WIP isolation

garlic/exp/nbody/tampi.nix

@@ -16,13 +16,15 @@ let
   varConfig = {
     cc = [ bsc.icc ];
     mpi = [ bsc.impi ];
+    #mpi = [ bsc.mpichDebug ];
     blocksize = [ 1024 ];
   };
 
   # Common configuration
   common = {
     # Compile time nbody config
-    gitBranch = "garlic/tampi+send+oss+task";
+    gitBranch = "garlic/mpi+send";
+    #gitBranch = "garlic/tampi+send+oss+task";
 
     # nbody runtime options
     particles = 1024*4;
@@ -30,15 +32,16 @@ let
 
     # Resources
     ntasksPerNode = "2";
-    nodes = "2";
+    nodes = "1";
 
     # Stage configuration
-    enableRunexp = true;
+    enableTrebuchet = true;
     enableSbatch    = true;
     enableControl   = true;
     enableExtrae    = false;
     enablePerf      = false;
     enableCtf       = false;
+    enableStrace    = true;
 
     # MN4 path
     nixPrefix = "/gpfs/projects/bsc15/nix";
@@ -90,6 +93,11 @@ let
     perfArgs = "sched record -a";
   };
 
+  nixsetup = {stage, conf, ...}: with conf; w.nixsetup {
+    program = stageProgram stage;
+    nixsetup = "${nixPrefix}/bin/nix-setup";
+  };
+
   isolate = {stage, conf, ...}: with conf; w.isolate {
     program = stageProgram stage;
     clusterName = "mn4";
@@ -110,8 +118,23 @@ let
     '';
   };
 
+  strace = {stage, conf, ...}: w.strace {
+    program = stageProgram stage;
+  };
+
   argv = {stage, conf, ...}: w.argv {
     program = stageProgram stage;
+    env = ''
+      #export I_MPI_PMI_LIBRARY=${bsc.slurm17-libpmi2}/lib/libpmi2.so
+      export I_MPI_DEBUG=+1000
+      #export I_MPI_FABRICS=shm
+
+      export MPICH_DBG_OUTPUT=VERBOSE
+      export MPICH_DBG_CLASS=ALL
+      export MPICH_DBG_OUTPUT=stdout
+
+      export FI_LOG_LEVEL=Info
+    '';
     argv = ''( -t ${toString conf.timesteps}
       -p ${toString conf.particles} )'';
   };
@@ -146,19 +169,25 @@ let
   };
 
   stages = with common; []
-    # Launch the experiment remotely
-    #++ optional enableRunexp runexp
-
     # Use sbatch to request resources first
-    ++ optional enableSbatch sbatch
+    ++ optionals enableSbatch [
+      sbatch
+      nixsetup
+      #isolate
+    ]
 
     # Repeats the next stages N times
-    ++ optionals enableControl [ isolate control ]
+    ++ optional enableControl 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 isolate ]
+    ++ [
+      #strace
+      srun
+      nixsetup
+      #isolate
+    ]
 
     # Intrumentation with extrae
     ++ optional enableExtrae extrae
@@ -169,6 +198,9 @@ let
     # Optionally profile nanos6 with the new ctf
     ++ optional enableCtf ctf
 
+    # Optionally enable strace
+    #++ optional enableStrace strace
+
     # Execute the nbody app with the argv and env vars
     ++ [ argv nbodyFn ];
 
@@ -177,7 +209,7 @@ let
 
   launcher = launch jobs;
 
-  runexp = stage: w.runexp {
+  trebuchet = stage: w.trebuchet {
     program = stageProgram stage;
     nixPrefix = common.nixPrefix;
   };
@@ -187,8 +219,7 @@ let
     conf = common;
   };
 
-  final = runexp (isolatedRun launcher);
+  final = trebuchet (isolatedRun launcher);
-  
 
 in
   # We simply run each program one after another

garlic/nbody/default.nix

@@ -16,7 +16,7 @@ with stdenv.lib;
 stdenv.mkDerivation rec {
   name = "nbody";
 
