Simplify paths

bsc/garlic/nbody/default.nix

@@ -1,46 +0,0 @@
-{
-  stdenv
-, cc
-, tampi ? null
-, mpi ? null
-, cflags ? null
-, gitBranch
-, gitURL ? "ssh://git@bscpm02.bsc.es/garlic/apps/nbody.git"
-, blocksize ? 2048
-}:
-
-with stdenv.lib;
-stdenv.mkDerivation rec {
-  name = "nbody";
-
-  src = /home/Computational/rarias/bscpkgs/manual/nbody;
-
-  #src = builtins.fetchGit {
-  #  url = "${gitURL}";
-  #  ref = "${gitBranch}";
-  #};
-  programPath = "/bin/nbody";
-
-  buildInputs = [
-    cc
-  ]
-  ++ optional (mpi != null) [ mpi ];
-
-  preBuild = (if cflags != null then ''
-    makeFlagsArray+=(CFLAGS="${cflags}")
-  '' else "");
-
-  makeFlags = [
-    "CC=${cc.cc.CC}"
-    "BS=${toString blocksize}"
-  ];
-
-  dontPatchShebangs = true;
-
-  installPhase = ''
-    echo ${tampi}
-    mkdir -p $out/bin
-    cp nbody* $out/bin/${name}
-  '';
-
-}

garlic/exp/default.nix

@@ -0,0 +1,64 @@
+{
+  pkgs
+, callPackage
+, callPackages
+}:
+
+let
+
+  garlic = {
+
+    # Load some helper functions to generate app variants
+    inherit (import ./gen.nix) genApps genApp genConfigs;
+
+    mpptest = callPackage ./mpptest { };
+
+    ppong = callPackage ./ppong {
+      mpi = pkgs.mpi;
+    };
+
+    nbody = callPackage ./nbody {
+      cc = pkgs.icc;
+      mpi = pkgs.impi;
+      tampi = pkgs.tampi;
+      gitBranch = "garlic/seq";
+    };
+
+    runWrappers = {
+      sbatch  = callPackage ./stages/sbatch.nix { };
+      srun    = callPackage ./stages/srun.nix { };
+      launch  = callPackage ./stages/launcher.nix { };
+      control = callPackage ./stages/control.nix { };
+      nixsetup= callPackage ./stages/nix-setup.nix { };
+      argv    = callPackage ./stages/argv.nix { };
+      statspy = callPackage ./stages/statspy.nix { };
+      extrae  = callPackage ./stages/extrae.nix { };
+      stagen  = callPackage ./stages/stagen.nix { };
+    };
+
+    # Perf is tied to a linux kernel specific version
+    linuxPackages = pkgs.linuxPackages_4_4;
+    perfWrapper = callPackage ./perf.nix {
+      perf = pkgs.linuxPackages.perf;
+    };
+
+    exp = {
+      noise = callPackage ./exp/noise.nix { };
+      nbody = {
+        bs = callPackage ./exp/nbody/bs.nix {
+          pkgs = pkgs // garlic;
+        };
+        mpi = callPackage ./exp/nbody/mpi.nix { };
+      };
+      osu = rec {
+        latency-internode = callPackage ./exp/osu/latency.nix { };
+        latency-intranode = callPackage ./exp/osu/latency.nix {
+          interNode = false;
+        };
+        latency = latency-internode;
+      };
+    };
+  };
+
+in
+  garlic

garlic/exp/nbody/bs.nix

@@ -97,7 +97,7 @@ let
       -p ${toString conf.particles} )'';
   };
 
