diff --git a/Snakefile b/Snakefile
index f02d73f6a7aaf6a10a385d5e08506386b56f9e1c..d0f291c9ff31b00e8edd9c65f60ddbdd8a7f9672 100644
--- a/Snakefile
+++ b/Snakefile
@@ -1,5 +1,5 @@
-PATH_HERE="/home/quentin/ghq/gitlab.inria.fr/qguillot/eval-folding-pfs"
-# PATH_HERE="/home/qguilloteau/eval-folding-pfs"
+# PATH_HERE="/home/quentin/ghq/gitlab.inria.fr/qguillot/eval-folding-pfs"
+PATH_HERE="/home/qguilloteau/eval-folding-pfs"
RESULT_FOLDER=f"{PATH_HERE}/data"
NIX_COMPANION_FILE=f"{PATH_HERE}/nix-user-chroot.sh"
@@ -14,43 +14,10 @@ FLAVOURS = [
]
NB_NODES = [
- 5, 9, 13, 17, 21, 25
- # 3,
- # 5,
- # 9,
- # 13,
- # 17,
- # 21
- # 4,
- # 6,
- # 8,
- # 12,
- # 16,
- # 24
-]
-
-DARSHAN_YEARS = [
- 2018,
- 2019,
- 2020,
- 2021
-]
-
-SECTIONS_PAPER = [
- "01_introduction",
- "02_cigri_example",
- "03_folding",
- "04_methodo",
- "05_eval"
-]
-
-FIGS = [
- "darshan_analysis.pdf",
- "boxplot_times.pdf",
- "ratio_folding.pdf",
- "ratio_folding_above_below.pdf",
- "speedup.pdf",
- "speedup_min.pdf"
+ 4,
+ 6,
+ 8,
+ 16
]
@@ -58,14 +25,14 @@ rule all:
input:
# expand(["nxc/build/composition::{file}"], file=FLAVOURS),
# expand(["{result_folder}/csv_zip/results_csv_ior_{nb_nodes}_nodes_{flavour}.zip"], result_folder=RESULT_FOLDER, flavour=FLAVOURS, nb_nodes=NB_NODES),
- # expand(["{path_here}/data/json_zip/results_ior_{nb_nodes}_nodes_{flavour}.zip"], path_here=PATH_HERE, flavour=FLAVOURS, nb_nodes=NB_NODES),
- # expand(["{result_folder}/csv/{nb_nodes}_{flavour}.csv"], result_folder=RESULT_FOLDER, flavour=FLAVOURS, nb_nodes=NB_NODES),
+ expand(["{path_here}/data/json_zip/results_ior_{nb_nodes}_nodes_{flavour}.zip"], path_here=PATH_HERE, flavour=FLAVOURS, nb_nodes=NB_NODES),
+ # expand(["{result_folder}/csv/{nb_nodes}_{flavour}.csv"], result_folder=RESULT_FOLDER, flavour=FLAVOURS, nb_nodes=NB_NODES)
# expand(["data/repeat/iter_{iter}/csv_zip/results_csv_ior_{nb_nodes}_nodes_{flavour}.zip"], iter=[1, 2, 3, 4, 5], nb_nodes=8, flavour=FLAVOURS),
# expand(["data/repeat/iter_{iter}/csv/{nb_nodes}_{flavour}.csv"], iter=[1, 2, 3, 4, 5], nb_nodes=8, flavour=FLAVOURS),
- # expand(["darshan_data/filtered_csv/darshan_{year}.csv"], year=DARSHAN_YEARS),
- "darshan_data/csv_full/darshan.csv",
- "paper/main.pdf",
- expand(["figs/{name}"], name=FIGS)
+ # "Rplots.pdf",
+ # "analysis/rmd/main.pdf",
+ # "analysis/repeat.pdf"
+ # expand(["{result_folder}/results_ior_{nb_nodes}_{flavour}.csv"], result_folder=RESULT_FOLDER, flavour=FLAVOURS, nb_nodes=NB_NODES),
rule build_nxc_image:
input:
@@ -90,18 +57,18 @@ rule run_ior:
rule json_to_csv:
input:
"analysis/ior_json_to_csv.py",
- "{PATH_HERE}/data/json_zip/results_ior_{nb_nodes}_nodes_{flavour}.zip"
+ "{RESULT_FOLDER}/results_ior_{nb_nodes}_nodes_{flavour}.zip"
output:
- "{PATH_HERE}/data/csv_zip/results_csv_ior_{nb_nodes}_nodes_{flavour}.zip"
+ "{RESULT_FOLDER}/csv_zip/results_csv_ior_{nb_nodes}_nodes_{flavour}.zip"
shell:
"nix develop .#python --command python3 {input} {output}"
rule generate_csv:
input:
- "{PATH_HERE}/analysis/zip_to_csv.R",
- "{PATH_HERE}/data/csv_zip/results_csv_ior_{nb_nodes}_nodes_{flavour}.zip"
+ "analysis/zip_to_csv.R",
+ "data/csv_zip/results_csv_ior_{nb_nodes}_nodes_{flavour}.zip"
output:
- "{PATH_HERE}/data/csv/{nb_nodes}_{flavour}.csv"
+ "data/csv/{nb_nodes}_{flavour}.csv"
shell:
"nix develop .#rshell --command Rscript {input} {output}"
@@ -126,8 +93,8 @@ rule repeat_analysis:
rule general_analysis:
input:
- "analysis/analysis2.R",
- expand(["{path_here}/data/csv/{nb_nodes}_{flavour}.csv"], path_here=PATH_HERE, flavour=FLAVOURS, nb_nodes=NB_NODES)
+ "analysis/analysis.R",
+ expand(["{result_folder}/csv/{nb_nodes}_{flavour}.csv"], result_folder=RESULT_FOLDER, flavour=FLAVOURS, nb_nodes=NB_NODES)
output:
"Rplots.pdf"
shell:
@@ -135,69 +102,13 @@ rule general_analysis:
rule paper:
input:
- "paper/main.tex",
- "paper/references.bib"
+ "analysis/rmd/main.Rmd",
+ expand(["{result_folder}/csv/{nb_nodes}_{flavour}.csv"], result_folder=RESULT_FOLDER, flavour=FLAVOURS, nb_nodes=NB_NODES)
output:
- "paper/main.pdf"
+ "analysis/rmd/main.pdf"
shell:
- "cd paper; nix develop .#paper --command rubber -d main.tex"
+ "nix develop .#rmdshell --command Rscript -e 'rmarkdown::render(\"analysis/rmd/main.Rmd\", \"pdf_document\")'"
-rule paper_tex:
- input:
- "paper/main.md",
- expand(["paper/sections/{section_name}.md"], section_name = SECTIONS_PAPER)
- output:
- "paper/main.tex"
- shell:
- "nix develop .#paper --command pandoc --from=markdown --to=latex --template=paper/template.tex --output={output} {input}"
-
-
-rule darshan_decompress:
- input:
- "darshan_data/ANL-ALCF-DARSHAN-THETA_{year}0101_{year}1231.csv.gz"
- output:
- "darshan_data/csv/darshan_{year}.csv"
- shell:
- "gunzip -k {input} -c > {output}"
-
-rule darshan_filter:
- input:
- "analysis/darshan_filtering.R",
- "darshan_data/csv/darshan_{year}.csv"
- output:
- "darshan_data/filtered_csv/darshan_{year}.csv"
- shell:
- "nix develop .#rshell --command Rscript {input} {wildcards.year} {output}"
-
-rule darshan_merged:
- input:
- "analysis/darshan_merged.R",
- expand(["darshan_data/filtered_csv/darshan_{year}.csv"], year=DARSHAN_YEARS)
- output:
- "darshan_data/csv_full/darshan.csv"
- shell:
- "nix develop .#rshell --command Rscript {input} {output}"
-
-rule darsahn_analysis:
- input:
- "analysis/darshan_analysis.R",
- "darshan_data/csv_full/darshan.csv"
- output:
- "figs/darshan_analysis.pdf"
- shell:
- "nix develop .#rshell --command Rscript {input} {output}"
-
-rule generate_plots:
- input:
- "analysis/plot_{plot_name}.R",
- expand(["{path_here}/data/csv/{nb_nodes}_{flavour}.csv"], path_here=PATH_HERE, flavour=FLAVOURS, nb_nodes=NB_NODES)
- output:
- "figs/{plot_name}.pdf"
- shell:
- "nix develop .#rshell --command Rscript {input} {output}"
-
-
-
# rule r_analysis:
diff --git a/flake.nix b/flake.nix
index 7e91c5e1a384e5c1fc0a87448b08f42de2f5bad9..478e19d14195633b2ad503cbb8b4cb11ea9cb818 100644
--- a/flake.nix
+++ b/flake.nix
@@ -52,9 +52,6 @@
buildInputs = with pkgs; [ myRstudio pandoc texlive.combined.scheme-full ];
};
- paper = pkgs.mkShell {
- buildInputs = with pkgs; [ pandoc texlive.combined.scheme-full rubber ];
- };
};
};
}
diff --git a/nxc/composition.nix b/nxc/composition.nix
index 2fbee585171e0468ba47036435fc76fb68d9c3a9..a1390b55cd9dee8d641cf04ba5998dc1170ef5f3 100644
--- a/nxc/composition.nix
+++ b/nxc/composition.nix
@@ -21,7 +21,7 @@
environment.systemPackages = with pkgs; [ ior openmpi scripts.start_ior_nodes scripts.generate_ior_config ];
fileSystems."/data" = {
- device = "server:/srv/shared";
+ device = "server:/";
fsType = "nfs";
};
};