Merge all branches

New apt list does not have Package: as the first entry for all packages

flake.lock

@@ -2,10 +2,10 @@
   "nodes": {
     "nixpkgs": {
       "locked": {
-        "lastModified": 1736867362,
-        "narHash": "sha256-i/UJ5I7HoqmFMwZEH6vAvBxOrjjOJNU739lnZnhUln8=",
-        "path": "/nix/store/2csx2kkb2hxyxhhmg2xs9jfyypikwwk6-source",
-        "rev": "9c6b49aeac36e2ed73a8c472f1546f6d9cf1addc",
+        "lastModified": 1752436162,
+        "narHash": "sha256-Kt1UIPi7kZqkSc5HVj6UY5YLHHEzPBkgpNUByuyxtlw=",
+        "path": "/nix/store/zk8v61cpk1wprp9ld5ayc1g5fq4pdkwv-source",
+        "rev": "dfcd5b901dbab46c9c6e80b265648481aafb01f8",
         "type": "path"
       },
       "original": {

flake.nix

@@ -3,15 +3,33 @@
 
   outputs = { self, nixpkgs, ...}:
   let
+    system = "x86_64-linux";
     pkgs = import nixpkgs {
+      inherit system;
       # For now we only support x86
-      system = "x86_64-linux";
       overlays = [ self.overlays.default ];
     };
   in
     {
       bscOverlay = import ./overlay.nix;
       overlays.default = self.bscOverlay;
-      legacyPackages.x86_64-linux = pkgs;
+
+      # full nixpkgs with our overlay applied
+      legacyPackages.${system} = pkgs;
+
+      # packages added by our overlay
+      packages.${system} =
+        let
+          inherit (builtins) attrNames removeAttrs;
+          inherit (nixpkgs.lib) flip filterAttrs getAttrs pipe isDerivation;
+        in
+          # extract the names of the packages from the overlay, then get the
+          # actual packages from the full package set with the overlay applied
+          pipe (self.overlays.default null null) [
+            attrNames
+            (flip getAttrs pkgs)
+            (flip removeAttrs [ "bsc" ])
+            (filterAttrs (_: isDerivation))
+          ];
     };
 }

overlay.nix

@@ -1,15 +1,22 @@
 final: /* Future last stage */
 prev:  /* Previous stage */
 
-with final.lib;
-
 let
-  callPackage = final.callPackage;
+  inherit (prev.lib) collect isDerivation mapAttrs;
+
+  inherit (final) callPackage;
 
   mkDeps = name: pkgs: final.runCommand name { }
     "printf '%s\n' ${toString (collect (x: x ? outPath) pkgs)} > $out";
 
-  bscPkgs = {
+  mkStrict = drv: if (isDerivation drv && drv ? overrideAttrs && !(drv ? strictDeps))
+    then drv.overrideAttrs { strictDeps = true; }
+    else drv;
+
+  bscPkgs = mapAttrs (_: mkStrict) {
+    aoccUnwrapped = callPackage ./pkgs/aocc/unwrapped.nix { };
+    aocc = callPackage ./pkgs/aocc/default.nix { };
+    stdenvAocc = final.overrideCC final.stdenv final.aocc;
     bench6 = callPackage ./pkgs/bench6/default.nix { };
     bigotes = callPackage ./pkgs/bigotes/default.nix { };
     clangOmpss2 = callPackage ./pkgs/llvm-ompss2/default.nix { };
@@ -17,8 +24,9 @@ let
     clangOmpss2Nodes = callPackage ./pkgs/llvm-ompss2/default.nix { ompss2rt = final.nodes; openmp = final.openmp; };
     clangOmpss2NodesOmpv = callPackage ./pkgs/llvm-ompss2/default.nix { ompss2rt = final.nodes; openmp = final.openmpv; };
     clangOmpss2Unwrapped = callPackage ./pkgs/llvm-ompss2/clang.nix { };
+    clsparse = callPackage ./pkgs/clsparse/package.nix { };
     #extrae = callPackage ./pkgs/extrae/default.nix { }; # Broken and outdated
-    gpi-2 = callPackage ./pkgs/gpi-2/default.nix { };
+    #gpi-2 = callPackage ./pkgs/gpi-2/default.nix { }; # Broken: https://jungle.bsc.es/git/rarias/bscpkgs/issues/7
     intel-apt = callPackage ./pkgs/intel-oneapi/packages.nix { };
     intelPackages_2023 = callPackage ./pkgs/intel-oneapi/2023.nix { };
     intelPackages_2024 = final.intel-apt.hpckit_2024;
@@ -49,8 +57,9 @@ let
     stdenvClangOmpss2Nanos6 = final.stdenv.override { cc = final.clangOmpss2Nanos6; allowedRequisites = null; };
     stdenvClangOmpss2Nodes = final.stdenv.override { cc = final.clangOmpss2Nodes; allowedRequisites = null; };
     stdenvClangOmpss2NodesOmpv = final.stdenv.override { cc = final.clangOmpss2NodesOmpv; allowedRequisites = null; };
-    tagaspi = callPackage ./pkgs/tagaspi/default.nix { };
+    #tagaspi = callPackage ./pkgs/tagaspi/default.nix { }; # Broken due gpi-2
     tampi = callPackage ./pkgs/tampi/default.nix { };
+    taopencl = callPackage ./pkgs/taopencl/default.nix { };
     tasycl = callPackage ./pkgs/tasycl/default.nix { };
     tasycl-acpp = callPackage ./pkgs/tasycl/default.nix { useIntel = false; };
     wxparaver = callPackage ./pkgs/paraver/default.nix { };

pkgs/aocc/default.nix

@@ -0,0 +1,16 @@
+{ wrapCCWith
+, aoccUnwrapped
+}:
+
+let
+  cc = aoccUnwrapped;
+in wrapCCWith {
+  inherit cc;
+
+  extraBuildCommands = ''
+    echo "-isystem ${cc}/include" >> $out/nix-support/cc-cflags
+
+    wrap aocc   $wrapper $ccPath/clang
+    wrap aocc++ $wrapper $ccPath/clang++
+  '';
+}

pkgs/aocc/unwrapped.nix

@@ -0,0 +1,51 @@
+{ lib
+, fetchurl
+, stdenv
+, autoPatchelfHook
+, rocmPackages
+, zlib
+, libffi
+, elfutils
+}:
+
+let
+  # in newer nixpkgs the runtime is hsakmt
+  rocmRuntime =
+    if rocmPackages ? hsakmt then
+      rocmPackages.hsakmt
+    else
+      rocmPackages.rocm-runtime;
+in
+stdenv.mkDerivation {
+  pname = "aocc-compiler";
+  version = "5.0.0";
+
+  src = fetchurl {
+    url = "https://download.amd.com/developer/eula/aocc/aocc-5-0/aocc-compiler-5.0.0.tar";
+    sha256 = "sha256-lm+sLSx1np3m6WnBCtp6ezBsET9/HgfqN2gp7IY4Dao=";
+  };
+
+  nativeBuildInputs = [ autoPatchelfHook ];
+  buildInputs = [
+    elfutils
+    zlib
+    rocmRuntime
+    stdenv.cc.cc.lib
+  ];
+  phases = [ "unpackPhase" "installPhase" "fixupPhase" ];
+  dontStrip = true;
+
+  installPhase = ''
+    mkdir -p $out
+    cp -a . $out/
+
+    ln -s ${lib.getLib libffi}/lib/libffi.so $out/lib/libffi.so.6
+  '';
+
+  passthru = {
+    inherit rocmRuntime;
+    isClang = true; # Needed for wrapCCWith
+  };
+
+  meta.mainProgram = "clang";
+}

