.
• A collapsible table was built and attached to the core racks in the receiving area. This table served as an extra surface to place section halves during sampling parties. The table top was designed to be removed and stored away at the end of the expedition.
• Figure 1. Plumbing for sink drainage diverted to carboy.
  The shelf supporting the amplifier in the core receiving area was deemed unstable, and a more suitable replacement shelf, with more surface area was assembled and installed.
• The wooden lids to the bins on the catwalk were replaced with weatherproof lids.

CORE DESCRIPTION

MARGRET HASTEDT
Description of the Hess Deep cores was arguably one of the highest priorities of the expedition. And with a total of 17 describers, DESClogik was heavily used. A number of hours were spent pre-expedition for the initial configuration of several templates based on input from the co-chiefs and another sailing petrologist.
Once the expedition began in earnest there was quite a bit of template modification to be done based on reviews from the three descriptive groups: Igneous Petrology, Alteration, and Structure. Three main templates were deployed – a macroscopic one for igneous and alteration combined, one just for structure, and the thin section template. We had a standby sediment template but it was not used.

Issues:

1. Piece-based vs. section-offset based descriptions: the co-chief scientists initially wanted each piece individually described in DESClogik. This mode continued for a few days but after some discussions with the science party everyone agreed to offset-based descriptions. The switchover spawned some cleanup on our parts to change the earlier piece-based descriptions back to offsets but this was desirable for simplicity and consistency reasons.
2. General DESC flakiness early in the cruise: we had a lot of Launcher errors under a variety of circumstances (such as simply attempting to log in or start an upload). This seemed to become less frequent over time, but never completely stopped. It was possibly caused by webservices or server issues, or more likely, complications from the piece lookup metadata column. See Developer's report for details.
3. Imperfect automatic piece lookups (metadata column) and general confusion over piece vs. bin lengths led to repeated cleanups in DESC to facilitate gap-free graphics on the VCDs.
4. Using copy/paste from Word into DESC cells can inadvertently add odd symbols. Particular culprits are long hyphens, smart quotes, and degree symbols.
5. For unknown reasons DESC sometimes reveals its bracketed classifications in tabular data entry screens even though it should not. This confuses users who think they need to 'clean up' the classifications. However, sometimes just selecting a DESC cell incorrectly displaying a classified value sets off a cascading disappearance of the brackets in a number of nearby cells. These incorrectly-classified cells also show up in the exports to Excel. Perhaps there is a screen-refresh problem at work here.
6. Formula columns may not display properly on download. Upon data entry the formula column operates as expected and you see values change as you populate cells involved in the formula. However, the formula column can be blank immediately after upload /download of the same row(s) of data. Change (i.e. edit) any of the cells used in the formula and it calculates and displays again immediately.
7. Exports from DESC occasionally show problems when opened in Excel. You will see a message along the lines of "Excel found unreadable content in {your spreadsheet name}. Do you want to recover the contents of this workbook? If you trust the source of this workbook, click Yes." So go ahead and click Yes, and you will see something close to the following:

We are not completely sure what causes these errors because it is not consistent – smaller exports don't exhibit this behavior. It seems to happen most often on exports that exceed a certain number of rows or from tabs that tend to see a lot of copy/paste activity such as the Unit Summary tab in the 345_macroscopic template. Much more detailed troubleshooting from the developers is in order to see if the creation/saving of the Excel file at DESClogik export is the issue.

DESC reporting efforts:

As is typical with hard rock expeditions, quite some effort was required to get the logged information within DESClogik into a form that was a) acceptable to the science party and b) usable by the Pubs Specialist for the VCD barrel sheets. First we created mockups of the text blocks for the VCDs based on older examples from previous hard rock cruises and populated using what the scientists had selected as the most relevant columns from the Unit Summary tab in DESC. After some discussion this was finalized and we worked with Dwight Hornbacher to automate the process (see Developer's report for details). In a nutshell, we now have a utility called DescToWord which will take a DESC or LIMS2excel export of the X345 Unit Summary tab and reformat it into this expedition's standard descriptive text block for each row (i.e. lithologic interval) and save it as an individual Word document. Due to some yet-unresolved issues these small Word documents must be post-processed to force them into Arial 8-point font with no line separators, done by macro on the entire directory at once. Then these are provided to the Pubs Specialist who does the final resizing and placement into the VCDs. Dwight's tool made creation of the text blocks fast and almost painless! The only hiccup we encountered was late in the cruise, when a couple of key columns in DESC were swapped around. This 'breaks' DescToWord because it is highly dependent on columns being in the same order as when it was originally programmed. Swapping them back into order either in DESC or in Excel easily fixes this issue.
The thin section report on the other hand continues to be a large amount of work. We began as above with a sample report in spreadsheet form for the scientists to review. The scientists (particularly the alteration group) had differing ideas on how they wanted their data reported. The end result was a number of rather elaborate equations to display the alteration data in mirrored table format: the left hand table shows secondary mineral summed percentages and a breakdown of the contributions of each primary mineral based on a formula, and the right-hand table displays the primary mineral original vs alteration percentages and their secondary minerals as logged in DESC.
The unfortunate side of the Excel-based thin section report is the large amount of effort required to populate it (both the Igneous and Alteration descriptions for each thin section could have up to three domains) as well as formatting cleanup (deleting empty rows, resizing others, and eliminating formatting marks due to the equations used). We also had a request to substitute "<0.1%" for values of "0%" which came out of a request to round calculated values to a single digit past the decimal point. Macros helped with certain tasks but most of it was done laboriously by hand. David Fackler is creating a web-based version of this report which eliminates these issues but it is not yet ready as of this writing.

DESC feature requests

1. Metadata lookup columns need to work across multiple tabs in a template. Ideally we admins should be able to enter identical qualifiers in another tab in the configuration file and have DESC populate it from the original tab based on a selected sample/interval, but all it does now is cause a Launcher error.
2. Formulas should be able to access the same cells for multiple calculations within the same tab. Right now if you use one cell's value for a given formula column you are not allowed to call it again for another formula. The second formula silently fails.

MAGNETICS LAB

MARGRET HASTEDT
Scientist: Tony Morris , Sarah Friedman, Andrew Horst
The paleomagnetics lab was only moderately used this cruise, due to the relative lack of material to measure. One Flexit tool was deployed to check for hole drift. The spinner magnetometer, thermal demagger and Kappabridge were used the most.

Problems reported

1. The spinner magnetometer had a spate of overflow messages one day. This followed several attempts at realigning the brass actuator to the holder after it had become misaligned during normal use. To reduce/eliminate the overflow messages, check the following 3 things:

• Keep a 1-meter separation (line of sight) between the pickup unit and its power supply. Move monitors as far from the pickup unit as practicable.
• Reseat the ground strap on the inside of the pickup unit's cover. Repeated cover removals to repair misalignments may render the contact less effective.
• Ensure that the pickup unit's cover is not touching the metal body under the black coil halves

1. The thermal demagger's timer begins its countdown to cooling the instant you start the heating cycle. This means that you need to carefully estimate the total time for a heating run in advance to ensure your samples reach thermal equilibrium when the oven reaches its setpoint temperature. We need to investigate how to better time the actual heating run to ensure consistency, which would be dependent on the thermal mass (total number of samples) in the oven at the time. The manual is not very useful in this regard.

1. Late breaking issue: the spinner lost its ability to rotate the automatic cubic sample handler at the worst possible time… right at the very end of the cruise when the scientists were just trying to finish some runs and the rest of us were sampling our brains out. Garrick saw a broken wire on the tiny motor that turns the shaft, but the scientists wanted to finish their measurements without switching spinners so they elected to run in semi-automatic mode. That simply means you have to rotate the cubic sample holder by hand into the 3 positions. It actually can be slightly faster than letting the spinner do it!

Miscellaneous

• The scientists occasionally used the DAFI software to monitor fields inside the SRM at the beginning of the cruise. That eventually ceased as we maintained the same heading within 5-10 degrees for the entire time we were on site U1415 (almost the entire cruise).
• The scientists employed a novel "thermal" demagnetizing protocol using liquid nitrogen dunks of samples inside the portable Mu-metal shields. This was first seen on Exp 335. The two shield sets are nested together to make a 6-layer shield for the greatest possible magnetic field attenuation. Cubes were immersed in a beaker of liquid nitrogen and allowed to come back to room temperature while inside the nested shields. In this way you can remove most or all of the drillstring overprint in one or two dunks. "Normal" thermal demags were performed after this initial stage. Note: the scientists determined that AF demags were not as effective for characterizing the complex multiple-component remanences of these samples. All samples were measured using the spinner magnetometer.
• Flexit tool #938 was deployed to assess hole drift at the request of the science party/Ops Manager. There was some concern that hole U1415J might have drifted off vertical based on observations of certain pieces of core as well as operational indicators. The drift study indicated a maximum of just a little over 3° at the bottom of the hole, and somewhat shallower on the way out.

Pmag chores for the tie-up period:

1. Yearly adsorber change is due in March.
2. Replace the Kevlar rope and chain
3. Coldhead replacement and Helium refill are required before the next sailing expedition.

PHYSICAL PROPERTY LAB

Thomas Gorgas
Exp345 was a hard rock expedition par excellence and offered many opportunities to test the current status-quo of our laboratory instrumentation for such deep earth materials. It was in particular exciting to see the (positive) performance differences compared to EXP335 ("Superfast") where some of the equipment and systems were not quite as capable as they are today.
In sum we acquired a total of measurements on the various instruments as follows:

The next paragraphs summarize the performance of the individual Physical-Property instruments that we used during EXP345, i.e., WRMSL; NGR; Therm-Con; XRF; P-Wave Gantry; MADMAX/Mettler-Balance-Pycnometer; SHIL; SHMSL.

Systems Status

SHMSL:

The Section-Half-Multi-Sensor Logger did function well throughout the entire expedition. There were no complaints or issues reported. The instrument was used both for "Whole-Round" and "Section-Half" line-scan imagery. The "VCD Scratch Setup" utility allows now to toggle between several template options for "print-outs" (IgPet/Alteration/Structure).

WRMSL

Throughout EXP345 the machine ran and operated within its range of expectations. However, some issues occurred and are briefly described:
Issue #1: Following up on comments from the EXP344 Tech-Report, we tested the core section advancement and thereby further elucidated the sensitivity of the laser sensor, which can cause a faulty core section advancement when progressing through the track sensory system. We concluded that the system was working according to expectation and that unwarranted advancement behaviors for the cores must have been caused by internal reflections of the laser light, bouncing sometimes irregularly from acrylic laser end caps. As a consequence, we covered those end caps with black electrical tape to avoiding unwarranted reflections of the laser signal. We also adjusted the laser position by a fraction of a degree as the sensor appeared to be not in an optimal vertical position, and thus emitting a light signal at a slight angle. Whether that adjustment indeed contributed to reducing the presence of this issue is unknown. Ultimately, the laser sensor ought to be replaced with a less sensitive optical sensor.
A code change to "fix" the advancement issue through modifications of the application code was removed after 2 weeks into the expedition as it caused some unforeseen problems within the LIMS Report domain (via D.Hornbacher; see: email note on 12/17/2012 and corresponding Tech Report).
In sum: We report that EXP345 whole round cores passed through the WRMSL track without stirring any "issue-complaints".
Issue #2: Some rock samples in U1415J-21R-1 contained an abundant amount of magnetite, which caused some of the data to "wrap around" the measurement scale on our Bartington instrument; the scale is limited to only "9999" (Si Units). Our PP scientists "un-wrapped" the over-scaled data points into the correct scale range for a proper VCD display, and placed them on DATA1 as part of the data back-up.
Suggestion & Improvements: Per request from shore to have "wire diagrams" for each machine in place, we started the process of creating "photographic image-based" wiring diagrams for the WRMSL (via Microsoft's VISIO application). We plan to continue with this effort on all other tracks and instruments. It is a visually-driven depiction of the wiring from sensors to PC-box and accessory electronic components (e.g., "Emergency Stop" buttons, etc.). As per this writing, ET G.v.Rendsburg has produced three such documents (for the WRMSL, STMSL and NGR).

NGR

Several issues with the instrument have been observed and tested now repeatedly over the past expeditions (EXP344S thru EXP345) and want to be addressed during the tie-up period in 2013. Our observations from EXP345 are essentially a "re-cap" of those from EXP344 and EXP344S, just adding some more numerical examples and graphical depictions of the various phenomena.
Issue #1: As our technical staff reported from EXP344, NGR-Detector #3 now consistently exhibits a severe drift behavior. It is noticeable after only a few minutes of running the measurement cycle. A long-term measurement on our CS/Co standards revealed a serious distortion of the expected energy [keV] bin and channel position of all three signal peaks.
We attempted to solve the issue by going through a prescribed "Bias Voltage Calibration Procedure" for all detectors, following the "Natural Gamma Radiation Logger Service Guide", but without achieving acceptable results for Detector #3. Our EXP344 Tech-Team concluded that the source of this and other problems (see below: "Spike on Detector #3) are "...hidden somewhere between NaI detector and Dual Spec Amplifier..." (Per verbatim: 344 Tech Report).
Figure 1 shows the severe drift on Detector #3 over a background measurement period of several hours. The two Co-peaks (located at 1170keV and 1339 keV, respectively) merge into an extended energy "lump", and thus become indistinguishable; the Cs-peak at 662 keV is also distorted. Figure 1: Peak distortion on Detector#3, with indistinguishable Co-peaks in the 1170 to 1330 [keV] range and a distorted Cs-peak around 662 keV highlights the pressing need to repair or replace Detector #3 (in the worst case scenario) or associated electronics. Right now our "best-guess" is that the issue is related to faulty electronic components and/or connectors, causing the observed troubles.
The previously "bias voltage" adjustment (see: "NGR Logger Service Guide") did not remedy the drift behavior of the compromised Detector #3. Alongside with acquiring a second background measurement over 22,000 seconds per calibration position (on 01/12/2013), we also performed a second standard Cs/Co-calibration to verify the amount of drift that had occurred since the start of EXP345's measurements (on 12/23/2012). The amount of drift in both [keV] and respective energy channel [CH] bin for all detectors within this 3-week period was as follows:

_Figure 2: Background measurements recorded during EXP345 reveal a "migration" of the characteristic ⁴⁰K-peak around Energy Channel-500[keV] for Detector #3. The signal quality of this peak is also visibly degraded compared to corresponding peaks on the other detectors_We used this calibration data set for all subsequent measurements on rock specimen until the end of EXP345. A screenshot of the 2^nd BACKGROUND measurement (01/12/2013) is captured in Figure 2. It showed once more the degradation of signal quality and accuracy/precision of signals recorded with Detector #3.

















