Merge branch 'saiph' into 'master'

Saiph

See merge request rarias/bscpkgs!6

NOISE

@@ -121,6 +121,3 @@ ABSTRACT
   within Nix, they will be copied with the current data and consequently 
   not updated during the Nix compilation process.
 
-  See saiph devMode option and its implications at   
-  bscpkgs/garlic/saiph/default.nix
-  

garlic/apps/saiph/default.nix

@@ -6,24 +6,26 @@
 , cc 
 , vtk
 , boost
-, devMode ? false
 , gitBranch ? "master"
 , numComm ? null
+, nbx ? null
+, nby ? null
+, nbz ? null
 , vectFlags ? null
 #, breakpointHook
 }:
 
+with stdenv.lib;
+
 stdenv.mkDerivation rec {
   name = "saiph";
 
-  src = (if (devMode == true) then ~/repos/saiph
+  src = builtins.fetchGit {
-         else
-	 builtins.fetchGit {
     url = "ssh://git@bscpm02.bsc.es/DSLs/saiph.git";
     ref = "${gitBranch}";
-         });
+  };
 
-  programPath = "/bin/ExHeat3D";
+  programPath = "/bin/Heat3D_vect";
 
   enableParallelBuilding = true;
   dontStrip = true;
@@ -46,22 +48,24 @@ stdenv.mkDerivation rec {
     cd saiphv2/cpp/src 
     export VTK_VERSION=8.2
     export VTK_HOME=${vtk}
-  ''
+    make clean
-  + (if (devMode == true) then "make clean" else "")
+  '';
-  ;
 
   makeFlags = [
     "-f" "Makefile.${cc.cc.CC}"
     "apps"
-    "APP=ExHeat3D"
+    "APP=Heat3D_vect"
-    ( if (numComm != null) then "NUM_COMM=${toString numComm}" else "" )
+  ] ++ optional (nbx != null) "NB_X=${toString nbx}"
-    ( if (vectFlags != null) then "VECT_FLAGS=${toString vectFlags}" else "" )
+    ++ optional (nby != null) "NB_Y=${toString nby}"
-  ];
+    ++ optional (nbz != null) "NB_Z=${toString nbz}"
+    ++ optional (numComm != null) "NUM_COMM=${toString numComm}"
+    ++ optional (vectFlags != null) "VECT_FLAGS=${toString vectFlags}"
+    ;
     
   installPhase = ''
     mkdir -p $out/lib
     mkdir -p $out/bin
     cp obj/libsaiphv2.so $out/lib/
-    cp bin/ExHeat3D $out/bin/
+    cp bin/Heat3D_vect $out/bin/
   '';
 }

garlic/exp/saiph/granularity.nix

@@ -0,0 +1,68 @@
+{
+  stdenv
+, stdexp
+, bsc
+, targetMachine
+, stages
+}:
+
+with stdenv.lib;
+
+let
+  # Initial variable configuration
+  varConf = with bsc; {
+    nb = [ 1 2 4 8 ];
+  };
+
+  # Generate the complete configuration for each unit
+  genConf = with bsc; c: targetMachine.config // rec {
+    expName = "saiph.granularity";
+    unitName = "${expName}.nbx-nby-nbz-${toString nbx}-${toString nby}-${toString nbz}";
+
+    # saiph options
+    nbx = c.nb;
+    nby = c.nb;
+    nbz = c.nb;
+    mpi = impi;
+    gitBranch = "garlic/tampi+isend+oss+task+simd";
+
+    # Repeat the execution of each unit 50 times
+    loops = 50;
+
+    # Resources
+    qos = "debug";
+    time = "00:30:00";
+    ntasksPerNode = 1;
+    nodes = 1;
+    cpuBind = "sockets,verbose";
+    jobName = "${unitName}-${gitBranch}";
+  };
+
+  # Compute the array of configurations
+  configs = stdexp.buildConfigs {
+    inherit varConf genConf;
+  };
+
+  exec = {nextStage, conf, ...}: with conf; stages.exec {
+    inherit nextStage;
+    env = ''
+      export OMP_NUM_THREADS=${toString hw.cpusPerSocket}
+      export NANOS6_REPORT_PREFIX="#"
+      export I_MPI_THREAD_SPLIT=1
+      export ASAN_SYMBOLIZER_PATH=${bsc.clangOmpss2Unwrapped}/bin/llvm-symbolizer
+    '';
+  };
+
+  program = {nextStage, conf, ...}: with conf;
+  let
+    customPkgs = stdexp.replaceMpi conf.mpi;
+  in
+    customPkgs.apps.saiph.override {
+      inherit nbx nby nbz mpi gitBranch;
+    };
+
+  pipeline = stdexp.stdPipeline ++ [ exec program ];
+
+in
+ 
+  stdexp.genExperiment { inherit configs pipeline; }

garlic/exp/saiph/numcomm.nix

@@ -20,7 +20,6 @@ let
     unitName = "${expName}.nc-${toString numComm}";
 
