Add patch to paraver to prevent focus stealing

https://github.com/bsc-performance-tools/wxparaver/issues/18

default.nix

@@ -1,11 +1,19 @@
 let
   bscOverlay = import ./overlay.nix;
 
-  # Pin the nixpkgs
-  nixpkgsPath = import ./nixpkgs.nix;
-
-  pkgs = import nixpkgsPath {
-    overlays = [ bscOverlay ];
+  # read flake.lock and determine revision from there
+  lock = builtins.fromJSON (builtins.readFile ./flake.lock);
+  inherit (lock.nodes.nixpkgs.locked) rev narHash;
+  fetchedNixpkgs = builtins.fetchTarball {
+    url = "https://github.com/NixOS/nixpkgs/archive/${rev}.tar.gz";
+    sha256 = narHash;
   };
-
-in pkgs
+in
+{ overlays ? [ ]
+, nixpkgs ? fetchedNixpkgs
+, ...
+}@attrs:
+import nixpkgs (
+  (builtins.removeAttrs attrs [ "overlays" "nixpkgs" ]) //
+  { overlays = [ bscOverlay ] ++ overlays; }
+)

nixpkgs.nix

@@ -1,9 +0,0 @@
-let
-  commit = "e4ad989506ec7d71f7302cc3067abd82730a4beb";
-in builtins.fetchTarball {
-    # Descriptive name to make the store path easier to identify
-    name = "nixpkgs-${commit}";
-    url = "https://github.com/nixos/nixpkgs/archive/${commit}.tar.gz";
-    # Hash obtained using `nix-prefetch-url --unpack <url>`
-    sha256 = "sha256-de9KYi8rSJpqvBfNwscWdalIJXPo8NjdIZcEJum1mH0=";
-}

overlay.nix

@@ -20,9 +20,8 @@ let
     #extrae = callPackage ./pkgs/extrae/default.nix { }; # Broken and outdated
     gpi-2 = callPackage ./pkgs/gpi-2/default.nix { };
     intelPackages_2023 = callPackage ./pkgs/intel-oneapi/2023.nix { };
-    intelPackages = final.intelPackages_2023;
     jemallocNanos6 = callPackage ./pkgs/nanos6/jemalloc.nix { };
-    #lmbench = callPackage ./pkgs/lmbench/default.nix { }; # Broken
+    lmbench = callPackage ./pkgs/lmbench/default.nix { };
     mcxx = callPackage ./pkgs/mcxx/default.nix { };
     nanos6 = callPackage ./pkgs/nanos6/default.nix { };
     nanos6Debug = final.nanos6.override { enableDebug = true; };
@@ -61,7 +60,6 @@ in bscPkgs // {
       #sigsegv = callPackage ./test/reproducers/sigsegv.nix { };
       hello-c = callPackage ./test/compilers/hello-c.nix { };
       hello-cpp = callPackage ./test/compilers/hello-cpp.nix { };
-      hello-sycl = callPackage ./test/compilers/hello-sycl.nix { };
       lto = callPackage ./test/compilers/lto.nix { };
       asan = callPackage ./test/compilers/asan.nix { };
       intel2023-icx-c   = hello-c.override   { stdenv = final.intelPackages_2023.stdenv; };

pkgs/bench6/default.nix

@@ -1,14 +1,22 @@
 {
   stdenv
+, bigotes
 , cmake
 , clangOmpss2
+, openmp
+, openmpv
 , nanos6
 , nodes
+, nosv
 , mpi
 , tampi
+, tagaspi
+, gpi-2
+, openblas
+, ovni
 , gitBranch ? "master"
 , gitURL ? "ssh://git@bscpm04.bsc.es/rarias/bench6.git"
-, gitCommit ? "1e6ce2aa8ad7b4eef38df1581d7ec48a8815f85d"
+, gitCommit ? "bf29a53113737c3aa74d2fe3d55f59868faea7b4"
 }:
 
 stdenv.mkDerivation rec {
@@ -21,9 +29,30 @@ stdenv.mkDerivation rec {
     rev = gitCommit;
   };
 
-  buildInputs = [ cmake clangOmpss2 nanos6 nodes mpi tampi ];
+  buildInputs = [
+    bigotes
+    cmake
+    clangOmpss2
+    openmp
+    openmpv
+    nanos6
+    nodes
+    nosv
+    mpi
+    tampi
+    tagaspi
+    gpi-2
+    openblas
+    openblas.dev
+    ovni
+  ];
+
+  env = {
+    NANOS6_HOME = nanos6;
+    NODES_HOME = nodes;
+    NOSV_HOME = nosv;
+  };
 
