Script to Export river h5s

[rburghol]

Note: This has been updated to a generic script: export_hsp_h5.R

• Objectives/Steps:
  • Renaming "alias" for Qout
  • Renaming "alias" for wd_mgd
  • Renaming "alias" for ps_mgd
  • Name: hsp_hydr.R
    • Use: hsp_hydr.R [river_segment_name] [scenario_name] [hydr_file_path]
    • Ex: Rscript HARParchive/HARP-2022-Summer/AutomatedScripts/hsp_hydr.R OR1_7700_7980 hsp2_2022 /media/model/p532/out/river/hsp2_2022
• Try to re-use as much as possible from the Land model Post-Processing Work Flow (each step is 1 separate script/function) #261
  • Single command line to output?
• See Data Dictionary #237 for details on h5 internal data path and columns
• h5 output File path (to harvest data):
  • Use: /media/model/[model_version]/out/river/[scenario]/h5/
  • Aka: $CBP_EXPORT_DIR/river/[scenario]/h5/
  • Ex: /media/model/p532/out/river/hsp2_2022/h5/
  • This has been coded into the hspf model run routines to move to this data location (see also: Add switch to use hsp2 executable cbp_wsm#64)
• Create an R script to add a run record to VAHydro via rest.
  • Need to send the output_file_path to VAHydro
• Analysis:
  • Base it on this: https://github.com/HARPgroup/om/blob/master/R/summarize/waterSupplyModelNode.R
  • For starters, Qout, wd_mgd (withdrawal), ps_mgd (point source) related analyses only.
    • We'll need you to find the variable names used in HSPF for wd_mgd and ps_mgd. See the hspf manual and the sample uci to
• Development notes:
  • Need to replicate behavior of fn_get_runfile() to grab water-year specific data if needed from these hsp2 CSV output files that we generated.
    • Need to clone om repo to to see fn_get_runfile code
  • The old functions uses vahydro_post_metric_to_scenprop(), which uses the REST data source to create properties, similar to the way you coded properties in the land segment analysis. vahydro_post_metric_to_scenprop() might be useful since it is very concise.

[juliabruneau]

Suggestions From HSPF Manual:

I'm most unsure about ps_mgd . The IVOL variable is the only one in the HYDR table that has anything to do with water entering the river segment.

These are also in the HYDR/table:

O1 - zeros
O2 - zeros
O3 - values (Rates of outflow from individual exits)

• O1+O2+O3 = RO
• Values in RO = Values in O3

OVOL1 - zeros
OVOL2 - zeros
OVOL3 - values (Volume of outflow from individual exits)

• OVOL1+OVOL2+OVOL3 = ROVOL
• Values in ROVOL = Values in OVOL3

[juliabruneau]

Data Harvesting Script for River Segments

Separate harvesting script created for river segments: batch_harvest_river.bat

Use: /opt/model/p53/p532c-sova$ bash ~/HARParchive/HARP-2022-Summer/AutomatedScripts/batch_harvest_river.bat hsp2_2022 OR1_7700_7980

H5 file path = $CBP_EXPORT_DIR/river/$scenario_name/h5/$basin'.h5'
Output file path = $CBP_EXPORT_DIR/river/$scenario_name/hydr/$basin

Ex:

juliasb@deq2:/opt/model/p53/p532c-sova$ bash ~/HARParchive/HARP-2022-Summer/AutomatedScripts/batch_harvest_river.bat hsp2_2022 OR1_7700_7980
Loading /opt/model/p53/p532c-sova/hspf.config
CBP_ROOT: /opt/model/p53/p532c-sova
CBP_EXPORT_DIR: /media/model/p532/out
Warning message:
In H5Dread(did, bit64conversion = "double") :
  integer precision lost while converting 64-bit integer from HDF5 to double in R.
Choose bit64conversion='bit64' to avoid data loss and see the vignette 'rhdf5' for more details about 64-bit integers.
hydr csv created

Found in:

juliasb@deq2:/media/model/p532/out/river/hsp2_2022/hydr$ ls
OR1_7700_7980_hydr.csv

[rburghol]