Issue #2: During NGR experiments on EXP345 hard rock specimen, Detector #3 continued to exhibit characteristic [cps] spikes (Figure 3, see: right-hand) over the first 100 channels. These peaks have been noticeably prevalent since EXP344S. Right now, it is still too early to provide "concrete solutions" to resolve this phenomenon - except to discard the data from the affected energy channels. Until we have conducted more thorough tests, it is too premature to draw firm conclusions from our observations up to date.
We also tested the NGR performance with the WRMSL electronics and motors shut down, which still produced the ultra-high counts-per-seconds (cps) on Detector #3. Ditto: the high-counts are not affected or influenced by the WMRSL electronics. Our tests also confirmed once more that Detector #3 requires a much longer "Live Time" count than all other detectors.
Issue #3: By Week-5, the NGR started to develop a distinct high-pitch noise, originating from the cooling fan area. The noise was like a high-frequency wax-and-wane sound. We used high-pressure air to blow out and through the electronics, which unlocked a lot of dust from the inside of the electronic components and filling the air space with dirt. This corrective measure helped temporarily to mitigate whatever the noise issue was. The noise level after the "cleaning" was around 70dB, which is 10dB below a noise contamination that warrants ear protection (see: Photo-Plate #1). We did not measure the noise level before the cleaning, but it was noticeably louder before than after the cleaning.

Photo-Plate 1: Noise levels right underneath the cooling fan area of the NGR were around 70db after cleaning the electronic components with high-pressure air.
Suggestions: For further testing and calibration purposes of the NGR logger, two new (hand-crafted) "Uranium Standard Cores" were produced onshore and brought to the ship. They are now are available for any NGR experiments. Corresponding paperwork for the U-enriched cores is placed together with the standards inside the NGR drawers and also available in digital format on the server. Another copy of the "Technical Sheet" is available in the "NGR Logging Service Guide" ringbook on the shelf above the NGR/Correlator-Station area.
Special Note: The NGR-oscilloscope was migrated from the top shelf above the "Corellator Station" to the ET's shop/office where it is better stored and placed than on its original storage location. Instead, several manuals and information on the various instruments are collected in various binders and ringbooks and placed on that shelf.
We also implemented a new "Snoop Tool" to monitor the cps-per-time-unit (i.e., every 5 seconds), which immediately highlighted that the compromised Energy-Bins of Detector #3 are Channel s 10-to-20 (via Bill Mills).

MADMAX:

In general, no problems were reported from the Mettler-Balance/Pycnometer station. All systems and the MADMAX application worked nearly flawlessly and reliably throughout the entire EXP345. However, reports of several failure points during EXP344 (see: corresponding Tech Report; also Developer's EXP344 Tech Report) indicated that the MADMAX station might be in need of a new PC-box. Up to date this has not been implemented for various reasons (via D.Fackler).
Some issues with the data depth entry (due to user error) were short lived and fixed via developer's effort (see: corresponding Developer Tech Report). Another error was reported during uploads, resulting in the following report message (Figure 4). It was caused by missing container numbers when corresponding data were entered into SAMPLE MASTER (normally "0" for rock measurements):












Figure 4: Error message from MADMAX was produced during upload due to missing container numbers. Clicking "OK" continued the upload and placing data correctly into the MADMAX interface dialog table.
This error did not prevent our users from uploading the data per se. They pretty much ignored the message, clicked "OK" and moved on. We subsequently entered the container number "0" into LIMS (via David Fackler), which was acknowledged by refreshing the MADMAX list as confirmation.

Vp-Gantry:

Following the insights from EXP344S (see: corresponding Tech Reports), we replaced the neoprene-rubber end caps with high-quality steel end caps. Measurements performed on acrylic blocks (our "Standard Material" of choice) and rock specimen with this new configuration indicated a much more favorable drift behavior than what users had to deal with in the past (e.g., see: Tech Reports 327 and 344S). Thus, a more consistent data set was acquired within a shorter amount of time because fewer standard/calibration and verification measurements were necessary to produce high-quality data.
Our PP-scientists always ran 10 replicates on the same sample while measuring the sound speed. This method allowed them to discern when the measurement has "settled" at a point of low data variability. The first 3-4 data points were normally discarded, producing a consistent sound speed value data set. Data variability was consistently as low as 1% for discrete measurements. Figure 5a & b highlights some results obtained with the modified GANTRY system.

















Figure 5: Mechanical and software improvements on the Gantry system produce better and more consistent result. Using steel end caps settle mechanically more robustly than the formerly used neoprene end caps (data and graph credits: Prof.B.Ildefonse, Montpellier).
Despite the significant improvements of the system, the following issues want to be mentioned:
Issue #1: We experienced one "homing" error of the transducers (on 12/22/2012), which was benign compared to what users had been exposed to in the past: endless trials of restarting the application, re-mapping the com-ports, and other drastic measures before the clamped transducers would release their grip. In our case, restarting the application and clicking the "Jog X" button as part of the "Actuator Utilities" sufficed to fix the problem.
Issue #2: One problem occurred with the LIMS data base system when scientists intended to upload data files and suddenly faced "uploading errors" via MUT; the MUT error message suggested that the files had been already uploaded properly (which was confirmed) and another copy placed in the local archive directory. It remains a bit of a mystery how this could have happened and so there was no measure taken by the developers. Most likely this situation was caused by some erroneous "User" workflow. However, it seems to be that the files had been uploaded in a different time-order than originally being recorded; this caused problems for the scientists regarding how they wanted to utilize the data for their particular data analysis.
Issue #3: One time, our logging scientist, Dr.Gilles Guerin, noticed a laser beam on his shirt while he was walking toward the area and recognized that the GANTRY laser was online – although no measurement was running and the system should have been offline. To turn the laser offline, it required us to restart the GANRTY experiment, home the transducers and properly exit from the application. The laser then turned off. It's important to double-check that the laser is off after closing the experiment.
Issue #4: We still experience occasionally a wrong X/Y/Z direction assignment within the LIMS REPORT domain (see: EXP344S Tech-Reports).
The most pressing issues are summarized once more as follows:
(per verbatim from Prof.B.Ildefonse, Montpellier):
"Thomas, Following the little exercise of this afternoon – 3 problems are to be solved:
red rows in the attached file (direct import from LIMS) should be deleted from LIMS. These are duplicated entries following uploading problems (see above: Issue #2)
yellow rows : change the direction of the measurement (X to Y or X to Z) as indicated in the file (see above: Issue #3)
it would be great to have the file creation time stamp (i.e., measurement time) in the LIMS report, instead of (or in addition to) the uploading time stamp in LIMS (see below: Suggestion #1)
It almost appears as if there are more data rows (of unknown origin) in LIMS than what we generate (again - see above: Issue #2)
Thanks – Benoit"
Suggestion #1: Based on aforementioned "Issue #2", we propose to log both time-stamps of the actual data-recording and the uploading process in the data base and make them retrievable via WTR or LIMS REPORT.
Suggestion #2: A pressure transducer/load cell was recently shipped to the JR's PP Lab and can now be integrated into the Vp-GANTRY experiment; its purpose is to measure the pressure per load cycle onto the acoustic piezo elements. Monitoring the pressure regime via this load cell can thus further enhance the repeatability of the measurement because of a better control over the temporary "squeeze" onto the acoustic elements. During EXP345 we prepared a small-scale "Arduino/LabView" project, which can be optimized and eventually executed during the upcoming tie-up period (the idea for this mini-project was inspired by a short training course on "Arduino Electronics" taught by ET Mr. Garrick van Rendsburg and Schlumberger Engineer Mr. Clay Furman.)

Therm-Con TeKa Station

EXP345 scientists used exclusively the half-space probes ("pucks") to acquire therm-con data on hard rock specimen. The following problems occurred:
Issue #1: Initially the QAQC data were not retrievable through the LIMS data base down/upload applications (LIMS & WTR) due to some changes that supposedly had been implemented during EXP344. The developer group addressed that short-lived issue promptly (see: corresponding Tech-Reports and emails from developers).
Issue #2: Sometimes TeKa data are not produced in the correct format to plot them in TeKa-Graph. To plot all TeKa data on TeKa-Graph, we used Mr.M.Meffert's "tc_convert.bat" and "to_ansi.bat" routines for converting unfavorable –to- usable data formats. Find those two routines under: T:\TAS\dml\software\labsystems\thermcon – and copy/paste them into your warranted data folder. Activating the "tc_convert.bat" routine finds every file in your selected data folder and converts data into the warranted format for a display with TeKa-Graph. It is a very useful routine to check the data quality. Check the TeKa Manual (Version 5.0, 2011) for more details on Teka-Graph, and then use the Meffert-code to decipher any TeKa therm-con data file for a proper display using TeKa-Graph.
Issue #3: Measurements on both MACOR standard and rock specimen with the small-sized Mini Half Space Probe (H51016) showed greater value variability (around 5%) than the large-size probe H11027 (smaller than 2% for most results on the MACOR standard). Scientists initially hoped that the small-sized puck could be used to reveal insights into "thermal anisotropy", which is related to the alignment and orientation of minerals. Due to the relatively large error observed during EXP345 rock sample measurements with the small-sized puck, our scientists decided not to use the H51016 probe any longer. Figure 6 highlights the different variability of the large-vs-small-sized probes for measurements both on the MACOR standard and a rock specimen from LEG 147.









Figure 6: Thermal conductivity measured on both MACOR (left-hand sight) and Leg 147 rock specimen (right-hand sight) show a greater data variability when obtained with the small-size (H51016) vs. large-size probe (H11027). (-- Data and graph credits: Prof.B.Ildefonse, Montpellier).
To make sure that we are not dealing again with some uncontrollable power issues, we also ran the TeKa instrument via the battery power alone, thus completely de-coupling the system from the ship's power. This is only possible as long as the FLEXIT tool is not running (because the latter requires an uninterrupted power resource at all times). Several test runs with the small-size probe attached to the MACOR standard (both inside and outside of the seawater bath) were satisfactory only within an accuracy range of 5% – which was not considered by the scientists to be accurate enough to confidently claim any firm conclusions about "thermal anisotropy".
Suggestion: Extract at least some portion of the complete Therm-Con analysis per LIMS REPORT or WTR. In particular the Therm-Con LET (ln extracted time) parameter as a data quality index is of particular value. We remember Dr.Kim from EXP317, who reported this particular value for each measurement on the therm-con log sheet. Thus, we recommend to offering this value as reportable data via our web-based data downloading tools.

XRF Hand-held scanner

The THERMO-FISHER hand-held XRF scanner was introduced to the scientists and sporadically used on rock samples during EXP345, but without producing results that contributed to the EXP345 scientific objectives. The Thermo-Fisher Niton XL3t GOLDD+ Handheld XRF was set up in He-purged mode for broad analysis of light (<Si) elements of geological interest. The instrument was placed right next to the Therm-Con station and operated by scientists who went through a short training routine (video and verbal/manual introduction to the instrument) in order to keep radiation (x-ray) doses as low as reasonably achievable (ALARA). The cubical-shaped bench top system for the scanner is shielded by lead-fabricated covers on three sides and a thick glass window toward the front. The unit is connected to a desktop PC for data capture and data processing. The PC, which had been shipped from shore together with the instrument, was decommissioned and the XRF Scanner software tagged onto the Therm-Con PC (via MCS team).
(Missed-) "Milestone"
Following recovery of hard rock core, the scientists intended to determine the usefulness of the data collected, and at that time determined the appropriateness of capturing and reporting this data. Accuracy and precision/repeatability tests were conducted on various rock standards using both the "dirty" vs. "clean" ship's power. Results of these tests exhibited very little variation in obtained results. However, the unit requires always a 30-min "cooling time" after about 6 measurements (at 150 seconds each) – two reasons, which made the instrument inefficient and non-attractive to our EXP345 users for the rock material that we recovered.
For measurements on actual rock specimen, a standard measurement was conducted both prior and after the actual rock data acquisition. On the surface of the heterogeneous rock samples, three representative areas were chosen and three measurements recorded for each sub-area. From the total of nine measurements an average was calculated, with the result representing the mineral assemblage of that particular rock sample (this seems to be a good approach to acquiring XRF-scanner data on such sample material – in case future sailing scientists decide to work with the XRF-scanner data).
For the reasons summarized above, the scientists concluded that the instrument was not producing the warranted results and terminated their experimental efforts (see: XRF_Report_revised_21jan_2013 – located under: uservol\7_Geochemistry\Handheld XRF\Report_345).

SHMSL

Following up on observations from the most recent past (see for example: Tech Report 344S), issues with the SHMSL are summarized as follows:

• The instrument exhibits a significant drift behavior and produces different results when measuring data at variable resolutions (e.g., [1cm] vs. [1mm] via observation by Prof.B.Ildefonse, Montpellier); similar behavior has been observed and reported during and post-EXP344S (via Dr.P.Ferretti).

• Sensitivity of the OCEAN OPTICS electronics to the thermal environment was identified as one possible main cause of the spectrophotometer drift. Both internal and external heat sources can apparently cause significant value jumps between calibrations. As a short term solution, a CPU heat sink and fan were attached and tested; the use of the "dark pixel" value as an internal real-time correction showed promising initial results.
• The Color-Calibration causes a significant "off-set" (see: 344S Tech-Report and follow-up discussions post-EXP344S); EXP345 cores U1415J-5R -&-6R are good examples for this unwarranted "off-set" behavior.
• Reasons for both the "off-set" and drift" are also discussed in a separate Tech-Report (via Bill Mills). However, data from re-measuring EXP345-core U1415I-4R suggest that the particular "off-set" issue might have been resolved after retrofitting the instrument.

Preliminary suggestions and solutions:

1. As a consequence of our findings the currently used OCEAN OPTICS sensor electronics was replaced with an older version of the same electronics. The newer electronic box is going to be sent to the company for calibration purposes. The older electronic box does not seem to be quite as sensitive to thermal changes and will be used until we receive a modified and/or re-calibrated OCEAN OPTICS unit.
2. Using a Teflon disc, color reflectivity values measured with the SHMSL currently always must differ from those produced by the company because they used two different bulb types of a different color temperature. DITTO: Improvements of the measurement system require additional tests performed on Teflon discs and White/Black standards to verify the nature and main reasons for the observed issues.
3. These tests ought to be performed with an electronic sensor that is less (or in the best case scenario: not at all) prone to thermal-induced drift. Consequently we suggest to:

• Isolate the thermal heat sources & sinks around the signal electronic box and sensors
• De-couple the entire system permanently from the ship's electrical system and run the experiment via a UPS power system. Electrical noise has been held responsible for problems with other instruments, e.g. Therm-Con, so it is not entirely far-fetched to possibly deal with a similar problem on the SHMSL as well.
• Re-organize and re-route all the cables with and around the entire instrument system (including to the PC-box and so forth), which might further reduce electrical noise.
• Ideally, we operate the instrument and conduct these tests under actual experimental conditions, using the same bulb type as the company did use to produce the color reflectivity data on our new Teflon discs (bytw: the discs are stored together with the old color tiles in the cabinet in the far end of the lab – port-side – close to the SHMSL.)

h1. IMAGING & MICROSCOPES
William Crawford

SPECIAL PROJECTS

INSTALLATION OF NEW SPOT MICROSCOPE CAMERA SYSTEMS. Replacement cameras were installed in the paleolab. The adaptors for the old cameras to the microscope were not compatible with the new cameras but a bit of scavenging and machining efforts were successful in operational systems. Proper adaptors need to be installed but we got by with successful results. 4,550 micrographs were taken and placed with the appropriate meta data into the data base. The newer systems coupled with the upgraded computers has made the capture and the live view faster.