-  enableParallelBuilding = false;
   cmakeFlags = [
     "-DCMAKE_C_COMPILER=clang"
     "-DCMAKE_CXX_COMPILER=clang++"

pkgs/intel-oneapi/2023.nix

@@ -313,9 +313,6 @@ let
       "intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic-common-${version}"
       "intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic-runtime-${version}"
       "intel-oneapi-compiler-dpcpp-cpp-classic-fortran-shared-runtime-${version}"
-      "intel-oneapi-compiler-shared-${version}"
-      "intel-oneapi-compiler-shared-common-${version}"
-      "intel-oneapi-compiler-shared-runtime-${version}"
     ];
     # From https://aur.archlinux.org/packages/intel-oneapi-compiler:
     # - intel-oneapi-compiler-cpp-eclipse-cfg-2023.0.0-25370_all.deb
@@ -332,9 +329,9 @@ let
     # - intel-oneapi-compiler-fortran-common-2023.0.0-2023.0.0-25370_all.deb
     # - intel-oneapi-compiler-fortran-runtime-2023.0.0-2023.0.0-25370_amd64.deb
     # - intel-oneapi-compiler-fortran-runtime-2023.0.0-25370_amd64.deb
-    # + intel-oneapi-compiler-shared-2023.0.0-2023.0.0-25370_amd64.deb
-    # + intel-oneapi-compiler-shared-common-2023.0.0-2023.0.0-25370_all.deb
-    # + intel-oneapi-compiler-shared-runtime-2023.0.0-2023.0.0-25370_amd64.deb
+    # - intel-oneapi-compiler-shared-2023.0.0-2023.0.0-25370_amd64.deb
+    # - intel-oneapi-compiler-shared-common-2023.0.0-2023.0.0-25370_all.deb
+    # - intel-oneapi-compiler-shared-runtime-2023.0.0-2023.0.0-25370_amd64.deb
     # - intel-oneapi-dpcpp-cpp-2023.0.0-2023.0.0-25370_amd64.deb
     # - intel-oneapi-openmp-2023.0.0-2023.0.0-25370_amd64.deb
     # - intel-oneapi-openmp-common-2023.0.0-2023.0.0-25370_all.deb
@@ -401,15 +398,6 @@ let
         echo "-L${intel-compiler-shared}/lib" >> $out/nix-support/cc-ldflags
         echo "-L${cc}/lib" >> $out/nix-support/cc-ldflags
 
-        echo "--gcc-toolchain=${mygcc.cc}" >> $out/nix-support/libcxx-cxxflags
-
-        for dir in ${mygcc.cc}/include/c++/*; do
-          echo "-isystem $dir" >> $out/nix-support/libcxx-cxxflags
-        done
-        for dir in ${mygcc.cc}/include/c++/*/${targetConfig}; do
-          echo "-isystem $dir" >> $out/nix-support/libcxx-cxxflags
-        done
-
         # Need the gcc in the path
         echo 'export "PATH=${mygcc}/bin:$PATH"' >> $out/nix-support/cc-wrapper-hook
 

pkgs/llvm-ompss2/default.nix

@@ -9,12 +9,14 @@
 , ompss2rt ? null
 }:
 
+with lib;
+
 let
   usingNodesAndOmpv = (openmp.pname == "openmp-v" && ompss2rt.pname == "nodes");
   sameNosv = openmp.nosv == ompss2rt.nosv;
 in
 
-assert lib.assertMsg (usingNodesAndOmpv -> sameNosv) "OpenMP-V and NODES must share the same nOS-V";
+assert assertMsg (usingNodesAndOmpv -> sameNosv) "OpenMP-V and NODES must share the same nOS-V";
 
 let
   homevar = if ompss2rt.pname == "nanos6" then "NANOS6_HOME" else "NODES_HOME";
@@ -34,14 +36,15 @@ let
   targetConfig = stdenv.targetPlatform.config;
   inherit gcc;
   cc = clangOmpss2Unwrapped;
+  gccVersion = with versions; let v = gcc.version; in concatStringsSep "." [(major v) (minor v) (patch v)];
 in wrapCCWith {
   inherit cc bintools;
   # extraPackages adds packages to depsTargetTargetPropagated
-  extraPackages = lib.optional (openmp != null) openmp;
+  extraPackages = optional (openmp != null) openmp;
   extraBuildCommands = ''
     echo "-target ${targetConfig}" >> $out/nix-support/cc-cflags
-    echo "-B${gcc.cc}/lib/gcc/${targetConfig}/${gcc.version}" >> $out/nix-support/cc-cflags
-    echo "-L${gcc.cc}/lib/gcc/${targetConfig}/${gcc.version}" >> $out/nix-support/cc-ldflags
+    echo "-B${gcc.cc}/lib/gcc/${targetConfig}/${gccVersion}" >> $out/nix-support/cc-cflags
+    echo "-L${gcc.cc}/lib/gcc/${targetConfig}/${gccVersion}" >> $out/nix-support/cc-ldflags
     echo "-L${gcc.cc.lib}/lib" >> $out/nix-support/cc-ldflags
 