pkgs/bench6/default.nix

@@ -1,14 +1,20 @@
 {
   stdenv
+, bigotes
 , cmake
 , clangOmpss2
+, openmp
+, openmpv
 , nanos6
 , nodes
+, nosv
 , mpi
 , tampi
+, openblas
+, ovni
 , gitBranch ? "master"
 , gitURL ? "ssh://git@bscpm04.bsc.es/rarias/bench6.git"
-, gitCommit ? "1e6ce2aa8ad7b4eef38df1581d7ec48a8815f85d"
+, gitCommit ? "bf29a53113737c3aa74d2fe3d55f59868faea7b4"
 }:
 
 stdenv.mkDerivation rec {
@@ -21,9 +27,31 @@ stdenv.mkDerivation rec {
     rev = gitCommit;
   };
 
-  buildInputs = [ cmake clangOmpss2 nanos6 nodes mpi tampi ];
+  nativeBuildInputs = [
+    cmake
+    clangOmpss2
+  ];
+
+  buildInputs = [
+    bigotes
+    openmp
+    openmpv
+    nanos6
+    nodes
+    nosv
+    mpi
+    tampi
+    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/bigotes/default.nix

@@ -4,7 +4,7 @@
 , cmake
 }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   pname = "bigotes";
   version = "9dce13";
   src = fetchFromGitHub {
@@ -13,5 +13,5 @@ stdenv.mkDerivation rec {
     rev = "9dce13446a8da30bea552d569d260d54e0188518";
     sha256 = "sha256-ktxM3pXiL8YXSK+/IKWYadijhYXqGoLY6adLk36iigE=";
   };
-  buildInputs = [ cmake ];
+  nativeBuildInputs = [ cmake ];
 }

pkgs/clsparse/install_target.patch

@@ -0,0 +1,53 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 3d139ed..15ffc14 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -176,32 +179,22 @@ if( BUILD_clSPARSE OR BUILD_SAMPLES )
+   if( BUILD_clSPARSE )
+     message( STATUS "Setting up clSPARSE external..." )
+ 
+-    if ( BUILD_SAMPLES )
+-      # If the user elects to build samples, then we must build and install clSPARSE
+-      # The install location is set as a subdirectory of the SuperBuild
+-      ExternalProject_Add(
+-        clSPARSE
+-        DEPENDS ${clSPARSE.Dependencies}
+-        SOURCE_DIR ${PROJECT_SOURCE_DIR}/src
+-        BINARY_DIR clSPARSE-build
+-        INSTALL_DIR clSPARSE-package
+-        CMAKE_ARGS ${clSPARSE.Cmake.Args} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+-        -DBUILD_CLVERSION=${BUILD_CLVERSION} -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
+-        -DUSE_SYSTEM_CL2HPP:BOOL=${USE_SYSTEM_CL2HPP}
+-      )
+-    else( )
+-      # If the user does not want to build samples, then build clSPARSE but don't automatically
+-      # install it
+-      ExternalProject_Add(
+-        clSPARSE
+-        DEPENDS ${clSPARSE.Dependencies}
+-        SOURCE_DIR ${PROJECT_SOURCE_DIR}/src
+-        BINARY_DIR clSPARSE-build
+-        CMAKE_ARGS ${clSPARSE.Cmake.Args} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+-        -DBUILD_CLVERSION=${BUILD_CLVERSION} -DUSE_SYSTEM_CL2HPP:BOOL=${USE_SYSTEM_CL2HPP}
+-        INSTALL_COMMAND ""
+-      )
+-    endif( )
++    ExternalProject_Add(
++      clSPARSE
++      DEPENDS ${clSPARSE.Dependencies}
++      SOURCE_DIR ${PROJECT_SOURCE_DIR}/src
++      BINARY_DIR clSPARSE-build
++      INSTALL_DIR clSPARSE-package
++      CMAKE_ARGS ${clSPARSE.Cmake.Args} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
++      -DBUILD_CLVERSION=${BUILD_CLVERSION} -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
++      -DUSE_SYSTEM_CL2HPP:BOOL=${USE_SYSTEM_CL2HPP}
++    )
++
++    install(
++      DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/clSPARSE-package/
++      DESTINATION ${CMAKE_INSTALL_PREFIX}
++      USE_SOURCE_PERMISSIONS
++    )
+ 
+   endif( )
+ 

pkgs/clsparse/package.nix

@@ -0,0 +1,70 @@
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  fetchpatch,
+  boost,
+  gtest,
+  ocl-icd,
+  opencl-headers,
+  opencl-clhpp,
+  cmake,
+}:
+
+stdenv.mkDerivation rec {
+  pname = "clsparse";
+  version = "0.10.2.0";
+
+  src = fetchFromGitHub {
+    owner = "clMathLibraries";
+    repo = "clSPARSE";
+    rev = "v${version}";
+    hash = "sha256-jIauCtUyPEIx7pFI3qH0WagV+t/fvro0OsGgONBJm0s=";
+  };
+
+  patches = [
+    ./pass_include_dir.patch
+    ./install_target.patch
+    (fetchpatch {
+      name = "remove-gettypecode.patch";
+      url = "https://patch-diff.githubusercontent.com/raw/clMathLibraries/clSPARSE/pull/210.patch";
+      hash = "sha256-9Q+tk7RMdWE4MCnbvWlsI0MIgBYKIWR2jIC1bICtIjU=";
+    })
+  ];
+
+  postInstallPhase = ''
+    mv $installDir/lib64 lib
+    ln -s lib/ lib64
+  '';
+
+  env.NIX_CFLAGS_COMPILE = "-std=c++17";
+
+  nativeBuildInputs = [
+    cmake
+  ];
+
+  buildInputs = [
+    boost
+    ocl-icd
+    opencl-headers
+    opencl-clhpp
+  ];
+
+  cmakeFlags = [
+    "-DBUILD_Boost=OFF"
+    "-DBUILD_gMock=OFF"
+    "-DBUILD_MTX=OFF"
+    "-DBUILD_SAMPLES=OFF"
+    "-DUSE_SYSTEM_CL2HPP=ON"
+    "-DGMOCK_ROOT=${gtest}"
+    "-DGTEST_INCLUDE_DIR=${gtest.src}/googletest/include"
+  ];
+
+  meta = {
+    description = "A software library containing Sparse functions written in OpenCL";
+    homepage = "https://github.com/clMathLibraries/clSPARSE";
+    license = lib.licenses.asl20;
+    maintainers = with lib.maintainers; [ leixb ];
+    platforms = lib.platforms.all;
+  };
+}

pkgs/clsparse/pass_include_dir.patch

@@ -0,0 +1,14 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 3d139ed..b7ea2d3 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -132,6 +132,9 @@ else( )
+       set( GMOCK_ROOT "$ENV{GMOCK_ROOT}" )
+     endif( )
+     list( APPEND clSPARSE.Cmake.Args -DGTEST_ROOT=${GMOCK_ROOT} )
++    if( DEFINED GTEST_INCLUDE_DIR )
++      list( APPEND clSPARSE.Cmake.Args -DGTEST_INCLUDE_DIR=${GTEST_INCLUDE_DIR} )
++    endif( )
+   endif( )
+ endif( )
+ 

pkgs/intel-oneapi/2023.nix

@@ -1,6 +1,5 @@
 { stdenv
 , fetchurl
-, ncurses
 , lib
 , dpkg
 , rsync
@@ -10,12 +9,9 @@
 , hwloc
 , zlib
 , autoPatchelfHook
-, symlinkJoin
 , libfabric
-, gcc
-, gcc7
+, gcc13
 , wrapCCWith
-, linuxHeaders
 }:
 
