Merge branch 'creams' into 'master'

Creams

See merge request rarias/bscpkgs!2

garlic/creams/default.nix

@@ -2,23 +2,45 @@
   stdenv
 , nanos6
 , mpi
+, openmpi
+, impi
 , tampi
 , mcxx
-, icc
+, gnuDef
+, intelDef
+, cc
+, gitBranch
 }:
 
+assert (mpi == impi || mpi == openmpi);
+
+let
+  mpiName = (if mpi == openmpi then
+    "OpenMPI"
+  else
+    "IntelMPI");
+
+  compName = (if cc == intelDef then
+    "Intel"
+  else
+    "GNU");
+
+in
 stdenv.mkDerivation rec {
   name = "creams";
 
+  # src = /home/Computational/pmartin1/creams-simplified;
   src = builtins.fetchGit {
     url = "ssh://git@bscpm02.bsc.es/pmartin1/creams-simplified.git";
-    ref = "MPI+OmpSs-2+TAMPI";
+    ref = "${gitBranch}";
   };
 
+  programPath = "/bin/creams.exe";
+
   buildInputs = [
     nanos6
     mpi
-    icc
+    cc
     tampi
     mcxx
   ];
@@ -27,12 +49,19 @@ stdenv.mkDerivation rec {
 
   configurePhase = ''
     export TAMPI_HOME=${tampi}
+
     . etc/bashrc
+
+    export FORTRAN_COMPILER=${compName}
+    export MPI_LIB=${mpiName}
+
+    echo
+
+    CREAMS_UPDATE_ENVIRONMENT
   '';
 
   installPhase = ''
     mkdir -p $out/bin
     cp -a build/* $out/bin
   '';
-
 }

garlic/creams/input.nix

@@ -0,0 +1,31 @@
+{
+  stdenv
+, granul ? 0
+, nprocz ? 0
+, gitBranch
+}:
+
+stdenv.mkDerivation rec {
+  name = "creams-input";
+
+  # src = /home/Computational/pmartin1/creams-simplified;
+  src = builtins.fetchGit {
+    url = "ssh://git@bscpm02.bsc.es/pmartin1/creams-simplified.git";
+    ref = "${gitBranch}";
+  };
+
+  phases = [ "unpackPhase" "patchPhase" "installPhase" ];
+
+  patchPhase = ''
+    patchShebangs SodTubeBenchmark/gridScript.sh
+  '';
+  
+  installPhase = ''
+    pushd SodTubeBenchmark
+      ./gridScript.sh 0 0 ${toString nprocz} ${toString granul}
+    popd
+
+    mkdir -p $out
+    cp -a SodTubeBenchmark $out/
+  '';
+}