-  bscOverlay = import ../../../../overlay.nix;
+  bscOverlay = import ../../../overlay.nix;
 
   genPkgs = newOverlay: nixpkgs {
     overlays = [

garlic/exp/nbody/tampi.nix

@@ -0,0 +1,165 @@
+{
+  stdenv
+, nixpkgs
+, pkgs
+, genApp
+, genConfigs
+, runWrappers
+}:
+
+with stdenv.lib;
+
+let
+  bsc = pkgs.bsc;
+
+  # Set variable configuration for the experiment
+  varConfig = {
+    cc = [ bsc.icc ];
+    mpi = [ bsc.impi bsc.openmpi ];
+    blocksize = [ 1024 ];
+  };
+
+  # Common configuration
+  common = {
+    # Compile time nbody config
+    gitBranch = "garlic/tampi+send+oss+task";
+
+    # nbody runtime options
+    particles = 1024*128;
+    timesteps = 20;
+
+    # Resources
+    ntasksPerNode = "48";
+    nodes = "1";
+
+    # Stage configuration
+    enableSbatch = true;
+    enableControl = true;
+    enableExtrae = false;
+    enablePerf = false;
+    enableCtf = false;
+
+    # MN4 path
+    nixPrefix = "/gpfs/projects/bsc15/nix";
+  };
+
+  # Compute the cartesian product of all configurations
+  configs = map (conf: conf // common) (genConfigs varConfig);
+
+  stageProgram = stage:
+    if stage ? programPath
+    then "${stage}${stage.programPath}" else "${stage}";
+
+  w = runWrappers;
+
+  sbatch = {stage, conf, ...}: with conf; w.sbatch {
+    program = stageProgram stage;
+    exclusive = true;
+    time = "02:00:00";
+    qos = "debug";
+    jobName = "nbody-bs";
+    inherit nixPrefix nodes ntasksPerNode;
+  };
+
+  control = {stage, conf, ...}: with conf; w.control {
+    program = stageProgram stage;
+  };
+
+  srun = {stage, conf, ...}: with conf; w.srun {
+    program = stageProgram stage;
+    srunOptions = "--cpu-bind=verbose,rank";
+    inherit nixPrefix;
+  };
+
+  statspy = {stage, conf, ...}: with conf; w.statspy {
+    program = stageProgram stage;
+  };
+
+  perf = {stage, conf, ...}: with conf; w.perf {
+    program = stageProgram stage;
+    perfArgs = "sched record -a";
+  };
+
+  nixsetup = {stage, conf, ...}: with conf; w.nixsetup {
+    program = stageProgram stage;
+  };
+
+  extrae = {stage, conf, ...}: w.extrae {
+    program = stageProgram stage;
+    traceLib = "mpi"; # mpi -> libtracempi.so
+    configFile = ./extrae.xml;
+  };
+
+  ctf = {stage, conf, ...}: w.argv {
+    program = stageProgram stage;
+    env = ''
+      export NANOS6=ctf
+      export NANOS6_CTF2PRV=0
+    '';
+  };
+
+  argv = {stage, conf, ...}: w.argv {
+    program = stageProgram stage;
+    env = ''
+      set -e
+      export I_MPI_THREAD_SPLIT=1
+    '';
+    argv = ''( -t ${toString conf.timesteps}
+      -p ${toString conf.particles} )'';
+  };
+
+  bscOverlay = import ../../../overlay.nix;
+
+  genPkgs = newOverlay: nixpkgs {
+    overlays = [
+      bscOverlay
+      newOverlay
+    ];
+  };
+
+  # We may be able to use overlays by invoking the fix function directly, but we
+  # have to get the definition of the bsc packages and the garlic ones as
+  # overlays.
+
+  nbodyFn = {stage, conf, ...}: with conf;
+    let
+      # We set the mpi implementation to the one specified in the conf, so all
+      # packages in bsc will use that one.
+      customPkgs = genPkgs (self: super: {
+        bsc = super.bsc // { mpi = conf.mpi; };
+      });
+    in
+    customPkgs.bsc.garlic.nbody.override {
+      inherit cc blocksize mpi gitBranch;
+    };
+
+  stages = with common; []
+    # Use sbatch to request resources first
+    ++ optional enableSbatch sbatch
+
+    # Repeats the next stages N times
+    ++ optionals enableControl [ nixsetup control ]
+
+    # Executes srun to launch the program in the requested nodes, and
+    # immediately after enters the nix environment again, as slurmstepd launches
+    # the next stages from outside the namespace.
+    ++ [ srun nixsetup ]
+
+    # Intrumentation with extrae
+    ++ optional enableExtrae extrae
+
+    # Optionally profile the next stages with perf
+    ++ optional enablePerf perf
+
+    # Optionally profile nanos6 with the new ctf
+    ++ optional enableCtf ctf
+
+    # Execute the nbody app with the argv and env vars
+    ++ [ argv nbodyFn ];
+
+  # List of actual programs to be executed
+  jobs = map (conf: w.stagen { inherit conf stages; }) configs;
+
+in
+  # We simply run each program one after another
+  w.launch jobs

