Add dvc pipelines #14

radistoubalidis · 2022-07-01T14:18:26Z

Signed-off-by: radis toubalidis rtoumpalidis@gmail.com

Description

The goal of this PR is :

create a dvc pipeline containing the stages as described in Standalone_GCBM\readme.txt
establish an action that when someone pushes a new run from a new branch is uses dvc to publish differences between the post-processing plots or other parameters.

Type of change

Please delete options that are not relevant.

New feature (non-breaking change which adds functionality)
This change requires a documentation update

How Has This Been Tested?

Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration

Additional Context (Please include any Screenshots/gifs if relevant)

Current stages:

tiler                       Outputs ..\..\logs\tiler_log.txt
recliner2gcbm_x64           Outputs logs\recliner_log.txt
add_species_vol_to_bio      Outputs logs\add_species_vol_to_bio.log
modify_root_parameters      Outputs logs\modify_root_parameters.log
modify_decay_parameters     Outputs logs\modify_decay_parameters.log
modify_turnover_parameters  Outputs logs\modify_turnover_parameters.log
modify_spinup_parameters    Outputs logs\modify_spinup_parameters.log
update_GCBM_configuration   Outputs ..\logs\update_gcbm_config.log
run_gcbm                    Outputs ..\logs\Moja_Debug.log
create_tiffs                Outputs ..\..\logs\create_tiffs.log, ..\..\processed_output\spatial
compile_results             Outputs ..\..\logs\compile_results.log
post_processing             Reports metrics\1900-1950_Deadwood_Tropical_Dry.json, metrics\1900-1950_Deadwoo…

DVC creates these files:

.dvc
dvc.lock --> it captures hashes of the dependencies (usually md5s)
dvc.yml --> which contains the stages of the pipeline

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

…ifeZone Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

aornugent · 2022-07-02T00:42:01Z

.dvc/config

@@ -0,0 +1,6 @@
+[core]
+    remote = processed_output
+['remote "gcbm_belize_logs"']


Can we add a comment alerting users to configure this to their own storage?

aornugent · 2022-07-02T00:44:53Z

Postprocessing/Tables/Pools_DOM_Sensitivity_forest_0_years.csv

-1900,Total Biomass,Tropical Dry,0.0014951294179772342
-1900,Total Biomass,Tropical Moist,6.140465519536419
-1900,Total Biomass,Tropical Premontane Wet,6.079037757144233
+1900,Deadwood,Tropical Dry,


@radistoubalidis - do you know why these tables have changed?

Don't know I'll look it up.

aornugent · 2022-07-02T00:48:15Z

Postprocessing/metrics/Deadwood.json

@@ -0,0 +1 @@
+{"Deadwood, Tropical Dry": {"pool_tc_sum_MEAN": "15624317.95", "area_sum_MEAN": "1142790.38", "pool_tc_per_ha_MEAN": "13.67"}, "Deadwood, Tropical Moist": {"pool_tc_sum_MEAN": "15802289.91", "area_sum_MEAN": "608498.41", "pool_tc_per_ha_MEAN": "25.97"}, "Deadwood, Tropical Premontane Wet": {"pool_tc_sum_MEAN": "13011268.76", "area_sum_MEAN": "417245.77", "pool_tc_per_ha_MEAN": "31.18"}}


This is cool. Does it refer to the mean over the lifetime of the simulation? Alternative/additional summary statistics might be start, mid- and endpoints. (e.g 1900, 1950, 2000) or decadal timestamps.

I wrote a simple script that calculates the mean value of for each indicator for each LifeZone so we can use it for dvc metrics. But I didn't use it yet cause there were some inconcistencies.

This is cool. Does it refer to the mean over the lifetime of the simulation? Alternative/additional summary statistics might be start, mid- and endpoints. (e.g 1900, 1950, 2000) or decadal timestamps.

Update : in b1fa0de I modified analyze.py to create a json metric file for start,mid and end endpoints .

aornugent · 2022-07-02T00:49:49Z

Standalone_GCBM/tools/CompileGCBMSpatialOutput/create_tiffs.bat


 REM Set Python path - change this to your Python installation directory.
-set GCBM_PYTHON=C:\Python37
+set GCBM_PYTHON=C:\Develop\Python\Python37


Can you use an environmental variable for this?

