BOX - beginning of expedition
EOX - end of expedition
The outgoing programmer(s) is(are) responsible for all of the end-of-expedition (EOX) activities.
This expedition is ending.
Make sure we are getting as complete a The goal is to ensure a good copy of the data gets back to HQ.
Please read this entire document and its companion. Expect to take 3 to 4 hours to complete this exercise. (I keep saying this only takes 15 minutes. But that really is just the individual database dump processes.) Do not hurry. If you are "fried"--work together.
0. Readiness assessment.
to be warehoused on shore as we can.
This document does not recapitulate all items on the checklist. If an item is in need of elaboration, please add to it.
0. Negotiate a time window
Work with the LO, ALOs, EPM, MCS, laboratory Technical Staff. Three weeks before the end of the expedition you should have an (increasingly clear) idea how and when these activities will transpire.
- When will the last core be on deck?
- When will we be in port?
- When do we need to be done collecting data for a given laboratory
...
- Are we done collecting data for this laboratory area
- ?
- Has all the data content that you want to go home been:
- is required to be warehoused been stored?
uploaded to the database
copied to data1 OR
copied to the - uservol (workspace toward creation of EXPEDITION PROCEEDINGS volume
- )
- Are you aware of the varieties of data that have been collected?
A review of data1 is helpful
Though we presently do not fill this out, a data disposition spreadsheet/form is available in s:\data1 . - that exercises this concern.
?Where is the data? A data disposition
It is helpful to the data librarian to have that filled out
If nonot done, obtain estimates when the data collection will be done. Schedule accordingly.
1. Notify everyone. Database snapshot in progress.
- Notify jr_developer and the shipboard technical staff that the EOX database backup is in progress.
- The database is available for reports, but content cannot be changed while this activity is in progress.
2. Make the database read only.
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At the SQL> prompt, run the last command.
Stop. Leave this window open for use below.
Technical note. This command prevents write access to any table content that resides in the storage facility under the "labware" table space. In our database implementation, this happens to be all tables owned by the LIMS schema. Use of Drill Report ("ops" schema) is not affected. Aspects of DescLogik software configuration are also still open to maintenance, though use of DescLogik itself is locked out by this change.
3. Full snapshot as oracle@k1.
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NOTE: While performing the EOX for expedition 384, it was discovered that the path represented by "data_pump_dir" did not exist. You can discover what the data_pump_dir is supposed to be using this query (logged in as your DBA account):
select * from dba_directories;
The results have a lot of stuff that's not useful, but the DATA_PUMP_DIR should be there. Currently it is /backup/LIMSJR/dpdump. Note that "backup" is singular (it used to be plural) and there is apparently some desire to change this, so keep that in mind. If you find that the folder does not exist, the command in this step will fail and you may need to get an MCS or a DBA on shore to help create it.
You can also try:
create directory data_pump_dir as '/backup/export';
grant read, write on directory data_pump_dir to transfer, system;
10/5/2021: Folder did not exist, as above, but MCS suggested I try creating it myself (in Putty, logged in as Oracle) using mkdir commands. That initially seemed to work, but it broke some kind of symbolic or virtual link that caused the file to be written to the wrong physical location (with reduced disk space), so not recommended.
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:
- routine core flow will be complete
- data is uploaded and copied to data1
- routine sampling will be complete
Pacing items are typically XRD (long powder prep times), MAD (24-hour oven drying time), SRM (typically last track run), some chemistry processes have lengthy sample prep and run procedures.
It is Ok to ask repeatedly. It is an exercise in planning and preparation which helps us collectively focus and prioritize the tasks to be done.
1. Deliver the EOX tech report
Deliver the end-of-expedition technical report to the (place in Confluence specified by the) LO.
Please post a PDF export of it to jrso-developer on Slack.
2. Establish when the final database snapshot will be taken
Recapitulation of 0. Continue talking to the LOs, ALOs, EPM, MCS, and laboratory Technical Staff to clarify this timing.
- It takes 20 minutes to run a full database export (for 61 GiB of data)--but we want it to be as complete as possible within the constraints of expedition activities.
- The MCS routinely stage expedition content for convenience of copying via Science Office and User Room workstations. Timing of that activity is a common communication at the end of the expedition.
3. Spot check data copy efforts
Recapitulation of 0, 2. Be an additional set of eyes and ears.
What data didn’t get into the database? What remains to be staged on data1 or uservol?
As-needed, provide support to get data in or find an appropriate staging location for it.
- Spot check instrument host data folders. Are they getting over to data1?
- If technical staff are new--are they aware of the scope of concerns for getting data back home?
- If technical staff are old hands--learn about what they do and why.
Often there is both expedition-specific and individual variance. Much room for improvement in the current process.
4. Honor moratorium
Once content is uploaded to LIMS, and raw files have gone to data1, and routine backup cycles have occurred: expedition-specific data may (in-general) be cleaned off of instrument hosts and workstations.