garlic/nbody/default.nix

@@ -0,0 +1,68 @@
+{
+  stdenv
+, cc
+, mpi ? null
+, tampi ? null
+, mcxx ? null
+, cflags ? null
+, gitBranch
+, gitURL ? "ssh://git@bscpm02.bsc.es/garlic/apps/nbody.git"
+, blocksize ? 2048
+}:
+
+assert !(tampi != null && mcxx == null);
+
+with stdenv.lib;
+stdenv.mkDerivation rec {
+  name = "nbody";
+
+  #src = /home/Computational/rarias/bscpkgs/manual/nbody;
+
+  src = builtins.fetchGit {
+    url = "${gitURL}";
+    ref = "${gitBranch}";
+  };
+  programPath = "/bin/nbody";
+
+  buildInputs = [
+    cc
+  ]
+  ++ optional (mpi != null) mpi
+  ++ optional (tampi != null) tampi
+  ++ optional (mcxx != null) mcxx;
+
+  preBuild = (if cflags != null then ''
+    makeFlagsArray+=(CFLAGS="${cflags}")
+  '' else "");
+
+  postPatch = ""
+
+  # This should be fixed in the Makefile as well.
+  + ''sed -i 's/libtampi.a/libtampi-c.a/g' Makefile
+  ''
+  # Dirty HACK until the nbody issue at:
+  # https://pm.bsc.es/gitlab/garlic/apps/nbody/-/issues/1
+  # is properly fixed.
+  +
+    (if (mpi.pname or "unknown") == "openmpi" then
+      ''sed -i 's/-lstdc++/-lstdc++ -lmpi_cxx/g' Makefile
+      ''
+    else
+      ""
+    );
+
+  makeFlags = [
+    "CC=${cc.cc.CC}"
+    "BS=${toString blocksize}"
+  ]
+  ++ optional (tampi != null) "TAMPI_HOME=${tampi}";
+
+  dontPatchShebangs = true;
+
+  installPhase = ''
+    echo ${tampi}
+    mkdir -p $out/bin
+    cp nbody* $out/bin/${name}
+  '';
+
+}

garlic/stages/argv.nix

@@ -6,7 +6,9 @@
 {
   program
 , env ? ""
-, argv # bash array as string, example: argv=''(-f "file with spaces" -t 10)''
+
+# bash array as string, example: argv=''(-f "file with spaces" -t 10)''
+, argv ? "()"
 }:
 
 stdenv.mkDerivation {

garlic/stages/gen.nix

@@ -0,0 +1,34 @@
+let
+  lib = import <nixpkgs/lib>;
+
+  gen = rec {
+    # genAttrSets "a" ["hello" "world"]
+    # [ { a = "hello"; } { a = "world"; } ]
+    genAttrSets = (name: arr: (map (x: {${name}=x; })) arr);
+
+    # addAttrSets "a" [1 2] {e=4;}
+    # [ { a = 1; e = 4; } { a = 2; e = 4; } ]
+    addAttrSets = (name: arr: set: (map (x: set // {${name}=x; })) arr);
+
+    # attrToList {a=1;}
+    # [ { name = "a"; value = 1; } ]
+    attrToList = (set: map (name: {name=name; value=set.${name};} ) (builtins.attrNames set));
+
+    # mergeConfig [{e=1;}] {name="a"; value=[1 2]
+    # [ { a = 1; e = 1; } { a = 2; e = 1; } ]
+    mergeConfig = (arr: new: lib.flatten ( map (x: addAttrSets new.name new.value x) arr));
+
+    # genConfigs {a=[1 2]; b=[3 4];}
+    # [ { a = 1; b = 3; } { a = 1; b = 4; } { a = 2; b = 3; } { a = 2; b = 4; } ]
+    genConfigs = (config: lib.foldl mergeConfig [{}] (attrToList config));
+
+    # Generate multiple app versions by override with each config
+    genApp = (app: configs: map (conf: app.override conf // {conf=conf;}) configs);
+
+    # Generate app version from an array of apps
+    genApps = (apps: configs:
+      lib.flatten (map (app: genApp app configs) apps));
+
+  };
+in
+  gen