     for dir in ${gcc.cc}/include/c++/*; do
@@ -55,12 +58,12 @@ in wrapCCWith {
 
     wrap clang++  $wrapper $ccPath/clang++
 
-  '' + lib.optionalString (openmp != null) ''
+  '' + optionalString (openmp != null) ''
     echo "export OPENMP_RUNTIME=${ompname}" >> $out/nix-support/cc-wrapper-hook
-  '' + lib.optionalString (ompss2rt != null) ''
+  '' + optionalString (ompss2rt != null) ''
     echo "export OMPSS2_RUNTIME=${rtname}" >> $out/nix-support/cc-wrapper-hook
     echo "export ${homevar}=${ompss2rt}"   >> $out/nix-support/cc-wrapper-hook
-  '' + lib.optionalString (ompss2rt != null && ompss2rt.pname == "nodes") ''
+  '' + optionalString (ompss2rt != null && ompss2rt.pname == "nodes") ''
     echo "export NOSV_HOME=${ompss2rt.nosv}" >> $out/nix-support/cc-wrapper-hook
   '';
 }

pkgs/llvm-ompss2/openmp.nix

@@ -68,6 +68,7 @@ stdenv.mkDerivation rec {
     rm -f $out/lib/libiomp*
   '' + lib.optionalString enableNosv ''
     rm -f $out/lib/libomp.*
+    rm -f $out/libllvmrt/libomp.*
   '';
 
   passthru = {

pkgs/lmbench/default.nix

@@ -1,19 +1,20 @@
 {
   lib,
   stdenv,
+  libtirpc,
   fetchFromGitHub
 }:
 
 stdenv.mkDerivation rec {
   pname = "lmbench";
-  version = "701c6c35";
+  version = "941a0dcc";
 
   # We use the intel repo as they have fixed some problems
   src = fetchFromGitHub {
     owner = "intel";
     repo = pname;
-    rev = "701c6c35b0270d4634fb1dc5272721340322b8ed";
-    sha256 = "0sf6zk03knkardsfd6qx7drpm56nhg53n885cylkggk83r38idyr";
+    rev = "941a0dcc0e7bdd9bb0dee05d7f620e77da8c43af";
+    sha256 = "sha256-SzwplRBO3V0R3m3p15n71ivYBMGoLsajFK2TapYxdqk=";
   };
 
   postUnpack = ''
@@ -24,12 +25,19 @@ stdenv.mkDerivation rec {
     sed -i "s@/bin/rm@rm@g" $(find . -name Makefile)
   '';
 
+  buildInputs = [ libtirpc ];
+  patches = [ ./fix-install.patch ];
+
   hardeningDisable = [ "all" ];
 
   enableParallelBuilding = false;
 
   preBuild = ''
-    makeFlagsArray+=(BASE=$out)
+    makeFlagsArray+=(
+      BASE=$out
+      CPPFLAGS=-I${libtirpc.dev}/include/tirpc
+      LDFLAGS=-ltirpc
+    )
   '';
 
   meta = {

pkgs/lmbench/fix-install.patch

@@ -0,0 +1,10 @@
+--- a/Makefile
++++ b/Makefile
+@@ -144,6 +144,7 @@ install-target:
+ 	if [ ! -d $(BASE)/include ]; then mkdir $(BASE)/include; fi
+ 	if [ ! -d $(BASE)/lib ]; then mkdir $(BASE)/lib; fi
+ 	cp $(EXES) $(BASE)/bin
++	cp $(OPT_EXES) $(BASE)/bin
+ 	cp $(INCS) $(BASE)/include
+ 	cp $O/lmbench.a $(BASE)/lib/libmbench.a
+ 	cd ../doc; env MAKEFLAGS="$(MAKEFLAGS)" make CC="${CC}" OS="${OS}" BASE="$(BASE)" install

pkgs/paraver/default.nix

@@ -1,5 +1,6 @@
 {
   stdenv
+, fetchFromGitHub
 , autoreconfHook
 , boost
 , libxml2
@@ -18,14 +19,17 @@ let
 in
 stdenv.mkDerivation rec {
   pname = "wxparaver";
-  version = "4.11.2";
+  version = "4.12.0";
 