These activities are the purview of laboratory technical staff. Often assistance is welcome.
There is precedent for this activity to be pushed to the (fresh) oncoming crew. Totally depending on timing of last core on deck and timing of arrival in port.
5. Conduct EOX database backup
Make the database read only
Run from PuTTY, Windows Terminal, Powershell, Hyperterminal.
You can run this step from SQL Developer too, but you'll need the command-line at the ODA for the data pump export command. If the oraenv script does not show LIMSJR1 as the default, contact the DBA (Sunil).
| Code Block |
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ssh oracle@k1.ship.iodp.tamu.edu
. oraenv
ORACLE_SID = [LIMSJR1] ? <Enter>
sql you_dba
sql>
alter tablespace labware read only;
exit
[oracle]$ |
Export the database content
| Code Block |
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cd /backup/export
ls -l
time expdp you_dba directory=dmpdir full=y logfile=limsjr_full-###-export.log dumpfile=limsjr_full-###.dmpdp |
Make the database read-write again
| Code Block |
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sql you_dba
Password:
sql>
alter tablespace labware read write;
exit
[oracle]$ |
Test the export file
Read the limsjr_full-###-export.log in k1:/backup/export.
- Are there any errors? No is good. If errors, find cause, maybe re-run.
- Review the number of samples for LIMS.SAMPLE, LIMS.TEST, LIMS.RESULT, OPS.RIS_DATA.
Log into the SHIPTEST instance. Run these commands to confirm ability to restore content from the file generated.
| Code Block |
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ssh oracle@k2.ship.iodp.tamu.edu
. oraenv
ORACLE_SID = [SHIPTEST] ? <Enter>
[oracle]$
time impdp you_shiptest_dba directory=dmpdir logfile=exp###-test-export.log dumpfile=limsjr_full-###.dmpdp tables=lims.sample,lims.test remap_schema=lims:transfer remap_table=lims.sample:xxx_sample,lims.test:xxx_test exclude=trigger table_exists_action=replace
time impdp you_shiptest_dba directory=dmpdir logfile=exp###-test-export.log dumpfile=limsjr_full-###.dmpdp schemas=geodp### remap_schema=geodp###:geodp###_review |
Use SQL Developer to review the content of the SHIPTEST TRANSFER.XXX_SAMPLE, XXX_TEST tables. Repeat for the restored GEODP###_REVIEW schema. Do not cleanup. Leave it for the oncoming crew to review.
Notify everyone that its done
Post the export log file on Slack jrso-developer. Note the size of the export file.
We will not zip it, nor send it over the wire. If needed to achieve earlier emplacement of content on shore, the person tagged with conducting the EOX Shore data processing will conduct those activities.
Email it to
- MCS - jr_mcs@ship.iodp.tamu.edu
- IT_OPS - it_ops@iodp.tamu.edu
- Data Librarian - database@iodp.tamu.edu
- programmers - programmers@iodp.tamu.edu
- DBAs - sunil@rajaconsultancy.com, murli@rajaconsultancy.com
In the email, note the size of the file and its location--if we're putting it in the right place, there's no need for the MCS to move it
4. Restore database read/write capability.
From the prompt [oracle@k1 ~]$
run these command, supply the appropriate credential
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Stop. Leave this window open for use below.
5. Compress the exports for transport. Cleanup.
From the prompt [oracle@k1 ~]$
run these commands
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Cut and paste the digest keys and file listing into a notification email. Enables remote users to verify the integrity of the files.
Please log these in a txt file in the \AD\support\'expedition named sub directory'\ see other expeditions for example.
Statistics. 367: 22 min to compress both files (~5 GiB to < 1 GiB); 345: 22 min 53 sec for bzip step. 351: full 137 min 46 for ~8 GiB content. 360: 67 min 27 sec for ~5 GiB file. 45-60 min for high recovery expeditions.
Exp 396: we had trouble initially because we ran out of disk space. This was apparently due to my creating the /backup/LIMSJR/dpdump folder under the Oracle account. This broke some kind of link-up that gives the backup folder lots of additional drive space. Don't do that.
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6. Notify everyone. Database snapshot process is complete.
Notify jr_developer and expedition technical staff that the process is done.
Speak with the MCS. They will pick up the data from here.
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The MCS pick up the full export from oemjr:/backup/export.
Inquire Enquire with the MCS. Ensure the (above) database content and the (below) ASMAN content are being taken to media for transport to HQ.
Take a copy of the export file
Login into the Oracle account at the ODA using WinSCP. Bring down a copy of the export file and its log to
- your laptop--or other transfer device; and
- stage a copy in \\novarupta\vol3\dml\oracle-data\
for future local reference OR until we have to clean/preen for space.
6. Provide courier services
The backup tapes created by the MCS return to HQ as soon as possible. If your travel itinerary supports that goal, let them know you can provide courier services.