 # The distribution of intel packages is a mess. We are doing the installation
@@ -30,6 +26,8 @@
 
 let
 
+  gcc = gcc13;
+
   v = {
     hpckit   = "2023.1.0";
     compiler = "2023.1.0";
@@ -98,14 +96,17 @@ let
       "intel-oneapi-mpi-${version}"
     ];
 
-    buildInputs = [
+    nativeBuildInputs = [
+      autoPatchelfHook
       rsync
+    ];
+
+    buildInputs = [
       libfabric
       zlib
       stdenv.cc.cc.lib
     ];
 
-    nativeBuildInputs = [ autoPatchelfHook ];
     phases = [ "installPhase" "fixupPhase" ];
     dontStrip = true;
     installPhase = ''
@@ -144,7 +145,6 @@ let
 
     buildInputs = [
       intel-mpi
-      rsync
       libffi_3_3
       libelf
       libxml2
@@ -152,7 +152,10 @@ let
       stdenv.cc.cc.lib
     ];
 
-    nativeBuildInputs = [ autoPatchelfHook ];
+    nativeBuildInputs = [
+      autoPatchelfHook
+      rsync
+    ];
     phases = [ "installPhase" "fixupPhase" ];
     dontStrip = true;
 
@@ -182,7 +185,6 @@ let
     buildInputs = [
       intel-mpi
       intel-tbb
-      rsync
       libffi_3_3
       libelf
       libxml2
@@ -191,7 +193,10 @@ let
       stdenv.cc.cc.lib
     ];
 
-    nativeBuildInputs = [ autoPatchelfHook ];
+    nativeBuildInputs = [
+      autoPatchelfHook
+      rsync
+    ];
     phases = [ "installPhase" "fixupPhase" ];
     dontStrip = true;
 
@@ -244,7 +249,6 @@ let
     buildInputs = [
       intel-mpi
       intel-compiler-shared
-      rsync
       libffi_3_3
       libelf
       libxml2
@@ -252,7 +256,10 @@ let
       stdenv.cc.cc.lib
     ];
 
-    nativeBuildInputs = [ autoPatchelfHook ];
+    nativeBuildInputs = [
+      autoPatchelfHook
+      rsync
+    ];
 
     phases = [ "installPhase" "fixupPhase" ];
 
@@ -301,10 +308,8 @@ 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}"
     ];
+    dontCheckForBrokenSymlinks = true;
     # From https://aur.archlinux.org/packages/intel-oneapi-compiler:
     # - intel-oneapi-compiler-cpp-eclipse-cfg-2023.0.0-25370_all.deb
     # + intel-oneapi-compiler-dpcpp-cpp-2023.0.0-2023.0.0-25370_amd64.deb
@@ -320,16 +325,15 @@ 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
 
     buildInputs = [
       intel-compiler-shared
-      rsync
       libffi_3_3
       libelf
       libxml2
@@ -337,7 +341,10 @@ let
       stdenv.cc.cc.lib
     ];
 
-    nativeBuildInputs = [ autoPatchelfHook ];
+    nativeBuildInputs = [
+      autoPatchelfHook
+      rsync
+    ];
     autoPatchelfIgnoreMissingDeps = [ "libtbb.so.12" "libtbbmalloc.so.2" "libze_loader.so.1" ];
 
     phases = [ "installPhase" "fixupPhase" ];
@@ -389,17 +396,10 @@ 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"' >> $out/nix-support/cc-wrapper-hook
+        # FIXME: We should find a better way to modify the PATH instead of using
+        # this ugly hack. See https://jungle.bsc.es/git/rarias/bscpkgs/issues/9
+        echo 'path_backup="${mygcc}/bin:$path_backup"' >> $out/nix-support/cc-wrapper-hook
 
         # Disable hardening by default
         echo "" > $out/nix-support/add-hardening.sh

pkgs/intel-oneapi/patch_intel.nix

@@ -5,7 +5,7 @@
 , autoPatchelfHook
 , wrapCCWith
 , overrideCC
-, gcc
+, gcc13
 , hwloc
 , libelf
 , libffi_3_3
@@ -33,6 +33,8 @@ makeOverridable (
 let
   inherit (builtins) attrValues filter mapAttrs removeAttrs;
 
+  gcc = gcc13;
+
   __components = removeAttrs components ["extraPackages"];
   _components = __components;
   # _components = lib.traceSeqN 2 {
@@ -50,6 +52,7 @@ let
         echo "-L${gcc.cc.lib}/lib" >> $out/nix-support/cc-ldflags
         echo "-L${cc}/lib" >> $out/nix-support/cc-ldflags
 
+        # echo "--gcc-toolchain=${gcc.cc}" >> $out/nix-support/libcxx-cxxflags
         echo "--gcc-toolchain=${gcc.cc}" >> $out/nix-support/cc-cflags
 
         # For some reason, If we don't resolve the realpath things go wrong
@@ -72,12 +75,12 @@ let
           echo "-isystem $dir" >> $out/nix-support/libcxx-cxxflags
         done
 
-        # Need the gcc in the path
-        echo 'export "PATH=${gcc}/bin:$PATH"' >> $out/nix-support/cc-wrapper-hook
+        # FIXME: We should find a better way to modify the PATH instead of using
+        # this ugly hack. See https://jungle.bsc.es/git/rarias/bscpkgs/issues/9
+        echo 'path_backup="${gcc.cc}/bin:$path_backup"' >> $out/nix-support/cc-wrapper-hook
 
         # Disable hardening by default
         echo "" > $out/nix-support/add-hardening.sh
-
       '' + extraBuildCommands;
     } // (removeAttrs args ["cc" "extraBuildCommands" "extraInstall"])
     ).overrideAttrs (old: {
@@ -110,6 +113,8 @@ stdenvNoCC.mkDerivation (finalAttrs: {
 
   autoPatchelfIgnoreMissingDeps = [ "libhwloc.so.5" "libcuda.so.1" "libze_loader.so.1" ];
 