Line Scan Camera.

Core recovery was minimal due to the nature of the Expedition. The images harvested were of the best of quality. The system produced images, which gleaned no complaints. Bill Mill's imaging profile system is providing very nice corrected images. The scanner remained consistent during the entire two months of operations requiring no adjustment for color or density. The lighting set up has not needed adjustment since Leg 320.
Partly because of the light recovery, the scientist chose to do two scans of each cut section half to images both wet and dry. Each section half. which was appropriate, were also imaged as a whole rounds and the resulting scans were hand pieced together in the imaging office. 48 whole round scans were completed. The condition of the hole(s) prevented successful logging efforts for comparison but the recovery produced very nice impressive whole round images.
Two of the scientist had prior experience with the whole round capture system and required no instruction or supervision. The adaption of the scanner to accommodate the whole rounds vs. the section halves were quick and straightforward.
The "end cap " scanning method is working successfully without complaint from the operators.

MICROSCOPES

Configuration and alignment. Heavy microscope use during the expedition of all upright binocular and stereomicroscopes. Heavy usage of the microscope image capture system was used as mentioned earlier. 4,550 micrographs were uploaded to lims. The microscopes were fitted with 2.5x through 40x objectives and stages modified for individual preferences and use.
To simplify the meta data coupling system. David Fackler installed config files in each imaging station, reflecting a generic set of objectives ranging from 1.2x-100x. This range covers all of our objectives, which we currently have for use. Choosing the correct objective and setting is key for the generation of the scale, which is produced with every image. After the addition of the new cameras, the scale was checked for accuracy.
The Zeiss medication of the New Discovery V8 stereoscope was done and received mixed to poor reviews. The method of attaching the analyzer to the objective is only a press fit to the objective itself via a split ring. The cross pol is adjusted at set up and there is no real method of viewing the specimen in single pol. The instinct of the operator is to twist the analyzer on the objective. This of course loosens the filter and it drops to the base which risk cracking and damaging the thin section sample itself. The built in light source in the stage makes the stage thicker and harder to view samples when not using the polarization options of the imaging station. As a result the use of the modified SV8 stereo scope by the scientist was minimal.
Overall Microscope Assessment Other than configuring the microscopes for specific needs in the first few weeks after departure, the microscopes required little attention other than cleaning and minor adjustments.

CLOSE-UP PHOTOGRAPHY

The close up capture station worked well. Contrasting to the low recovery, 983 close-up photographs were taken including approximately 450 of those being close ups of Thin-sections. The close ups of the thin sections was a special request which required modification of the Picat to do so. The picat system was moved temporarily to the close up workstation to utilize the strobe-flash type lighting and the Capture One software. The close-up capture system was used to place the thin section images in the close up category of the file system. This was done with the advice and knowledge of David Fackler who tracked the production of these unique data entries and placed all of the special images on user vol. I was very pleased to the modification of the lighting system was successful and produced superior images. This can be attributed to several things. First of all using strobe light allows the power to use smaller F/stops there for sharper images. The colors of the light produced by the strobes are industry standards and correct using standard camera color balance settings. Finally the duration of the strobe vs. the shutter required for correct exposure using incandescent light eliminated any vibration the ship was producing which could degrade the image. The combination of both incandescent and strobe in a custom light box could provide the live view big screen bi-refringence display as well as better quality capture in one unit.
I was very pleased with the result and produced what has to be called Artwork of the very detailed thin section. 6 prints were made and given to the Co-Chiefs after display in the Galley.
Emily Fisher should be and with vibratos congratulated and recognized for providing excellent thin section services. She was pleasant to work with and quick, sometimes turning out 12 per day. The thin sections she produced were consistent in thickness and polished to a high degree. This allowed the production of some of the best images I have seen to date of thin section samples.

Video and still efforts

Still and video efforts were as per standard with lots of activity surrounding Christmas and New Years. Lisa Crowder led the way with the organizing of the Christmas show and singing. We were fortunate to have several musicians on board all playing different instruments and different styles including Violin and Trumpet. A video was captured of the activities of Christmas and B roll of activities during the cruise.
Extra video was requested and shot for the Education and Outreach team. This was the best team I have seen on board and produced untold amounts of live broadcast mostly to France and England. Due to the time differences, they worked all hours tirelessly.
All of the video camera and still equipment worked flawlessly. The newly repaired/replaced remote microphone coupled with the new digital video camera produced excellent audio quality with low background noise with used with the Lavalier microphones.
I did research and self-study of the newly installed Apple Final Cut Pro X video editing software. The format and interface is totally different from Final Cut Pro 7 and requires some effort to master. Improvements with organizing and meta data is more reflective of industry standards and efforts to achieve good results as for as digital Asset management.
I am producing an unedited assemble edit of some 900 clips available for the crew and the scientist.
On a side note, one of the best features of the Picat thin section system is its versatility and able to be modified as technology grows. Case in point is the imaging system attached can be upgraded needed. An attempt was made to attach the Hasselblad camera system to the picat. The Hasselblad camera shoots 39 mega pixels vs, 21 mega pixels with the canon system. Having a much higher resolution image of the thin sections would be wonderful as it would, in effect, allow the computer display of the images to be a virtual microscope. The Hasselblad micro lens did not allow a full sensor image to be recorded there for negated the advantage of the sharper and better sensor. The program might consider the purchase of the proper lenses or adaptors to allow this to happen. I am not a fan of the Hasselblad work flow as I find it clunky and restrictive as well as proprietary. Having said that I also feel these issues could be worked around and tremendous results gleamed.
Considerable time and effort went into organizing and maintaining the various digital assets.

Vit recordings

As a part of normal workflow, it was established the Imaging Specialist be brought in as part of the VIT archiving system. In the process of this work flow model, the file is duplicated and another copy is given to Engineering. In doing so a collection of the re-entries are archived on the hard drive. 26 VIT recordings were duplicated and then Ripped to Mp4 format and place on Volume 1 under engineering/video. Also still images at times were requested and produced from the video footage.

STATS

327 GB video
48 GB still images
48 Whole round images
Sections 345-U1415P: 22R1-3, 23R1-2 remain to be stitched and uploaded
LSIMG
147: 15 sections scanned
345: 137 sections scanned

CLOSEUP
total:
147: 14
345: 983
thin section closeups: 489 snapshots of 143 TS
TSIMAGE
147: 48
345: 357
MICROIMG
147: 151
345: 3058

CHEMISTRY LAB TECHNICIANS REPORT

Lisa Brandt, Rachel Gray

Ampulator

The ampulator was not used.

Balances

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

Cary Spectrophotometer

We aligned the source mirror and lamp as described in the documentation that came with the instrument. The values at 885 nm are still jumpy. I believe we made some progress, as it now seems to be stable to 2 decimal places, when at first it was much more erratic. This needs to be checked out some more.

CHNS

Samples were analyzed for C, H, and S content (all four peaks appeared, N was excluded by scientists). After being powdered, samples were dried for 12h at 110^oC to drive off any absorbed water vapor. Samples were run at about 40{}{+}1 mg (not including V₂O₅), and we replaced the reactors after 100-125 analyses (due to loss of sensitivity and heavy use of V₂O₅).
We performed 531 analyses (including samples, blanks, calibration standards, &c) for 53 samples. The 10:1 ratio represents bypass samples between every standard and sample to ensure against unreacted powder from the previous sample oxidizing with the current sample, as well as several "ActualBlank" samples (a tin capsule plus V₂O₅) interspersed throughout the run. We also used various rock standards as to calibrate the instrument as opposed to the Thermo CN Soil Standard, L-cysteine, or sulfanilamide (although we did run sulfanilamide standards as a backup). DTS-1, JGb-1, JP-1, MRG-1, SCO-1, SY-2, and W147-895D were used as rock standards, and SDO-1 and JG-3 were not suited to the expected geochemical content of recovered material.
The previous issue regarding non-present or overlapping H, S peaks was resolved by bypassing the water trap, thereby eliminating the gas pressure drop in the trap (what we hypothesized to be the problem). The CHNS should always be run in this setup if H, S, or both are desired; only reinstall the water trap if neither H nor S will be measured. Also, sample runs should be the full 1200s for H, S detection. All of this will be mentioned in the new instrument manual, after the software is updated.

Coulometer

The coulometer was not used.

Freeze-dryer

No issues arose with the freeze-dryer.

Gas Lines/manifold

No issues arose with the gas system. A few leaky spots in the Argon line were tightened before the first ICP run.

GC3/NGA

GC3 and NGA were not used.

Hydrogen generators

No issues to report.

IC

The IC was not used.

ICP

The ICP was used to analyze about 53 samples. No problems with the hardware. The ICP analyzer software did not work. The main chemist tried using ICP Analyzer at the beginning of the cruise, using an old data set from her previous expedition. Evidently, at some point the software was changed to where on the final tab, the software queries LIMS and adds the Leg/Site/Hole/Core sample information along with the text ID. This is a nice addition, since the scientists don't care about text ID's. HOWEVER, the software crashes if the samples are not there. Since the database is wiped every cruise, this means you can't test or demonstrate the software by processing an old batch through the software. Also, many of the calibration elements were not displaying correctly.
Since the scientists couldn't play with the software, and the developers were busy with DescLogik issues, they just built their own spreadsheet to calculate the data. The issue that ICP Analyzer is not working has been sent to shore, and acknowledged, and should be fixed by South Alaska.

SRA

The SRA was not used.

titrations

alkalinity

The alkalinity/Chloride computer was replaced at the beginning of the expedition with a new Z420 workstation. The Alkalinity and Chloride software was installed on the new computer. We also brought over the LabView data files from the old computer so that old rates and data are accessible on the new box. We then ran some test samples and standards. In order to get the data uploaded, we had to install the Password Exchange program. Data was then able to be uploaded to LIMS.

Water system

The prefilter and MPS cartridges were replaced.

Misc

fridges

The middle incubator was defrosted. We then left it turned off and pulled out since they will be working on the floor in that area during the tie up.

Random

Physical counts were performed.

An inventory of chemicals present under the fume hoods was performed. We then found NFPA triangle ratings for all of the chemicals. The fume hoods and chem lab doors were then labeled with the triangles as well, to help in a potential fire situation.

XRD & SAMPLE PREP LABS

Kristin BRONK

Summary

This expedition was a low recovery hard rock cruise with 78 XRD samples and 53 ICP samples. The equipment worked well with a few hiccups mostly involving new computer installs. The new version of the XRD evaluation software was used for the first time this expedition. A new bead maker was received and installed this expedition!

• XRD samples: 78
• ICP samples: 53

MethodsThe

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

• 40 kV, 40 mA
• Scan angles: 4 – 70° 2 ¿
• Step Size: 0.0087
• Scan Speed: 1 s/step
• Div Slit: 0.3° = 0.6 mm

A scientist also collected the cutting debris and water from the saw as we split the rocks. He then centrifuged and filtered the water multiple times to be left with an 'average' powder to XRD from the entire split core. There was much debate of the value of this data and it ultimately was decided he would take the powders home as personal samples.

Equipment and Software

Overall, the equipment worked well, with the few problems noted below, most dealing with new computer installs. The new version of EVA (v1.4) was used for the first time this cruise with few hiccups.
A new bead maker was installed at the beginning of the expedition!

Problems/Issues

New bead maker

The new bead maker is running well with a few items noted below. The old bead maker is currently crated in the pallet stores and we can decide at what point we want to send if back to College Station. A few things to note in the installation:
I had an issue using the old melting temperatures (700°C and 1050°C). These readings on the new machine were not fully melting a flux bead. I sent an email to Kuro who confirmed that our crucibles are style CJ-30 and the crucible constant (set on the right side of the machine, inside the door) is 5.10. This helped the melting somewhat, but not completely. I still raised the numbers on the monitor output by ~150°C and produced great beads. I have asked the ETs to order a thermocouple that works with their Omega meter so we can verify it is getting to the temperature the bead maker monitor indicates.
Most of the existing hardware from the previous bead maker was used. One thing we did change was the water fittings on back of the machine – the slightly larger ones from the old machine were used to fit existing tubing.
The quartz ring that the Pt crucible sits in was moved to the new machine as it keeps the crucible more stable during agitation.
The quartz cooling plate was moved from the old machine and stored in the bead maker spare drawer

New lap wheel

The new polishing plate with magnetic back for XRD samples is stored in a cardboard holder in ICP prep area cabinet.

Balance software

When beginning to weigh standard for beads, the balance began to give lower readings after adding more weight. A new version of the balance software had been installed on the new computer but the balances were not 'talking' correctly to the computer. David and Dwight troubleshot the problem and decided to install the older balance software, which corrected the issue.

Crucible holders for furnace

The first batch of ICP samples ignited in the furnace had to be redone as black powder/flakes from the holders got inside the crucibles. One holder seems to be in much better shape than the other, but both could be replaced. I've written to Brad and Roy asking if something could be fabricated in Victoria or College Station.

Water leak and floor damage

I think we may have determined at least part of what caused the floor damage under the Haskris. As we were emptying the shelf to install the new bead maker I noticed the chill water lines seem to have condensation around the connections/valve where there is no foam insulation. A large bead of water forms around the valve and eventually trickles down the insulation to the floor. (A very slow process, but over years it could add up.) This would also explain the water spot under the valve that is developing on the wooden counter holding the bead maker. We tightened all the connections as best we could, but by week 6 the condensation trickle returned. Perhaps during tie-up, the connections could be changed or better insulated?

Methanol vs. Isopropanol vs. Acetone for sonicating ICP samples

Scientist Margot Godard was surprised to see our cook book listed methanol or acetone for sonicating ICP samples. She pulled up old methods from her previous expeditions listing isopropanol and requested I use it as well and suggested we change our methods to use IPA

Sound proofing of Haskris

Tim built a sound enclosure for the Haskris. It seems to help the noise somewhat. We will buy paint in Victoria or send it in the shipment to paint during the second part of the tie-up.

