Initial commit

.gitignore

+# Benchmarks and document export output
+*.tex
+*.bbl
+*.aux
+*.blg
+*.fdb_latexmk
+*.fls
+*.log
+*.txt
+*.out
+*.toc
+*.nav
+*.snm
+*.vrb
+*.pdf
+!styles/**/*.pdf
+*.html
+*.json
+svg-inkscape
+_minted*
+figures/*.svg
+public/figures/*
+*.csv
+
+# Tangled source code
+*.sh
+*.R
+*.scm
+
+# Singularity images
+*.gz.squashfs
+
+# Swap and backup files
+*~
+\#*\#
+.\#*

.gitlab-ci.yml

+stages:
+  - "Extract source code"
+  - "Performing benchmarks"
+  - "Post-processing results"
+  - "Publishing"
+
+tangle:
+  stage: "Extract source code"
+  tags: ["guix"]
+  script:
+    - >
+      guix shell --pure git emacs emacs-org -- emacs --batch --no-init-file
+      -l org --eval '(progn (setq org-src-preserve-indentation t) (dolist (file
+      (directory-files-recursively "." "\\.org$"))
+      (org-babel-tangle-file file)))'
+  rules:
+    - if: '$CI_COMMIT_BRANCH == "master"'
+  artifacts:
+    paths:
+      - benchmarks/run.sh
+      - benchmarks/definitions.csv
+      - plot.R
+      - experiments.scm
+      - post-processing.scm
+      - channels.scm
+  
+test-fembem:
+  stage: "Performing benchmarks"
+  tags: ["guix"]
+  script:
+    - >
+      guix time-machine -C channels.scm -- shell --pure -m experiments.scm --
+      ./benchmarks/run.sh -d ./benchmarks/definitions.csv
+      -o ./benchmarks/results
+  rules:
+    - if: '$CI_COMMIT_BRANCH == "master"'
+  artifacts:
+    paths:
+      - benchmarks/results
+
+figures:
+  stage: "Post-processing results"
+  tags: ["guix"]
+  script:
+    - >
+      guix time-machine -C channels.scm -- shell --pure
+      -m post-processing.scm -- Rscript ./plot.R
+      ./benchmarks/results/results.csv
+  rules:
+    - if: '$CI_COMMIT_BRANCH == "master"'
+  artifacts:
+    paths:
+      - figures/*.svg
+
+pages:
+  stage: "Publishing"
+  tags: ["guix"]
+  script:
+    - >
+      guix time-machine -C channels.scm -- shell --pure
+      -m post-processing.scm -- emacs --batch --no-init-file --load publish.el
+      --eval '(org-publish "study")'
+    - >
+      guix time-machine -C channels.scm -- shell --pure
+      -m post-processing.scm -- emacs --batch --no-init-file --load publish.el
+      --eval '(org-publish "study-static")'
+    - mv ./public/study-article.html ./public/index.html
+  rules:
+    - if: '$CI_COMMIT_BRANCH == "master"'
+  artifacts:
+    paths:
+      - public

README.md

+# test_FEMBEM: Advanced setup
+
+[![pipeline status](https://gitlab.inria.fr/tuto-techno-guix-hpc/test_fembem/advanced-setup/badges/master/pipeline.svg)](https://gitlab.inria.fr/tuto-techno-guix-hpc/test_fembem/advanced-setup/-/commits/master)
+[![SWH](https://archive.softwareheritage.org/badge/origin/https://gitlab.inria.fr/tuto-techno-guix-hpc/test_fembem/advanced-setup/)](https://archive.softwareheritage.org/browse/origin/?origin_url=https://gitlab.inria.fr/tuto-techno-guix-hpc/test_fembem/advanced-setup)
+[![SWH](https://archive.softwareheritage.org/badge/swh:1:dir:b90252438cb45ead88474107ca6845689d57b885/)](https://archive.softwareheritage.org/swh:1:dir:b90252438cb45ead88474107ca6845689d57b885;origin=https://gitlab.inria.fr/tuto-techno-guix-hpc/test_fembem/advanced-setup;visit=swh:1:snp:79f450e0f43828f56f261d81b3e86aaab18362eb;anchor=swh:1:rev:1afd45f51a79560da1e76a790a3b46caf564ed43)
+
+This repository contains a copy of an experimental study relying on the
+open-source version of the `test_FEMBEM` solver test suite [3]. In this case, we
+**do rely** rely on the GNU Guix [1] transactional package manager and literate
+programming [2] to ensure reproducibility of the research study. We refer to
+this version of the study as to *Advanced setup*.
+
+## Where to find the original study?
+
+You can find all the materials and reproducing guidelines
+[here](https://tuto-techno-guix-hpc.gitlabpages.inria.fr/test_fembem/advanced-setup).
+
+## References
+
+1. GNU Guix software distribution and transactional package manager
+   [https://guix.gnu.org](https://guix.gnu.org).
+2. Literate Programming, Donald E. Knuth, 1984
+   [https://doi.org/10.1093/comjnl/27.2.97](https://doi.org/10.1093/comjnl/27.2.97).
+3. test_FEMBEM, a simple application for testing dense and sparse solvers with
+   pseudo-FEM or pseudo-BEM matrices
+   [https://gitlab.inria.fr/solverstack/test_fembem](https://gitlab.inria.fr/solverstack/test_fembem).