+  dontCheckForBrokenSymlinks = true;
+
   nativeBuildInputs = [ autoPatchelfHook ];
   installPhase = ''
     cp -r $src/opt/intel/oneapi/ $out
@@ -157,6 +162,7 @@ stdenvNoCC.mkDerivation (finalAttrs: {
 
         sed -i 's/.*isCxx=0/isCxx=1/' $out/bin/icpx
 
+        # oneMath looks for sycl libraries in bin/../lib
         ln -s ${finalAttrs.finalPackage.pkgs.compiler}/lib $out/lib
         ln -s ${finalAttrs.finalPackage.pkgs.compiler}/include $out/include
       '';

pkgs/llvm-ompss2/clang.nix

@@ -16,19 +16,19 @@
 , useGit ? false
 , gitUrl ? "ssh://git@bscpm04.bsc.es/llvm-ompss/llvm-mono.git"
 , gitBranch ? "master"
-, gitCommit ? "8c0d267c04d7fc3fb923078f510fcd5f4719a6cc"
+, gitCommit ? "880e2341c56bad1dc14e8c369fb3356bec19018e"
 }:
 
 let
   stdenv = llvmPackages_latest.stdenv;
 
   release = rec {
-    version = "2024.11";
+    version = "2025.06";
     src = fetchFromGitHub {
       owner = "bsc-pm";
       repo = "llvm";
       rev = "refs/tags/github-release-${version}";
-      hash = "sha256-pF0qa987nLkIJPUrXh1srzBkLPfb31skIegD0bl34Kg=";
+      hash = "sha256-ww9PpRmtz/M9IyLiZ8rAehx2UW4VpQt+svf4XfKBzKo=";
     };
   };
 
@@ -43,32 +43,36 @@ let
 
   source = if (useGit) then git else release;
 
-in stdenv.mkDerivation rec {
+in stdenv.mkDerivation {
   pname = "clang-ompss2";
   inherit (source) src version;
 
   enableParallelBuilding = true;
-  isClang = true;
 
   passthru = {
     CC = "clang";
     CXX = "clang++";
+
+    isClang = true;
+    isClangWithOmpss = true;
+
+    inherit gcc zlib;
   };
 
-  isClangWithOmpss = true;
-
-  nativeBuildInputs = [ zlib ];
-
-  buildInputs = [
-    which
+  nativeBuildInputs = [
     bash
+    cmake
+    elfutils
+    llvmPackages_latest.lld
+    pkg-config
     python3
     perl
-    cmake
-    llvmPackages_latest.lld
-    elfutils
+    which
+    zlib
+  ];
+
+  buildInputs = [
     libffi
-    pkg-config
     zlib
     gcc.cc.lib # Required for libstdc++.so.6
   ];

pkgs/llvm-ompss2/default.nix

@@ -39,34 +39,12 @@ let
   cc = clangOmpss2Unwrapped;
   gccVersion = with versions; let v = gcc.version; in concatStringsSep "." [(major v) (minor v) (patch v)];
 
-  resetIntelCCFlags = let tconf = builtins.replaceStrings ["-"] ["_"] targetConfig;
-  in writeShellScript "remove-intel.sh" ''
-    if [ "$NIX_CC_WRAPPER_INTEL" = 1 ]; then
-      unset NIX_CFLAGS_COMPILE_${tconf}
-      unset NIX_CFLAGS_COMPILE_BEFORE_${tconf}
-      unset NIX_CFLAGS_LINK_${tconf}
-      unset NIX_CXXSTDLIB_COMPILE_${tconf}
-      unset NIX_CXXSTDLIB_LINK_${tconf}
-      unset NIX_GNATFLAGS_COMPILE_${tconf}
-
-      unset NIX_CC_WRAPPER_FLAGS_SET_${tconf}
-    # unset NIX_BINTOOLS_WRAPPER_FLAGS_${tconf}
-    fi
-  '';
-
-in wrapCCWith {
-  inherit cc bintools;
-  # extraPackages adds packages to depsTargetTargetPropagated
-  extraPackages = optional (openmp != null) openmp;
   extraBuildCommands = ''
     echo "-target ${targetConfig}" >> $out/nix-support/cc-cflags
     echo "-B${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 ${gcc.cc}/lib/gcc/${targetConfig}/*/include; do
-      echo "-isystem $dir" >> $out/nix-support/cc-cflags
-    done
     for dir in ${gcc.cc}/include/c++/*; do
       echo "-isystem $dir" >> $out/nix-support/libcxx-cxxflags
     done
@@ -77,19 +55,50 @@ in wrapCCWith {
     echo "--gcc-toolchain=${gcc}" >> $out/nix-support/cc-cflags
 
     wrap clang++  $wrapper $ccPath/clang++
-
-    sed -i 's|# Flirting.*|&\nsource ${resetIntelCCFlags}|' $out/bin/clang
-    sed -i 's|# Flirting.*|&\nsource ${resetIntelCCFlags}|' $out/bin/clang++
-
-    echo "" > $out/nix-support/add-hardening.sh
-
-  '' + lib.optionalString (openmp != null) ''
-    echo "export OPENMP_RUNTIME=${ompname}" >> $out/nix-support/cc-wrapper-hook
-  '' + optionalString (ompss2rt != null) ''
-    echo "export OMPSS2_RUNTIME=${rtname}" >> $out/nix-support/cc-wrapper-hook
-    echo "export ${homevar}=${ompss2rt}"   >> $out/nix-support/cc-wrapper-hook
-  '' + optionalString (ompss2rt != null && ompss2rt.pname == "nodes") ''
-    echo "export NOSV_HOME=${ompss2rt.nosv}" >> $out/nix-support/cc-wrapper-hook
   '';
-}
 
+  envExports = lib.optionalString (openmp != null) ''
+      echo "export OPENMP_RUNTIME=${ompname}" >> $out/nix-support/cc-wrapper-hook
+    '' + optionalString (ompss2rt != null) ''
+      echo "export OMPSS2_RUNTIME=${rtname}" >> $out/nix-support/cc-wrapper-hook
+      echo "export ${homevar}=${ompss2rt}"   >> $out/nix-support/cc-wrapper-hook
+    '' + optionalString (ompss2rt != null && ompss2rt.pname == "nodes") ''
+      echo "export NOSV_HOME=${ompss2rt.nosv}" >> $out/nix-support/cc-wrapper-hook
+    '';
+
+  extraPackages = optional (openmp != null) openmp;
+
+  wrappedCC = wrapCCWith {
+    # extraPackages adds packages to depsTargetTargetPropagated
+    inherit cc bintools extraPackages;
+    extraBuildCommands = extraBuildCommands + envExports;
+  };
+
+  resetIntelCCFlags = let tconf = builtins.replaceStrings ["-"] ["_"] targetConfig;
+  in writeShellScript "remove-intel.sh" ''
+    if [ "''${NIX_CC_WRAPPER_INTEL:-0}" = 1 ]; then
+      unset NIX_CFLAGS_COMPILE_${tconf}
+      unset NIX_CC_WRAPPER_FLAGS_SET_${tconf}
+
+      if (( "''${NIX_DEBUG:-0}" >= 1 )); then
+        echo "ompss2: cleaned NIX_CFLAGS_COMPILE_${tconf} (invokation from intel compiler detected)"
+      fi
+    fi
+  '';
+
+  intelExtraBuildCommands = ''
+    sed -i 's|# Flirting.*|source ${resetIntelCCFlags}\n\n&|' $out/bin/clang
+    sed -i 's|# Flirting.*|source ${resetIntelCCFlags}\n\n&|' $out/bin/clang++
+  '';
+
+  wrappedCCIntel = wrapCCWith {
+    inherit cc bintools extraPackages;
+    # extraPackages adds packages to depsTargetTargetPropagated
+    extraBuildCommands = intelExtraBuildCommands + envExports;
+  };
+
+in wrappedCC.overrideAttrs (oldAttrs: {
+    passthru = oldAttrs.passthru // {
+      forIcpx = wrappedCCIntel;
+    };
+  })

pkgs/lmbench/default.nix

@@ -17,16 +17,12 @@ stdenv.mkDerivation rec {
     sha256 = "sha256-SzwplRBO3V0R3m3p15n71ivYBMGoLsajFK2TapYxdqk=";
   };
 