XRD of thin sections?

A scientist was curious if we had the capability of running thin sections in the D4. Curious as well, I asked the machinist to mill down one of our steel sample holders to where a thin section slide, plus a tiny bit of tape, would lay at the right height for the diffractometer. Unfortunately, the process of milling down the sides caused the sample grabber to be unable to pick it up. I don't think it's something we need to investigate further now, just a project out of curiosity. The sample holder is stored in the drawer with the other sample holders.

New computer for D4

With the movement to upgrade all computers running XP to Windows 7, I wrote Bruker asking about compatibility of our current software versions. See email below. Essentially, everything needs to be upgraded. The quote has been passed to Brad, David, and Paul F. with my recommendation to send a computer to Bruker for software installation and have it sent to the ship in Victoria. David seemed to think we would go that route, but I have not heard officially and no orders have been placed to my knowledge. You may need to double check with shore that a computer gets sent to Bruker Madison.
**************************************************************************
>>> "Gray, Daniel" <Daniel.Gray@bruker-axs.com> 1/18/2013 4:48 PM >>>
Hello Kristin,
I can at least get you started. With a software upgrade, you can bump up to Win 7 32 bit. So, it appears that you already upgrade to the DIFFRAC.EVA software, however we are currently on V3 now I believe. All except for Commander will need to be upgrade to the DIFFRAC.SUITE software. Commander will need an Update.
The software and new PC will have to be quoted through your salesman, so I will forward this on to him.
I am assuming that you will not be ported in the US any time soon? If this is the case, we should be able to build up the PC with the new software in the office. I will have you email me a copy of the configuration. When you get the PC, I can Webex in to finish it off.
Please let me know if this would work for you?
Regards,
Dan Gray
On Jan 18, 2013, at 8:09 AM, "JR Kristin Bronk" <jr_bronk_k@ship.iodp.tamu.edu> wrote:
Hello,
My apologies if this has been sent to the wrong person, but I would appreciate it if it could be forwarded to the appropriate representative.
We have a D4 Endeavor on our research ship and are currently trying to upgrade older computers running instruments. Our D4 is running the below software on an older machine with XP.
DIFFRAC plus XRD Commander (v 2.6.0)
DIFFRAC EVA v1.4 (purchased 2012)
DIFFRAC plus Basic Evaluation Package (release 2007)
D4 Tools v3.02 (2006)
DIFFRAC plus TOPAS (v 3)
DIFFRAC plus TOPAS Structure Database (release 2006)
We are researching if it is possible to run the D4 on a newer computer running 32-bit or 64-bit Windows 7. We are already running EVA 1.4 on Win 7 machines successfully, but are mostly concerned with Commander, D4 Tools, XRD Wizard etc being compatible with a new computer to control the D4. Is this possible? And if not, is there updated software available that is compatible with Win7?
Thanks in advance for your help,
Kristin

THIN SECTION LAB

EMILY FISHER

Summary

There were a total of 143 thin section requests of gabbros and troctolites.

Special projects

Finished remaining thin section requests from expedition 344, thin section 19-36, made of basalts.

Problems encountered

None

Miscellaneous

Routine equipment maintenance as needed.

UNDERWAY GEOPHYSICS & FANTAIL REPORT

William Mills

SURVEYS

VSP

• No VSP surveys were conducted.

MagnetometeR DATA

• The magnetometer was towed on transits to and from Hess Deep. On the final transit, the software was ran on a new Z420 without issue.

BATHYMETRIC DATA

• Bathymetric data was collected on all transits to and from Hess Deep.
• Because of the water depth and steep topography data from the ship's 3.5 bathymetric system could not relied upon to provide and accurate depth. For drill depth purposes, the site survey values were used.

• A series of 14 near-bottom surveys were conducted during Expedition 345 to characterize the seafloor and shallow subsurface of the Site U1415 area (Table U1415-B-T1). The purpose of these surveys was to observe and characterize the nature of the seafloor and its local slope, and the thickness of the subsurface material covering more competent basement, with the ultimate goal of siting drill holes. The surveys were either exploratory, to characterize the area surrounding the proposed drill sites (HD-01B to -03B) and to assess the viability of additional areas, or targeted, to characterize a specific hole location. All of the surveys involved visual observations, five of these surveys also collected seismic data using a 3.5 kHz near bottom seismic source (Table U1415-B-T1). [science report extract]

These surveys were conducted using a 3.6 kHz pinger mounted to the VIT frame as a source and recording with our hull mounted 3.5 system using the software's passive modes. After resolving initial problems with the hardware, we were able to get surprisingly good records from a very difficult geology (broken rock). See VIT kHz Sub-bottom Profile Survey section at the end of this report for more details.

Lab Changes

During the transit out to our first site:

• Installed the replacement floor tiles
• Installed three more Vidmar storage cabinets and anchored all cabinets to the bulkhead.
• Still waiting on countertop material which should arrive in Victoria.

New Instument HOSTS

The underway Geophysical lab is scheduled to receive to new instrument hosts. During this expedition, the MCS provided a spare system for us to experiment with and determine if we were going to have any problems running old applications. Except for the SB Logger, we have successfully installed (including security keys) all of the applications and tested them in realtime. Currently WinFrog 2 has been replaced and we are running both Bathy2010 software and the Magnetometer Sea Spy software at the same time.
The above diagram shows how the serial ports are configured to support running both applications on the same PC. Once all of the instrument hosts have been installed, this diagram will have to be updates and the cables re-tagged. This diagram has been posted on the bulletin board for reference.
Note, the old WinFrog computer is still sitting in the lab. We should hang onto it until all of the new instrument hosts are in.

SB LOGGER:

The software is strictly XP and Triton has no plans to upgrade Win 7 and our new Z420 PCs do not support XP drivers. This means that SB Logger must stay on its current XP box or be replaced with a new application. The hardware that SB Logger uses can be upgraded to Win7.

Bathy 2010

The OLD BATHY 2010 EMBEDDED COMPUTER

I'm referring to the old embedded computer that lived with the DSP electronics (middle rack). It has been turned off for the last 6 months and no issues arose, so we completely removed the system. The parts have been boxed and should be sent home for surplus from Victoria. The computer's power supply is still in the chassis and is used to power the fan, but the ETs will probably replace with a 12v power supply before the end of the expedition.

Bathy Software Issues

• Still no SEG-Y being produced in real time;
• GUI and Marker zoom still don't work;
• And a new twist! The zoom window is not scaling as shown below. The $PNTI 103 command is not sending the scaling message. In the Zoom return data ($PNTI 121) shows the top of the Zoom box with no bottom. This is also shown in the display ..just the top but no bottom value. It appears to repeat just one value for the full widow (lines).

Inspection of ODEC and the comma delimited files do not show any problems with the data collected and the files can be converted to SEGY-Y. The depth values are spot on; just no zoom display!
Because the issues appeared after removing the old Bathy board computer we initially thought that we had accidently ground something on the board. Therefore, we replaced each board one at a time but the issue did not go away. I will call the vendor to go over this problem (and other issues) and try to this resolved. But for now we are getting good depths, you just can't do a SEGY-Y conversion on the "zoom" data.
VIT 3.5 kHz Sub-bottom Profile Survey

Setup Overview

Figure 1: Hardware ConfigurationIn order to provide sediment thickness data to the science party, Co-Chief Scientist, Dr. John Snow, arranged for the loan of a self-contained, deep water, 3.5kHz pinger from Dr. Hartely of Woods Hole Oceanographic Institute. To acquire a sub-bottom profile, the pinger was lowered to the ocean floor while attached to the ship's VIT frame (re-entry camera system). The acoustic return from the pinger was acquired by the ship's sonar system and processed by equipment in the ship Under Way Geophysical Lab.
The Figure 1 shows the final hardware configuration which evolved over the course of the expedition. What is discussed below is related to the final configuration. Detail that led to this configuration are discussed in the Hardware and Software Issues section.
Acoustic returns captured by our 3.5 kHz array and processed using the Bathy 2010 Digital Signal Processing (DSP) electronics. The Bathy 2010 control software interfaced allowed us to configure the DSP for pre-acquisition processing (timing, filtering and initial amplification). The analog output, from the Bathy 2010's DSP, was split into an unmodified signal path and a second signal path that received further amplification. The unmodified signal was digitized using a National Instrument high-resolution digitizer board (NI PCI-5124) controlled by a LabView application that acquire, display and record voltages (along with time, ship's position and pinger offset data).
The second signal was further amplified using an ITHACO 455 amplifier and then split again with one line going to the EPC 9802 thermal graphic printer and the second to a PC running Triton's SB Logger software. Using another National Instrument dynamic signal acquisition board (NI PCI-4474), the SB logger software acquire, display and recorded the data in standard SEG-Y format.
The EPC printer control and time/position annotation was managed via another LabView application. GPS position data was provided by the WinFrog navigation software and beacon offset data was provided by the Nautronics RS925 Acoustic Tracking software (part of the ship's Automatic Station Keeping system –ASK).

Hardware and Software Specifics and Comments

3.5 kHz Sub-bottom Profiling System:

Description [Ref: Leg 200 IR Explanatory notes p.35]:
Ocean Research Equipment, Accusonic pinger (model 263), consisting of a 4.252-kHz transducer interconnected with a 5-in-diameter, 33-in-long pressure housing containing a battery pack, a storage capacitor, and electronics, was mounted on the VIT frame. This free-running pinger produces a 2-ms pulse at a 1-s repetition rate. Its half-power beam width is 65°. To distinguish it from other sonic devices, each ninth ping is skipped. The transducer's active face is about one-third of the wavelength of its characteristic frequency; therefore, there is only a single front and rear lobe to its directivity pattern.
Our initial survey was quite successful with the system operating for 9 hours. Subsequent surveys were more problematic with the system shutting down after 2 hours of operation. After several days of intensive repairs the unit was capable of completing long surveys at full power. See ET's troubleshooting report at the end of this document for more details.
Figure 1: Custom frame built by SEIM crew for attaching the pinger to the VIT frame.
Figure 2: VIT frame with the ORE Accusonic pinger attached
<span style="color: #243f60">Figure 2: VIT frame with the ORE Accusonic</span> <span style="color: #243f60">pinger attached</span>

Bathy 2010 Bathymetric and Sub-Bottom Profiler

Our initial plans were to use only the Bathy 2010 hardware and software in "passive" mode acquisition. During our initial testing, with the pinger hung over the side of the ship, we discovered that in order to record the return signal, you had to start acquisition by clicking the "ping" icon. This counter intuitive action cause the system's DSP to "free run" at 1-sec interval without sending an outgoing pulse from the transducer. Unfortunately, this caused several unavoidable problems for the way we wanted to use the system:

1. Figure 3: Receiver Output showing the initial signal clamping by the DSP.In the "free" run mode there was no provision in the software to sync the start of acquisition to the incoming pulse, which meant that your returns marched across the 1-sec window making post processing and visual analysis difficult.

1. Figure 4: Noise pattern left on the data.As part of the DSP cycle, the receiver would clamp down on the first ~10 ms of the 1 sec acquisition window (Figure 3). In normal operating mode, this would prevent the out-going pulse from overwhelm the receiver; but in passive mode it created a pattern across the record (Figure 4) and suppressed the return signal when received at the top of the 1-sec window. This is a flaw in the Bathy 2010's passive mode and most likely related to limitations in the hardware.

To overcome this problem, we did the following:

1. The Bathy 20210 system was put into "active" mode with the outgoing pulse attenuated (-42db), CW mode selected and the range set to 1200m. This created a 12 second window of passive listening with the outgoing pulse showing up on every 12^th record.

1. Figure 5: Photo showing the analog output for the 3.5 kHz signal.Although we continued to record data on the Bathy 2010, this data is unusable. Primary data was collected on a LabView application that was developed at the beginning of the expedition (Bathy Master.vi) and uses the analog signal from the Bathy 2010's DSP analog out (Figure 5).

Bathy Master Application

Running on a spate PC from the Bathy 2010 software, The Bathy Master application used the following National Instrument DAQ Board to digitize the analog output:
The NI PCI-5124 is a high-resolution digitizer with a large dynamic range, software-selectable 50 Ω or 1 MΩ input, ranges from 200 mV to 20 V, and ability to acquire more than 1 million waveforms in onboard memory.
Direct return from pingerSeafloorSub-surfaceFigure 6: Acoustic returned signalDigitized data was presented as both an oscilloscope trace (Figure 6) and as intensity chart (Figure 7). Data was digitized at a rate 100000 data points/sec for a 250ms period (25000 records).




Figure 7: Acoustic traces displayed as an intensity chartDirect return from pingerSeafloorSub-surface
The returned wave to the ship consists of three parts. The first is a direct wave from the pinger itself. The second arrival was the seafloor reflection, and the difference between the two gave the height of the pinger off the bottom. Any subsequent returns are from the subbottom structures such as the sediment/basement interface or layering within the sediment.