@juliabruneau can you paste a sample of the first few lines of the output CSV file into the issue main body, so we can see the columns available and sample data? The head command is useful for that, so, something like: head /media/model/p532/out/river/hsp2_2022/hydr/OR1_7700_7980_hydr.csv should spit out the top 5-10 lines (FYI: tail does just the opposite, showing the last few lines of a file)

Also, I think:

• ROVOL is definitely NOT wd_mgd, it is Qout as in the outflow from the river channel. wd_mgd is the withdrawal.
• IVOL similarly, is the sum of all inflows to the river channel, point source discharges will be a single component of this, but not the entirety as upstream inflow, and runoff/baseflow/interflow will also be part of this.
• wd_mgd (withdrawals) will be DIVR or OUTDGT or something? Can we link to the data dictionary so we see the options in the HYDR table?
• ps_mgd is point source discharge, so, something that enters a stream from a wastewater discharge.
• In our sample UCI file, [OR1_7700_7980.uci(https://raw.githubusercontent.com/HARPgroup/HSPsquared/master/tests/test_cbp_river/OR1_7700_7980.uci):
  • the point source comes in as DSN 3000 -- can we find this data? We have some experience looking at things in the EXT SOURCES block of a uci, maybe it is stored in the h5 in the TIMESERIES or other? Refer to our earlier issues to find this. And then please document whatever you find in the issue body.
  • The withdrawal comes in as DSN 3007 and 3008 (DIVR and DIVA). Same as point source, it will be interesting to see if this gets imported to the h5 file.
• It may be that the OUTDGT or whatever it is is not contained in the HYDR table. In which case we need to search the h5 file for it, and if that proves unfruitful, we might have to hack the hsp2 code to make it so, which will be fun :)

[glenncampagna]

Findings about point source in river h5 file

• Since point source flow is DSN 3000 in the UCI, we checked the TS3000 table within the TIMESERIES group in OR1_7700_7980.h5, and found only values of 0. In fact, all timeseries tables in the 3000s are populated with only 0s, making us think if point sources are in the h5 file they are elsewhere, but we found no occurrence of DIVR, DIVA, or OUTDGT

[rburghol]

Ok, there but empty us good. One thing we'll need to do is insure that we have a segment that SHOULD have point sources, or withdrawals for that matter. I'll try to find one! For now, get the aliases in there and focus on batch script.

[glenncampagna]

Testing our R script which will perform analysis and send exports from hydr table to VAhydro

Script: hsp_hydr.R https://github.com/HARPgroup/HARParchive/blob/master/HARP-2022-Summer/AutomatedScripts/hsp_hydr.R

• When doing a test run with Rscript HARParchive/HARP-2022-Summer/AutomatedScripts/hsp_hydr.R OR1_7700_7980 hsp2_2022 /media/model/p532/out/river/hsp2_2022/hydr/OR1_7700_7980_hydr.csv we get the error:

[1] "REST AUTH INFO HAS BEEN SUPPLIED"
[1] "RETRIEVING REST TOKEN"
[1] "Login attempt successful"
[1] "token = KWZItnbXkT161Uk-dNzzSFsc5kxABzUU2NmjHrP_2ac"
Warning messages:
1: no DISPLAY variable so Tk is not available 
2: In system("timedatectl", intern = TRUE) :
  running command 'timedatectl' had status 1
Error in if (input == "" || length(grep("\\n|\\r", input))) { : 
  missing value where TRUE/FALSE needed
Calls: fread
Execution halted

It appears this happens before the hydr data table is created and any analysis performed. Any ideas/ suggestions? @rburghol

[rburghol]

Two thjngs:

• Is the file path correct?
• Run "R" from the command line (literally, type capital R and enter)
• paste in each command, except for the "argv" commands, where you should set the values to whatever you would have passed as arguments -- if you are stumped on this, talk to @juliabruneau who did this last week. A critical method of debugging.

Keep me posted!

[glenncampagna]

We have our hsp_hydr.R script working and theoretically sending constants and graphs soon to VAhydro, but aren't sure where to check on these because we don't see an existing river feature in VAHydro for OR1_7700_7980. This was why we'd thought to save the river segment originally @rburghol
We only see the features A51011_OR1...(HUC8) and A51037_OR1...(HUC8)

[rburghol]

Awesome work today. To find the River segment OR1_7700_7980, check with @megpritch and @nicoledarling as they just went through this process.

