Parmest update of util convert_params_to_vars. #3339

smartin71 · 2024-08-10T21:34:39Z

Fixes # .

Summary/Motivation:

This is step 1 of a set of internal changes to parmest related to issue:
#3252

Changes proposed in this PR:

Revamped util function convert_params_to_vars to avoid the use of parameter names as strings.
Now using component IDs both internally to the convert function and in the API.

Legal Acknowledgement

By contributing to this software project, I have read the contribution guide and agree to the following terms and conditions for my contribution:

I agree my contributions are submitted under the BSD license.
I represent I am authorized to make the contributions and grant the license. If my employer has rights to intellectual property that includes these contributions, I represent that I have received permission to make contributions and grant the required license on behalf of that employer.

pyomo/contrib/parmest/utils/model_utils.py

jsiirola

This looks pretty good, but there is a big performance bug that should be addressed.

jsiirola · 2024-08-15T14:45:35Z

pyomo/contrib/parmest/utils/model_utils.py

+            indexed_param_CUIDs += [
+                ComponentUID(theta_obj) for _, theta_obj in theta_object.items()
+            ]


It would be more clear / more efficient to use list's extend() and dict's values():

indexed_param_CUIDs.extend( ComponentUID(theta_obj) for theta_obj in theta_object.values() )

Changed as suggested.

jsiirola · 2024-08-15T14:47:15Z

pyomo/contrib/parmest/utils/model_utils.py

+            var_theta_objects = [
+                var_theta_obj for _, var_theta_obj in theta_var_object.items()
+            ]


If you are only using the values from a dict, it is more clear / more efficient to use values():

var_theta_objects = list(var_theta_obj.values())

Changed as suggested.

jsiirola · 2024-08-15T14:50:26Z

pyomo/contrib/parmest/utils/model_utils.py


    # Convert Params to Vars in Expressions
    for expr in model.component_data_objects(pyo.Expression):
        if expr.active and any(
-            v.name in param_names for v in identify_mutable_parameters(expr)
+            ComponentUID(v) in param_CUIDs for v in identify_mutable_parameters(expr)


This is very inefficient (quadratic in the number of params). If you are going to test membership, param_CUIDs needs to be a set / dict / mapping object (so that lookups are O(1) and not O(n)).

Converted list to set for the lookups at the end of the function.

codecov · 2024-08-16T15:37:03Z

Codecov Report

Attention: Patch coverage is 93.33333% with 1 line in your changes missing coverage. Please review.

Project coverage is 88.53%. Comparing base (7f779ab) to head (7ea02db).
Report is 158 commits behind head on main.

Files	Patch %	Lines
pyomo/contrib/parmest/utils/model_utils.py	90.90%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff            @@
##             main    #3339    +/-   ##
========================================
  Coverage   88.52%   88.53%            
========================================
  Files         868      868            
  Lines       98436    98771   +335     
========================================
+ Hits        87144    87450   +306     
- Misses      11292    11321    +29

Flag	Coverage Δ
linux	`86.05% <93.33%> (+0.01%)`	⬆️
osx	`75.63% <6.66%> (-0.03%)`	⬇️
other	`86.55% <93.33%> (+0.01%)`	⬆️
win	`83.86% <93.33%> (+0.02%)`	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

blnicho

I think this still needs some work. There are some bugs in this function when params to be converted to vars live on blocks. This PR didn't necessarily introduce the bugs but I think we should fix them while we're overhauling this function. Here is a small example demonstrating one of the bugs:

from pyomo.environ import *
from pyomo.contrib.parmest.utils import convert_params_to_vars

m = ConcreteModel()
m.p1 = Param(initialize=1, mutable=True)
m.b = Block()
m.b.p2 = Param(initialize=2, mutable=True)

param_cuids = [ComponentUID(m.p1), ComponentUID(m.b.p2)]
m2 = convert_params_to_vars(m, param_cuids)

this fails with an AttributeError:
AttributeError: 'ScalarParam' object has no attribute 'unfix'

blnicho · 2024-08-19T17:59:17Z

pyomo/contrib/parmest/parmest.py

@@ -440,8 +440,8 @@ def TotalCost_rule(model):
            )

        # Convert theta Params to Vars, and unfix theta Vars
-        theta_names = [k.name for k, v in model.unknown_parameters.items()]
-        parmest_model = utils.convert_params_to_vars(model, theta_names, fix_vars=False)
+        theta_CUIDs = [v for k, v in model.unknown_parameters.items()]


Suggested change

theta_CUIDs = [v for k, v in model.unknown_parameters.items()]

theta_CUIDs = list(model.unknown_parameters.values())

blnicho · 2024-08-19T18:19:16Z

pyomo/contrib/parmest/tests/test_utils.py

@@ -46,12 +50,12 @@ def test_convert_param_to_var(self):
        exp = ReactorDesignExperiment(data, 0)
        instance = exp.get_labeled_model()

-        theta_names = ['k1', 'k2', 'k3']
+        param_CUIDs = [v for k, v in instance.unknown_parameters.items()]


Suggested change

param_CUIDs = [v for k, v in instance.unknown_parameters.items()]

param_CUIDs = list(instance.unknown_parameters.values())

blnicho · 2024-08-19T18:33:24Z

pyomo/contrib/parmest/utils/model_utils.py


+            # get indexed Params
+            param_theta_objects = [theta_obj for _, theta_obj in theta_object.items()]