-  src = builtins.fetchGit {
-    url = "https://github.com/bsc-performance-tools/wxparaver.git";
-    rev = "129e6b4a4f061e5a319049db8db1620f5de3bd70"; # v4.11.2 (missing tag)
-    ref = "master";
+  src = fetchFromGitHub {
+    owner = "bsc-performance-tools";
+    repo = "wxparaver";
+    rev = "v${version}";
+    sha256 = "sha256-YsO5gsuEFQdki3lQudEqgo5WXOt/fPdvNw5OxZQ86Zo=";
   };
 
+  patches = [ ./do-not-steal-focus-on-redraw.patch ];
+
   hardeningDisable = [ "all" ];
 
   # Fix the PARAVER_HOME variable

pkgs/paraver/do-not-steal-focus-on-redraw.patch

@@ -0,0 +1,26 @@
+From 2b185e1b5ce52808b3026334851dbcd5a640ed4d Mon Sep 17 00:00:00 2001
+From: aleixbonerib <aleix.boneribo@bsc.es>
+Date: Mon, 10 Jun 2024 20:59:45 +0200
+Subject: [PATCH] fix: do not set focus on redraw
+
+Some wm can change the window size without focusing. Right now, when the
+plot is resized it takes back focus.
+---
+ src/gtimeline.cpp | 1 -
+ 1 file changed, 1 deletion(-)
+
+diff --git a/src/gtimeline.cpp b/src/gtimeline.cpp
+index 23ebef2..a896066 100644
+--- a/src/gtimeline.cpp
++++ b/src/gtimeline.cpp
+@@ -899,7 +899,6 @@ void gTimeline::redraw()
+ 
+   drawZone->Refresh();
+ 
+-  SetFocus();
+ }
+ 
+ 
+-- 
+2.44.1
+

pkgs/paraver/dont-expand-colors.patch

@@ -11,7 +11,7 @@ diff --git a/api/semanticcolor.cpp b/api/semanticcolor.cpp
 index 9f86960..22859eb 100644
 --- a/api/semanticcolor.cpp
 +++ b/api/semanticcolor.cpp
-@@ -232,8 +232,9 @@ rgb CodeColor::getColor( PRV_UINT32 pos ) const
+@@ -295,8 +295,9 @@ rgb SemanticColor::getColor( PRV_UINT32 pos ) const
  {
    if( pos == 0 && ParaverConfig::getInstance()->getColorsTimelineUseZero() )
      return ParaverConfig::getInstance()->getColorsTimelineColorZero();
@@ -22,26 +22,26 @@ index 9f86960..22859eb 100644
 +  return colors[ pos + 1 ];
  }
  
- void CodeColor::setColor( PRV_UINT32 whichPos, rgb whichColor )
-@@ -250,6 +251,12 @@ void CodeColor::setColor( PRV_UINT32 whichPos, rgb whichColor )
+ void SemanticColor::setColor( PRV_UINT32 whichPos, rgb whichColor )
+@@ -314,6 +315,12 @@ void SemanticColor::setColor( PRV_UINT32 whichPos, rgb whichColor )
    colors[ whichPos ] = whichColor;
  }
  
-+void CodeColor::cutAfter( PRV_UINT32 pos )
++void SemanticColor::cutAfter( PRV_UINT32 pos )
 +{
 +  if ( pos < colors.size() )
 +    colors.erase( colors.begin() + pos, colors.end() );
 +}
 +
- void CodeColor::setCustomColor( TSemanticValue whichValue, rgb color ) 
+ void SemanticColor::setCustomColor( TSemanticValue whichValue, rgb color ) 
  {
    customPalette[ whichValue ] = color;
 diff --git a/api/semanticcolor.h b/api/semanticcolor.h
 index a079556..bddf3d8 100644
 --- a/api/semanticcolor.h
 +++ b/api/semanticcolor.h
-@@ -98,6 +98,7 @@ class CodeColor: public SemanticColor
- 
+@@ -114,6 +114,7 @@ class SemanticColor
+     // Code Color methods
      PRV_UINT32 getNumColors() const;
      void setColor( PRV_UINT32 pos, rgb color );
 +    void cutAfter( PRV_UINT32 pos );
@@ -61,7 +61,7 @@ index b0d2050..ee2ab69 100644
    for ( auto it : semanticColors )
    {
      std::tie( tmpColor.red, tmpColor.green, tmpColor.blue ) = it.second;
-     myCodeColor.setColor( it.first, tmpColor );
+     mySemanticColor.setColor( it.first, tmpColor );
 +	if (it.first > maxValue)
 +      maxValue = it.first;
    }
@@ -69,7 +69,7 @@ index b0d2050..ee2ab69 100644
 +  // Cut the palette after the highest defined value, so there are no
 +  // extra expanded values
 +  if ( !pcfParser.expandColors )
-+	myCodeColor.cutAfter(maxValue);
++	mySemanticColor.cutAfter(maxValue);
 +
    myEventLabels = EventLabels( pcfParser );
    myStateLabels = StateLabels( pcfParser );

