Basic Troubleshooting Guide for SIO-CalCOFI's Program Network

Connection to Network & Data Server Directories

• All SIO-CalCOFI programs are designed to be on a common network and the data server (\\seaserv2\data) drive mapped as Q: (or other available letter; set individual program cfg files to the chosen letter). If networking is unavailable, all programs can operate locally by setting drive paths to local letters (ie C:\CODES\2014\1411\...). Base files generated by CESL may be "sneaker-netted" by flash drive - map the datapath to the flash drive (ie F:\Codes\2014\1411\...). Be sure to unmount the flash drive before removing it from the source PC.
• Expected data directory structure: Q:\CODES\YYYY\YYMM\ (ie Q:\CODES\2014\1411\). Subdirectories expected:
  • ..\1411\CHL\
  • ..\1411\CSV\ and ..\1411\CSV\BAK\
  • ..\1411\CTD\  - requires a readme.txt file in order to copy zip files; file content is unimportant but its presence is needed for the zip command to work
  • ..\1411\EVENTS\  - currpos.csv (GPS or MET position), eventnumber.txt (event number), orderocc.txt (station number)
  • ..\1411\LOGS\  - sample log location: CTDBackup-generated base sample log file 1411001.log, 1411002.log... which are loaded into CESL which generates 1411001.slog, 1411002.slog...
  • ..\1411\MAPS\ - location of preliminary contour maps that are generated from CTD mrk or asc files by DECODR
  • ..\1411\MRK\  - secondary location of CTD mrk, hdr, nav, hex, xmlcon files
  • ..\1411\NUT\  - nutrient data dir; data & run files must be copied by the nutrient analyst to the data server using ztree or filesync
  • ..\1411\O2\  - oxygen data dir; data & run files must be copied by the oxygen analyst to the data server using ztree or filesync
  • ..\1411\PROCESS\  - processing log dir; logs for each processing step for each station are recorded in sta files
  • ..\1411\PRODO\  - primary productivity data dir which includes DECODR-PIC-generated bottle files (ie 1411pbtl, prd001, prd007...) HOBO daily incubation temperature files, & Almanac-generated incubation Start-End LAN-Civil Twilight files.
  • ..\1411\SALT\  - salinity data dir; contains CESL-generated salt base files (ie salt001, salt002...); sample analysis files (ie H00102, H00202...), print files (ie salt001.prn), run files (ie salt001.csv), conductivity reading files (ie salt001.con), network-browsable html file.
  • ..\1411\STACST\  - legacy station cast description file still generated by CESL but replaced by YYMMcasts.csv (ie 1411casts.csv) in the CSV subdir.
  • ..\1411\UWAY\  - developmental dir for underway data; MET data currently are logged in the events subdir
  • ..\1411\WEATHER\ - legacy weather file location, still generated but replaced by YYMMcasts.csv (ie 1411casts.csv) in the CSV subdir.

Seasoft Troubleshooting

• Seasoft uses a series of display files which should be pre-set from previous cruises. If starting from scratch, get a head start by copying the configuration (.psa) & display files (.dsa) from the backup dir (Q:\Software\SeaBird\SeasaveV7CastSettings\)
• Temperature, Conductivity-Salinity, & Oxygen pairs should agree pretty closely if recent calibration coefficients are entered properly. These coefficients can be imported digitally so key-entry mistakes should not be an issue. If you see significant disagreement between sensor pairs, check the correctness of the sensor configuration - are the sensor serial #s on the correct port?  The primary & secondary T, C or O2 may be switched. To correct a problem, change the calibration coefficients appropriately. If there is a hardware problem, replace the suspect sensor with the backup & update the coefficients.
• CTDBlade1 is our primary Windows7 data acquistion system.
  • Attach the deck unit 'signal data' serial cable to the primary com port;
  • Attach the deck unit 'modem cable' to the usb2serial adapter connected to the front panel usb.
  • GPS with GLL string is connected to the deck unit GPS port; a serial to two-pin Seabird cable will facilitate this connection.
  • Attach the Surface Par, if available, to the deck unit Surface Par port;
  • Attach the Remote Depth readout box to the deck unit port and run the cable to the winch control console area. The remote depth readout box is not backlit so frontal lighting is necessary to view the numbers at night.
• CTDBlade2 is our backup WindowsXP data acquisition system. Settings from CTDBlade1 should be copied so immediate switching over is easily accomplished after deck unit cabling is moved from on blade to the other.
• A backup deck unit is available if the primary deck unit fails. Please note the backup is version 1 without support for the remote depth readout box or secondary conductivity alignctd offset. All other ports are functional.