-  postUnpack = ''
-    export sourceRoot="$sourceRoot/src"
-  '';
-
   postPatch = ''
     sed -i "s@/bin/rm@rm@g" $(find . -name Makefile)
   '';
 
   buildInputs = [ libtirpc ];
-  patches = [ ./fix-install.patch ];
+  patches = [ ./fix-install.patch ./gcc-14.patch ];
 
   hardeningDisable = [ "all" ];
 
@@ -34,7 +30,9 @@ stdenv.mkDerivation rec {
 
   preBuild = ''
     makeFlagsArray+=(
+      -C src
       BASE=$out
+      CFLAGS=-Wno-implicit-int
       CPPFLAGS=-I${libtirpc.dev}/include/tirpc
       LDFLAGS=-ltirpc
     )

pkgs/lmbench/fix-install.patch

@@ -1,5 +1,5 @@
---- a/Makefile
-+++ b/Makefile
+--- a/src/Makefile
++++ b/src/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

pkgs/lmbench/gcc-14.patch

@@ -0,0 +1,77 @@
+From a3c6e7d303cd8368e8d4e35be7cbc1997e801257 Mon Sep 17 00:00:00 2001
+From: Rodrigo Arias Mallo <rodrigo.arias@bsc.es>
+Date: Mon, 21 Jul 2025 17:38:58 +0200
+Subject: [PATCH] Misc fixes to build with gcc 14
+
+---
+ src/bench.h      | 2 ++
+ src/lat_select.c | 2 +-
+ src/lib_debug.c  | 1 +
+ src/lib_sched.c  | 2 +-
+ src/lib_timing.c | 2 +-
+ 5 files changed, 6 insertions(+), 3 deletions(-)
+
+diff --git a/src/bench.h b/src/bench.h
+index 8166408..4da9079 100644
+--- a/src/bench.h
++++ b/src/bench.h
+@@ -320,4 +320,6 @@ extern int handle_scheduler(int childno, int benchproc, int nbenchprocs);
+ extern char *rpc_xact_1();
+ extern char *client_rpc_xact_1();
+ 
++void lmbench_usage(int argc, char *argv[], char* usage);
++
+ #endif /* _BENCH_H */
+diff --git a/src/lat_select.c b/src/lat_select.c
+index 583b505..39df369 100644
+--- a/src/lat_select.c
++++ b/src/lat_select.c
+@@ -164,7 +164,7 @@ doit(iter_t iterations, void * cookie)
+ 	state_t * 	state = (state_t *)cookie;
+ 	fd_set		nosave;
+ 	static struct timeval tv;
+-	static count = 0;
++	static int count = 0;
+ 	
+ 	tv.tv_sec = 0;
+ 	tv.tv_usec = 0;
+diff --git a/src/lib_debug.c b/src/lib_debug.c
+index e8347dd..cf65312 100644
+--- a/src/lib_debug.c
++++ b/src/lib_debug.c
+@@ -1,5 +1,6 @@
+ #include "bench.h"
+ #include "lib_debug.h"
++#include <math.h>
+ 
+ /*
+  * return micro-seconds / iteration at the the fraction point.
+diff --git a/src/lib_sched.c b/src/lib_sched.c
+index aa83ae0..4f16bbf 100644
+--- a/src/lib_sched.c
++++ b/src/lib_sched.c
+@@ -91,7 +91,7 @@ handle_scheduler(int childno, int benchproc, int nbenchprocs)
+ 			     childno * (nbenchprocs + 1) + benchproc);
+ 	} else {
+ 		/* default action: do nothing */
+-		return;
++		return 0;
+ 	}
+ 
+ 	return sched_pin(cpu % sched_ncpus());
+diff --git a/src/lib_timing.c b/src/lib_timing.c
+index af8cf68..7ec9652 100644
+--- a/src/lib_timing.c
++++ b/src/lib_timing.c
+@@ -1623,7 +1623,7 @@ bread(void* buf, long nbytes)
+ void
+ touch(char *buf, int nbytes)
+ {
+-	static	psize;
++	static int psize;
+ 
+ 	if (!psize) {
+ 		psize = getpagesize();
+-- 
+2.49.0
+

pkgs/mcxx/default.nix

@@ -32,19 +32,22 @@ stdenv.mkDerivation rec {
 
   enableParallelBuilding = true;
 
-  buildInputs = [
+  nativeBuildInputs = [
     autoreconfHook
-    nanos6
-    gperf
+    bison
+    flex
     python3
     gfortran
     pkg-config
-    sqlite.dev
-    bison
-    flex
+    gperf
     gcc
   ];
 
+  buildInputs = [
+    nanos6
+    sqlite.dev
+  ];
+
   patches = [ ./intel.patch ];
 
   preConfigure = ''

pkgs/nanos6/default.nix

@@ -19,7 +19,7 @@
 , useGit ? false
 , gitUrl ? "ssh://git@bscpm04.bsc.es/nanos6/nanos6"
 , gitBranch ? "master"
-, gitCommit ? "9f54c988e0a8b9c011d9d526acdb8d76f18fcae4"
+, gitCommit ? "f82762b66c82b5174a8eaad33f6c2f335ac759b4"
 }:
 
 assert enableJemalloc -> (jemallocNanos6 != null);
@@ -28,12 +28,12 @@ with lib;
 
 let
   release = rec {
-    version = "4.2";
+    version = "4.3";
     src = fetchFromGitHub {
       owner = "bsc-pm";
       repo = "nanos6";
       rev = "version-${version}";
-      hash = "sha256-tBrRGLCjSFYdmVGPAC2DzYY6HJyZGUOMeykujafn7+4=";
+      hash = "sha256-/c6WiKBsAo/01uvMRmjv0PMucbrgvaGmbxlPE6q+dfE=";
     };
   };
 
@@ -88,11 +88,19 @@ in
     dontStrip = enableDebug;
     separateDebugInfo = true;
 
-    buildInputs = [
+    nativeBuildInputs = [
       autoconf
       automake
       libtool
       pkg-config
+
+      # TODO: papi_version is needed for configure:
+      # ./configure: line 27378: papi_version: command not found
+      # This probably breaks cross-compilation
+      papi
+    ];
+
+    buildInputs = [
       boost
       numactl
       hwloc
@@ -104,7 +112,7 @@ in
     postInstall = ''
       mkdir -p $out/nix-support
       echo "export NANOS6_HOME=$out" >> $out/nix-support/setup-hook
-    ''; 
+    '';
 
     meta = with lib; {
       homepage = "https://github.com/bsc-pm/nanos6";

pkgs/nosv/default.nix

@@ -6,24 +6,26 @@
 , pkg-config
 , numactl
 , hwloc
+, papi
+, enablePapi ? true
 , cacheline ? 64 # bits
 , ovni ? null
 , useGit ? false
 , gitUrl ? "git@gitlab-internal.bsc.es:nos-v/nos-v.git"
 , gitBranch ? "master"
-, gitCommit ? "cfd361bd1dd30c96da405e6bbaa7e78f5f93dfda"
+, gitCommit ? "9f47063873c3aa9d6a47482a82c5000a8c813dd8"
 }:
 
 with lib;
 
 let
   release = rec {
-    version = "3.1.0";
+    version = "3.2.0";
     src = fetchFromGitHub {
       owner = "bsc-pm";
       repo = "nos-v";
       rev = "${version}";
-      hash = "sha256-Pkre+ZZsREDxJLCoIoPN1HQDuUa2H1IQyKB3omg6qaU=";
+      hash = "sha256-yaz92426EM8trdkBJlISmAoG9KJCDTvoAW/HKrasvOw=";
     };
   };
 