garlic/exp/creams/ss+hybrid.nix

@@ -0,0 +1,180 @@
+{
+  stdenv
+, nixpkgs
+, pkgs
+, genApp
+, genConfigs
+, runWrappers
+}:
+
+with stdenv.lib;
+
+let
+  bsc = pkgs.bsc;
+
+  # Set variable configuration for the experiment
+  varConfig = {
+    cc  = [ bsc.icc  ]; # [ bsc.icc  pkgs.gfortran10 ];
+
+    mpi = [ bsc.impi ]; # [ bsc.impi bsc.openmpi-mn4 ];
+
+    input = [
+      { nodes=1 ; nprocz=2 ; granul=37; time= "10:00:00"; }
+      { nodes=2 ; nprocz=4 ; granul=19; time= "05:00:00"; }
+      { nodes=4 ; nprocz=8 ; granul=10; time= "03:00:00"; }
+      { nodes=8 ; nprocz=16; granul=9 ; time= "02:00:00"; }
+      { nodes=16; nprocz=32; granul=9 ; time= "01:00:00"; }
+    ];
+
+    gitBranch = [ "garlic/mpi+isend+oss+task"
+                  "garlic/mpi+send+omp+fork"
+                  "garlic/mpi+send+oss+task"
+                  "garlic/tampi+isend+oss+task"
+    ];
+  };
+
+  # Common configuration
+  common = {
+    # Resources
+    ntasksPerNode   = 2;
+    #ntasksPerSocket = 1; // Add this variable to nix
+
+    # 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 "${stage}";
+
+  w = runWrappers;
+
+  sbatch = {stage, conf, ...}: with conf; w.sbatch {
+    nodes = input.nodes;
+    program = stageProgram stage;
+    exclusive = true;
+    time = input.time;
+    #qos = "debug";
+    jobName = "creams-ss-${toString input.nodes}-${toString gitBranch}";
+    inherit nixPrefix ntasksPerNode;
+  };
+
+  control = {stage, conf, ...}: with conf; w.control {
+    program = stageProgram stage;
+  };
+
+  srun = {stage, conf, ...}: with conf; w.srun {
+    program = stageProgram stage;
+    srunOptions = "--cpu-bind=verbose,socket";
+    inherit nixPrefix;
+  };
+
+  statspy = {stage, conf, ...}: with conf; w.statspy {
+    program = stageProgram stage;
+  };
+
+  perf = {stage, conf, ...}: with conf; w.perf {
+    program = stageProgram stage;
+    perfArgs = "sched record -a";
+  };
+
+  nixsetup = {stage, conf, ...}: with conf; w.nixsetup {
+    program = stageProgram stage;
+    nixsetup = "${nixPrefix}/bin/nix-setup";
+  };
+
+  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
+    '';
+  };
+
+  bscOverlay = import ../../../overlay.nix;
+
+  genPkgs = newOverlay: nixpkgs {
+    overlays = [
+      bscOverlay
+      newOverlay
+    ];
+  };
+
+  inputDataset = {stage, conf, ...}:
+  let
+    input = bsc.garlic.creamsInput.override {
+      gitBranch = conf.gitBranch;
+      granul = conf.input.granul;
+      nprocz = conf.input.nprocz;
+    };
+  in w.argv
+  {
+    program = stageProgram stage;
+    env = ''
+      cp -r ${input}/SodTubeBenchmark/* .
+      chmod +w -R .
+    '';
+  };
+
+  # 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.
+
+  creamsFn = {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.creams.override {
+      inherit cc 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 app with the argv and env vars
+    ++ [ inputDataset creamsFn ];
+
+  # 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/exp/creams/ss+pure.nix

@@ -0,0 +1,176 @@
+{
+  stdenv
+, nixpkgs
+, pkgs
+, genApp
+, genConfigs
+, runWrappers
+}:
+
+with stdenv.lib;
+
+let
+  bsc = pkgs.bsc;
+
+  # Set variable configuration for the experiment
+  varConfig = {
+    cc  = [ bsc.icc  ]; # [ bsc.icc  pkgs.gfortran10 ];
+
+    mpi = [ bsc.impi ]; # [ bsc.impi bsc.openmpi-mn4 ];
+
+    input = [
+      { nodes=1 ; nprocz=48 ; granul=0; time= "10:00:00";  }
+      { nodes=2 ; nprocz=96 ; granul=0; time= "05:00:00";  }
+      { nodes=4 ; nprocz=192; granul=0; time= "03:00:00";  }
+      { nodes=8 ; nprocz=384; granul=0; time= "02:00:00";  }
+      { nodes=16; nprocz=768; granul=0; time= "01:00:00";  }
+    ];
+
+    gitBranch = [ "garlic/mpi+send+seq" ];
+  };
+
+  # Common configuration
+  common = {
+    # Resources
+    ntasksPerNode   = 48;
+    #ntasksPerSocket = 24; // Add this variable to nix
+
+    # 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 "${stage}";
+
+  w = runWrappers;
+
+  sbatch = {stage, conf, ...}: with conf; w.sbatch {
+    nodes = input.nodes;
+    program = stageProgram stage;
+    exclusive = true;
+    time = input.time;
+    #qos = "debug";
+    jobName = "creams-ss-${toString input.nodes}-${toString gitBranch}";
+    inherit nixPrefix ntasksPerNode;
+  };
+
+  control = {stage, conf, ...}: with conf; w.control {
+    program = stageProgram stage;
+  };
+
+  srun = {stage, conf, ...}: with conf; w.srun {
+    program = stageProgram stage;
+    srunOptions = "--cpu-bind=verbose,rank";
+    inherit nixPrefix;
+  };
+
+  statspy = {stage, conf, ...}: with conf; w.statspy {
+    program = stageProgram stage;
+  };
+
+  perf = {stage, conf, ...}: with conf; w.perf {
+    program = stageProgram stage;
+    perfArgs = "sched record -a";
+  };
+
+  nixsetup = {stage, conf, ...}: with conf; w.nixsetup {
+    program = stageProgram stage;
+    nixsetup = "${nixPrefix}/bin/nix-setup";
+  };
+
+  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
+    '';
+  };
+
+  bscOverlay = import ../../../overlay.nix;
+
+  genPkgs = newOverlay: nixpkgs {
+    overlays = [
+      bscOverlay
+      newOverlay
+    ];
+  };
+
+  inputDataset = {stage, conf, ...}:
+  let
+    input = bsc.garlic.creamsInput.override {
+      gitBranch = conf.gitBranch;
+      granul = conf.input.granul;
+      nprocz = conf.input.nprocz;
+    };
+  in w.argv
+  {
+    program = stageProgram stage;
+    env = ''
+      cp -r ${input}/SodTubeBenchmark/* .
+      chmod +w -R .
+    '';
+  };
+
+  # 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.
+
+  creamsFn = {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.creams.override {
+      inherit cc 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 app with the argv and env vars
+    ++ [ inputDataset creamsFn ];
+
+  # 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/stages/sbatch.nix