pkgs/paraver/fix-libxml2-deprecation.patch

@@ -0,0 +1,23 @@
+commit 60aa3ffa05f6b40db191a880e9e622d608744c1f
+Author: Aleix Boné <aleix.boneribo@bsc.es>
+Date:   Sun Jul 21 12:11:30 2025 +0200
+
+    fix libxml2 deprecated macro
+
+diff --git a/configure.ac b/configure.ac
+index 7fe1876..3ce1091 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -46,7 +46,10 @@ AC_PROG_CPP
+ AC_PROG_CXXCPP
+ AC_PROG_SED
+ 
+-AM_PATH_XML2
++PKG_PROG_PKG_CONFIG
++PKG_CHECK_MODULES([XML], [libxml-2.0])
++
++AC_SUBST(XML_CPPFLAGS, $XML_CFLAGS)
+ 
+ AX_BOOST_BASE(1.36)
+ AX_BOOST_SERIALIZATION
+

pkgs/paraver/kernel.nix

@@ -1,5 +1,6 @@
 {
   stdenv
+, fetchFromGitHub
 , autoreconfHook
 , boost
 , libxml2
@@ -16,17 +17,19 @@ let
 in
 stdenv.mkDerivation rec {
   pname = "paraver-kernel";
-  version = "${src.shortRev}";
+  version = "4.12.0";
 
-  src = builtins.fetchGit {
-    url = "https://github.com/bsc-performance-tools/paraver-kernel.git";
-    rev = "2e167da3cee78ca11e31b74faefb23f12bac2b8c"; # master (missing tag)
-    ref = "master";
+  src = fetchFromGitHub {
+    owner = "bsc-performance-tools";
+    repo = "paraver-kernel";
+    rev = "v${version}";
+    sha256 = "sha256-Xs7g8ITZhPt00v7o2WlTddbou8C8Rc9kBMFpl2WsCS4=";
   };
 
   patches = [
     # https://github.com/bsc-performance-tools/paraver-kernel/pull/11
     ./dont-expand-colors.patch
+    ./fix-libxml2-deprecation.patch
   ];
 
   hardeningDisable = [ "all" ];

test/compilers/hello-sycl.nix

@@ -1,55 +0,0 @@
-{ intelPackages,  writeText, strace }:
-
-let
-  stdenv = intelPackages.stdenv;
-  hello_sycl = writeText "hello.cpp" ''
-    #include <sycl/sycl.hpp>
-
-    class hello_world;
-
-    int main(int argc, char** argv) try {
-        auto device_selector = sycl::default_selector_v;
-
-        sycl::queue queue(device_selector);
-
-        std::cout << "Running on: "
-                  << queue.get_device().get_info<sycl::info::device::name>()
-                  << std::endl;
-
-        queue.submit([&] (sycl::handler& cgh) {
-            auto os = sycl::stream{128, 128, cgh};
-            cgh.single_task<hello_world>([=]() {
-                os << "Hello World! (on device)\n";
-            });
-        });
-
-        return 0;
-    } catch (sycl::exception &e) {
-        std::cout << "SYCL exception: " << e.what() << std::endl;
-        return 0; // we excpect to fail since no devices should be available;
-    }
-  '';
-in
-
-stdenv.mkDerivation {
-  version = "0.0.1";
-  name = "hello-sycl";
-  buildInputs = [ stdenv strace ];
-  src = hello_sycl;
-  dontUnpack = true;
-  dontConfigure = true;
-  NIX_DEBUG = 0;
-  buildPhase = ''
-    cp $src hello.cpp
-    set -x
-    echo CXX=$CXX
-    command -v $CXX
-    $CXX -fsycl hello.cpp -o hello
-    ./hello
-    set +x
-  '';
-
-  installPhase = ''
-    touch $out
-  '';
-}