@@ -56,5 +58,5 @@ in
       numactl
       hwloc
       ovni
-    ];
+    ] ++ lib.optionals enablePapi [ papi ];
   }

pkgs/onemath/default.nix

@@ -1,40 +1,51 @@
 { lib
-, intelPackages
-, withCFlags
 , fetchFromGitHub
 , cmake
-, cudaPackages
-, enableNvidia ? true
-, withHipTargets ? null # only one target at a time supported
-, rocmPackages
-, enableMkl ? true
+, withCFlags
+, intelPackages
+
+, mklSupport ? true
+
+, config
+
+, cudaSupport ? config.cudaSupport
+, cudaPackages ? { }
+
+, rocmSupport ? config.rocmSupport
+, hipTargets ? null # only one target at a time supported
+, rocmPackages ? { }
 }:
 
 let
-  enableHip = withHipTargets != null;
+  # rocmSupport is not enough, we need a specific target
+  enableHip = rocmSupport && hipTargets != null;
 
-  stdenv = withCFlags (lib.optionals enableNvidia [ "--cuda-path=${cudaPackages.cudatoolkit}" ]) intelPackages.stdenv;
+  stdenv = withCFlags (lib.optionals cudaSupport [ "--cuda-path=${cudaPackages.cudatoolkit}" ]) intelPackages.stdenv;
 in
+
+  # at least one backend has to be enabled
+  assert mklSupport || cudaSupport || enableHip;
+
 stdenv.mkDerivation rec {
   pname = "oneMath";
-  version = "0.7";
+  version = "0.8";
 
   src = fetchFromGitHub {
     owner = "uxlfoundation";
     repo = "oneMath";
     rev = "v${version}";
-    sha256 = "sha256-De04PUmI68Jx4rJ+MRb+RepayZCapgnouCUCrAu6G38=";
+    sha256 = "sha256-xK8lKI3oqKlx3xtvdScpMq+HXAuoYCP0BZdkEqnJP5o=";
   };
 
   cmakeFlags = [
-    (lib.cmakeBool "ENABLE_MKLCPU_BACKEND"    enableMkl)
-    (lib.cmakeBool "ENABLE_MKLGPU_BACKEND"    enableMkl)
+    (lib.cmakeBool "ENABLE_MKLCPU_BACKEND"    mklSupport)
+    (lib.cmakeBool "ENABLE_MKLGPU_BACKEND"    mklSupport)
 
-    (lib.cmakeBool "ENABLE_CUBLAS_BACKEND"    enableNvidia)
-    (lib.cmakeBool "ENABLE_CUFFT_BACKEND"     enableNvidia)
-    (lib.cmakeBool "ENABLE_CURAND_BACKEND"    enableNvidia)
-    (lib.cmakeBool "ENABLE_CUSOLVER_BACKEND"  enableNvidia)
-    (lib.cmakeBool "ENABLE_CUSPARSE_BACKEND"  enableNvidia)
+    (lib.cmakeBool "ENABLE_CUBLAS_BACKEND"    cudaSupport)
+    (lib.cmakeBool "ENABLE_CUFFT_BACKEND"     cudaSupport)
+    (lib.cmakeBool "ENABLE_CURAND_BACKEND"    cudaSupport)
+    (lib.cmakeBool "ENABLE_CUSOLVER_BACKEND"  cudaSupport)
+    (lib.cmakeBool "ENABLE_CUSPARSE_BACKEND"  cudaSupport)
 
     (lib.cmakeBool "ENABLE_ROCBLAS_BACKEND"   enableHip)
     (lib.cmakeBool "ENABLE_ROCFFT_BACKEND"    enableHip)
@@ -45,11 +56,11 @@ stdenv.mkDerivation rec {
     (lib.cmakeBool "BUILD_FUNCTIONAL_TESTS" false)
     (lib.cmakeBool "BUILD_EXAMPLES" false)
   ] ++ lib.optionals enableHip [
-    (lib.cmakeFeature "HIP_TARGETS" withHipTargets)
+    (lib.cmakeFeature "HIP_TARGETS" hipTargets)
   ];
 
   nativeBuildInputs = [ cmake ];
-  buildInputs = lib.optionals (enableMkl) [
+  buildInputs = lib.optionals (mklSupport) [
     intelPackages.mkl
     intelPackages.tbb
   ] ++ lib.optionals (enableHip) [
@@ -59,7 +70,7 @@ stdenv.mkDerivation rec {
     rocmPackages.rocsolver
     rocmPackages.rocrand
     rocmPackages.rocsparse
-  ] ++ lib.optionals (enableNvidia) [
+  ] ++ lib.optionals (cudaSupport) [
     (lib.getDev cudaPackages.cuda_cudart)
     cudaPackages.cudatoolkit
 

pkgs/osu/default.nix

@@ -24,9 +24,10 @@ stdenv.mkDerivation rec {
 
   doCheck = true;
   enableParallelBuilding = true;
+  nativeBuildInputs = [ mpiAll ];
   buildInputs = [ mpiAll ];
   hardeningDisable = [ "all" ];
-  configureFlags = [ 
+  configureFlags = [
       "CC=mpicc"
       "CXX=mpicxx"
   ];
@@ -40,7 +41,7 @@ stdenv.mkDerivation rec {
 
   meta = {
     description = "OSU Micro-Benchmarks";
-    homepage = http://mvapich.cse.ohio-state.edu/benchmarks/;
+    homepage = "http://mvapich.cse.ohio-state.edu/benchmarks/";
     maintainers = [ ];
     platforms = lib.platforms.all;
   };

pkgs/ovni/default.nix

@@ -7,23 +7,21 @@
 , useGit ? false
 , gitBranch ? "master"
 , gitUrl ? "ssh://git@bscpm04.bsc.es/rarias/ovni.git"
-, gitCommit ? "a7103f8510d1ec124c3e01ceb47d1e443e98bbf4"
+, gitCommit ? "e4f62382076f0cf0b1d08175cf57cc0bc51abc61"
 , enableDebug ? false
 # Only enable MPI if the build is native (fails on cross-compilation)
 , useMpi ? (stdenv.buildPlatform.canExecute stdenv.hostPlatform)
 }:
 