I refactored all the python paths in bat files in 5296555

aornugent · 2022-07-02T00:51:20Z

dvc.yaml

@@ -0,0 +1,116 @@
+stages:
+  tiler:
+    cmd: C:\Develop\Python\Python37\python.exe ..\..\tools\Tiler\tiler.py


If you add python to PATH this could be cmd: python ..\..\tools\Tiler\tiler.py

For some reason, even though I added python37 to my PATH this stage fails when I try to run it with python instead of the whole path. But I 'll note it on the pipeline readme

Update :
In 237d2a5 I added a vars list in dvc.yml where the local python path is included so it can be used as a var in the stages

aornugent

This looks awesome, well done @radistoubalidis! The only thing missing is a README update to describe the new pipeline and steps to reproduce.

I'm not quite sure why the sensitivity figures have changed. It suggests that you're getting different results somehow. Or, alternatively, the problem could be that the post-processing pipeline is missing a grouping variable - this can sometimes cause the sawtooth pattern you see in the new figures. I'll double check the R code and get back to you.

radistoubalidis · 2022-07-02T13:08:16Z

This looks awesome, well done @radistoubalidis! The only thing missing is a README update to describe the new pipeline and steps to reproduce.

I'm not quite sure why the sensitivity figures have changed. It suggests that you're getting different results somehow. Or, alternatively, the problem could be that the post-processing pipeline is missing a grouping variable - this can sometimes cause the sawtooth pattern you see in the new figures. I'll double check the R code and get back to you.

I noticed it too about the figures, they're not the same with HEAD , I'll try to modify the pipeline so the outputs come out the same as in HEAD

UPDATE :
I have not verified that this is the reason why sensitivity figures have changed but ,I noticed that in run_all.bat the simulation start/end are different than the step by step workflow (e.g. in update_gcbm_configuration.bat they are [2010,2020] and in run_all.bat they are [1900,2050]

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

…t to post_processing metrics in dvc Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

radistoubalidis · 2022-07-05T13:02:04Z

@aornugent the changes after your review (updated):

In cb38bcd completed Notebook for ArchieIndex db
In 7944bde Completed dvc pipeline readme
In 237d2a5 created a var in dvc.yaml for the python path (in pipeline readme it explains how to modify to your to local path)
In b1fa0de I added metrics in the post_processing stage ([1900-1950], [1951-2000], [2001-2050])
In 5296555 I refactored all the python paths in .bat files same to master
In 3657937 I updated analyze.py to create a metrics json file for each period for each indicator for each lifezone . So we have :
- 3 periods 1900-1950, 1951-2000, 2001-2050
- 4 indicator types Deadwood, Litter, Soil Carbon, Total Biomass
- 3 Lifezones Tropical Dry, Tropical Moist, Tropical Premontane Wet
In total 36 metrics json files with dvc metrics show output:

Path                                                          area_sum_mean    pool_tc_per_ha_mean    pool_tc_sum_mean
metrics\1900-1950_Deadwood_Tropical_Dry.json                  1142790.3823     8.46574                9674571.56838   
metrics\1900-1950_Deadwood_Tropical_Moist.json                608498.40961     19.67003               11969184.86104  
metrics\1900-1950_Deadwood_Tropical_Premontane_Wet.json       417245.76511     23.20835               9683586.49465   
metrics\1900-1950_Litter_Tropical_Dry.json                    1142790.3823     7.63421                8724307.19108   
metrics\1900-1950_Litter_Tropical_Moist.json                  608498.40961     15.89514               9672169.16877   
metrics\1900-1950_Litter_Tropical_Premontane_Wet.json         417245.76511     19.54048               8153183.07648   
metrics\1900-1950_Soil Carbon_Tropical_Dry.json               1142790.3823     18.18886               20786056.03202  
metrics\1900-1950_Soil Carbon_Tropical_Moist.json             608498.40961     69.2994                42168571.67542  
metrics\1900-1950_Soil Carbon_Tropical_Premontane_Wet.json    417245.76511     73.05651               30482518.25375  
metrics\1900-1950_Total Biomass_Tropical_Dry.json             1142790.3823     73.47453               83965986.06718  
metrics\1900-1950_Total Biomass_Tropical_Moist.json           608498.40961     128.64026              78277394.92039  
metrics\1900-1950_Total Biomass_Tropical_Premontane_Wet.json  417245.76511     131.66177              54935317.14342  
metrics\1951-2000_Deadwood_Tropical_Dry.json                  1142790.3823     15.45497               17661793.48354  
metrics\1951-2000_Deadwood_Tropical_Moist.json                608498.40961     26.51319               16133235.92611  
metrics\1951-2000_Deadwood_Tropical_Premontane_Wet.json       417245.76511     32.0702                13381156.01564  
metrics\1951-2000_Litter_Tropical_Dry.json                    1142790.3823     15.90142               18171994.72645  
metrics\1951-2000_Litter_Tropical_Moist.json                  608498.40961     27.23009               16569467.89581  
metrics\1951-2000_Litter_Tropical_Premontane_Wet.json         417245.76511     35.09762               14644334.00538
metrics\1951-2000_Soil Carbon_Tropical_Dry.json               1142790.3823     26.80044               30627284.39216
metrics\1951-2000_Soil Carbon_Tropical_Moist.json             608498.40961     76.61108               46617719.93404
metrics\1951-2000_Soil Carbon_Tropical_Premontane_Wet.json    417245.76511     81.71437               34094976.88782
metrics\1951-2000_Total Biomass_Tropical_Dry.json             1142790.3823     114.36661              130697056.55196
metrics\1951-2000_Total Biomass_Tropical_Moist.json           608498.40961     197.02668              119890421.62813
metrics\1951-2000_Total Biomass_Tropical_Premontane_Wet.json  417245.76511     207.90839              86748893.20024
metrics\2001-2050_Deadwood_Tropical_Dry.json                  1142790.3823     15.90271               18173464.67515
metrics\2001-2050_Deadwood_Tropical_Moist.json                608498.40961     29.2953                17826146.29171
metrics\2001-2050_Deadwood_Tropical_Premontane_Wet.json       417245.76511     36.33499               15160622.39384
metrics\2001-2050_Litter_Tropical_Dry.json                    1142790.3823     16.55106               18914397.27665
metrics\2001-2050_Litter_Tropical_Moist.json                  608498.40961     30.41606               18508123.58862
metrics\2001-2050_Litter_Tropical_Premontane_Wet.json         417245.76511     40.59053               16936228.41531
metrics\2001-2050_Soil Carbon_Tropical_Dry.json               1142790.3823     35.42651               40485069.6378
metrics\2001-2050_Soil Carbon_Tropical_Moist.json             608498.40961     86.52913               52652839.85377
metrics\2001-2050_Soil Carbon_Tropical_Premontane_Wet.json    417245.76511     94.05828               39245418.40241
metrics\2001-2050_Total Biomass_Tropical_Dry.json             1142790.3823     114.65017              131021114.07375
metrics\2001-2050_Total Biomass_Tropical_Moist.json           608498.40961     208.71101              127000315.77753
metrics\2001-2050_Total Biomass_Tropical_Premontane_Wet.json  417245.76511     223.22683              93140448.19134