Since we have to wait to get the point source abd withdrawals sorted out, let's move forward on the flow analysis -- if you haven't already done that! The R script above, "waterSupplyModelNode.R" has many metrics that it calculates as a function of the Qout variable. If you can replicate all of those that would be excellent.

[glenncampagna]

We modified our hsp_hydr.R script to create a model run within OR1_7700_7980 - Club Creek. We had to change the type from vahydro to cbp532 to do this. Should we have called the feature with hydrocode vahydrosw_wshed_OR1_7700_7980 and the vahydro ftype instead?

We are in the process of incorporating the Qout metrics into our script and testing

[juliabruneau]

Update on hsp_hydr.R flow analysis:

Based on waterSupplyModelNode.R:

Exported Constants:
Mean Qout - Qout_mean
30-day Low Flow - l30_Qout
90-day Low Flow - l90_Qout
August Low Flow - alf
September 10th Percentile - sept_10
7-day Low Flow Over 10 Years - x7q10
Output File Path - /media/model/p532/out/river/hsp2_2022/hydr/[river_segment_name]_hydr.csv

• Successful export to VAHydro:
  

Planned Exported Plots:
Qout vs Time

Potential Exported Constants (after calculating wd/ps_cumulative):
Mean Withdrawals - wd_mgd
Mean Point Source - ps_mgd
net_consumption_mgd = wd_cumulative - ps_cumulative
Qbaseline = Qout + (ws_cumulative - ps_cumulative)
consumptive_use_frac = 1.0 - (Qout / Qbaseline)
daily_consumptive_use_fraction = mean(consumptive_use_frac)

• Still working on generating the water year time series for further use
• Is there anything else we should analyze? Especially with generating plots?

[glenncampagna]

We added a container for Qout in VAhydro for better organization:

Here is the figure of Qout we generated:

It might help us out to remove the existing scenario hsp2_2022 from this river seg because there are some duplicates from testing, then we can run and have everything in the right place and no duplicates
Link to scenario: http://deq1.bse.vt.edu/d.dh/om-model-info/6850637/dh_properties

[juliabruneau]

@rburghol
Should we export the updated constants and graph into the cbp532 or vahydro ftype?

• @juliabruneau These should definitely be on the vahydro ftype. Pop your code that you are using to do the query up here if you are still having a hard time with that. Did you all check with Nicole and Megan, as they just resolved a similar issue.

[glenncampagna]

Updated use for script to analyze river seg hydr files:

Script: hsp_hydr.R https://github.com/HARPgroup/HARParchive/blob/master/HARP-2022-Summer/AutomatedScripts/hsp_hydr.R
Use: Rscript hsp_hydr.R [river seg] [scenario name] [scenario folder path to locate hydr csv]
Example: Rscript HARParchive/HARP-2022-Summer/AutomatedScripts/hsp_hydr.R OR1_7700_7980 hsp2_2022 /media/model/p532/out/river/hsp2_2022

[rburghol]

@juliabruneau @glenncampagna
Couple things -- the adding of Qout aliases etc should be done separately from the analysis step, so can you:

• split that out into another script that 1) reads the file, 2) creates the aliases/unit conversion, and 3) saves the file.
• move the analysis to a totally separate script
• Change the unit conversion for cfs to MGD to 1.547, rather than 1.55, it's what we use everywhere else so we can be consistent.

The separate scripts ask is cause I'd like the Qout and other columns to always be there for any script to operate on, and thus we wont have to do multiple conversions if we access then with different analytical routines.

[juliabruneau]

@juliabruneau @glenncampagna Couple things -- the adding of Qout aliases etc should be done separately from the analysis step, so can you:

• split that out into another script that 1) reads the file, 2) creates the aliases/unit conversion, and 3) saves the file.
• move the analysis to a totally separate script
• Change the unit conversion for cfs to MGD to 1.547, rather than 1.55, it's what we use everywhere else so we can be consistent.

The separate scripts ask is cause I'd like the Qout and other columns to always be there for any script to operate on, and thus we wont have to do multiple conversions if we access then with different analytical routines.