overlay.nix

@@ -2,20 +2,19 @@ self:  /* Future last stage */
 super: /* Previous stage */
 
 let
-  #callPackage = self.callPackage;
   inherit (self.lib) callPackageWith;
   inherit (self.lib) callPackagesWith;
   callPackage = callPackageWith (self // self.bsc);
 
+  # --------------------------------------------------------- #
+  #  BSC Packages
+  # --------------------------------------------------------- #
+
   bsc = {
     # Default MPI implementation to use. Will be overwritten by the
     # experiments.
     mpi = self.bsc.openmpi;
 
-    # --------------------------------------------------------- #
-    #  BSC Packages
-    # --------------------------------------------------------- #
-
     perf = callPackage ./bsc/perf/default.nix {
       kernel = self.linuxPackages_4_9.kernel;
       systemtap = self.linuxPackages_4_9.systemtap;
@@ -76,34 +75,29 @@ let
 
     openmpi = self.bsc.openmpi-mn4;
 
-    fftw = callPackage ./bsc/fftw/default.nix {
+    fftw = callPackage ./bsc/fftw/default.nix { };
-      mpi = self.bsc.mpi;
+
+    extrae = callPackage ./bsc/extrae/default.nix { };
+
+    tampi = callPackage ./bsc/tampi/default.nix { };
+
+    mcxxGit = callPackage ./bsc/mcxx/default.nix {
+      bison = self.bison_3_5;
     };
 
-    extrae = callPackage ./bsc/extrae/default.nix {
+    mcxxRarias = callPackage ./bsc/mcxx/rarias.nix {
-      mpi = self.bsc.mpi;
+      bison = self.bison_3_5;
     };
 
-    tampi = callPackage ./bsc/tampi/default.nix {
+    mcxx = self.bsc.mcxxGit;
-      mpi = self.bsc.mpi;
-    };
-
-    mcxx = callPackage ./bsc/mcxx/default.nix { };
-
-    mcxx-rarias = callPackage ./bsc/mcxx/rarias.nix { };
 
     # Use nanos6 git by default
-    nanos6 = self.nanos6-git;
+    nanos6 = self.bsc.nanos6-git;
-    nanos6-latest = callPackage ./bsc/nanos6/default.nix {
+    nanos6-latest = callPackage ./bsc/nanos6/default.nix { };
-      extrae = self.bsc.extrae;
-    };
 
-    nanos6-git = callPackage ./bsc/nanos6/git.nix {
+    nanos6-git = callPackage ./bsc/nanos6/git.nix { };
-      extrae = self.bsc.extrae;
-    };
 
     vtk = callPackage ./bsc/vtk/default.nix {
-      mpi = self.bsc.mpi;
       inherit (self.xorg) libX11 xorgproto libXt;
     };
 
@@ -130,47 +124,57 @@ let
 
     mpptest = callPackage ./bsc/mpptest/default.nix { };
 
-
     garlic = {
 
       # Load some helper functions to generate app variants
-      inherit (import ./bsc/garlic/gen.nix) genApps genApp genConfigs;
+      inherit (import ./garlic/gen.nix) genApps genApp genConfigs;
 
-      mpptest = callPackage ./bsc/garlic/mpptest { };
+      mpptest = callPackage ./garlic/mpptest { };
 
