Move apps into garlic/apps

garlic/apps/cpic/default.nix

@@ -0,0 +1,41 @@
+{
+  stdenv
+, libconfig
+, nanos6
+, mpi
+, uthash
+, fftw
+, tampi
+, hdf5
+}:
+
+stdenv.mkDerivation rec {
+  name = "cpic";
+
+  # Use my current cpic version, so I can test changes without commits
+  #src = /home/Computational/rarias/cpic;
+
+  src = builtins.fetchGit {
+    url = "https://github.com/rodarima/cpic";
+#    rev = "73bd70448587f0925b89e24c8f17e412ea3958e6";
+    ref = "simd";
+  };
+
+  enableParallelBuilding = true;
+  dontStrip = true;
+
+  buildInputs = [
+    libconfig
+    nanos6
+    mpi
+    uthash
+    fftw
+    tampi
+    hdf5
+  ];
+
+  installPhase = ''
+    mkdir -p $out/bin
+    cp cpic $out/bin/cpic
+  '';
+}

garlic/apps/creams/default.nix

@@ -0,0 +1,67 @@
+{
+  stdenv
+, nanos6
+, mpi
+, openmpi
+, impi
+, tampi
+, mcxx
+, 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 = "${gitBranch}";
+  };
+
+  programPath = "/bin/creams.exe";
+
+  buildInputs = [
+    nanos6
+    mpi
+    cc
+    tampi
+    mcxx
+  ];
+
+  hardeningDisable = [ "all" ];
+
+  configurePhase = ''
+    export TAMPI_HOME=${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/apps/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/apps/fwi/default.nix

@@ -0,0 +1,52 @@
+{
+  stdenv
+, nanos6
+, mpi
+, tampi
+, mcxx
+, icc
+}:
+
+stdenv.mkDerivation rec {
+  name = "nbody";
+  variant = "4_MPI_ompss";
+
+  src = builtins.fetchGit {
+    url = "https://gitlab.com/srodrb/BSC-FWI.git";
+    ref = "ompss-mpi-nocache";
+  };
+
+  postUnpack = "sourceRoot=$sourceRoot/${variant}";
+
+  enableParallelBuilding = true;
+
+  buildInputs = [
+    nanos6
+    mpi
+    icc
+    tampi
+    mcxx
+  ];
+
+  # FIXME: This is an ugly hack.
+  # When using _GNU_SOURCE or any other definition used in features.h, we need
+  # to define them before mcc includes nanos6.h from the command line. So the
+  # only chance is by setting it at the command line with -D. Using the DEFINES
+  # below, reaches the command line of the preprocessing stage with gcc.
+  preBuild = ''
+    export DEFINES=-D_GNU_SOURCE
+  '';
+
+  makeFlags = [
+    "NZF=108"
+    "NXF=108"
+    "NYF=208"
+    "PRECISION=float"
+  ];
+
+  installPhase = ''
+    mkdir -p $out/bin
+    cp fwi.* $out/bin
+    cp ModelGenerator $out/bin
+  '';
+}

garlic/apps/heat/default.nix

@@ -0,0 +1,32 @@
+{
+  stdenv
+, nanos6
+, mpi
+, tampi
+, mcxx
+, icc
+}:
+
+stdenv.mkDerivation rec {
+  name = "heat";
+
+  src = builtins.fetchGit {
+    url = "ssh://git@bscpm02.bsc.es/benchmarks/ompss-2/heat-conflict-kevin.git";
+    #rev = "25fde23e5ad5f5e2e58418ed269bc2b44642aa17";
+    ref = "master";
+  };
+
+  buildInputs = [
+    nanos6
+    mpi
+    icc
+    tampi
+    mcxx
+  ];
+
+  installPhase = ''
+    mkdir -p $out/bin
+    cp heat_* $out/bin/
+  '';
+
+}

garlic/apps/hpccg/default.nix

@@ -0,0 +1,44 @@
+{
+  stdenv
+, nanos6
+, mpi
+, mcxx
+, tampi
+, icc
+}:
+
+stdenv.mkDerivation rec {
+  name = "hpccg";
+
+  src = builtins.fetchGit {
+    url = "ssh://git@bscpm02.bsc.es/mmaronas/HPCCG.git";
+    ref = "mmaronas-development";
+  };
+
+  buildInputs = [
+    nanos6
+    mpi
+    icc
+    tampi
+    mcxx
+  ];
+
+  # The hpccg app fails to compile in parallel. Makefile must be fixed before.
+  enableParallelBuilding = false;
+
+  postPatch = ''
+    sed -i 's/mpic++/mpiicpc/g' Makefile
+    sed -i 's/g++/icpc/g' Makefile
+    mkdir obj
+  '';
+
+  makeFlags =  [
+    "USE_MPI=-DUSING_MPI"
+    "TAMPI_HOME=${tampi}"
+  ];
+
+  installPhase = ''
+    mkdir -p $out/bin
+    cp test_HPCCG* $out/bin
+  '';
+}