Working on creating the two scripts - one for creating the aliases and one for the analysis.

Just to clarify @rburghol :

• Would you like to have everything in cfs, or have the PS and WS in mgd? The original script had them in mgd, but we are working with cfs in Qout.
  • Generally we do WD/PS in mgd, and flow in cfs. If it has units in the name, obviously do that (like wd_mgd, and ps_mgd). Some stuff will be oddball unis like cfs/sqmi (Runit variants).
• Would you also like me to rename the new file that gets created with something like "_hydr_cfs.csv" OR would you like the file to just contain the specific columns that got converted, for example: "_rovol_cfs.csv"?
  • No need to rename, just save over the original. And they all go in that one single file that way as well. It is just an extended set of outputs.

[juliabruneau]

Two Rscripts for River Segments:

Name: hsp_hydr_conversion.R
Use: Rscipt hsp_hydr_conversion.R [river seg] [scenario name] [scenario folder path to locate hydr csv]
Ex: Rscript HARParchive/HARP-2022-Summer/AutomatedScripts/hsp_hydr_conversion.R OR1_7700_7980 hsp2_2022 /media/model/p532/out/river/hsp2_2022
Output: CSV files with added column for wanted unit conversion (proof below - ROVOL_cfs at the end:)

  GNU nano 4.8                                                                                  OR1_7700_7980_hydr.csv
"index","DEP","IVOL","O1","O2","O3","OVOL1","OVOL2","OVOL3","PRSUPY","RO","ROVOL","SAREA","TAU","USTAR","VOL","VOLEV","date","week","month","year","ROVOL_cfs"
1984-01-01 01:00:00,0.24150724709034,8.84726428985596,0,0,2.05518269538879,0,0,0.122939802706242,0,2.05518269538879,0.122939802706242,67.4736633300781,0.0234425533562899,0

Name: hsp_hydr_analysis.R
Use: Rscipt hsp_hydr_analysis.R [river seg] [scenario name] [scenario folder path to locate hydr csv]
Ex: Rscript HARParchive/HARP-2022-Summer/AutomatedScripts/hsp_hydr_analysis.R OR1_7700_7980 hsp2_2022 /media/model/p532/out/river/hsp2_2022
Ouput: Constants and graphs into VAHydro

[rburghol]

Hey @glenncampagna @juliabruneau I am trying to run the summary script for river segments, but this is not working for Rockfish. I want to integrate these into the run_river.csh script, but will hold off until I can get this to work. I have pulled the HARP Archvie repository at 9:15 AM, so I think it is the most recent code.

Tried:

cd /opt/model/p53/p532c-sova
. hspf_config
Rscript $CBP_ROOT/run/export/hsp_hydr_analysis.R JL2_6850_6890 hsp2_2022 $CBP_EXPORT_DIR/river/hsp2_2022`

Help?

Integrated:

cp ../../HARParchive/HARP-2022-Summer/AutomatedScripts/hsp_hydr_analysis.R ./run/export/

[juliabruneau]

Hey @glenncampagna @juliabruneau I am trying to run the summary script for river segments, but this is not working for Rockfish. I want to integrate these into the run_river.csh script, but will hold off until I can get this to work. I have pulled the HARP Archvie repository at 9:15 AM, so I think it is the most recent code.

Tried:

cd /opt/model/p53/p532c-sova
. hspf_config
Rscript $CBP_ROOT/run/export/hsp_hydr_analysis.R JL2_6850_6890 hsp2_2022 $CBP_EXPORT_DIR/river/hsp2_2022`

Help?

Integrated:

cp ../../HARParchive/HARP-2022-Summer/AutomatedScripts/hsp_hydr_analysis.R ./run/export/

We ran the Rscript like you did, and found the error 'no rows to aggregate'. This is because we want to do our analysis script in cfs, and that means that we use the conversion script that generates Qout (cfs). The river seg didn't have the conversion script ran on it for some reason.

We ran the conversion on the hydr.csv now and that should fix the issue.

Note: the way the scripts are structured, the hydr conversion script should be run before the hydr analysis script is run

[rburghol]

Oh!

The river seg didn't have the conversion script ran on it for some reason.

That's cause I didn't include that in the run_river.csh work flow - thanks!