-with lib;
-
 let
   release = rec {
-    version = "1.11.0";
+    version = "1.12.0";
     src = fetchFromGitHub {
       owner = "bsc-pm";
       repo = "ovni";
       rev = "${version}";
-      hash = "sha256-DEZUK1dvbPGH5WYkZ2hpP5PShkMxXkHOqMwgYUHHxeM=";
-    } // { shortRev = "a7103f8"; };
+      hash = "sha256-H04JvsVKrdqr3ON7JhU0g17jjlg/jzQ7eTfx9vUNd3E=";
+    } // { shortRev = "a73afcf"; };
   };
 
   git = rec {
@@ -45,8 +43,7 @@ in
     postPatch = ''
       patchShebangs --build test/
     '';
-    nativeBuildInputs = [ cmake ];
-    buildInputs = lib.optionals (useMpi) [ mpi ];
+    nativeBuildInputs = [ cmake ] ++ lib.optionals (useMpi) [ mpi ];
     cmakeBuildType = if (enableDebug) then "Debug" else "Release";
     cmakeFlags = [
       "-DOVNI_GIT_COMMIT=${src.shortRev}"

pkgs/paraver/default.nix

@@ -1,5 +1,6 @@
 {
   stdenv
+, fetchFromGitHub
 , autoreconfHook
 , boost
 , libxml2
@@ -18,14 +19,23 @@ 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
+
+    # Fix for boost >=1.87 (thanks to gamezelda)
+    # https://aur.archlinux.org/cgit/aur.git/commit/?h=wxparaver&id=b0dcd08c472536e0a1a3cc1dfbc4c77d9f5e0d47
+    ./fix-boost-87.patch
+  ];
+
   hardeningDisable = [ "all" ];
 
   # Fix the PARAVER_HOME variable
@@ -50,17 +60,17 @@ stdenv.mkDerivation rec {
   ];
 
   nativeBuildInputs = [
+    autoconf
+    automake
+    autoreconfHook
     wrapGAppsHook
   ];
 
   buildInputs = [
-    autoreconfHook
     boost
     libxml2.dev
     xml2
     wx
-    autoconf
-    automake
     paraverKernel
     openssl.dev
   ];

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-boost-87.patch

@@ -0,0 +1,87 @@
+From 7ecd888e2ebb9e8c5582851d3c50bff61022708e Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Joan=20Bruguera=20Mic=C3=B3?= <joanbrugueram@gmail.com>
+Date: Sat, 29 Mar 2025 18:14:25 +0000
+Subject: [PATCH] tutorialsdownload: Fix Boost ASIO 1.87.0 removals
+
+---
+ src/tutorialsdownload.cpp | 25 ++++++++++++-------------
+ 1 file changed, 12 insertions(+), 13 deletions(-)
+
+diff --git a/src/tutorialsdownload.cpp b/src/tutorialsdownload.cpp
+index a1921fd..6ce9dc2 100644
+--- a/src/tutorialsdownload.cpp
++++ b/src/tutorialsdownload.cpp
+@@ -121,13 +121,13 @@ void TutorialsProgress::updateInstall( int whichValue )
+ class client
+ {
+   public:
+-    client( boost::asio::io_service& io_service,
++    client( boost::asio::io_context& io_context,
+             boost::asio::ssl::context& context,
+             const std::string& server, const std::string& path,
+             ofstream& storeFile,
+             TutorialsProgress *progress )
+-            : resolver_( io_service ),
+-              socket_( io_service, context ),
++            : resolver_( io_context ),
++              socket_( io_context, context ),
+               store_( storeFile ),
+               progress_( progress )
+     {
+@@ -143,8 +143,7 @@ class client
+ 
+         // Start an asynchronous resolve to translate the server and service names
+         // into a list of endpoints.
+-        tcp::resolver::query query( server, "https" );
+-        resolver_.async_resolve( query,
++        resolver_.async_resolve( server, "https",
+                                  boost::bind( &client::handle_resolve,
+                                               this,
+                                               boost::asio::placeholders::error,
+@@ -154,7 +153,7 @@ class client
+   private:
+ 
+     void handle_resolve( const boost::system::error_code& err,
+-                         tcp::resolver::iterator endpoint_iterator )
++                         const tcp::resolver::results_type& endpoints )
+     {
+       if ( !err )
+       {
+@@ -162,7 +161,7 @@ class client
+         socket_.set_verify_callback( boost::bind( &client::verify_certificate, this, _1, _2 ) );
+ 
+         boost::asio::async_connect( socket_.lowest_layer(), 
+-                                    endpoint_iterator,
++                                    endpoints,
+                                     boost::bind( &client::handle_connect, 
+                                                  this,
+                                                  boost::asio::placeholders::error ) );
+@@ -536,9 +535,9 @@ bool TutorialsDownload::downloadTutorialsList() const
+     boost::asio::ssl::context ctx( boost::asio::ssl::context::sslv23 );
+     ctx.set_default_verify_paths();
+ 
+-    boost::asio::io_service io_service;
+-    client c( io_service, ctx, server, path, storeFile, nullptr );
+-    io_service.run();
++    boost::asio::io_context io_context;
++    client c( io_context, ctx, server, path, storeFile, nullptr );
++    io_context.run();
+ 
+     doneDownload = true;
+   }
+@@ -580,9 +579,9 @@ bool TutorialsDownload::download( const TutorialData& whichTutorial, string& tut
+     boost::asio::ssl::context ctx( boost::asio::ssl::context::sslv23 );
+     ctx.set_default_verify_paths();
+ 
+-    boost::asio::io_service io_service;
+-    client c( io_service, ctx, std::string( server.mb_str() ), std::string( path.mb_str() ), storeFile, &progress );
+-    io_service.run();
++    boost::asio::io_context io_context;
++    client c( io_context, ctx, std::string( server.mb_str() ), std::string( path.mb_str() ), storeFile, &progress );
++    io_context.run();
+   }
+   catch ( ParaverKernelException& e )
+   {
+-- 
+2.49.0
+

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

@@ -1,32 +1,32 @@
 {
   stdenv
+, fetchFromGitHub
 , autoreconfHook
 , boost
 , libxml2
 , xml2
-, wxGTK32
 , autoconf
 , automake
 , pkg-config
 , zlib
 }:
 
-let
-  wx = wxGTK32;
-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
+    # TODO: add this back if it's still relevant
+    # ./dont-expand-colors.patch
+    ./fix-libxml2-deprecation.patch
   ];
 
   hardeningDisable = [ "all" ];
@@ -44,14 +44,17 @@ stdenv.mkDerivation rec {
     "--enable-openmp"
   ];
 
-  buildInputs = [
+  nativeBuildInputs = [
     autoreconfHook
-    boost
-    libxml2.dev
-    xml2
     autoconf
     automake
     pkg-config
+  ];
+
+  buildInputs = [
+    boost
+    libxml2.dev
+    xml2
     zlib
   ];
 }

pkgs/paraver/release.nix

@@ -61,13 +61,16 @@ stdenv.mkDerivation rec {
     "--with-wx-config=${wx}/bin/wx-config"
   ];
 
