V2.1.0 (verificarlo#50)

* Update fuzzy to Verificarlo v2.1.0:
  - Update python version to 3.8.20
  - Update numpy version to 1.24.4
  - Update scipy version to 1.10.1
  - Update scikit-learn version to 1.2.2

* Add fuzzy pytorch docker image

* Update verificarlo version in github workflow

* update workflow

* Fix docker image for pytorch

* Update workflow

* Update README + fix build_fuzzy_libmath script

* update verificarlo version

* Add missing files

* Add blas test

* Update fuzzy pytorch

* Add the patched version of verificarlo

Author: yohanchatelain

.github/workflows/build-fuzzy.yml

@@ -5,7 +5,7 @@ on:
     branches: ['*']
 
 env:
-  VERIFICARLO_VERSION: v2.0.0
+  VERIFICARLO_VERSION: v2.1.0
 
 jobs:
   fuzzy:
@@ -18,32 +18,32 @@ jobs:
         include:
           - NAME: Lapack + Libmath
             DOCKER_FROM: ""
-            DOCKER_TO: fuzzy_v2.0.0-lapack
-            DOCKER_IMAGE: verificarlo/fuzzy:v2.0.0-lapack
+            DOCKER_TO: fuzzy_v2.1.0-lapack
+            DOCKER_IMAGE: verificarlo/fuzzy:v2.1.0-lapack
             DOCKER_FILE: ./docker/base/ubuntu-20.04/Dockerfile.ubuntu-20.04-0-lapack-libmath
 
           - NAME: Python
-            DOCKER_FROM: fuzzy_v2.0.0-lapack
-            DOCKER_TO: fuzzy_v2.0.0-lapack-python3.8.5
-            DOCKER_IMAGE: verificarlo/fuzzy:v2.0.0-lapack-python3.8.5
+            DOCKER_FROM: fuzzy_v2.1.0-lapack
+            DOCKER_TO: fuzzy_v2.1.0-lapack-python3.8.20
+            DOCKER_IMAGE: verificarlo/fuzzy:v2.1.0-lapack-python3.8.20
             DOCKER_FILE: ./docker/base/ubuntu-20.04/Dockerfile.ubuntu-20.04-1-python
 
           - NAME: Numpy
-            DOCKER_FROM: fuzzy_v2.0.0-lapack-python3.8.5
-            DOCKER_TO: fuzzy_v2.0.0-lapack-python3.8.5-numpy
-            DOCKER_IMAGE: verificarlo/fuzzy:v2.0.0-lapack-python3.8.5-numpy
+            DOCKER_FROM: fuzzy_v2.1.0-lapack-python3.8.20
+            DOCKER_TO: fuzzy_v2.1.0-lapack-python3.8.20-numpy
+            DOCKER_IMAGE: verificarlo/fuzzy:v2.1.0-lapack-python3.8.20-numpy
             DOCKER_FILE: ./docker/base/ubuntu-20.04/Dockerfile.ubuntu-20.04-2-numpy
 
           - NAME: Scipy
-            DOCKER_FROM: fuzzy_v2.0.0-lapack-python3.8.5-numpy
-            DOCKER_TO: fuzzy_v2.0.0-lapack-python3.8.5-numpy-scipy
-            DOCKER_IMAGE: verificarlo/fuzzy:v2.0.0-lapack-python3.8.5-numpy-scipy
+            DOCKER_FROM: fuzzy_v2.1.0-lapack-python3.8.20-numpy
+            DOCKER_TO: fuzzy_v2.1.0-lapack-python3.8.20-numpy-scipy
+            DOCKER_IMAGE: verificarlo/fuzzy:v2.1.0-lapack-python3.8.20-numpy-scipy
             DOCKER_FILE: ./docker/base/ubuntu-20.04/Dockerfile.ubuntu-20.04-3-scipy
 