-  #src = /home/Computational/rarias/bscpkgs/manual/nbody;
+  #src = ~/nbody;
 
   src = builtins.fetchGit {
     url = "${gitURL}";

garlic/stages/isolate/stage1

@@ -16,16 +16,31 @@ nixjoin="@nixPrefix@@nixtools@/bin/nix-join"
 env=(
   PATH="@nixPrefix@@busybox@/bin:@busybox@/bin:@extraPath@"
   $(env | grep ^SLURM || true)
+  $(env | grep ^PMI || true)
   $(env | grep ^GARLIC_OUT || true)
+  $(env | grep ^USER || true)
+  HOME="/homeless-shelter"
 )
 
-#-m @nixPrefix@ \
+mounts=(
-join_flags="-m /etc \
+	#-m @nixPrefix@
-	-m /.statelite/tmpfs/etc \
+	#FIXME: Use only the strictly neccesary from /etc
-	-m /sys \
+	-m /etc
-	-m /var/run/munge \
+	# The /etc/hosts file is a symlink to this etc/
-	-m /gpfs/projects/bsc15 \
+	-m /.statelite/tmpfs/etc
-	-m /bin:@nixPrefix@@busybox@/bin"
+	-m /sys
+	-m /dev
+	-m /proc
+	# nscd cache: doesn't exist (?)
+	#-m /var/run/nscd
+	# Needed for munge auth
+	-m /var/run/munge
+	# FIXME: We should only need nix and the output path
+	-m /gpfs/projects/bsc15
+	-m /bin:@nixPrefix@@busybox@/bin
+)
+
+join_flags="${mounts[@]}"
 
 exec $nixjoin -v -i $join_flags $nixhome -- \
 	env -i "${env[@]}" @out@/bin/stage2

garlic/stages/strace.nix

@@ -0,0 +1,23 @@
+{
+  stdenv
+, bash
+, strace
+}:
+
+{
+  program
+}:
+
+stdenv.mkDerivation {
+  name = "strace";
+  preferLocalBuild = true;
+  phases = [ "installPhase" ];
+  installPhase = ''
+    cat > $out <<EOF
+    #!/bin/sh
+    
+    exec ${strace}/bin/strace -f ${program}
+    EOF
+    chmod +x $out
+  '';
+}

garlic/stages/trebuchet/default.nix

@@ -11,15 +11,15 @@
 }:
 
 stdenv.mkDerivation {
-  name = "runexp";
+  name = "trebuchet";
   preferLocalBuild = true;
   phases = [ "unpackPhase" "installPhase" ];
   dontPatchShebangs = true;
   src = ./.;
   inherit sshHost nixPrefix nixtools targetCluster program;
   installPhase = ''
-    substituteAllInPlace runexp
+    substituteAllInPlace trebuchet
-    cp runexp $out
+    cp trebuchet $out
     chmod +x $out
   '';
 }

garlic/stages/trebuchet/trebuchet

@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/bin/sh -ex
 # @upload-to-mn@
 
 # This program runs the current experiment in the ./result symlink in

overlay.nix

@@ -28,7 +28,7 @@ let
 
     mpich = callPackage ./bsc/mpich/default.nix { };
 
-    mpichDebug = self.mpich.override { enableDebug = true; };
+    mpichDebug = self.bsc.mpich.override { enableDebug = true; };
 
     # Updated version of libpsm2: TODO push upstream.
     #libpsm2 = callPackage ./bsc/libpsm2/default.nix { };
@@ -207,7 +207,8 @@ let
         envRecord = callPackage ./garlic/stages/envRecord.nix { };
         valgrind  = callPackage ./garlic/stages/valgrind.nix { };
         isolate   = callPackage ./garlic/stages/isolate { };
-        runexp    = callPackage ./garlic/stages/runexp { };
+        trebuchet = callPackage ./garlic/stages/trebuchet { };
+        strace    = callPackage ./garlic/stages/strace.nix { };
       };
 
       # Tests (move to bsc ?)