+  nativeBuildInputs = [
+    autoconf
+    automake
+  ];
+
   buildInputs = [
     boost
     xml2
     libxml2.dev
     wx
-    autoconf
-    automake
     openssl.dev
   ];
 

pkgs/sonar/default.nix

@@ -18,8 +18,12 @@ stdenv.mkDerivation rec {
   hardeningDisable = [ "all" ];
   dontStrip = true;
   configureFlags = [ "--with-ovni=${ovni}" ];
-  buildInputs = [
+
+  nativeBuildInputs = [
     autoreconfHook
+  ];
+
+  buildInputs = [
     ovni
     mpi
   ];

pkgs/tacuda/default.nix

@@ -0,0 +1,61 @@
+{ stdenv
+, lib
+, withCFlags
+, fetchFromGitHub
+, automake
+, autoconf
+, libtool
+, gnumake
+, autoreconfHook
+, boost
+
+, useGit ? false
+, gitUrl ? "git@gitlab-internal.bsc.es:task-awareness/tacuda/tacuda.git"
+, gitBranch ? "main"
+, gitCommit ? ""
+}:
+
+let
+  release = rec {
+    version = "2.1.0";
+    src = fetchFromGitHub {
+      owner = "bsc-pm";
+      repo = "tacuda";
+      rev = version;
+      hash = "";
+    };
+  };
+
+  git = rec {
+    version = src.shortRev;
+    src = builtins.fetchGit {
+      url = gitUrl;
+      ref = gitBranch;
+      rev = gitCommit;
+    };
+  };
+
+  source = if (useGit) then git else release;
+
+in
+
+stdenv.mkDerivation {
+  pname = "tacuda";
+  inherit (source) src version;
+
+  enableParallelBuilding = true;
+  separateDebugInfo = true;
+
+  nativeBuildInputs = [
+    autoreconfHook
+    automake
+    autoconf
+    libtool
+    gnumake
+  ];
+
+  buildInputs = [
+    boost
+  ];
+
+}

pkgs/tampi/default.nix

@@ -8,14 +8,13 @@
 , gnumake
 , boost
 , mpi
-, gcc
 , autoreconfHook
 , enableOvni ? true
 , ovni ? null
 , useGit ? false
 , gitUrl ? "ssh://git@bscpm04.bsc.es/interoperability/tampi.git"
 , gitBranch ? "master"
-, gitCommit ? "a5c93bf8ab045b71ad4a8d5e2c991ce774db5cbc"
+, gitCommit ? "f6455db9d3124ae36e715a4874fd49720e79f20a"
 }:
 
 with lib;
@@ -24,12 +23,12 @@ assert enableOvni -> (ovni != null);
 
 let
   release = rec {
-    version = "4.0";
+    version = "4.1";
     src = fetchFromGitHub {
       owner = "bsc-pm";
       repo = "tampi";
       rev = "v${version}";
-      hash = "sha256-R7ew5tsrxGReTvOeeZe1FD0oThBhOHoDGv6Mo2sbmDg=";
+      hash = "sha256-SwfPSnwcZnRnSgNvCD5sFSUJRpWINqI5I4adj5Hh+XY=";
     };
   };
   git = rec {
@@ -41,20 +40,23 @@ let
     };
   };
   source = if (useGit) then git else release;
-in stdenv.mkDerivation rec {
+in stdenv.mkDerivation {
   pname = "tampi";
   inherit (source) src version;
   enableParallelBuilding = true;
   separateDebugInfo = true;
-  buildInputs = [
-    autoreconfHook
-    automake
+
+  nativeBuildInputs = [
     autoconf
-    libtool
+    automake
+    autoreconfHook
     gnumake
+    libtool
+  ];
+
+  buildInputs = [
     boost
     mpi
-    gcc
   ] ++ optional (enableOvni) ovni;
   configureFlags = optional (enableOvni) "--with-ovni=${ovni}";
   dontDisableStatic = true;

pkgs/taopencl/default.nix

@@ -0,0 +1,46 @@
+{
+  stdenv
+, automake
+, autoconf
+, libtool
+, gnumake
+, boost
+, mpi
+, gcc
+, autoreconfHook
+, ocl-icd
+, opencl-headers
+}:
+
+stdenv.mkDerivation (finalAttrs: {
+  pname = "taopencl";
+  version = finalAttrs.src.shortRev;
+
+  src = builtins.fetchGit {
+    url =  "git@gitlab-internal.bsc.es:task-awareness/taopencl/taopencl.git";
+    ref = "master";
+    rev = "c3b7b32ae8fa4af7ceff598532a881f8f1490aaf";
+  };
+
+  enableParallelBuilding = true;
+  separateDebugInfo = true;
+
+  configureFlags = [
+    "--with-opencl-lib=${ocl-icd}/lib"
+    "--with-opencl-include=${opencl-headers}/include"
+  ];
+
+  buildInputs = [
+    autoreconfHook
+    automake
+    autoconf
+    libtool
+    gnumake
+    boost
+    mpi
+    gcc
+  ];
+
+  dontDisableStatic = true;
+  hardeningDisable = [ "all" ];
+})

pkgs/tasycl/default.nix

@@ -9,7 +9,6 @@
 , gnumake
 , autoreconfHook
 , boost
-, opensycl ? null
 , adaptivecpp ? null
 , useIntel ? true
 
@@ -19,17 +18,9 @@
 , gitCommit ? "78f98dcf60a66e0eaa3b4ebcf55be076bec64825"
 }:
 
-assert (useIntel || opensycl != null || adaptivecpp != null);
+assert (useIntel || adaptivecpp != null);
 
 let
-  # opensycl has migrated to adaptivecpp
-  acpp-flags =
-    if adaptivecpp == null then
-      [ "-L${opensycl}/lib" "-lhipSYCL-rt" "-I${opensycl}/include" ]
-    else
-      [ "-L${adaptivecpp}/lib" "-lacpp-rt" "-I${adaptivecpp}/include" ]
-  ;
-
   variant = if useIntel then "intel" else "acpp";
 
   syclStdenv =
@@ -38,7 +29,7 @@ let
       # intel disables all optimizations
       withCFlags ["-O3"] intelPackages.stdenv
     else
-      withCFlags acpp-flags stdenv
+      withCFlags [ "-L${adaptivecpp}/lib" "-lacpp-rt" "-I${adaptivecpp}/include" ] stdenv
   ;
 
   release = rec {

test/compilers/icpx-ompss2.nix

@@ -1,4 +1,4 @@
-{ writeText, intelPackages, nodes, nosv, clangOmpss2Nodes, clangOmpss2Unwrapped, clangOmpss2, strace }:
+{ writeText, intelPackages, nodes, nosv, clangOmpss2Nodes, strace }:
 
 let
   hello_cpp = writeText "hello.cpp" ''
@@ -44,6 +44,10 @@ intelPackages.stdenv.mkDerivation {
   dontUnpack = true;
   dontConfigure = true;
 
+  # NODES requires access to /sys/devices to request NUMA information. It will
+  # fail to run otherwise, so we disable the sandbox for this test.
+  __noChroot = true;
+
   env.NODES_HOME = nodes;
 
   NIX_DEBUG = 0;
@@ -54,9 +58,9 @@ intelPackages.stdenv.mkDerivation {
     echo NODES_HOME=$NODES_HOME
     command -v $CXX
 
-    icpx -fsycl \
-        -fsycl-host-compiler=${clangOmpss2Nodes}/bin/clang++ \
-        -fsycl-host-compiler-options='-fompss-2=libnodes' \
+    icpx -Wno-deprecated-declarations -fsycl \
+        -fsycl-host-compiler=${clangOmpss2Nodes.forIcpx}/bin/clang++ \
+        -fsycl-host-compiler-options='-Wno-deprecated-declarations -fompss-2=libnodes' \
         -lnodes -lnosv \
         $NODES_HOME/lib/nodes-main-wrapper.o \
         hello.cpp -o hello