add snakefile

Snakefile

+PATH_HERE="/home/quentin/ghq/gitlab.inria.fr/nixos-compose/hpc-io/orangefs"
+RESULT_FOLDER=f"{PATH_HERE}/data"
+
+
+FLAVOURS = [
+    "g5k-image"
+]
+
+NB_CPU_NODES = [
+    8, 16, 24, 32
+]
+
+NB_IO_NODES = [
+    1, 2, 4
+]
+
+
+BLOCK_SIZES = [
+    "1M",
+    "10M",
+    "100M"
+    # "1G",
+]
+
+FIGS = [
+    "ratio_folding.pdf"
+]
+
+
+EXPES_RESULTS = expand(["{path_here}/data/json_zip/results_ior_{nb_cpu_nodes}_cpu_nodes_{nb_io_nodes}_io_nodes_{block_size}_block_size_{flavour}.zip"], path_here=PATH_HERE,
+                                                                                                                                                        flavour=FLAVOURS,
+                                                                                                                                                        nb_cpu_nodes=NB_CPU_NODES,
+                                                                                                                                                        nb_io_nodes=NB_IO_NODES,
+                                                                                                                                                        block_size=BLOCK_SIZES)
+
+
+
+rule all:
+    input:
+        EXPES_RESULTS,
+        expand(["figs/{name}"], name=FIGS)
+
+
+rule build_nxc_image:
+    input:
+        "nxc/flake.nix",
+        "nxc/flake.lock",
+        "nxc/composition.nix",
+        "nxc/my_scripts.nix",
+        "nxc/script_ior.nix"
+    output:
+        "nxc/build/composition::{flavour}"
+    shell:
+        "cd nxc; nix develop --command nxc build -f {wildcards.flavour}"
+
+rule run_ior:
+    input:
+        "nxc/build/composition::{flavour}"
+    output:
+        "{PATH_HERE}/data/json_zip/results_ior_{nb_cpu_nodes}_cpu_nodes_{nb_io_nodes}_io_nodes_{block_size}_block_size_{flavour}.zip"
+    shell:
+        "cd nxc; nix develop --command python3 script.py --nxc_build_file {PATH_HERE}/{input} --nb_cpu_nodes {wildcards.nb_cpu_nodes} --nb_io_nodes {wildcards.nb_io_nodes} --block_size {wildcards.block_size} --result_dir {RESULT_FOLDER} --flavour {wildcards.flavour} --outfile {output} --walltime 5"
+
+
+rule json_to_csv:
+    input:
+        "analysis/ior_json_to_csv.py",
+        "{PATH_HERE}/data/json_zip/results_ior_{nb_cpu_nodes}_cpu_nodes_{nb_io_nodes}_io_nodes_{block_size}_block_size_{flavour}.zip"
+    output:
+        "{PATH_HERE}/data/csv_zip/results_csv_ior_{nb_cpu_nodes}_cpu_nodes_{nb_io_nodes}_io_nodes_{block_size}_block_size_{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_cpu_nodes}_cpu_nodes_{nb_io_nodes}_io_nodes_{block_size}_block_size_{flavour}.zip"
+    output:
+        "{PATH_HERE}/data/csv/{nb_cpu_nodes}_{nb_io_nodes}_{block_size}_{flavour}.csv"
+    shell:
+        "nix develop .#rshell --command Rscript {input} {output} {wildcards.nb_cpu_nodes} {wildcards.nb_io_nodes} {wildcards.block_size}"
+
+rule generate_plots:
+    input:
+        "analysis/plot_{plot_name}.R",
+        expand(["{path_here}/data/csv/{nb_cpu_nodes}_{nb_io_nodes}_{block_size}_{flavour}.csv"], path_here=PATH_HERE, flavour=FLAVOURS, nb_cpu_nodes=NB_CPU_NODES, nb_io_nodes=NB_IO_NODES, block_size=BLOCK_SIZES),
+    output:
+        "figs/{plot_name}.pdf"
+    shell:
+        "nix develop .#rshell --command Rscript {input} {output}"

flake.lock

+{
+  "nodes": {
+    "nixpkgs": {
+      "locked": {
+        "lastModified": 1659446231,
+        "narHash": "sha256-hekabNdTdgR/iLsgce5TGWmfIDZ86qjPhxDg/8TlzhE=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "eabc38219184cc3e04a974fe31857d8e0eac098d",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "ref": "nixos-21.11",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "root": {
+      "inputs": {
+        "nixpkgs": "nixpkgs"
+      }
+    }
+  },
+  "root": "root",
+  "version": 7
+}

flake.nix

+{
+  description = "A very basic flake";
+
+  inputs = {
+    nixpkgs.url = "github:NixOS/nixpkgs/nixos-21.11";
+  };
+
+  outputs = { self, nixpkgs }:
+  let
+    system = "x86_64-linux";
+    pkgs = import nixpkgs { inherit system; };
+
+    rPkgs = with pkgs.rPackages; [
+      tidyverse
+      modelr
+      ggh4x
+    ];
+
+    myR = pkgs.rWrapper.override { packages = rPkgs; };
+
+    rmdPkgs = with pkgs.rPackages; [
+        rmarkdown
+        markdown
+        knitr
+        tinytex
+        magick
+        codetools
+      ];
+
+      myRmd = pkgs.rWrapper.override { packages = rPkgs ++ rmdPkgs; };
+      myRstudio = pkgs.rstudioWrapper.override { packages = rPkgs ++ rmdPkgs; };
+  in
+  {
+    devShells.${system} = {
+      default = pkgs.mkShell {
+        buildInputs = [ pkgs.graphviz pkgs.snakemake ];
+      };
+
+      python = pkgs.mkShell {
+        buildInputs = [
+          pkgs.python3
+        ];
+      };
+
+      rshell = pkgs.mkShell {
+        buildInputs = [ myR ];
+      };
+
+      rmdshell = pkgs.mkShell {
+        buildInputs = with pkgs; [ myRmd pandoc texlive.combined.scheme-full ];
+      };
+
+      rmddev = pkgs.mkShell {
+        buildInputs = with pkgs; [ myRstudio pandoc texlive.combined.scheme-full ];
+      };
+
+    };
+  };
+}
+