The software also creates an ASCII data log of the raw voltages, ship's position and beacon offset. To determine the actual position of the VIT frame a standard positioning beacon was attached and the offset data measured by the ship's hydrophone using the RS925 software.
Note: The beacon positions where not correctly calculated during the first survey and should not be used.
Data post-processing was done by Logging Staff Scientist, Gilles Guerin using just the captured voltages from this application. An example is shown in Figure 8.
Figure 8: Processed data from the 3.5 kHz VIT pinger.BathyMaster Data Log Format and Explanation:
The data log uses tags to structure the data. Between the start and end tags, data is tab delimited. Except for the waveform data, each data type is identified by name:value pair.
Ship's position data from the WinFrog navigation software;START_GPS
UTC:23 DEC 12 - 16h 36m 60s, z 0
LON:20 15.134400' N
LAT:1010 32.866820' W
HDG:129.5
END_GPS
T0: offset of the first data point from the start of acquisition;
dT: the time difference between data points;STARTPING{_}:
T0:-1.400061E-2
dT:2.000000E-6
START_WAVE:
-0.3523-0.3745-0.3745-0.3523-0.3634-0.3468-0.3523-0.3468-0.3523-0.3357-0.3246-0.3246-0.3135-0.3080-0.3024-0.2747-0.2692-0.2470……..
Raw voltages of the returned waveform;

………………..-0.2470-0.2359-0.2304-0.2193-0.1805-0.1805-0.1750-0.0863-0.0586-0.0475-0.0530-0.0309-0.0530-0.0253-0.0198-0.0364-0.0364-0.0253-0.0253-0.0031-0.0087
END_WAVE
END_PING
For each beacon tracked by the RS925 software, the following section is repeated. See Figure 9.
B: beacon number (Beacon 1 is on the seafloor and beacon 4 is mounted to the VIT);
X: offset (Ship relative coordinate in meters in the starboard direction)
Y: offset (Ship relative coordinate in meters in the forward direction)
D: offset (Ship relative depth in meters – fixed value set by the ASK operator)
P: degree (Ship's pitch)
R: degree (Ship's roll)
H: degree (Ship's gyro heading)
E: error (0=no error)
SX: not used
SY: not used
SQ: not used
BecLon: longitude (calculated from the ship's GPS position and beacon offsets)
BecLat: latitude (calculated from the ship's GPS position and beacon offsets)
BecUTC: time (GPS UTC time)







START_BEACON
23Dec 2012 16:53:50:687
B:1
X:-342.7
Y:286.5
D:4855.0
P:-0.4
R:0.3
H:129.8
E:0
SX:-36111133.2
SY:10000000.0
SH:0.0
SQ:0
BecLon:20 15.372632' N
BecLat:1010 32.908794' W
BecUTC:23 DEC 2012 - 16h 53m 50s, z +1
23Dec 2012 16:53:50:937
B:4
X:0.8
Y:-4.2
D:4855.0
P:-0.5
R:0.4
H:129.8
E:0
SX:-36111133.2
SY:10000000.0
SH:0.0
SQ:0
BecLon:20 15.132235' N
BecLat:1010 32.867066' W
BecUTC:23 DEC 2012 - 16h 53m 50s, z +1
END_BEACON
START_GPS ……

Nautronics RS925 Software

Figure 9: Diagram showing the beacon offset coordinate system.
To determine the location of the VIT relative to the ship, a standard position beacon was attached to the VIT frame (Figure 2). Data from the Nautronics RS925 acoustic software (part of the Automatic Station Keeping system, ASK) was transmitted on the network from a spare communication port on the back-up system. Using the GPS position and heading data from WinFrog, an offset was calculated for the pinger's position. Figure 9 shows the coordinate system used by the RS925 to report the beacon's position. The Z coordinate (depth) is set by the user which in our case was the seafloor depth. This can create an apparent position error as the beacon is lowered. Figure 10 shows how the VIT appears to be at a great distance from the ship and move inward as the beacon gets closer to the depth value in use. In the future we could integrate the VIT line depth and correct the position in real time. Such information could be used to see the effects of current on the drill string or pinpoint the exact seafloor position of a hole.

Beacon Watch Software Figure 10: Screen shot from the BeaconWatch application showing hoe the error in the depth value can affect the beacon's apparent position.

This is another LabView application that was developed at the beginning of the expedition to collect RS925 beacon offset information and calculate the bearing and range from the ship and the beacon's latitude and longitude. The calculations are made relative to the ship's GPS position as corrected to the moonpool.
Both beacon and GPS dats is shared with the BathyMaster program to annotate the data log records.
As seen in Figure 11, the beacon position data has a large spread as compared to the GPS data, but a mean of 30 seconds is very stable.
Figure 11: GPS position data is shown in blue and Beacon position data in purple.

EPC 9802 thermal graphic printer

For printing, we a dusted off the old EPC thermal printers and with a little work were able to get them on line. We ended up using just one but both had problems with the pinch rollers that deteriorated extruding a sticky substance. The sticky rollers would eventually grab the paper and wind it up on the pinch roller until jamb or tore the paper. Replacement parts have been ordered. Also, our stock of thermal paper has deteriorated, as well. We opened a newest roll but it was difficult to achieve a nice contrast on the print out at low voltages. To see any trace, we had run the signal through the ITHACO amplifiers and raise the voltage which also increased the noise. Data was pronted on all surveys but the print out has little science value.
Recommendation: New paper should always be purchased for any expedition that plans on using the printers. Thermal paper just doesn't store well.
In the past the EPC printers were controlled and annotated using the LabView UnderWay Watch program. While this program is no longer relevant (or usable) to the work in the Underway Lab, code controlling the EPC printers was copied and complied into a new application "EPC Master" This application's only task is to control and annotate the EPC printer output. Time and navigation data for annotation is obtained from WinFrog.

Triton SB Logger Software

Figure 12: Output from the Triton SB Logger softwareLater on in the expedition, we started the Triton SB Logger software (normally used for seismic survey) to acquire and record data in SEG-Y format. Unable to trigger acquisition from the first arrival, this data suffers from "data walk" issues; although, in periods where the depth of the VIT was held steady, we collected some very nice records (Figure 9) given the depth and the nature of the ocean floor.
SB Logger uses the following National Instrument board:
The National Instruments PCI-4474 is a four-channel dynamic signal acquisition board and can simultaneously digitize input signals over a bandwidth from DC to 45 kHz on all channels.

Data Flow and Application Dependences

Figure 13: Data Flow between applications

Figure 14: The pinger consists of two separate modules which are connected with a two core interconnecting cable.

ET's 3.5KHz Pinger Trouble Shooting Report

Ocean Research Equipment, Accusonic 263 pinger was built in the late '70s and has seen some rough times. We received operational information from the technical staff at WHOI but no vendor diagrams or manuals. All attempts to find this information on the internet failed. The company, Ocean Research Equipment, is no longer around but has been absorbed by various companies over the years. EdgeTech (EdgeTech.com) is its current re-incarnation. There, we talk one of their staff (Dave Fraser) who had worked on the system long ago. He was surprise to hear that one was still operational. He had no manuals on the system but gave us some advice and things to look for. Also, we received some good advice from Dr. Hartley who looks after the equipment that is owned by WHOI.
After our initial survey of 9 hours, the system would shut down after two hours of operation ( just as we would start the survey). Initially this appeared to be a battery charging issue. But after several more failures the system was opened up for inspection (Figure 15). From our inspections, we made the following repairs:
Electronics Module:

1. Damaged current limiting resistors were replaced with a single 2 Ohm 20 Watt resistor.
2. Heat damaged solder was removed and replaced to prevent dry joints in the solder.
3. The external charger is not designed correctly and will maintain the 200 mA necessary to charge the batteries but drops to 28 mA.
4. Two of the batteries in the pinger were faulty.

Figure 15: Electronics modules.
Transducer Module:

1. Damaged contacts to the ceramic disks were repaired and silicone was used in an attempt to keep the soldered wire connections in place.
2. The ceramic transducer supply cable was extended from the base of the transducer housing to the transducer package.
3. Damage to the blue supply wire was identified at the point where it feeds through the transducer housing, this was repaired.
4. Various attempts were made to repair the rubber cover to keep the oil from leaking out and water from entering the chamber.

Interconnecting Cables:

1. Figure 16: Transducer and housing:One pin connection in the connector is pushed into the sealed rubber part of the connector and repairing this is not possible. This cable would need to be replaced.

Dr. Hartley has arranged for long term loan of the system as long as we can put to use. For stable long term operations we need to do the following:

1. Purchase a new rubber cap. Because of dry-rot, salt water is leaking into the chamber. Because you can longer purchase parts, we'll return the cap to CS and see if the folks at Hempstead Poly Urethane can make a replacement.
2. The correct oil needs to be purchased and stocked onboard.
3. The silicone, supporting the wires on the piezoelectric elements, needs to be removed. It is not compatible with the oil and is coming apart.
4. Also we should look into replacing the NiCad batteries with Lithium ION.

Fantail EQUIPMENT

Starboard Winch

• No problems to report.

Port Winch

• The level wind continues to be a problem. We need to look into a replacement for the system.

Deck Crane

• Randy did a thorough job of removing the rust from the crane wherever a needle gun could reach, primed and painted.
• New safety stickers will need to be ordered to replace the ones that flaked off.
• The red metal box (list safety sensor) was completely rotted.
• Regarding the colors used to repaint the crane. Well this is what happens when you delegate and fail to oversee the job!?

ET REPORT

Garrick Van Rensburg & Randy Gjesvold
Summary: This was a hard rock leg.
ET Shop: Conducted Lab View and AdruinoTraining: Set up training for all who are interested in basic electronics. Updated Lab Status Reports.
DHML: Used as a workshop during this expedition.
Rig Instrumentation: Received reflectors for the pipe counter. They have been turned over to Siem.
Core Lab: Permanently attached a metric ruler to the core entry table top rail with brass screws. Moved all of the stores from under the Digital Photography area to the aft most Vidmars under the Whole Round Multi Sensor Track and the Fast Track. Re attached the white standard to the SMSL after a modification to embed it. Conducted voltage checks on the NGR. Installed weather tight speakers above the core receiving platform. Added a heat sink to the Ocean Optics amp to stabilize heat fluctuations. Manufactured a table and installed it at the base of the core receiving racks. Created pictograms for the WRMSL, Fast Track and NGR. Spinner Magnetometer began having issues with the microswitches. Looking into hardening the ribbon cables so that the vibration won't continue to damage them.
Core Splitting Room: The forward most tile saw had wobbling issues. The saw was removed and re installed closer to the operator a few inches to enhance the balance of the saw. Continued to have twisting problems. A brace was installed to counteract the twisting during use. Manufactured a table to hold core attached to the core receiving racks.
Liquid N₂ Gen recharged Dec 16, 27 and Jan 07, 17, 27 and Feb 02 or roughly every 16 days depending on sea conditions. The -86 Freezer battery pack went flat. The batteries were replaced.
X-Ray: Assisted the X-Ray tech in measuring the temperature in the new bead maker.
Conference Room: Found the fwd TV power cable missing and the remote control covered in dried Coke. Replaced the power cord. Cleaned up the remote control with Isopropyl Alcohol. Tapped out two 2X4 and two 1X1 pices of aluminum unistrut for feet for a shelf system being manufactured for the Conference Room. Working on the Video Conference computer system.
Upper Tween Deck: Installed a second speaker to the stereo system.
Lower Tween Deck: IT Cable Test Meter failed. Found that the power supply had gone bad. Rigged up an LA-200 DC power supply for temporary power. This will be returned when a new power supply for the meter is procured.
Gym: Inflated Speed Bag. Reset the Audio settings on the gym amplifier to improve audio quality. Found a screw near the back end of the new treadmill. During investigation found a plastic support from the cover on the back right hand side of the new treadmill broken off and lying underneath the machine. Removed the cover and found that both supports were broken. Epoxied the supports back in place and re installed it. Cooling fan near the Siem Lounge started to squeak as it turned. Added some WD-40 to the turning mechanism and the squeak quieted. Added lubrication to the other fans as well. New Treadmill began having problems with the speed and elevation function. Would only go up or down one setting at a time. Found that if you touched the heart rate monitor and ran the speed or elevation functions up they would run up and down as they are supposed to. Cleaned the contacts from the circuit cards and the wires coming from the upper control display assembly. Stationary Bike started making rattling noises. Found that the chain had loosened from use and was dragging on the chain guard. Moved the front wheel forward to tighten the chain. Changed out one of the brake pads because it was worn out.
Science Lounge: Replaced batteries to the remotes. They have disappeared again. Re set the system so the audio works correctly. BD has been renamed Bluray DVD to ease confusion. Found the intake vent to the UPS Power Supply mostly clogged with lint. It was removed and cleaned. This will need to be cleaned at least once per leg to avoid overheating the UPS. Optoma Projector lamp failed Jan 22 2013. New lamp has been installed. Replacement is on order. There is 1 spare on board in hold stores.
Subsea: 3.5 KHz pinger ceased to function. Removed from VIT and took to Subsea shop for repair. Found the batteries dead. Batteries re charged. It appears the Pinger lasts about 10 hours on a charge. During investigation found two dead cells. These were replaced. Also discovered the battery charger was not charging correctly. The battery cells were removed and charged individually. Conducted a 24 hour endurance test on the catwalk and it worked fine. Tested while open and found the output to the hydrophone was 960 VDC. It will be run again at the earliest opportunity.
Fantail: Cleaned slide rails and added Dry Slide Lubricant on the Maggy Reel Wind. Greased the fittings on the Port Reel Wind, Starboard Reel wind and the Crane. Chipped, painted and inspected the fantail crane. Inspected power connector.
Underway Lab: Assisted in the installation of new floor tiles in the lab. This required removing the table and most of the cabinets. Trimmed the outer tiles to fit with the Jig Saw. Moved ET Spares to the new cabinets in the forward end of the lab. Energized the EPC printer and it began shredding paper. The lower pinch roller would just roll up the paper and not pass it on. Roller was cleaned. No change. Added talcum powder to bring down the stickiness. It's working so far. Wave Tech Sun Filter no longer functional. Being sent back to College Station.
Misc: Assisted in the stores loads. Brady Printer was brought in non functional. Found the batteries had gone flat. These were replaced.

CURATORIAL REPORT

Chad Broyles
December 11, 2012-February 12, 2013
Puntarenas, Costa Rica to Balboa, Panama

Summary

Samples -A total of 1,439 samples were taken for Expedition 345. 893 were personal samples, and 546 were routine shipboard samples. This does not include ICP powder splits that are currently being processed. 138 residues from Leg 147 were processed on Exp. 345 for shipboard analysis. Additionally, 330 personal samples were taken for shipboard scientists from Leg 147.
Shipments -

• Core – 75 meters of core was recovered on Expedition 345. 20 boxes (Archive & Working) are being shipped to the GCR.
• Residues – The following table outlines the number of Exp. 345 shipboard sample residues that were requested by scientists.

Most Leg 147 ICP powder residues were requested by shipboard scientists on Exp. 345. Other residues and returned samples (e.g. TSB) from Leg 147 were also requested. Residue distribution was documented in the LIMS database.
Thin Sections- Emily prepared a total of 144 thin sections. This includes several duplicates that were made. Please see the Thin Section Inventory sent along with this document for a complete listing. A complete list is also available from LIMS Web Tabular Reports by searching Exp. 345, with a Test List qualifier of TS. An excel spread sheet of this inventory is also being sent to the USIO Curator and GCR Superintendent.