           - NAME: Scikit-Learn
-            DOCKER_FROM: fuzzy_v2.0.0-lapack-python3.8.5-numpy-scipy
-            DOCKER_TO: fuzzy_v2.0.0-lapack-python3.8.5-numpy-scipy-sklearn
-            DOCKER_IMAGE: verificarlo/fuzzy:v2.0.0-lapack-python3.8.5-numpy-scipy-sklearn
+            DOCKER_FROM: fuzzy_v2.1.0-lapack-python3.8.20-numpy-scipy
+            DOCKER_TO: fuzzy_v2.1.0-lapack-python3.8.20-numpy-scipy-sklearn
+            DOCKER_IMAGE: verificarlo/fuzzy:v2.1.0-lapack-python3.8.20-numpy-scipy-sklearn
             DOCKER_FILE: ./docker/base/ubuntu-20.04/Dockerfile.ubuntu-20.04-4-sklearn
 
     name: ${{ matrix.NAME }}
@@ -56,57 +56,58 @@ jobs:
         id: changes
 
       - name: Print list of changed files
-        run: echo ${{ steps.changes.outputs.all }}
+        run: echo ${{ steps.changes.outputs.files }}
 
       - name: If Dockerfiles have been updated, cancel running upstream jobs
-        if: contains(steps.changes.outputs.all, ${{ env.RUN_IF_CHANGED }})
+        if: contains(steps.changes.outputs.all_changed_files, '${{ env.RUN_IF_CHANGED }}')
         continue-on-error: true
         uses: n1hility/cancel-previous-runs@v3
         with:
-          token: ${{ secrets.GH_ACCESS_TOKEN }}
+          token: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Determine if images will be pushed to Docker, and login as needed
-        if: contains(steps.changes.outputs.all, ${{ env.RUN_IF_CHANGED }})
+        if: contains(steps.changes.outputs.all_changed_files, '${{ env.RUN_IF_CHANGED }}')
         run: |
           if ([ "${{github.event_name}}" == "push" ] && [ "${{github.ref}}" == "refs/heads/master" ])
           then
               echo This is a push to master: we will push to Docker Hub
               echo "PUSH=true" >> "$GITHUB_ENV"
+              export PUSH=true
               docker login -u ${{ secrets.DOCKER_HUB_USERNAME }} -p ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
           else
               echo This is a PR or non-master push: we will not push to Docker Hub
               echo "PUSH=false" >> "$GITHUB_ENV"
           fi
 
       - name: Download Docker artifacts, if available
-        if: contains(steps.changes.outputs.all, ${{ env.RUN_IF_CHANGED }})
+        if: contains(steps.changes.outputs.all_changed_files, '${{ env.RUN_IF_CHANGED }}') && matrix.DOCKER_FROM != ''
+        continue-on-error: true
         uses: actions/download-artifact@v4
         with:
           name: ${{ matrix.DOCKER_FROM }}
           path: /tmp
 
-      - name: (optionally) Load, Build, and (optionally) Push Docker image
-        if: contains(steps.changes.outputs.all, ${{ env.RUN_IF_CHANGED }})
+      - name: Build and Push Docker image
+        if: contains(steps.changes.outputs.all_changed_files, '${{ env.RUN_IF_CHANGED }}')
         run: |
-          if [ ! -z ${{ matrix.DOCKER_FROM }} ]
+          if [ -n "${{ matrix.DOCKER_FROM }}" ] && [ -f "/tmp/${{ matrix.DOCKER_FROM }}.tar" ]
           then
             docker load --input /tmp/${{ matrix.DOCKER_FROM }}.tar
             docker image ls -a
           fi
 
           docker build ./ -t ${{ matrix.DOCKER_IMAGE }} \
                           -f ${{ matrix.DOCKER_FILE }} \
-                          --build-arg VERIFICARLO_VERSION=v2.0.0
+                          --build-arg VERIFICARLO_VERSION=v2.1.0
 
           docker save ${{ matrix.DOCKER_IMAGE }} -o /tmp/${{ matrix.DOCKER_TO }}.tar
-
-          if ${{ env.PUSH }}
+          if [ "$PUSH" = "true" ]
           then
             docker push ${{ matrix.DOCKER_IMAGE }}
           fi
 