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

radistoubalidis · 2022-07-12T13:41:40Z

Output of dvc metrics show

Path                                                                         area_sum_mean    pool_tc_per_ha_mean    pool_tc_sum_mean
Postprocessing\metrics\1900-1950_Deadwood_Tropical_Dry.json                  1142790.3823     9.02374                10312240.27057
Postprocessing\metrics\1900-1950_Deadwood_Tropical_Moist.json                608498.40961     21.44724               13050609.96778
Postprocessing\metrics\1900-1950_Deadwood_Tropical_Premontane_Wet.json       417245.76511     24.6368                10279599.85621
Postprocessing\metrics\1900-1950_Litter_Tropical_Dry.json                    1142790.3823     7.51629                8589542.73961
Postprocessing\metrics\1900-1950_Litter_Tropical_Moist.json                  608498.40961     15.67057               9535513.88722
Postprocessing\metrics\1900-1950_Litter_Tropical_Premontane_Wet.json         417245.76511     19.05744               7951634.95976
Postprocessing\metrics\1900-1950_Soil Carbon_Tropical_Dry.json               1142790.3823     18.27207               20881145.04849
Postprocessing\metrics\1900-1950_Soil Carbon_Tropical_Moist.json             608498.40961     69.44361               42256326.8329
Postprocessing\metrics\1900-1950_Soil Carbon_Tropical_Premontane_Wet.json    417245.76511     73.32265               30593565.30046
Postprocessing\metrics\1900-1950_Total Biomass_Tropical_Dry.json             1142790.3823     73.47453               83965986.06718
Postprocessing\metrics\1900-1950_Total Biomass_Tropical_Moist.json           608498.40961     128.64026              78277394.92039
Postprocessing\metrics\1900-1950_Total Biomass_Tropical_Premontane_Wet.json  417245.76511     131.66177              54935317.14342
Postprocessing\metrics\1951-2000_Deadwood_Tropical_Dry.json                  1142790.3823     16.68079               19062652.0933
Postprocessing\metrics\1951-2000_Deadwood_Tropical_Moist.json                608498.40961     28.58334               17392918.97526
Postprocessing\metrics\1951-2000_Deadwood_Tropical_Premontane_Wet.json       417245.76511     33.75245               14083067.18984
Postprocessing\metrics\1951-2000_Litter_Tropical_Dry.json                    1142790.3823     15.67846               17917198.28353
Postprocessing\metrics\1951-2000_Litter_Tropical_Moist.json                  608498.40961     26.8251                16323028.91383
Postprocessing\metrics\1951-2000_Litter_Tropical_Premontane_Wet.json         417245.76511     34.24219               14287409.81653
Postprocessing\metrics\1951-2000_Soil Carbon_Tropical_Dry.json               1142790.3823     26.90024               30741339.14617
Postprocessing\metrics\1951-2000_Soil Carbon_Tropical_Moist.json             608498.40961     76.80424               46735260.33606
Postprocessing\metrics\1951-2000_Soil Carbon_Tropical_Premontane_Wet.json    417245.76511     82.09022               34251795.1364
Postprocessing\metrics\1951-2000_Total Biomass_Tropical_Dry.json             1142790.3823     114.36661              130697056.55196
Postprocessing\metrics\1951-2000_Total Biomass_Tropical_Moist.json           608498.40961     197.02668              119890421.62813
Postprocessing\metrics\1951-2000_Total Biomass_Tropical_Premontane_Wet.json  417245.76511     207.90839              86748893.20024
Postprocessing\metrics\2001-2050_Deadwood_Tropical_Dry.json                  1142790.3823     16.23329               18551242.10796
Postprocessing\metrics\2001-2050_Deadwood_Tropical_Moist.json                608498.40961     31.16315               18962725.98408
Postprocessing\metrics\2001-2050_Deadwood_Tropical_Premontane_Wet.json       417245.76511     37.4451                15623808.56073
Postprocessing\metrics\2001-2050_Litter_Tropical_Dry.json                    1142790.3823     14.93973               17072980.27577
Postprocessing\metrics\2001-2050_Litter_Tropical_Moist.json                  608498.40961     27.97692               17023913.2908
Postprocessing\metrics\2001-2050_Litter_Tropical_Premontane_Wet.json         417245.76511     36.8938                15393783.85856
Postprocessing\metrics\2001-2050_Soil Carbon_Tropical_Dry.json               1142790.3823     33.60477               38403209.25278
Postprocessing\metrics\2001-2050_Soil Carbon_Tropical_Moist.json             608498.40961     84.92637               51677560.85901
Postprocessing\metrics\2001-2050_Soil Carbon_Tropical_Premontane_Wet.json    417245.76511     92.26118               38495586.80793
Postprocessing\metrics\2001-2050_Total Biomass_Tropical_Dry.json             1142790.3823     104.68105              119628496.69294
Postprocessing\metrics\2001-2050_Total Biomass_Tropical_Moist.json           608498.40961     194.4306               118310712.98961
Postprocessing\metrics\2001-2050_Total Biomass_Tropical_Premontane_Wet.json  417245.76511     207.51839              86586169.15699

…e order Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

radistoubalidis · 2022-07-14T17:43:34Z

In fd9b236
I updated add_species_vol_to_bio.py and the modify_<type>_parameters.py scripts to store logging messages in a file in /log directory.

This is needed because dvc as a default does not define an order in the pipeline stages , it does it only if for each i-th stage with output x its next one i+1-th has x as a dependency.By creating a log file for each stage we achieve pipeline execution in order.