Leg 147 Core Sections

The following sites (archive and working halves) were sent to the ship: 894G, 895D, and 895E.
Core Description- The co-chief scientists chose a suite of representative core sections from Leg 147. Core section data was transferred from JANUS to LIMS to the section half level. It was found that the curated lengths of the sections did not transfer properly. This was corrected before we could do any further work on the cores. Piece information for core sections was entered manually as this is unique to the LIMS database. The following is a list of Leg 147 Cores that were re-described on Exp. 345:

Physical Properties (MADC) measurements on Leg 147 Residues-The Physical Properties Scientists chose a set of Leg 147 mini cores that were used for Moisture and Density (MADC) measurements. The following samples were manually entered into the LIMS database for MADC measurements:

ICP Analysis on Leg 147 Residues-The following powder residues were picked by Exp. 345 geochemists for ICP analysis:

Sampling of Exp. 344 Core Material

Expedition 344 did not receive hard rock material until the last few days of their cruise. They were limited on core processing time, with a short transit towards the end. Staff Scientist Dr. Katerina Petronotis (Exp. 344) requested that we pull sections from the Hold Refrigerator Store, and take 18 Thin Section Billets for Exp. 344 shipboard analysis and make the thin sections. This was requested 3 weeks into Exp. 345 when we had received a decent amount of core and were quite busy with processing our own samples. I would suggest that in the future any issues like this be ironed out in port, so we know what to expect ahead of time. We had 2 weeks of down time before we received the first core on deck on Exp. 345. However, we pulled the cores and cut the TSBs as ordered by the Lab Officer. Our thin section technician, made the subsequent thin sections from these billets. Gemma Maxwell entered all of this data into LIMS at the Gulf Coast Repository. Bill Mills is hand carrying these thin sections from the ship to the GCR. At this time, the thin sections need to be entered into the LIMS database as Exp. 344 data was not available to us when the thin sections were finished.

345 Hard Rock Core Processing

Exp. 345 core processing followed the same procedures implemented on Expeditions 324 and 330. The main exception was 360 degree whole round image scans. This occurred before the core was split and labeled. Due to the possibility of losing top to bottom sequencing of the core material, only a few trusted scientists were allowed to do this. Upon completion of 360 degree imaging, the scanning scientists carefully placed the core back into binned liners in the exact order it was removed. From here marine lab technicians split and labeled the core material.
Daily Shipboard Sampling-Each day, in the afternoon the co-chiefs, staff scientist, team facilitators, and I would gather around the sample table to discuss shipboard sampling. At this time, facilitators would describe why they had chosen specific samples. Samples consisted of thin section billets (TSB), XRD, ICP, and PP/PMAG. The scientists then marked their samples with a blue china wax pencil, and filled out appropriate TSB forms. Once all shipboard samples had been marked, Lisa Crowder (ALO) and meI, would cut and enter all samples. XRD and ICP samples were placed in labeled bins under the sample table. Thin section billets were placed in a labeled box, in the core lab. The thin section technician would pick these up when he came on shift.
Piece Length Measurement-Exp. 345 scientists showed interest in measuring the actual length of the piece (cm). On past expeditions, this has been equated with the bin length that the piece fit into. On this expedition the igneous petrologists kept a spread sheet where they measured pieces that were large enough. This measurement was defined as the longest axis of the archive half. I then entered the piece lengths into LIMS via Sample Master for each archive piece measured.
Collection of Saw Residue (1941IODP)- Dr. Robert Wintsh (Indiana State University) put in a sample request 1941IODP to collect water and residue produced from splitting the core material. This was approved by the Sampling Allocation Committee (SAC). This was done in lieu of cutting a thin slab off of each piece of rock to obtain a bulk geochemistry sample. This was done on a whole core by core basis. This required modifying the drainage system on our saws. The saws were completely removed. We switch positions of the larger and smaller MK saws. The larger MK saw was used exclusively for this purpose. When collecting this water and residue the drain pipe was removed and a spout was connected to the drain. The spout emptied into a large plastic container. Dr. Wintsh was responsible for providing the containers and collecting saw residue once the cutting was complete. When his saw cuttings were dried, I entered the sample into the LIMS database.
TSB Checkout Sheet- There was great interest in looking at the billets that the thin sections were made from. We ran into a problem in that one scientist took it upon himself to take the TSBs from the Thin Section Lab as he pleased. In an effort to have more control over this we created a check out system where I kept the billets and the scientists filled in a sheet of those they would like to see. I dispersed the billets accordingly and they returned them when they were finished. This seemed to work very well, and the billets were all accounted for and did not become unorganized.

End of Expedition Sample Party

The end of this expedition consisted of a 6 day transit from the Hess Deep to Panama City, Panama.
The following guidelines were used for each sample party.

• Cores were laid out from Exp. 345 & Leg 147.

• New research proposals were submitted from assembled research groups for Exp. 345 and Leg 147. Any samples that came from Leg 147 core material were submitted via the JANUS Sample Request system on line (http://iodp.tamu.edu/curation/samples.html).

• Once proposals had been approved by the SAC, I associated each sample request with sample request codes (first four letters of scientists' last name).

• Scientist filled out a pre-formatted Excel spreadsheet outlining each sample they were requesting. This form included Exp, Site, Hole, Core, Section, Interval, research group, and what type (e.g. TSB) of sample/size they would like. 

• Groups of scientists went through and marked samples with personalized Sample Request Code Label Dots (provided by the curator). This was done in an organized and specific order.

• Dot stickers were returned to the curator.

• All scientists then left the cores alone. Sample Allocation Committee (SAC) reviewed samples, and resolved initial conflicts.

• Each scientist made a second pass, updating sample request forms. At this time, sample location cannot be changed! Also, at this time each scientist or group marks the exact sample he/she would like to get with a blue china marker. All conflicts were then resolved by the SAC.

• Technical staff committee (Curator/ALO) verifies location of samples corresponds with each form.

• Technical staff cut all samples and entered them into the LIMS data base via Sample Master. All samples were labeled, bagged, and boxed by the technical staff.

Action Item

Thin Sections – Several thin sections made on Exp. 345 have been requested for loan by shipboard scientists. A complete list of borrowed thin sections is being sent to the USIO Curator and GCR Superintendent. Thin sections will first be sent to the GCR for inventory, and distributed on loan to requesting scientists.
Exp. 344 Core Shipment – Expedition 344 cores will be shipped with Expedition 345 cores from Victoria, Canada to the Gulf Coast Repository in College Station, Texas. This will occur immediately after the transit from Balboa, Panama to Victoria, Canada. Exp. 334 sections that were sent for Exp. 344 are also being shipped to the GCR. Problems Encountered
Super Saw - We did not receive long sections (1 meter plus) of cored material. We cut one of the longest pieces received from U1415I- 4R-1 with the super saw. The user has much less control cutting material with this saw than cutting it by hand on the smaller saws. This in turn, produced a significant saw mark on the archive half of the piece. From this point on we used the hand saws in order to minimize saw marks on the cut face of the core material. If possible, I suggest using the hand saw when cutting hard rock material. This is with the understanding that sometimes a piece will be recovered that is simply too long to cut on the smaller saws, and the super saw must be used

Computer Software and Hardware

Sample Master- Sample Master behaved for the most part with usual random crashes for no particular reason.
Ghost Cores - We received several "Ghost" cores on this expedition. These mainly consisted of several rock pieces or 'rollers'. However we did receive a 1.5 meter section of ghost material with long cored pieces. Sample Master did not upload this information into the database with desired results (i.e. ghost cores effected the depth calculation of other cores) David Fackler spent many hours sorting out this issue. Ghost Core Definition (Type = G): A ghost core's contents come from an already drilled part of the hole (i.e., the extent of a ghost core lies completely within the drilled or cored portion of a hole.) It is a re-drilled interval. However, it can yield a significant amount of rock material that either fell into the hole and was subsequently emplaced into the core barrel, or was re-drilled (e.g. a ledge that slumps over into the hole that we core again). It is similar to junk baskets where you ream out certain depth intervals in the hole and anything that falls in is collected in the junk basket. However in the case of a ghost core, you are re-drilling with a core barrel inside that collects the material. During the first part of the expedition we could not enter this into the data base without affecting the depth of other cores since ghost cores come in between real cores. Mike Storms and Kevin Grigar kept a spread sheet that outlined the exact intervals where the ghost cores were re-drilled for 345-U1415. For example U1415J-7G was re-drilled from 29.0-34.9 meters. We recovered 1.54 meters of core material. As far as curation was concerned we curated these cores like we would any other core material except it was logged under the Ghost Core. We curated it from the bottom to the top marking oriented pieces, and tried to piece together anything that fit. Rock pieces were spaced out using dividers, and a split line was drawn as usual. The curated length and piece lengths were recorded, entered, and uploaded into the database. In the case of U1415J 7G it expanded into two sections with a final curated length of 2.05 meters. This kept in mind that the core material from 7G came from a re-drilled interval of 29.0-34.9 meters. In reality the material could have come from any part of the hole if material fell in and was collected in the core barrel. For curation, it was important to document this material and curate it as we would normal core material. In the case of Exp. 345, ghost cores were very important because of low recovery and the Ghost yielded scientific information about the hole that was not recovered previously. Mike Storms recorded ghost core depths using his spread sheet. In the end, Ghost cores were handled as they should and did no effect depth calculations for other cores in the hole.

Web Tabular Report

It appeared that Sample Master did not have the ability to edit piece information. I later found that Sample Master does change this information in the database. However updates are not transferred to WTR. So it appears that no change has been made, when actually it has.
h1. PUBLICATIONS REPORT
TIM FULTON

Summary

Expedition 345 was a low recovery hardrock expedition. The data entry in DESClogik and output through LIMS2Excel and Desc export seemed to work well. A hardrock VCD template was developed using Exp 335 as a starting point. There were a few minor adjustments made to the column arrangement. The fabric columns that were overlapped on Exp 335 were separated for this expedition.

VCD - descriptions

The biggest issue was adding the description column. Do to the formatting of the text the description process is virtually entirely manual. With the version of Strater that we have the text that is in the unit summary tabs must be formatted using word. A download and format process was developed on this cruise for the descriptions. The "description" word document is then saved as a pdf and that is opened in Illustrator, sized and spaced for consistency. Once that is done the VCD pdf is then opened in Illustrator and the description text is then copied into the description column.

VCD – primary mineralogy

The primary mineralogy had to be exported directly from DESClogik with the desc export. LIMS2excel was unable to pull all of the primary mineralogy into a single tab. It was a very simple work around to map it via the Desc export.
All other processes for the publication specialist were routine with no problems to report.

Equipment & Software Performance Summary

• The latest version - Strater 3 was used on the Publication Office PC and ran smoothly.
• Adobe Illustrator, Photoshop, & Bridge ran fine. No issues to report.
• The Publications Office Mac and PC ran fine. No issues to report.
• Microsoft Excel & Word worked fine as well.
• GroupWise worked fine for emails.
• The copy machine worked well.

DEVELOPER'S REPORT

Dwight HornBACHER, and David Fackler
Hess Deep —Puntarenas, Costa Rica to Balboa, Panama12 December 2012 – 12 February 2013

Overview

This document highlights changes to the JOIDES Resolution laboratory data management environment during Expedition 345.
Selected issues are highlighted, but not reviewed in exhaustive detail. In general, see the ship activity log and Pending pages of various products on the developer site for additional detail: https://sites.google.com/a/scientific-ocean-drilling.org/developer-page.

Curation and Core Handling

SampleMaster

No change. Operating with release 2.2.4.3 since Exp 344.
NOTED:
Ghost material. The ghost designation was resurrected and applied to selected hole maintenance operations which also often returned sample material.

• LIMS and WTR reporting systems require corrections to report these appropriately on the various hole, core, section summary reports.
• Ghosts are to be ignored (as are drilled intervals) for computation of recovery, penetration, and advancement.
• The depths assigned to ghost operations always overlap other regions of cored material. The effects of this ripple through various systems—not breaking them, but also often not working as an end-user would require. E.g. Some systems present overlapping images (Limspeak). Some systems clearly retrieve data by depth, and only sort by depth—where sorting by site, hole, core, section and depth would have provided clear presentation (LimsOnLine data editing).

Sample data for expedition 147 cores was migrated into LIMS to support expedition activities on this material. Only HOLE, CORE, SECT, SHLF samples were migrated using the Janus2Lims utility. Piece logs were manually entered (not available in Janus). Thin sections and billets were cataloged manually: not sensible to migrate automatically as Janus doesn't carry any sample parent-child relationship, and the cataloging conventions for this type of sample have changed sufficiently to go forward this way.
Additional issues noted with SampleMaster operations here.
Toward release 2.2.4.4: project changes were committed so that future SampleMaster builds from trunk will occur against FarPoint 6.0 spreadsheet. Ran it this way from code for handling of a variety of day-to-day SampleMaster use-cases.

LaserEngraver aka LazerKatjie

No change. Operational with release 2.1.0.2 since Exp 342. Used consistently on all sections.
NOTED: Sample hierarchy browser failed to operate due to an ampersand applied in a hole description. Work-around: edit out the ampersand with SampleMaster. Finding the offending record requires debugging in LabVIEW to obtain the offset of the offending character. Seen twice now. Content was properly escaped according to standards. Noted in LazerKatjie product log.

Geology

DESCLogik

No change. Operating with release 3.23.6.9 since Exp 344.
NOTED: On-going list of issues attached to the DescLogik product logs: see DESC crash screencaps.docx. Review of database LIMS.ERRORLOG indicated more errors this expedition than with previous expedition version.
Most columns are multiply qualified (0-4 qualifiers, 1 value entry field). Lims2Excel in general supports specification of only two search qualifiers. Led to the usual series of VCD production cycle questions: "Why does this data show up?", "Why doesn't this data show up?" as the process and tools are adapted to the custom report specifications for the expedition.

Virtual core composite generation

No change. Operating with release 2.0.3.2 since Exp 336.
NOTED: Due to hard-rock core flows, COREPHOTOS are initially generated using whole round surface slices. But this is temporary: archive half split section surface scans are always done after whole round surface slices. This expeditions work flows also generated wet and dry images. As long as the archive half section dry is scanned last, the current program does the right thing: the program always uses the last LSIMG test applied against the archive section half, if a previous COREPHOTO exists, it is replaced.
Code changes were made to ensure the utility would still compile against recent [circa 2011] LIMS services library changes. The code is checked-in, not released for production use.

Affine and Splice CSV to XML format Converter

No change. Not used. Release ? available since Exp 342.

Splice Parser

No change. Not used. Release ? available since Exp ?.

AffineSpliceUploader

No change. Not used. Release ? available since Exp ?.

Closeup, Microphoto, Thinsection Capture

No change. Operating with release 2.0.0.8 since Exp 344S.
ImageCapture2. This alternative version of the CloseupCapture program is removed from distribution.
New cameras and computers. Five new Spot Flex cameras were sent to Expedition 345. Four were installed and configured on Z420 instrument hosts during the transit to site. The systems now using a Z420 are noted in this planning spreadsheet. The ImageCapture software configuration files were modified: (1) to reflect current configurations and serial numbers; (2) to simplify the construction the WS_CONFIG.xml. Example on the development site at this link.

