Cookies problem (#93)

* Rename cookies-problem to igatools-cookies-problem * Add fenics-cookie-problem * Updated README * ensure N (mesh size) is integer * change docker location in readme * Rename folder to fenics-cookies-problem * add source code subsection to README for CI * updated readme for model and benchmark * added back original readmes by ben * going over changes with Ben * removing parabolic benchmark * deleted temporary test output files * removed igatools cookies version * removed time benchmark class * fixed links to other files in the repo --------- Co-authored-by: Ben Kent <[email protected]> Co-authored-by: Lorenzo Tamellini <[email protected]>
UM-Bridge · Aug 1, 2024 · 06a3cf0 · 06a3cf0
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diff --git a/benchmarks/cookies-problem-propagation/README.md b/benchmarks/cookies-problem-propagation/README.md
@@ -2,15 +2,16 @@
 
 ## Overview
 
-This benchmark runs a forward uncertainty quantification problem for the [cookies model](https://github.com/UM-Bridge/benchmarks/tree/main/models/cookies-problem/README.md) using the [Sparse Grids Matlab Kit](https://github.com/lorenzo-tamellini/sparse-grids-matlab-kit) interface to UM-Bridge. See below for full description.
+This benchmark runs a forward uncertainty quantification problem for the [cookies model](https://github.com/UM-Bridge/benchmarks/tree/main/models/fenics-cookies-problem/README.md) using the [Sparse Grids Matlab Kit](https://github.com/lorenzo-tamellini/sparse-grids-matlab-kit) interface to UM-Bridge. See below for full description.
 
 ## Authors
+- [Benjamin Kent]([email protected])
 - [Massimiliano Martinelli](mailto:[email protected])
 - [Lorenzo Tamellini](mailto:[email protected])
 
 ## Run
 ```
-docker run -it -p 4242:4242 linusseelinger/cookies-problem
+docker run -it -p 4242:4242 linusseelinger/cookiebenchmark
 ```
 
 ## Properties
@@ -24,7 +25,7 @@ benchmark | Sets the config options for the forward UQ benchmark (see below)
 Mapping | Dimensions   | Description
 ---     |---           |---
 input   | [8]          | These values modify the conductivity coefficient in the 8 cookies. They are i.i.d. uniform random variables in the range [-0.99, -0.2] (software does not check that inputs are within the bound) 
-output  | \[1\]        | The integral of the solution over the central subdomain (see definition of $\Psi$ at [cookies model](https://github.com/UM-Bridge/benchmarks/tree/main/models/cookies-problem/README.md) for info)
+output  | \[1\]        | The integral of the solution over the central subdomain (see definition of $$\Psi$$ at [cookies model](https://github.com/UM-Bridge/benchmarks/tree/main/models/fenics-cookies-problem/README.md) for info)
 
 Feature       | Supported
 ---           |---
@@ -33,11 +34,9 @@ Gradient      | False
 ApplyJacobian | False
 ApplyHessian  | False
 
-Config        | Type    | Default value   	| Can be changed in benchmark model	| Description
----           |---      |---      		|---		  			| ---	
-NumThreads    | integer | 1     		| yes					| Number of physical cores to be used by the solver 
-BasisDegree   | integer | 4       		| no					| Default degree of spline basis (must be a positive integer)
-Fidelity      | integer | 2       		| no					| Controls the number of mesh elements (must be a positive integer, see below for details)
+Config      | Type    | Default value | Description
+---         |---      |---      		| ---	
+None        |
 
 
 ## Mount directories
@@ -47,18 +46,25 @@ None            |
 
 ## Source code
 
-[Benchmark sources available at this folder.](https://github.com/UM-Bridge/benchmarks/tree/main/benchmarks/cookies-problem)
+[Benchmark sources available at this folder.](https://github.com/UM-Bridge/benchmarks/tree/main/benchmarks/cookies-problem-propagation)
 
 ## Description
 
-![cookies-problem](https://raw.githubusercontent.com/UM-Bridge/benchmarks/main/models/cookies-problem/cookies_domain.png "geometry of the cookies problem")
+![cookies-problem](https://raw.githubusercontent.com/UM-Bridge/benchmarks/main/models/fenics-cookies-problem/cookies_domain.png "geometry of the cookies problem")
 
-The benchmark implements a forward uncertainty quantification problem for the [cookies model](https://github.com/UM-Bridge/benchmarks/tree/main/models/cookies-problem/README.md). More specifically, we assume that the uncertain parameters $y_n$ appearing in the definition of the diffusion coefficient are uniform i.i.d. random variables on the range $[-0.99, -0.2]$ and we aim at computing the expected value of the quantity of interest (i.e., output of the model) $\Psi$, which is defined as the integral of the solution over $F$.
+The benchmark implements a forward uncertainty quantification problem for the elliptic version of the [cookies model](https://github.com/UM-Bridge/benchmarks/tree/main/models/fenics-cookies-problem/README.md). More specifically, we assume that the uncertain parameters $$y_n$$ appearing in the definition of the diffusion coefficient are uniform i.i.d. random variables on the range $$[-0.99, -0.2]$$ and we aim at computing the expected value of the quantity of interest (i.e., output of the model) $$\Psi$$, which is defined as the integral of the solution over $$F$$.
 