CTD Troubleshooting

• If sensor issues are discovered by monitoring the sensor data during the 2 minute soak, bring the CTD back on board and replace the problem sensor. If time is tight, this may be done after the cast if a redundant sensor (T, C, or O2) is working properly.
• Mistrips - if a carousel trigger is not allowing a bottle to close, check the trigger is able to travel freely, friction-free. Clean the trigger with a Q-tip and ethanol. Be sure a freshwater rinse hose is operational/available & that all CTD operators are rinsing the carousel after each cast. If the trigger continues to mistrip, replace the trigger from the spare trigger inventory.
• Venting the ISUS battery - as the ISUS battery charges, hydrogen gas can build up in the battery casing. Be sure to vent the battery before the cast particularly if charging for more than 2 hours and in the sun. Use a Kim-wipe to remove any water on or near the vent before opening so moisture does not leak into the battery case.
• If a bottle valve is leaking, cracked, or hard-to-open - replace it. Note that hard-to-open valves may just be overtightened - back it off a few turns and test the looseness. This may unstick a sticky valve, if not replace with a valve from the spare valve inventory.

CTDBackup Troubleshooting - instructions for settings & operation

• CTDBackup.cfg is located in C:\ctdbackup\ subdir. Be sure the drive paths and backup locations settings are correct and available. See the CTDBackup program instructions for more details.
• The ctdbackup desktop icon should be shortcut-key mapped to <CTRL><ALT>B. This may be checked or accomplished by right-clicking the ctdbackup icon, selecting properties then selecting the shortcut key field and pressing <CTRL><ALT>B simultaneously then Apply. If shortcut-key does not work, double-click the desktop icon to perform the backup. A CESL electronic sample log base file will be built from the CTDATDepth.csv event file, and the CTD .hdr & .mrk files.

CESL Troubleshooting - instructions for settings & operation

• CESL.cfg is located in the C:\CESL\ dir - start CESL and select File/Edit CESL.cfg to check and edit settings. Filepaths are set here so be sure \\Seaserv2\Data is mapped & available (usually as Q:) and the O2 PC box file dir is mapped & available (usually as O:\).
• Printer connectivity is also important - if unavailable over the network then configure the default printer as PDF or install one locally.
• CESL expects a base sample file to be available but if unavailable CESL will try to use the .hdr, .nav, .mrk files instead. If those are also unavailable, CESL has a Create Log option where the sample log may be filled out interactively. Enter the order occupied, max depth (ie 515), number of bottles - note clicking the Extra 10m bottle will auto-increment the bottle count by 1, select the Type (I, II, or III) & Include Stnd Depths if you want the typical bottle depths to be pre-entered (ie Type I - 515, 440, 370...). Uncheck the Include Stnd Depths for prodo casts or try it and see how it works. If pre-filling depths does not work properly, select Create Log again and start over. Key-entry of CTD depths, CTD T & S may be done manually but I recommend importing the CTD asc data when available.
• CESL generates sample form printout, salt base file, O2 box file, sta.csv & casts.csv, chl base file & filter form.

CELogGPS Troubleshooting - instructions for settings & operation

• CELogGPS requires GPS input either directly via a GPS device or from the currpos.csv file located in the Events subdir on the network drive. The source of the currpos.csv file can be a GPS or MET string created by the METcapture program on SIO vessels.
• If the GPS time & position is not updating, check the USB GPS connectivity or restart the METcapture program.
• All screen settings, options & activities listed are configured using txt files in the C:\CELogGPS subdir; txt filenames are defined in C:\CELogGPS\CELogGPS.cfg file.

PSAL Troubleshooting - instructions for settings & operation

• PSal.cfg is located in C:\PSAL\ dir - start PSAL and select Edit PSAL.cfg from the menu to check and edit settings. Standard values, data & file paths are set here so be sure \\Seaserv2\Data\ is mapped and available (usually Q:).
• CESL generates salt base files (ie salt001, salt002...) which typically are located on Q: (ie Q:\CODES\2014\1401\Salt\).
• A dedicated printer is usually attached directly to the PSal computer. Printing to a network printer is not advised so change the default printer to PDF if necessary. A salt###.prn file will be generated for each session and may be printed later.
• Typical problems with PSal are serial port related - be sure the Portasal is connected directly to the PC com port (com 1). A null modem is not needed so use a standard 25 - 9 pin serial cable. The com connection light will not appear green unless the [START] button is clicked in the program. If the PC and Portasal handshake properly the red "light" will turn green.
• PSAL supports serial air temperature input via an usb2serial adapter. If this fails even though the thermomter is connected and turned on, check the com port setting in Windows Device Manager. Set the com port to 2 or edit the psal.cfg to the assigned number. If the air-temperature auto-logging is problematic, key-enter the air temperature manually.

Oxygen Troubleshooting

• The Oxygen Autotitrator and software are an ODF-developed package and problems should be solved by reading its documentation.
• Missing box files or sample numbers may be corrected by re-loading a station into CESL, correcting the problem then resaving the box file using the File/Save O2 Box File Only option.
• Auto-titrator data files must be copied to the dataserver Q:\CODES\2014\1401\O2\ directory manually or by using filesync or zTree.

Nutrient Troubleshooting

• The nutrient autoanalyzer and software are a Seal developed package and troubleshooting recommendations related to sample analysis should come from Seal documentation.
• DECODR will recognize individual stations in the same file (run together) by labling a 'blank cup' run between station samples as sta### (ie sta001, sta002) in the autotitrator .txt file.