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

aornugent · 2023-03-11T00:04:36Z

@radistoubalidis or @aldeav - can we please update this branch to develop? @aldeav has fixed a bug in the postprocessing code to remedy the saw-tooth lines in the output figures.

radistoubalidis added 25 commits June 22, 2022 14:51

Added dvc to repo and tiler stage

2ab395d

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

Added untracked files

fd95c6e

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

add reclner2gcbm stage

c6dd4c9

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

added add_species_vol_to_bio stage

c032a07

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

added modify_root_parameters stage

bab3896

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

added modify_turnover_parameters stage

6537a28

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

added modify_decay_parameters stage

1015897

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

added modify_spinup_parameters stage

7758687

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

added update_GCBM_configuratrion stage

5929812

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

added run_gcbm stage

351cd31

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

added create_tiffs and compile_results stages

4bbfe3c

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

stop tracking Standalone_GCBM\logs\tiler_log.txt

bdadf23

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

stop tracking Standalone_GCBM\logs\create_tiffs.log

da83da7

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

stop tracking Standalone_GCBM\logs\update_gcbm_config.log

c53ef52

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

stop tracking Standalone_GCBM\logs\Moja_Debug.log

0ec2f53

added dvc repo on gdrive to track log files

807c70d

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

stoped tracking processed_output/spatial

adc8f34

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

added spatial output to remote storage

4b24f60

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

updates dependencies in compile_results,run_gcbm stages

d030f2d

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

updates dependencies in multiple stages

9ddf387

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

adds post_processing stage in pipeline

5ff3db1

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

updates deps in post_processing stage

6dc2a69

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

updates multiple stages dependencies

e2aa8f4

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

adds script that calculates mean values for each indicator for each L…

d2a83d6

…ifeZone Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

updates json format of metrics

2195c6d

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

aornugent reviewed Jul 2, 2022

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radistoubalidis added 11 commits July 4, 2022 11:31

adds overview for ArchiveIndex_Beta_Install.mdb

1a782cb

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

updates overview.ipynb

f6a9087

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

adds dvc pipeline readme

ef35803

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

updates dvcpipeline readme

87ed4ee

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

updates dvc pipeline readme

e866830

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

updates dvc pipeline readme

3ad7d94

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

adds export to csv option in query

cb38bcd

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

declares and uses python path as var in dvc.yml

237d2a5

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

updates pipeline readme

7944bde

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

updates analyze.py to calculate metrics for every 50 years and adds i…

b1fa0de

…t to post_processing metrics in dvc Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

refactor python paths in bat files back to original

5296555

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

radistoubalidis requested a review from aornugent July 5, 2022 13:03

radistoubalidis added 3 commits July 7, 2022 14:46

modifies analyze.py to update metrics in post_processing stage

6c11636

Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

casts json values as floats so dvc can recognize them

3657937

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implemented clean run

7775c63

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radistoubalidis force-pushed the add_dvc_pipelines branch from a7aa8e3 to 7775c63 Compare July 12, 2022 13:38

sets logging to write in file on modify scripts for dvc pipeline stag…

fd9b236

…e order Signed-off-by: radis toubalidis <rtoumpalidis@gmail.com>

update pipeline.md to current changes

347aec5

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radistoubalidis mentioned this pull request Aug 1, 2022

Establish pipeline moja-global/GCBM.Colombia#8

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aornugent commented Mar 11, 2023

		@@ -0,0 +1 @@
		{"Deadwood, Tropical Dry": {"pool_tc_sum_MEAN": "15624317.95", "area_sum_MEAN": "1142790.38", "pool_tc_per_ha_MEAN": "13.67"}, "Deadwood, Tropical Moist": {"pool_tc_sum_MEAN": "15802289.91", "area_sum_MEAN": "608498.41", "pool_tc_per_ha_MEAN": "25.97"}, "Deadwood, Tropical Premontane Wet": {"pool_tc_sum_MEAN": "13011268.76", "area_sum_MEAN": "417245.77", "pool_tc_per_ha_MEAN": "31.18"}}

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radistoubalidis commented Jul 1, 2022 • edited

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radistoubalidis Jul 4, 2022 • edited

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radistoubalidis commented Jul 2, 2022 • edited

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