Geophysics

Whole core systems

Whole-round logger (WRMSL), Special task logger (STMSL)

Changed. Operating with release 3.0.2.0 since Exp 345.
NOTED:
Release 3.0.2.0 after repair of positioning errors arising from failed top-of-material detection. After a formal vetting, testing period, was used without issue for the duration of the expedition.
STMSL was not used this expedition. Remained dismantled so JAMSTEC instrument (rock strain gauge) would be available for use into expedition 345.

Natural gamma (NGR)

No change. Operating with release 3.0.0.0 since Exp 330.
NOTED:
High total counts still occurring in detector 3, counts increased by another order of magnitude. The extra events incur counting dead time which leads to elapsed counting times 5-10 minutes longer than normal, leading to an overall extension of run-time.
Notes from the 344 evaluation of the issue indicate fault probably lies in the Spec 295 photo-multiplier-tube (PMT) base and electronics, or in the electronics of the NaI detector. We presently do not have a spare Spec 295 PMT base on-board.

Split core systems

Section half image logger (SHIL)

Operating with release 2.6.3 since Exp 344 and with the 2.6.x series since 344S.
NOTED:
Whole round surface images were generated this expedition. And wet and dry split surface scans were generated. For some material, both archive and working halves were scanned. Typical hard-rock core-flow. Which images should be used for which downstream processes is not always clear in this scenario. Mechanisms for finer granularity of image selection in downstream workflows are desirable. The specific requirements for these alternative products are different. They can be more clearly cataloged as-such.
Uploader [MUT] handling for LSIMGs should be modified to store whole round surface scans against the section. At present, they by default attach to section half—as scanned from a d-tube end-cap.
Much SHIL 3.0 hardware and software work and testing toward release. See LO notes.

Sonic velocity (GANTRY)

No change. Operating with release 2.0.3.4 since Exp 344S.

Reflectance and susceptibility (SHMSL)

Changed. Operating at release 5.0 since Exp .
NOTED: See LO report to LWG. Color reflectance module and tools were modified to accommodate for sensor temperature fluctuations due to use and environment. Acquisition and data reduction algorithms re-worked to accommodate for that behavior.

Discrete sample systems

Thermal conductivity (TCON)

No change. Operating with vendor release 5.0.0 build 7 since Exp 335.
NOTED: The LIMS Reports were modified so this data would display appropriately. Statistics gathering code underneath the ReportOverview were modified to show the correct number of rows of data available.

Moisture and density (MAD)

No change. Operating with release 2.0.0.8 since Exp 344.
NOTED: Z420 instrument host was configured as replacement. System failed to talk to Pycnometer hardware. Retained current xw4400 host for expedition 345 production operations. Z420 was then re-used for other development work. To be resolved before deployment in Victoria.

Penetration Strength

Not used. Release 1.0.0.3 available since Exp 340T.

Paleomagnetics

Kappa Bridge KLY-4S

Changed. Not used. Vendor release ? available since Exp 335.
NOTED: No change to the vendor software, but did upgrade National Instruments serial drivers to release 9.1 on this box to see if it will correct issue with utility ["Up" and "Down"] software's ability to raise and lower the sample holder. Installed, not yet tested.

Superconducting magnetometer (SRM section)

No change. Operating with release ? since Exp 339.

Superconducting magnetometer (SRM discrete)

No change. Operating with release ? since Exp ?.

Demag and Internal Field Intelligence (DAFI)

No change. Not used. Not further developed this expedition. Libraries available to hook in heading information from the Underway lab.

Underway

Navigation, bathymetry feed

No change. Operational at release 1.0 since 340T.
NOTED: Numerous changes to systems in Underway from which this utility gets its data feeds. See LO notes.

JR Navigation, Site Fix, Heading

Changed. Operational at release ? since 345.
NOTED: See LO notes.

Geochemistry

Alkalinity

Changed. Not used. Operating at release 3.0.0.0 since Exp 335.
NOTED: Deployed on Z420 instrument host hardware. The switch was successfully made, tested, and approved by the chemists. The xw4400 hardware previously used is retired from Chemistry and stored in lower tween IT.

CHNS

No change. Not used. Operating at release ? since Exp ?. Applies the WorkListGenerator.

Coulometer + Cahn Balance

No change. Not used. Operating at release 1.0.0.0 since Exp ?.

Mettler-Toledo Dual Balance

No change. Balance software operating at release since Exp ?. Computer hardware is shared between Mettler-Toledo and SRAnalyzer system.

Gas bottle monitoring

No change. Operating at release 2.0.0.3 since Sep 2011. Monitor program continues to be run on the NGA/GC3 system.

NGA/GC3

No change. Not used. Data upload supported by release ? of MUT since ?.

GC-MSD

Long retired for shipboard use. Box pulled off the shelf in chemistry. Packaged for shipment to HQ via Victoria. Includes a set of GPIB cables. Thank you MCS.

ICPAnalyzer

At release 1.0.4.0 since May 2012. Broken for hard-rock use. Unclear whether it is functional for sediment expedition use either. Product is still functional for management of standards used in the ICP methods.
NOTED: Not used this expedition. Release 1.0.4.0 and 1.0.3.5 fails to show calibration plots for the major elements required for hard-rock analysis. And [non-intuitively] requires database connectivity to complete data reduction, when all the data is available in the local file being processed.
The code was reviewed, changes begun, then tabled when Thin Section Reporting and Ghost related issues became the priority. See the product log for more information.

SpreadSheet Uploader

No change. Operating at release 3.0.1.2 since Exp 344.
Applied to upload stitched whole round surface images, CHNS data, and ICPAES content (in an extremely limited way compared to what ICPAnalyzer normally provides).

X-ray fluorescence

Used. There is no USIO custom software or data upload process for this system. It is setup as-required by expedition. System setup next to Thermcon with its own dedicated box. The data is stored in Excel files as part of the expedition proceedings of the physical properties group.

X-ray diffraction

Changed. Java Balance operating at release ? since Exp 345. Hardware was upgraded to a Z420 during 344 transit to Costa Rica. The Java-based variant of the Mettler-Toledo dual balance control system was installed on the new hardware.
New versions of peak analysis software [TOPAS, DIFFRAC] were distributed to equipment in the "Sediment" lab. Hardware is shared with the microscopy system there. One USB key is for TOPAS, DIFFRAC; the other is for the Spot Camera software.
In the same lab, Java balance for the Mettler-Toledo dual balance system installed on the Z420. [The box was staged the previous expedition, but not completely configured.]

Rig Instrumentation Systems

Depth Overlay and WITS Communication

No change. Operating with release 4.0b5 of DOWcomm since 344S.
NOTED: Very reliable. The failures observed are readily traceable to root causes:

• Seen once. Startech providing WITS feed [in Ops office] stopped responding. No WITS transmission, no browser access. Fix: unplug and plug in again to reset.

• Seen once. RigWatch slave in Ops office stopped forwarding the WITS feed to the RigWatch master. NACAgent was sufficiently out-of-policy [old version, out-of-date] that the box was quarantined. MCS updated the NACAgent.

• Seen once. Veeder RS422 network junction box was powered off [unknown reason]. Turned power back on to enable access to the devices on that network.

RigWatch

No change. Operating with release 8 since ?.
NOTED: RigWatch has a fixed limit on the number of rows of Live Data that may be recorded at 1-second intervals. Data collection stops when that limit is hit. Actually hitting the limit requires additional reconfiguration over the normal routine of starting a new Job file. The "DateBase" parameter must be set to a new starting date and time [from the Setup screen] for RigWatch to proceed as usual.

Other

Oracle

No change. Oracle release 11.2.0.2.0g in use since May 2012.
NOTED: Data model removals and modifications (locations as noted):
Removed operations tables (unused): OPS_RIS_DETAIL, OPS_RIS_MAIN (ship, shore, shore test). Removed LIMS tables (unused): ANALVALID8, LIMS_EXCEPTION_LOG (ship, shore, test). Revised the get depth function (ship). Updates to stored procedures for ReportOverview population of Thermal Conductivity summary (ship). Retain values to the millimeter precision for intervals presented on sample labels (X_SECT_OFFSET, X_SECT_OFFSET_BOT). Drop unused package (version 1) for depth computation (ship)—actually not used; PKG_RESULTDEPTH_2 is still required until the "old" vs. "new" depth usage is completely addressed and tested.
Seen once. DescLogik activity was stalled because two users conducting DESC modifications managed to lock the same row of data for modifications. Normal operations were not able to continue with that dataset until the lock contention was broken. Work-around: stop and restart all Tomcat nodes. This cleared all database sessions and their locks. Post-mortem: SQL Developer provides lock contention reports. The specific sessions involved are identified. Repair of this kind issue can be done with more finesse once the offending sessions are identified.
Seen once. Early morning occurrence, no lab activity at the time, but the drillers were at the end of their tour. Indications seen by the drillers indicated Oracle was not responding to logins or other requests. Current reading of the Oracle alert logs indicates that under some rare condition, the Oracle listener shuts down. It takes several minutes for the cluster services to notice the failure and then correct it. Review of the logs show this has been occurring at rare intervals since May (the limit of current logs on-line).

Data Loaders

MegaUploadaTron5001 (MUT)

No change. Operating at release 2.0.8.4 since Exp 342.
NOTED: Do still encounter stations running release 2.0.8.3. No compelling reason to upgrade unless a fix was made targeting the specific system. Before next hard-rock expedition, should revisit how we catalog WET scans of split surfaces, whole round surface slices, and whole round surface stitches. MUT should be revised to support cataloging whole round surface products against section rather than section half. Worked-around this by applying Spreadsheet Uploader to upload stitched images. Applied LimsOnLine data editing tool to re-parent the whole round surface slices.

Data Editors

Lims-On-Line

No change. Operating at release 0.3.5 since Feb 2012.

• Routinely used by PMAG and PP technicians to cancel selected runs of track data.
• Applied in chemistry to move 1 incorrectly cataloged analysis to its proper parent.
• Applied by Curation a few times to move samples to the correct parent.
• Applied routinely by developers to move whole round surface scan slices to be parented by section, rather than section half.

NOTED: LOL selects analytical data by depth range. The sample browser interface allows the selection of a specific section, but when presenting analytical observations, includes those from all material in the section-defined interval. Shows up particularly with "ghost" cores.

SQL Developer

Changed. Build box and development desktop upgraded to release 3.2.20.10.0.

Reporting Systems

Desc2Word

New. Custom report for creating the unit summaries applied to VCDs.
Java network launch protocol application. Directly (JDBC) queries the Oracle database for template structure and content. Presents the content as a Word document (using library docx4j to provide manipulation of the XML underlying the Office docx format).

Thin Section Report

Delivered by Hastedt and Gorgas as Excel spreadsheets constructed based on DescLogik exports with effective though not-as-complete-as-desired Excel macro automation.
NOTED: A .NET version of thin section reports exists (deployed on "tasapps"). But we do not have code for it. Fackler examined resurrecting the java-based thin section reports from expeditions 324, 330 but opted for a different development path based the requirements and specifications for the current Exp 345 thin section report layout. The outcome of that effort is still not complete and was of no value in reducing the effort to produce reports for this expedition. The HTML/CSS/Javascript version of the report is visible here.

WebTabular reports

Changed. Operating at release 3.0.0.11 since Exp 345. The associated release of resteasy-lims-webservices 4.4.7.1 was rolled back.

LIMS Reports

Changed. Operating at release 4.0.7 since Exp 345.
NOTED: Updated the thermal conductivity report so as to display the content available in the database—previously wasn't. Tied to release 4.0.7 of resteasy-reports.
To make the LIMS Reports preferentially more visible/accessible, added a link to the shipboard "home" page (http://ship.iodp.tamu.edu). To be revisited.

DESCReport

No change. Not used. Operating at release 1.3 since 345.

LIMSPeak

No change. Operating at release 1.8.0 since 344S.
NOTED: Images of ghost material overlap cored material. To be corrected.

INT

No change. Not used.

LIMS2Excel

Several changes. Operating with release 8.2.0.1 since Exp 345.
NOTED: DescLogik templates created this expedition carry from 0 to 4 qualifiers to guarantee the unique identification of a columns content in LIMS. Lims2Excel is at most capable of distinguishing two qualifiers. In some cases this is not sufficient to guarantee that the correct data is returned for publications needs in feeding barrel sheet production. Recent changes are noted here.

Drill Report

New program created and deployed on this expedition. Purpose is to replace the daily paper IADC drilling report. Program uses a web interface and AJAX/Web services to maintain the report database. Output is a PDF file. Uses associated web service resteasy-drillreport.

Culling Utility

No change. Not used.

Libraries

IODPUtils. No change.