garlic/apps/hpcg/default.nix

@@ -0,0 +1,46 @@
+{
+  stdenv
+, nanos6
+, mpi
+, mcxx
+, tampi
+, icc
+}:
+
+stdenv.mkDerivation rec {
+  name = "hpcg";
+
+  src = builtins.fetchGit {
+    url = "ssh://git@bscpm02.bsc.es/rpenacob/hpcg.git";
+    ref = "symgs_coloring_more_than_one_block_per_task_halos_blocking_discreete";
+  };
+
+  prePatch = ''
+    #export NIX_DEBUG=6
+  '';
+
+  patches = [ ./tampi.patch ];
+
+  buildInputs = [
+    nanos6
+    mpi
+    icc
+    tampi
+    mcxx
+  ];
+
+  enableParallelBuilding = true;
+
+  configurePhase = ''
+    export TAMPI_HOME=${tampi}
+    mkdir build
+    cd build
+    ../configure MPI_ICPC_OSS
+  '';
+
+  installPhase = ''
+    mkdir -p $out/bin
+    cp bin/* $out/bin/
+  '';
+
+}

garlic/apps/hpcg/tampi.patch

@@ -0,0 +1,13 @@
+--- a/setup/Make.MPI_ICPC_OSS	2020-07-13 16:02:33.272257865 +0200
++++ b/setup/Make.MPI_ICPC_OSS	2020-07-13 16:04:34.344413390 +0200
+@@ -91,8 +91,8 @@
+ # - HPCG includes / libraries / specifics -------------------------------
+ # ----------------------------------------------------------------------
+ #
+-HPCG_INCLUDES = -I$(INCdir) -I$(INCdir)/$(arch) $(MPinc) -I{TAMPI_HOME}/include
+-HPCG_LIBS     = ${TAMPI_HOME}/lib/libtampi.a
++HPCG_INCLUDES = -I$(INCdir) -I$(INCdir)/$(arch) $(MPinc) -I$(TAMPI_HOME)/include
++HPCG_LIBS     = -l:libtampi.a 
+ #
+ # - Compile time options -----------------------------------------------
+ #

garlic/apps/lulesh/default.nix

@@ -0,0 +1,31 @@
+{
+  stdenv
+, mpi
+, mcxx
+, icc
+}:
+
+stdenv.mkDerivation rec {
+  name = "lulesh";
+
+  src = builtins.fetchGit {
+    url = "ssh://git@bscpm02.bsc.es/mmaronas/lulesh.git";
+    ref = "master";
+  };
+
+  dontConfigure = true;
+
+  buildInputs = [
+    mpi
+    icc
+    mcxx
+  ];
+
+  enableParallelBuilding = true;
+
+  installPhase = ''
+    mkdir -p $out/bin
+    find . -name 'lulesh*' -type f -executable -exec cp \{\} $out/bin/ \;
+  '';
+
+}

garlic/apps/nbody/default.nix

@@ -0,0 +1,52 @@
+{
+  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 = ~/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="${cflags}")
+  '' else "");
+
+  makeFlags = [
+    "CC=${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/apps/ppong/default.nix

@@ -0,0 +1,34 @@
+{
+  stdenv
+, mpi
+, fetchurl
+}:
+
+stdenv.mkDerivation {
+  name = "ppong";
+
+  src = fetchurl {
+    url = "http://www.csl.mtu.edu/cs4331/common/PPong.c";
+    sha256 = "0d1w72gq9627448cb7ykknhgp2wszwd117dlbalbrpf7d0la8yc0";
+  };
+
+  unpackCmd = ''
+    mkdir src
+    cp $src src/ppong.c
+  '';
+
+  dontConfigure = true;
+
+  buildPhase = ''
+    echo mpicc -include stdlib.h ppong.c -o ppong
+    mpicc -include stdlib.h ppong.c -o ppong
+  '';
+
+  installPhase = ''
+    mkdir -p $out/bin
+    cp ppong $out/bin/ppong
+    ln -s $out/bin/ppong $out/bin/run
+  '';
+
+  buildInputs = [ mpi ];
+}

garlic/apps/saiph/default.nix

@@ -0,0 +1,67 @@
+{
+  stdenv
+, nanos6
+, mpi
+, tampi
+, cc 
+, vtk
+, boost
+, devMode ? false
+, gitBranch ? "master"
+, numComm ? null
+, vectFlags ? null
+#, breakpointHook
+}:
+
+stdenv.mkDerivation rec {
+  name = "saiph";
+
+  src = (if (devMode == true) then ~/repos/saiph
+         else
+	 builtins.fetchGit {
+           url = "ssh://git@bscpm02.bsc.es/DSLs/saiph.git";
+           ref = "${gitBranch}";
+         });
+
+  programPath = "/bin/ExHeat3D";
+
+  enableParallelBuilding = true;
+  dontStrip = true;
+  enableDebugging = true;
+
+  buildInputs = [
+    nanos6
+    mpi
+    tampi
+    cc
+    vtk
+    boost
+#    breakpointHook
+  ];
+
+  # Required for nanos6
+  hardeningDisable = [ "bindnow" ];
+  
+  preBuild = ''
+    cd saiphv2/cpp/src 
+    export VTK_VERSION=8.2
+    export VTK_HOME=${vtk}
+  ''
+  + (if (devMode == true) then "make clean" else "")
+  ;
+
+  makeFlags = [
+    "-f" "Makefile.${cc.cc.CC}"
+    "apps"
+    "APP=ExHeat3D"
+    ( if (numComm != null) then "NUM_COMM=${toString numComm}" else "" )
+    ( if (vectFlags != null) then "VECT_FLAGS=${toString vectFlags}" else "" )
+  ];
+
+  installPhase = ''
+    mkdir -p $out/lib
+    mkdir -p $out/bin
+    cp obj/libsaiphv2.so $out/lib/
+    cp bin/ExHeat3D $out/bin/
+  '';
+}