-      ppong = callPackage ./bsc/garlic/ppong {
+      ppong = callPackage ./garlic/ppong {
         mpi = self.bsc.mpi;
       };
 
-      nbody = callPackage ./bsc/garlic/nbody {
+      nbody = callPackage ./garlic/nbody {
         cc = self.bsc.icc;
-        mpi = self.bsc.impi;
+        mpi = self.bsc.mpi;
         tampi = self.bsc.tampi;
+        mcxx = self.bsc.mcxx;
         gitBranch = "garlic/seq";
       };
 
+      # Execution wrappers
       runWrappers = {
-        sbatch  = callPackage ./bsc/garlic/sbatch.nix { };
+        sbatch    = callPackage ./garlic/stages/sbatch.nix { };
-        srun    = callPackage ./bsc/garlic/srun.nix { };
+        srun      = callPackage ./garlic/stages/srun.nix { };
-        launch  = callPackage ./bsc/garlic/launcher.nix { };
+        launch    = callPackage ./garlic/stages/launcher.nix { };
-        control = callPackage ./bsc/garlic/control.nix { };
+        control   = callPackage ./garlic/stages/control.nix { };
-        nixsetup= callPackage ./bsc/garlic/nix-setup.nix { };
+        nixsetup  = callPackage ./garlic/stages/nix-setup.nix { };
-        argv    = callPackage ./bsc/garlic/argv.nix { };
+        argv      = callPackage ./garlic/stages/argv.nix { };
-        statspy = callPackage ./bsc/garlic/statspy.nix { };
+        statspy   = callPackage ./garlic/stages/statspy.nix { };
-        extrae  = callPackage ./bsc/garlic/extrae.nix { };
+        extrae    = callPackage ./garlic/stages/extrae.nix { };
-        stagen  = callPackage ./bsc/garlic/stagen.nix { };
+        stagen    = callPackage ./garlic/stages/stagen.nix { };
+        perf      = callPackage ./garlic/stages/perf.nix { };
       };
 
       # Perf is tied to a linux kernel specific version
-      linuxPackages = self.linuxPackages_4_4;
+      #linuxPackages = self.linuxPackages_4_4;
-      perfWrapper = callPackage ./bsc/garlic/perf.nix {
+      #perfWrapper = callPackage ./garlic/perf.nix {
-        perf = self.linuxPackages.perf;
+      #  perf = self.linuxPackages.perf;
-      };
+      #};
 
       exp = {
-        noise = callPackage ./bsc/garlic/exp/noise.nix { };
+        noise = callPackage ./garlic/exp/noise.nix { };
         nbody = {
-          bs = callPackage ./bsc/garlic/exp/nbody/bs.nix {
+          bs = callPackage ./garlic/exp/nbody/bs.nix {
+            pkgs = self // self.bsc.garlic;
+            nixpkgs = import <nixpkgs>;
+            genApp = self.bsc.garlic.genApp;
+            genConfigs = self.bsc.garlic.genConfigs;
+            runWrappers = self.bsc.garlic.runWrappers;
+          };
+
+          tampi = callPackage ./garlic/exp/nbody/tampi.nix {
             pkgs = self // self.bsc.garlic;
             nixpkgs = import <nixpkgs>;
             genApp = self.bsc.garlic.genApp;
@@ -180,8 +184,8 @@ let
 #          mpi = callPackage ./bsc/garlic/exp/nbody/mpi.nix { };
         };
         osu = rec {
-          latency-internode = callPackage ./bsc/garlic/exp/osu/latency.nix { };
+          latency-internode = callPackage ./garlic/exp/osu/latency.nix { };
-          latency-intranode = callPackage ./bsc/garlic/exp/osu/latency.nix {
+          latency-intranode = callPackage ./garlic/exp/osu/latency.nix {
             interNode = false;
           };
           latency = latency-internode;
@@ -193,4 +197,10 @@ let
 in
   {
     bsc = bsc;
+
+    # Alias
+    garlic = bsc.garlic;
+
+    # Alias
+    exp = bsc.garlic.exp;
   }