@@ -28,7 +28,7 @@ with stdenv.lib;
 let
 
   sbatchOpt = name: value: optionalString (value!=null)
-    "#SBATCH --${name}=${value}\n";
+    "#SBATCH --${name}=${toString value}\n";
   sbatchEnable = name: value: optionalString (value!=null)
     "#SBATCH --${name}\n";
 

overlay.nix

@@ -143,14 +143,20 @@ let
 #        tampi = tampi;
 #      };
 #
-#      creams = callPackage ./garlic/creams {
-#        stdenv = pkgs.gcc9Stdenv;
-#        mpi = intel-mpi;
-#        tampi = tampi.override {
-#          mpi = intel-mpi;
-#        };
-#      };
-#
+      creams = callPackage ./garlic/creams {
+        gnuDef   = self.gfortran10 ; # Default GNU   compiler version
+        intelDef = self.bsc.icc    ; # Default Intel compiler version
+
+        gitBranch = "garlic/mpi+send+seq";
+
+        cc  = self.bsc.icc; # self.bsc.icc OR self.gfortran10;
+        mpi = self.bsc.mpi; # self.bsc.mpi OR self.bsc.openmpi-mn4;
+      };
+
+      creamsInput = callPackage ./garlic/creams/input.nix {
+        gitBranch = "garlic/mpi+send+seq";
+      };
+
 #      lulesh = callPackage ./garlic/lulesh {
 #        mpi = intel-mpi;
 #      };
@@ -231,6 +237,25 @@ let
           };
         };
 
+        creams = {
+          ss = {
+            pure = callPackage ./garlic/exp/creams/ss+pure.nix {
+              pkgs = self // self.bsc.garlic;
+              nixpkgs = import <nixpkgs>;
+              genApp = self.bsc.garlic.genApp;
+              genConfigs = self.bsc.garlic.genConfigs;
+              runWrappers = self.bsc.garlic.runWrappers;
+            };
+            hybrid = callPackage ./garlic/exp/creams/ss+hybrid.nix {
+              pkgs = self // self.bsc.garlic;
+              nixpkgs = import <nixpkgs>;
+              genApp = self.bsc.garlic.genApp;
+              genConfigs = self.bsc.garlic.genConfigs;
+              runWrappers = self.bsc.garlic.runWrappers;
+            };
+          };
+        };
+
         osu = rec {
           latency-internode = callPackage ./garlic/exp/osu/latency.nix { };
           latency-intranode = callPackage ./garlic/exp/osu/latency.nix {