       - name: Upload Docker artifacts
-        if: contains(steps.changes.outputs.all, ${{ env.RUN_IF_CHANGED }})
+        if: contains(steps.changes.outputs.all_changed_files, '${{ env.RUN_IF_CHANGED }}')
         uses: actions/upload-artifact@v4
         with:
           name: ${{ matrix.DOCKER_TO }}
@@ -117,9 +118,9 @@ jobs:
     runs-on: ubuntu-20.04
     env:
       RUN_IF_CHANGED: docker
-      DOCKER_FROM: fuzzy_v2.0.0-lapack-python3.8.5-numpy-scipy-sklearn
+      DOCKER_FROM: fuzzy_v2.1.0-lapack-python3.8.20-numpy-scipy-sklearn
       DOCKER_IMAGE: verificarlo/fuzzy
-      DOCKER_FROM_TAG: v2.0.0-lapack-python3.8.5-numpy-scipy-sklearn
+      DOCKER_FROM_TAG: v2.1.0-lapack-python3.8.20-numpy-scipy-sklearn
 
     steps:
       - name: Checkout repository
@@ -130,16 +131,16 @@ jobs:
         id: changes
 
       - name: Print list of changed files
-        run: echo ${{ steps.changes.outputs.all }}
+        run: echo ${{ steps.changes.outputs.all_changed_files }}
 
       - name: If Dockerfiles have been updated, cancel running upstream jobs
-        if: contains(steps.changes.outputs.all, ${{ env.RUN_IF_CHANGED }})
+        if: contains(steps.changes.outputs.all_changed_files, '${{ env.RUN_IF_CHANGED }}')
         uses: n1hility/cancel-previous-runs@v3
         with:
-          token: ${{ secrets.GH_ACCESS_TOKEN }}
+          token: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Determine if images will be pushed to Docker, and login as needed
-        if: contains(steps.changes.outputs.all, ${{ env.RUN_IF_CHANGED }})
+        if: contains(steps.changes.outputs.all_changed_files, '${{ env.RUN_IF_CHANGED }}')
         run: |
           if ([ "${{github.event_name}}" == "push" ] && [ "${{github.ref}}" == "refs/heads/master" ])
           then
@@ -152,22 +153,22 @@ jobs:
           fi
 
       - name: Download Docker artifacts, if available
-        if: contains(steps.changes.outputs.all, ${{ env.RUN_IF_CHANGED }})
+        if: contains(steps.changes.outputs.all_changed_files, '${{ env.RUN_IF_CHANGED }}')
         uses: actions/download-artifact@v4
         with:
           name: ${{ env.DOCKER_FROM }}
           path: /tmp
 
-      - name: (optionally) Load, Rename, and Push Docker image
-        if: contains(steps.changes.outputs.all, ${{ env.RUN_IF_CHANGED }})
+      - name: Load, Rename, and Push Docker image
+        if: contains(steps.changes.outputs.all_changed_files, '${{ env.RUN_IF_CHANGED }}')
         run: |
           docker load --input /tmp/${{ env.DOCKER_FROM }}.tar
           docker image ls -a
 
           docker image tag ${{ env.DOCKER_IMAGE }}:${{ env.DOCKER_FROM_TAG }} \
                           ${{ env.DOCKER_IMAGE }}:latest
 
-          if ${{ env.PUSH }}
+          if [ "$PUSH" = "true" ]
           then
             docker push ${{ env.DOCKER_IMAGE }}:latest
-          fi
+          fi

README.md

@@ -1,4 +1,4 @@
-# Fuzzy v2.0.0
+# Fuzzy v2.1.0
 
 [![DOI](https://zenodo.org/badge/218554957.svg)](https://zenodo.org/badge/latestdoi/218554957)
 [![Build Fuzzy Environments](https://github.com/verificarlo/fuzzy/actions/workflows/build-fuzzy.yml/badge.svg?branch=master)](https://github.com/verificarlo/fuzzy/actions/workflows/build-fuzzy.yml)
@@ -7,7 +7,28 @@
 
 *A fuzzy ecosystem for evaluating the effect of numerical error on computational tools.*
 