-The PDE is solved with an IGA solver that uses as basis splines of degree $p=4$ and maximal regularity, i.e. of continuity $3$, and the mesh has $200 \times 200$ elements (i.e., the fidelity config parameter is set to $2$). The structure of this benchmark is identical to the one discussed in [[Bäck et al.,2011]](https://doi.org/10.1007/978-3-642-15337-2_3); however, raw numbers are different since in [[Bäck et al.,2011]](https://doi.org/10.1007/978-3-642-15337-2_3) the PDE solver employed was different (standard FEM with piecewise linear basis) and the mesh was also different.
+The benchmark configuration of the docker uses all config options set to their default values, see againg the [cookies model page](https://github.com/UM-Bridge/benchmarks/tree/main/models/fenics-cookies-problem/README.md). The structure of this benchmark thus is identical to the one discussed in [[Bäck et al.,2011]](https://doi.org/10.1007/978-3-642-15337-2_3); however, raw numbers are different since in [[Bäck et al.,2011]](https://doi.org/10.1007/978-3-642-15337-2_3) a different mesh was used.
 
+As a reference value, we provide the approximation of the expected value computed with a standard Smolyak sparse grid, based on Clenshaw--Curtis points, for levels $$w=0,1,\ldots,5$$, see e.g. [[Piazzola et al.,2024]](https://doi.org/10.1145/3630023). 
 
-As a reference value, we provide the approximation of the expected value computed with a standard Smolyak sparse grid, based on Clenshaw--Curtis points, for level $w=5$, see e.g. [[Piazzola et al.,2023]](https://doi.org/10.48550/arXiv.2203.09314). The resulting sparse grid has 15713 points, and the corresponding approximation of the expected value is $0.064196096847169$.
+Sparse grid $$w$$ | number of collocation points    | Estimate of $$\Psi$$ 
+----------------  |-------------------------------- |-------------------
+0                 | 1                               | 0.062255257529767
+1                 | 17                              | 0.064176316082952
+2                 | 145                             | 0.064206407272061
+3                 | 849                             | 0.064202639076811
+4                 | 3937                            | 0.064202350667514
+5                 | 15713                           | 0.064202367186117
 
-
-The script available [here](https://github.com/UM-Bridge/benchmarks/tree/main/benchmarks/cookies-problem/run_forward_benchmark_in_matlab.m) generates the results, using the Sparse Grids Matlab Kit [[Piazzola et al.,2023]](https://doi.org/10.48550/arXiv.2203.09314) for generating sparse grids. The Grids Matlab Kit is available on Github [here](https://github.com/lorenzo-tamellini/sparse-grids-matlab-kit) and a dedicated website with full resources including user manual is available [here](https://sites.google.com/view/sparse-grids-kit).
+The script available [here](https://github.com/UM-Bridge/benchmarks/tree/main/benchmarks/cookies-problem-propagation/run_forward_benchmark_in_matlab.m) generates the results, using the Sparse Grids Matlab Kit [[Piazzola et al.,2024]](https://doi.org/10.1145/3630023) for generating sparse grids. The Grids Matlab Kit is available on Github [here](https://github.com/lorenzo-tamellini/sparse-grids-matlab-kit) and a dedicated website with full resources including user manual is available [here](https://sites.google.com/view/sparse-grids-kit).
diff --git a/benchmarks/cookies-problem-propagation/run_forward_benchmark_in_matlab.m b/benchmarks/cookies-problem-propagation/run_forward_benchmark_in_matlab.m
@@ -14,7 +14,8 @@
 % 2) add sparse grids matlab kit and um-bridge matlab client to path
 % addpath(genpath('~/GIT_projects/Github/sparse-grids-matlab-kit/')) % this is version 23.5 Robert
 % addpath(genpath('~/GIT_projects/Github/umbridge/matlab/'))
-
+addpath(genpath('../../../sparse-grids-matlab-kit/'))
+addpath(genpath('../../../umbridge'))
 
 % 3) to save results on file (sparse grids in .txt / .mat, results in .txt / .mat), set the flag below to true
 saving_stuff = true;
@@ -31,7 +32,7 @@
 model = HTTPModel(uri,'benchmark');
 
 % config cookie solver with num threades
-config = struct('NumThreads',4);
+config = struct();
 
 
 % wrap model in an @-function too
@@ -50,7 +51,7 @@
 knots = @(n) knots_CC(n,-0.99,-0.2);
 lev2knots = @lev2knots_doubling;
 idxset_rule = @(i) sum(i-1);
-idxset_level_max = 1; % <--- controls max size of sparse grid
+idxset_level_max = 5; % <--- controls max size of sparse grid
 
 
 % To recycle evaluations from one grid to the next, we need some containers

diff --git a/models/cookies-problem/Dockerfile b/models/cookies-problem/Dockerfile
diff --git a/models/cookies-problem/README.md b/models/cookies-problem/README.md
diff --git a/models/cookies-problem/draw_geometry.m b/models/cookies-problem/draw_geometry.m
diff --git a/models/cookies-problem/umbridge-server.py b/models/cookies-problem/umbridge-server.py
diff --git a/models/fenics-cookies-problem/Dockerfile b/models/fenics-cookies-problem/Dockerfile
@@ -0,0 +1,19 @@
+FROM ubuntu:mantic
+
+# Install fenics and python packages
+RUN apt update
+RUN DEBIAN_FRONTEND=noninteractive apt install -y bash fenics python3-pip
+RUN pip3 install --break-system-packages umbridge
+
+# Expose port for UM-BRIDGE server
+EXPOSE 4242
+
+RUN apt update
+
+# Set up internal folders and files
+WORKDIR /
+COPY umbridge-server.py /
+COPY cookiepde.py /
+
+# Start Python UM-BRDIGE server
+CMD python3 umbridge-server.py