Suggested change

param_theta_objects = [theta_obj for _, theta_obj in theta_object.items()]

param_theta_objects = list(theta_object.values())

blnicho · 2024-08-19T18:45:03Z

pyomo/contrib/parmest/utils/model_utils.py

+        param_CUIDs = indexed_param_CUIDs
+
+    # convert to a set for look up efficiency
+    param_CUIDs_set = set(param_CUIDs)

    # Convert Params to Vars in Expressions
    for expr in model.component_data_objects(pyo.Expression):
        if expr.active and any(


Expression components are not "activatable" so this logic can be simplified to:

if any(ComponentUID(v) in param_CUIDs_set for v in identify_mutable_parameters(expr) ):

blnicho · 2024-08-19T19:03:13Z

pyomo/contrib/parmest/utils/model_utils.py


        # Param
        if theta_object.is_parameter_type():
+
            # Delete Param, add Var
            vals = theta_object.extract_values()
            model.del_component(theta_object)


I don't think this will work on hierarchical models. I think we need to add more tests for edge cases.

I think I fixed this and added a test.

blnicho · 2024-08-19T19:06:16Z

pyomo/contrib/parmest/utils/model_utils.py

-        param_names = indexed_param_names
+    # Update the list of param_CUIDs if the parameters were indexed
+    if len(indexed_param_CUIDs) > 0:
+        param_CUIDs = indexed_param_CUIDs


Why do we replace param_CUIDs here instead of extending it?

I think we have to replace it because it might not have the indexed variables, only the main variable. For example "theta" (param_CUIDs) vs. "theta[asymptote]" and "theta[rate_constant]" (indexed_param_CUIDs).

blnicho · 2024-08-19T19:07:18Z

pyomo/contrib/parmest/utils/model_utils.py

+            # get indexed Params
+            param_theta_objects = [theta_obj for _, theta_obj in theta_object.items()]
+
+            # get indexed Param names


Suggested change

# get indexed Param names

# get indexed Param CUIDs

smartin71 added 5 commits August 10, 2024 13:06

First attempt at new params-to-vars code.

a5d949e

Removed all strings from convert_params_to_vars in parmest utils.

e534e32

Black formatted.

0ae57d4

Removed deprecated convert_params_to_vars function.

7b64490

Re-blacked.

efa6465

mrmundt reviewed Aug 13, 2024

View reviewed changes

pyomo/contrib/parmest/utils/model_utils.py Outdated Show resolved Hide resolved

Removed left over code from model_utils.

7ea02db

mrmundt approved these changes Aug 13, 2024

View reviewed changes

blnicho self-requested a review August 13, 2024 18:50

jsiirola requested changes Aug 15, 2024

View reviewed changes

jsiirola added the AT: PRE-TEST INSPECTED label Aug 16, 2024

pyomo-autotest removed the AT: PRE-TEST INSPECTED label Aug 16, 2024

Fixed efficiency bugs in parmest model_utils.py.

394a6d6

blnicho requested changes Aug 19, 2024

View reviewed changes

smartin71 added 4 commits August 20, 2024 08:07

Bethany's changed, not including block/hierarchical model changes.

0545ecf

Forgot black on Bethany's changes.

d432500

Fixed hierarchical/block model bug.

577aea3

And black.

92c23f0

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Parmest update of util convert_params_to_vars. #3339

Parmest update of util convert_params_to_vars. #3339

smartin71 commented Aug 10, 2024

jsiirola left a comment

jsiirola Aug 15, 2024

smartin71 Aug 19, 2024

jsiirola Aug 15, 2024

smartin71 Aug 19, 2024

jsiirola Aug 15, 2024

smartin71 Aug 19, 2024

codecov bot commented Aug 16, 2024 •

edited

Loading

blnicho left a comment

blnicho Aug 19, 2024

smartin71 Aug 20, 2024

blnicho Aug 19, 2024

smartin71 Aug 20, 2024

blnicho Aug 19, 2024

smartin71 Aug 20, 2024

blnicho Aug 19, 2024

smartin71 Aug 20, 2024

blnicho Aug 19, 2024

smartin71 Aug 20, 2024

blnicho Aug 19, 2024

smartin71 Aug 20, 2024

blnicho Aug 19, 2024

smartin71 Aug 20, 2024

	theta_CUIDs = [v for k, v in model.unknown_parameters.items()]
	theta_CUIDs = list(model.unknown_parameters.values())

	param_CUIDs = [v for k, v in instance.unknown_parameters.items()]
	param_CUIDs = list(instance.unknown_parameters.values())


		# get indexed Params
		param_theta_objects = [theta_obj for _, theta_obj in theta_object.items()]

	param_theta_objects = [theta_obj for _, theta_obj in theta_object.items()]
	param_theta_objects = list(theta_object.values())

Parmest update of util convert_params_to_vars. #3339

Are you sure you want to change the base?

Parmest update of util convert_params_to_vars. #3339

Conversation

smartin71 commented Aug 10, 2024

Fixes # .

Summary/Motivation:

Changes proposed in this PR:

Legal Acknowledgement

jsiirola left a comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

codecov bot commented Aug 16, 2024 • edited Loading

Codecov Report

blnicho left a comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

codecov bot commented Aug 16, 2024 •

edited

Loading