references.bib

+@misc{testFEMBEM,
+  title        = {
+    {test\_FEMBEM, a simple application for testing dense and sparse solvers
+    with pseudo-FEM or pseudo-BEM matrices}
+  },
+  howpublished = {\url{https://gitlab.inria.fr/solverstack/test_fembem}}
+}
+
+@misc{hmat-oss,
+  title        = {{hmat-oss}},
+  howpublished = {\url{https://github.com/jeromerobert/hmat-oss}}
+}
+
+@phdthesis{Lize14,
+  title        = {
+    {Résolution Directe Rapide pour les Éléments Finis de Frontière en
+    Électromagnétisme et Acoustique : \(\mathcal{H}\)-Matrices. Parallélisme et
+    Applications Industrielles.}
+  },
+  author       = {Benoît Lizé},
+  year         = 2014,
+  school       = {Université Paris 13}
+}
+
+@misc{chameleon,
+  title        = {
+    {Chameleon, a dense linear algebra software for heterogeneous architectures}
+  },
+  howpublished = {\url{https://gitlab.inria.fr/solverstack/chameleon}}
+}
+
+@misc{cpu,
+  title        = {
+    {Intel(R) Xeon(R) Processor W3520 8M Cache 2.66 GHz 4.80 GTs Intel QPI
+    Product Specifications}
+  },
+  howpublished = {
+    \url{https://ark.intel.com/content/www/us/en/ark/products/39718/intel-xeon-processor-w3520-8m-cache-2-66-ghz-4-80-gts-intel-qpi.html}
+  }
+}
+
+@misc{ggplot2,
+  title = {{ggplot2, a system for declaratively creating graphics}},
+  howpublished = {\url{https://ggplot2.tidyverse.org/}}
+}
+
+@article{Knuth84,
+  title = {{Literate Programming}},
+  author = {Knuth, Donald E.},
+  year = 1984,
+  month = may,
+  journal = {{Comput. J.}},
+  publisher = {Oxford University Press, Inc.},
+  address = {USA},
+  volume = 27,
+  number = 2,
+  pages = {97–111},
+  doi = {10.1093/comjnl/27.2.97},
+  issn = {0010-4620},
+  url = {https://doi.org/10.1093/comjnl/27.2.97},
+  issue_date = {May 1984},
+  numpages = 15
+}
+
+@book{Dominik18,
+  title = {{The Org Mode 9.1 Reference Manual}},
+  author = {Dominik, Carsten},
+  year = 2018,
+  publisher = {12th Media Services},
+  isbn = 9781680921656
+}
+
+@misc{emacs,
+  title = {
+    {GNU Emacs: An extensible, customizable, free/libre text editor — and
+    more.}
+  },
+  howpublished = {\url{https://www.gnu.org/software/emacs/}}
+}
+
+@misc{OrgTangle,
+  title = {{Org mode documentation (Extracting source code)}},
+  howpublished = {\url{https://orgmode.org/manual/Extracting-Source-Code.html}}
+}
+
+@misc{OrgEval,
+  title = {{Org mode documentation (Evaluating source code)}},
+  howpublished = {\url{https://orgmode.org/manual/Evaluating-Code-Blocks.html}}
+}
+
+@misc{OrgExport,
+  title = {{Org mode documentation (Exporting)}},
+  howpublished = {\url{https://orgmode.org/manual/Exporting.html}}
+}
+
+@misc{guix,
+  title = {{GNU Guix software distribution and transactional package manager}},
+  howpublished = {\url{https://guix.gnu.org}}
+}
+
+@misc{guix-pack,
+  title = {{Invoking \texttt{guix pack} (GNU Guix Reference Manual)}},
+  howpublished = {
+    \url{https://guix.gnu.org/manual/en/html_node/Invoking-guix-pack.html}
+  }
+}
+
+@misc{guix-manifests,
+  title        = {{GNU Guix Cookbook: Basic setup with manifests}},
+  howpublished = {  
+    \url{https://guix.gnu.org/cookbook/en/html_node/Basic-setup-with-manifests.html}
+  }
+}
+
+@techreport{Study,
+  title        = {
+    {Minimal working example of an experimental study written in Org mode}
+  },
+  author       = {Fel{\v s}{\"o}ci, Marek},
+  year         = 3014,
+  month        = Feb,
+  number       = {RR-9999},
+  url          = {https://hal.inria.fr/example-report},
+  type         = {Research Report},
+  institution  = {{Inria Nancy Grand-Est, Laboratoire ICube Illkirch}}
+}
+
+@techreport{Reproduce,
+  title        = {
+    {Minimal working example of an experimental study written in Org mode:
+    reproducing guidelines}
+  },
+  author       = {Fel{\v s}{\"o}ci, Marek},
+  year         = 3014,
+  month        = Feb,
+  number       = {RT-9999},
+  url          = {https://hal.inria.fr/example-report},
+  type         = {Technical Report},
+  institution  = {{Inria Nancy Grand-Est, Laboratoire ICube Illkirch}}
+}