     # saiph options
-    devMode = false;
     inherit (c) numComm;
     mpi = impi;
     gitBranch = "garlic/tampi+isend+oss+task+simd";
@@ -57,7 +56,7 @@ let
     customPkgs = stdexp.replaceMpi conf.mpi;
   in
     customPkgs.apps.saiph.override {
-      inherit devMode numComm mpi gitBranch;
+      inherit numComm mpi gitBranch;
     };
 
   pipeline = stdexp.stdPipeline ++ [ exec program ];

garlic/fig/saiph/granularity.R

@@ -0,0 +1,100 @@
+library(ggplot2)
+library(dplyr)
+library(scales)
+library(jsonlite)
+
+args=commandArgs(trailingOnly=TRUE)
+
+# Read the timetable from args[1]
+input_file = "input.json"
+if (length(args)>0) { input_file = args[1] }
+
+# Load the dataset in NDJSON format
+dataset = jsonlite::stream_in(file(input_file)) %>%
+	jsonlite::flatten()
+
+
+# We only need the nblocks and time
+df = select(dataset, config.nbx, time) %>%
+	rename(nbx=config.nbx)
+
+df$nbx = as.factor(df$nbx)
+
+# Normalize the time by the median
+D=group_by(df, nbx) %>%
+	mutate(tnorm = time / median(time) - 1) %>%
+	mutate(bad = max(ifelse(abs(tnorm) >= 0.01, 1, 0)))
+
+D$bad = as.factor(D$bad)
+
+
+print(D)
+
+ppi=300
+h=5
+w=5
+
+png("box.png", width=w*ppi, height=h*ppi, res=ppi)
+#
+#
+#
+# Create the plot with the normalized time vs nblocks
+p = ggplot(data=D, aes(x=nbx, y=tnorm, color=bad)) +
+
+	# Labels
+	labs(x="nbx", y="Normalized time",
+              title=sprintf("Saiph-Heat3D normalized time"), 
+              subtitle=input_file) +
+
+	# Center the title
+	#theme(plot.title = element_text(hjust = 0.5)) +
+
+	# Black and white mode (useful for printing)
+	#theme_bw() +
+
+	# Add the maximum allowed error lines
+	geom_hline(yintercept=c(-0.01, 0.01),
+		linetype="dashed", color="gray") +
+
+	# Draw boxplots
+	geom_boxplot() +
+	scale_color_manual(values=c("black", "brown")) +
+
+	#scale_y_continuous(breaks = scales::pretty_breaks(n = 10)) +
+
+	theme_bw() +
+
+	theme(plot.subtitle=element_text(size=8)) +
+        theme(legend.position = "none")
+	#theme(legend.position = c(0.85, 0.85))
+
+
+
+
+# Render the plot
+print(p)
+
+## Save the png image
+dev.off()
+#
+png("scatter.png", width=w*ppi, height=h*ppi, res=ppi)
+#
+## Create the plot with the normalized time vs nblocks
+p = ggplot(D, aes(x=nbx, y=time)) +
+
+	labs(x="nbx", y="Time (s)",
+              title=sprintf("Saiph-Heat3D granularity"), 
+              subtitle=input_file) +
+	theme_bw() +
+	theme(plot.subtitle=element_text(size=8)) +
+	theme(legend.position = c(0.5, 0.88)) +
+
+	geom_point(shape=21, size=3) +
+	#scale_x_continuous(trans=log2_trans()) +
+	scale_y_continuous(trans=log2_trans())
+
+# Render the plot
+print(p)
+
+# Save the png image
+dev.off()

overlay.nix

@@ -330,6 +330,7 @@ let
 
         saiph = {
           numcomm = callPackage ./garlic/exp/saiph/numcomm.nix { };
+          granularity = callPackage ./garlic/exp/saiph/granularity.nix { };
         };
 
         creams = {
@@ -371,6 +372,7 @@ let
 
         saiph = with exp.saiph; {
           numcomm = merge [ numcomm ];
+          granularity = merge [ granularity ];
         };
 
         heat = with exp.heat; {
@@ -402,6 +404,13 @@ let
           };
         };
 
+        saiph = {
+          granularity = with ds.saiph; pp.rPlot {
+            script = ./garlic/fig/saiph/granularity.R;
+	    dataset = granularity;
+          };
+        };
+
         heat = {
           test = with ds.heat; pp.rPlot {
             script = ./garlic/fig/heat/test.R;