Web Services

SUSE OES Tomcat Servers [Ararat, Rainier, Shasta]

NOTED: Last significant refresh was in May 2012, associated with upgrade to Tomcat 7, Java 7.
ChangePassword. No change this reporting period. Release unchanged since May 2012.
DESCReport. No change. Operating at release 1.3-tomcat since Oct 2012.
ReportOverview. No change. Operating at release 3.1.2 since Exp 342 (May 2012). Changed how summary record counts are computed for thermal conductivity observations. Effected by PL/SQL in the database, not by change to the display code.
UWQ. Changed. Operating at release UWQ-4.0.7 since Exp 345. Thermal conductivity report once again displays a row for each observation.
WTR. Changed. Operating at release 3.0.0.11-PJR-20121216040333-fackler. Dropped support for non-functioning display of depths by splice.
depth-services. Removed, then rolled back. Operating at release 2.5.1.2-PJR-b79-20110902153606-fackler. Studied effects of retiring this service: computes sample and result depth values that are still used by a number of programs. Computes lengths for HOLE, CORE that the new depth routine doesn't.
lims-log. No change. Operating at release 1.1.0.1-PJR-b4-20110904210505-fackler.
ops. No change. Operating at release 2.0.1.0-PJR-b26-20110926101422-morgan.
probe. No change. Operating at release ?.
resteasy-affinesplice-webservices. No change. Operating at release ? since ?.
resteasy-desclogik-services. Redeployed. At release 1.6.8.7-PJR-20120914010615-fackler.
resteasy-drillreport. No change. Operating at release 1.0.0.2-PJR-20121205143915-foster since Exp 344 (Dec 2012).
resteasy-error-reporting. No change. Operating at release 2.2.0.2-PJR-20120528164701-hornbacher.
resteasy-lims-sync. No change. Operating at release 0.9.5.2-PJR-b320-20120106055221-bennight. Every 4 hours trickles home currently available data.
resteasy-image-tiling. Removed on all SUSE nodes. Service can only be used on the system providing the file backing store: the Solaris cluster.
resteasy-lims-webservices. Changed several times, then rolled back. Operating at release 4.4.6.10-PJR-20121202204402-morgan since Exp 344. DO NOT USE release 4.4.7.1. Changes incorporated there break display of data in Limspeak. Release rolled back and changeset moved off of trunk until correct handling of getResultsFastWithDepths is implemented.
resteasy-monitor. No change. Operating at release 1.0.0.1-PJR-b13-20110903171554-fackler
resteasy-printer. No change. Operating at release 2.0.1.5-PJR-b60-20110914204137-blaisdell
resteasy-reports. Changed. Operating at release 4.0.6[sic]-PJR-20121228024040-hornbacher since Exp 345. Corrects display of thermal conductivity data in conjunction with release 4.0.7 of the UWQ portion of LIMS Reports.
resteasy-reqmgmt. No change. Operating at release 0.2.0.1-PJR-b33-20110905143055-fackler.
resteasy-role-management. No change. Operating at release 0.9.0.1-PJR-b182-20111103145826-bennight
sampling-services. No change. Operating at release 1.3.0.1-PJR-b9-20110905030644-fackler

Solaris Tomcat Server

Sites. Minor changes in tasapps/index.html to reflect Lims2Excel release while keeping older version available. Added statistics page supported by resteasy-desclogik-service.
labnotebookWebDav. Unchanged.
resteasy-asman. Unchanged. At release 2.5.0.1. 2.5.0.1-PJR-b67-20111125070258-blaisdell
resteasy-image-tiling. Unchanged. At release 2.0.0.1. 2.0.0.1-PJR-b12-20110905111358-fackler
NOTED: This Tomcat Server is being restarted by the cluster services on a once-a-day to every-other-day basis. Root cause unknown. The "flap" was as frequent as once every 15 minutes under the unusual conditions: all cluster services were being serviced from one node; a backlog of image tiles was being recomputed for a batch of 1500 images; maintenance was being conducted on DHCP services; and a tape drive controller was failing. "Flap" appears to occur more frequently under heavy disk I/O load: backups, image tiling. Further monitoring and analysis required for resolution. Failing tape drive will be replaced in Victoria.
Image tiles are NOT automatically generated for thin sections (TSIMAGE), microscope images (MICROIMG), or closeups (CLOSEUP). This is a function that should be initiated upon successful upload of an image via ImageCapture.

Developer Resources

Desktops

Updated applications on the developer desktop (see INSTALLED.txt on the dev account desktop). The equipment Is configured for most development uses. For local backup purposes, installed the 1 TB travel drive OZY in the system. Retains a slightly longer history of content than is retained on the Novell Network.

Servers

Load Balancer Apache at Solaris. No change in production configuration.
Resilient Load Balancing. No change in production configuration.
Tomcat 7 Java 7 SUSE Linux OES. No change in production configuration.
NOTED: Operated this expedition on two load balancer nodes: Ararat, Shasta. Rainier was retained for standby.
Subversion code repositories. No change in production configuration.
Subversion repository replication mechanism. No change. Run reliably all expedition.

SYSTEM MANAGER'S REPORT

Andrew Trefethn and Mike HODGE

Servers

Servers (Microsoft):

• Windows Server was stable, nothing to report.

Servers (Solaris):

• While routine monitoring of /var/adm/messages logfile on both nodes discovered repeating error messages;

  • Jan 16 22:01:36 pico wa: [ID 902828 kern.notice] wa23: Command transport failed

  • Jan 16 22:01:36 pico wa: [ID 902828 kern.notice] wa23: biowait() returned error=5 bioerror=5

  • Logged an SR 3-667901300 with Oracle to identify the cause. Their analysis pointed to HP Ultrium 3-SCSI_1 (drive 0) in the tape library.
  • Logged call HP4691299502 with HP and provided HP_LTT diagnostic results for their analysis. Their analysis pointed to the same drive. To confirm, moved the drive from slot 0 to slot 1 and problem moved to slot 1.
  • HP would not ship a drive at this time. Before arrival at Victoria the MCS will have to reopen this case and have a drive shipped at that time.
  • Both Sun nodes occasionally log errors, of which, HP has stated are parity errors caused by the failing tape drive. Generally, to clear error logging requires rebooting the tape library, restart CommVault and the Sun media agents. Frequency varies but generally can go a couple of days before an instance occur requiring a reboot.
• Implemented Oracle crontab script entry to clear log_###.xml files out of alert folder. Script at;
  • /oracle/scripts/cron_alert_cleanup.sh
  • Done on both nodes
• The developers on Expedition 344 started capturing Daily Drilling Reports and storing them at /web/cumulus/asman/catalogs/DROPS/DROPS. Over time this folder will grow accumulating reports. Mike Storms agreed to only keep the last 2 Scientific Expeditions of reports. They want this available for reference on current expeditions. Because of tie-up and non-expedition periods this may mean keeping upwards of 6 to 8 months of files. This has been annotated in the "MCS SOP Check List.docx" document.
• There were two reasons for why DHCP services were only able to run on Sun node=pico. 1) The last IP pool added to DHCP manager (192.168.180.X) was somehow corrupted causing errors. 2) Because of the addition of IP pool 192.168.170.X the cluster agent START_TIMEOUT default of 300 seconds was not long enough for the agent to build its required resources before timing out and failing back to where it originated, in this case, pico. The solution was to remove the 180 pool since it was not being utilized and increase the START_TIMEOUT to 900 seconds. Depending on what processes are currently running on a particular node, it takes anywhere from 6 to 8 minutes before DHCP resources will mount on a node.
  • NOTE: Sun engineer working this SR stated that this is an indicator that our Sun equipment may be due for upgrades to newer hardware.
  • Sun case # for reference on this matter is SR 3-6663379891.

Servers (Novell):

• The Novell servers worked fine all expeditions. All services have run on their server since beginning of Exp345.
• Of note is at the beginning of Exp345 when extensive cleanup of prior expedition data occurred, the servers became unstable and required a reboot of all three nodes. The symptom started out with Scratch becoming unresponsive and could not access the volume. Tried rebooting the server, in this case rainier, but it would not shutdown. Had to do a forced power down with the power button. This forced VOL2 to migrate to another server. Upon trying to access the contents of VOL2 at a workstation, saw the content of VOL1 instead. At this point did a complete all OES node shutdown. This cleared the problem and restored systems to normalcy. The point of this entry is to make reference of some type of issues may be showing up due to the massive folder/files deletions that occurred at the beginning of an expedition. This has been observed on prior expeditions. Something to be aware of and monitor.

EVA4000 Storage:

• No issues to report with the EVA - worked as intended.

Network:

• The Fluke Optiview Network Analyzer power brick failed. Replacement unit has been ordered. To keep the unit operational had to cut the power plug from the brick and attached it to a DC power supply loaned to us from the ETs. Set the voltage to 15VDC @ 4A on the power supply, connected the power plug cord to the power supply and placed the unit at the base of the network rack in the data center. Once a new power brick has been obtained, the power supply needs to be returned to the ETs.
• Discovered the docking station for LT51608 laptop in Corelab C42 network locker can only display one resolution on both of its video out ports – VGA and DVI. It is currently set for HDMI 720p (1280 x 720) for feed to VBrick encoder. The PC-to-TV adapter can only handle max resolution of 1024 x 768. Until a VGA-to-RCA composite HDMI adapter can be located, will not be able to feed Rigwatch content to ship's CCTV network.
• The CoChiefs for Expedition 345 wanted to collect beacon data from the beacon PC in DP Control Center and visual see the beacon display in DP. Configured a StarTech device for serial port on beacon PC and configured an Axis IP camera for the beacon display. Connected to a Trendnet switch and setup all on B49-004 (ge.3.18) (WAP) port in DP. Encountered problems configuring the port so swapped B49-002 (ge.3.22) with B49-004 drop in Bridge B49 network locker and was able to make all operational.
• After expedition Notes:
• MCSs are to collect all equipment from DP at end of the expedition.
• Switch B49-002 (ge.3.22) with B49-004 (ge.3.18) drops in B49.
• B49-004 (ge.3.18) needs to be reconfigured as a WAP port again.
• Was discovered that B49-001 and B49-002 are missing and need to be located, if possible. Victoria tie-up?

Workstations

Pc Workstations:

• Microscopy Lab PCs were swapped with HP Z420s with the exception of PC51589 Picat station.
• Identify Finder – After applying an image to a Z420, it is necessary to enable Identity Finder by following the procedure at U:\MCS Procedures\Identity Finder\Configuring a Windows Computer for Identity Finder.docx. Identity Finder was enabled on Windows workstations, but not instrument host computers. Identity Finder has not been installed on OSX computers.
• SpiceWorks – communication between the SpiceWorks server and windows computers needed encouragement by running a batch file called wmiRebuild.bat which can be found at U:\Software\pc\Spiceworks.
• Netlimiter – This software is installed on the Skype station PC52509, from the administrator's account. The purpose of this software is to regulate the bandwidth an application uses. It has a simple interface listing all the software and the administrator is able to enter the bandwidth limit by specifying a number of kilobytes or megabytes.

MAC Workstations:

• Have to periodically inspect the Video distribution units. Regularly find units where XMBC has a message box requesting to relaunch the application.

Printers:

• Had one incident where the Sharp copier froze with a "Please Wait" message on the console. The console was un-responsive. Cycling the console power switch did not clear the message. Was not able to find a master power switch so pulled the power cord. This cleared the problem

Satellite/Internet/Phones:

• Encountered two outages due to weather conditions at LES. First incident was over two hours in duration. Second incident was ~30 minutes.
• Due to ship's heading most of this expedition was done on the bow dome. Aft dome blocked by derrick.

Other Equipment:

• Discovered during researching tape drive issues that we had two tapes that hit their Media Retirement Thresholds and became marked as bad tapes. Because of this, automated a bad tape report to run every Tuesday. HP engineer suggested that our tapes are becoming aged and should consider replacing our tapes on some criterion we decide. On a weekly basis, the full backup tape report is made available. Another new report for bad tapes is now available entitled "Storage information Report".
• Discovered the hard way that the ribbon cable for the Startech 2S1P PCIe Parallel Serial Combo Card is not keyed, can be installed in either direction. The ribbon cable connector has a slight tab on it and the PCB has a break in the line drawn around the connector is your only clue.

Special Projects:

• Visimeet – close inspection proved someone had modified the connections of different cables once again. When the cables were reattached properly Visimeet was tested but failed. After inspecting all the cables and connectors without detecting any problems, the computer was removed from the cabinet for better visibility. Internally at the rear of the Gentner mixer wires were found broken and pulled away. A solution allowing ease of access and high visibility was required for maintenance purposes. Tim Bronk built a cabinet from extruded aluminum and smoked plastic for this purpose. The cabinet has been bolted to the wall. The computer and Gentner mixer have been placed in the new cabinet. Wire looms have provided excellent cable management. Visibility is excellent and cabling appears to be simplified. All cables have been labeled to provide easy reinsertion. The Visimeet software has been tested successfully.
• Worked with Bill Mills to implement SB_Logger on HP Z420 PC with Windows 7 64-bit then next with 32-bit OS. No-joy. SB_Logger has a .dll file that explicitly states that it is not compatible with newer OS. Next tried Windows XP Mode and was able to successfully get SB_Logger to work. However, requirements are for 4 serial ports and a PCIe expansion card to connect to external devices. Windows XP Mode, being a virtualized environment, explicitly allows only two com ports. And, unless the PCIe card is a modem, does not have provisions to communicate with PCIe cards. What this means for the time being, unless shore decides to abandon seismic data collection and processing, is that we need to keep the seismic xw4400 PC along with adequate spare xw4400 PCs.
• Updated UPS spreadsheet, attempted to standardize AMS listing so as to not have this spreadsheet to keep updated. On-going. Discovered missing UPS 52155, last seen on Exp344S in LTSCI. Current location unknown. Spreadsheet at;
  • • U:\JR_Staterooms_Decks_AMS\UPS_Locations.xls
• Cumulus – imported the TechDoc catalog without incident. Karen Graber wanted the Techdoc log file. We discovered the logging had not been initiated since the Cumulus server installation. Logging has been turned on and will be available the next time Karen Graber asks for the TechDoc log file.
• Created a spreadsheet to identify all StarTech serial-to-ethernet deployments. Spreadsheet at;
  • • U:\JR_Staterooms_Decks_AMS\JR_StarTech_deployment.xlsx
    • Don't know password to three units.
• Bill Mills configured LT51917 Augmentix laptop with serial port analyzer software on a prior expedition. Used for connecting to PLC serial ports on Splitting Room saw and NGR track. Captured Frontline Serial Analyzer software and located in MCSZONE\software\PC volume. Mills also brought us all the hardware and cables for the analyzer for safe keeping. Located in LTIT E1-E3 VidMar cabinet.
• Setup HP Z420 PC52515 with Windows 7 64-Bit OS for Bill Mills' WinFrog and SHIL replacement testing. PC last seen in DHML for SHIL replacement testing.
• Discovered the hard way that the IR pickup for the large Samsung displays is on a tab that slides up and down on the back side of the monitor. Bridge Planning area remote quit working due to this tab was pushed up and not allowing line of site between remote and pickup, slid the tab down and remote started working again.
• VDU Mac mini computers have been attached to the walls with locking security mounting trays. The keys to security mounts are in the key drawer in the MCS office.

e344 To-do for e345:

• Install remaining WAPs. Victoria tie-up.
• Investigate the problem migrating net services to Etna. Resolved.
• Install replacement drive in Z420 in core network locker. Done.
• Install replacement drive in starboard imaging Mac and turn off Time Machine. Done.
• Uninstall CorelDraw from PC52511 in CoreLab. This license is for the Yeop and should then be installed on that machine. Done.
• The drillers on this crew have asked if they can get a dual monitor and wireless keyboard/mouse setup for the Samplemaster PC in the drill shack. Actually they were asking if we could plug our computer into the TV they have in front of them so they could switch back and forth from TV to computer when they have to enter information into Samplemaster. They say they need this so they don't have to leave to brake handle to enter information. Could you talk to the drillers/OIM/Ops Super. on your crew and ask if this is needed and if so perhaps come up with a proposal on how to do it. Bubba and Charlie said NO.
• The open office mac 52631 needs to be re-imaged as it has software installed on it that does not belong to IODP. Will attempt during transit to Panama but teachers are utilizing the system extensively.
• Verbal from Grant at e344/e345 portcall was to mount Gym network locker WAP in secure location. Done.

TO-DO:

• Install remaining WAPs.
• A project for Victoria tie-up is to locate B49-001 & 002 on Bridge. Currently, their location is unknown.
• Deploy MAD_Pycnometer PC52524 during Victoria tie-up.
• Image PC52523 UWGL (Win7 32-Bit), new UWGL PC setup, need to capture an image.