-[![Fuzzy Marimo](https://github.com/verificarlo/fuzzy/raw/master/img/fuzzy.png)](./img/fuzzy.png)
+<div align="center">
+  <a href="./img/fuzzy.png">
+    <img src="https://github.com/verificarlo/fuzzy/raw/master/img/fuzzy.png" alt="Fuzzy Marimo">
+  </a>
+</div>
+
+## Table of Contents
+- [Fuzzy v2.1.0](#fuzzy-v210)
+  - [Table of Contents](#table-of-contents)
+  - [Motivation](#motivation)
+  - [Usage](#usage)
+      - [Building \& booting the environment](#building--booting-the-environment)
+      - [Adding your software](#adding-your-software)
+      - [Fuzzy-libmath](#fuzzy-libmath)
+      - [Using Fuzzy in Multi-stage builds](#using-fuzzy-in-multi-stage-builds)
+      - [Running Fuzzy workflows](#running-fuzzy-workflows)
+      - [Quick overview of Monte Carlo Arithmetic](#quick-overview-of-monte-carlo-arithmetic)
+      - [Common failures](#common-failures)
+  - [Contributing](#contributing)
+  - [Presentation](#presentation)
+  - [References](#references)
+  - [License](#license)
 
 ## Motivation
 
@@ -40,7 +61,7 @@ programs can be evaluated, reducing the overhead on both tool developers and con
 You can get started with *Fuzzy* quite simply, just launch a
 [Docker](https://www.docker.com/) container as follows:
 
-```
+```bash
 docker run -ti verificarlo/fuzzy
 ```
 
@@ -54,7 +75,7 @@ build chain, you'll find instrumented versions of `libmath`, `lapack`, `python3`
 `numpy`, and several other recompiled libraries.
 
 An example for how to verify your installation for Python could be the following:
-```
+```bash
 $ python3 -c "print([sum([.001]*1000) for _ in range(3)])"
 [1.0, 0.9999999999999997, 1.0000000000000007, 1.0000000000000002]
 ```
@@ -70,7 +91,7 @@ The next step is to make sure the environment is configured to introduce perturb
 the way you expect. You can start with a configuration which performs perturbations
 akin to randomizing machine error with the following:
 
-```
+```bash
 echo "libinterflop_mca.so -m mca --precision-binary32=24 --precision-binary64=53" > $VFC_BACKENDS_FROM_FILE
 ```
 
@@ -113,7 +134,7 @@ the fastest and can be used if one does not require high accuracy. To switch
 from one version to another, please use the `set-fuzzy-libmath` tool already
 installed in the docker image as follow:
 
-```
+```bash
 usage: set-fuzzy-libmath [-h] --version {no-fuzzy,standard,quad,mpfr}
 
 optional arguments:
@@ -133,14 +154,47 @@ Fuzzy libmath version to use:
                     Slowest version but gives the correct rounding.
 ```
 
+
+> [!TIP] 
+> The script [build_fuzzy_libmath_dockerfile.sh](docker/resources/build_fuzzy_libmath_dockerfile.sh) helps you turn your Docker image into a fuzzy-libmath one.
+
+```bash
+usage: ./build_fuzzy_libmath_dockerfile.sh <DOCKER_IMAGE> <TAG> [FUZZY_IMAGE]
+          <DOCKER_IMAGE>: Name of the base Docker image to build
+          <TAG>:          Tag of the new image to build
+          [FUZZY_IMAGE]:  Name of the fuzzy image to copy from (optional)
+                          Requires a fuzzy version >= 0.9.1
+```
+
+To test your instrumentation:
+
+**Python**
+```python
+>>> import math
+>>> from collections import Counter
+>>> Counter( math.cos(42) for i in range(1000) )
+Counter({-0.39998531498835127: 506, -0.3999853149883513: 249, -0.3999853149883512: 245})
+```
+
+**Octave**
+```matlab
+>>> x = repmath(42, 1000);
+>>> y = cos(x);
+>>> printf("%.17f\n", unique(y))
+-0.39998531498835133
+-0.39998531498835127
+-0.39998531498835121
+```
+
+
 #### Using Fuzzy in Multi-stage builds
 Fuzzy provides a set of recompiled shared objects and tools that facilitate adding
 Monte Carlo Arithmetic to tools. If you've got a Docker container which relies on
 some of these libraries, you can easily add *Fuzzy* with a [Multi-stage Docker build](https://docs.docker.com/develop/develop-images/multistage-build/).
 
 For example:
 
-```
+```bash
 FROM verificarlo/fuzzy:latest as fuzzy
 
 # Your target image