Add install check for OpenMP{,-V}

See: https://lkml.org/lkml/2025/4/9/1709

flake.lock

@@ -2,16 +2,16 @@
   "nodes": {
     "nixpkgs": {
       "locked": {
-        "lastModified": 1752436162,
+        "lastModified": 1764522689,
-        "narHash": "sha256-Kt1UIPi7kZqkSc5HVj6UY5YLHHEzPBkgpNUByuyxtlw=",
+        "narHash": "sha256-SqUuBFjhl/kpDiVaKLQBoD8TLD+/cTUzzgVFoaHrkqY=",
         "owner": "NixOS",
         "repo": "nixpkgs",
-        "rev": "dfcd5b901dbab46c9c6e80b265648481aafb01f8",
+        "rev": "8bb5646e0bed5dbd3ab08c7a7cc15b75ab4e1d0f",
         "type": "github"
       },
       "original": {
         "owner": "NixOS",
-        "ref": "nixos-25.05",
+        "ref": "nixos-25.11",
         "repo": "nixpkgs",
         "type": "github"
       }

flake.nix

@@ -1,6 +1,6 @@
 {
   inputs = {
-    nixpkgs.url = "github:NixOS/nixpkgs/nixos-25.05";
+    nixpkgs.url = "github:NixOS/nixpkgs/nixos-25.11";
   };
 
   outputs = { self, nixpkgs, ... }:

m/common/base/env.nix

@@ -1,12 +1,12 @@
-{ pkgs, config, ... }:
+{ pkgs, ... }:
 
 {
   environment.systemPackages = with pkgs; [
     vim wget git htop tmux pciutils tcpdump ripgrep nix-index nixos-option
     nix-diff ipmitool freeipmi ethtool lm_sensors cmake gnumake file tree
-    ncdu config.boot.kernelPackages.perf ldns pv
+    ncdu perf ldns pv
-    # From bsckgs overlay
+    # From jungle overlay
-    osumb
+    osumb nixgen
   ];
 
   programs.direnv.enable = true;

m/common/base/watchdog.nix

@@ -5,5 +5,5 @@
   boot.kernelModules = [ "ipmi_watchdog" ];
 
   # Enable systemd watchdog with 30 s interval
-  systemd.watchdog.runtimeTime = "30s";
+  systemd.settings.Manager.RuntimeWatchdogSec = 30;
 }

m/fox/configuration.nix

@@ -93,20 +93,4 @@
     wantedBy = [ "multi-user.target" ];
     serviceConfig.ExecStart = script;
   };
-
-  # Only allow SSH connections from users who have a SLURM allocation
-  # See: https://slurm.schedmd.com/pam_slurm_adopt.html
-  security.pam.services.sshd.rules.account.slurm = {
-    control = "required";
-    enable = true;
-    modulePath = "${pkgs.slurm}/lib/security/pam_slurm_adopt.so";
-    args = [ "log_level=debug5" ];
-    order = 999999; # Make it last one
-  };
-
-  # Disable systemd session (pam_systemd.so) as it will conflict with the
-  # pam_slurm_adopt.so module. What happens is that the shell is first adopted
-  # into the slurmstepd task and then into the systemd session, which is not
-  # what we want, otherwise it will linger even if all jobs are gone.
-  security.pam.services.sshd.startSession = lib.mkForce false;
 }

m/module/debuginfod.nix

@@ -1,3 +1,10 @@
 {
-  services.nixseparatedebuginfod.enable = true;
+  services.nixseparatedebuginfod2 = {
+    enable = true;
+    substituters = [
+      "local:"
+      "https://cache.nixos.org"
+      "http://hut/cache"
+    ];
+  };
 }

m/module/slurm-client.nix

@@ -1,4 +1,4 @@
-{ lib, ... }:
+{ lib, pkgs, ... }:
 
 {
   imports = [
@@ -21,4 +21,20 @@
   };
 
   services.slurm.client.enable = true;
+
+  # Only allow SSH connections from users who have a SLURM allocation
+  # See: https://slurm.schedmd.com/pam_slurm_adopt.html
+  security.pam.services.sshd.rules.account.slurm = {
+    control = "required";
+    enable = true;
+    modulePath = "${pkgs.slurm}/lib/security/pam_slurm_adopt.so";
+    args = [ "log_level=debug5" ];
+    order = 999999; # Make it last one
+  };
+
+  # Disable systemd session (pam_systemd.so) as it will conflict with the
+  # pam_slurm_adopt.so module. What happens is that the shell is first adopted
+  # into the slurmstepd task and then into the systemd session, which is not
+  # what we want, otherwise it will linger even if all jobs are gone.
+  security.pam.services.sshd.startSession = lib.mkForce false;
 }

m/module/slurm-common.nix

@@ -1,31 +1,6 @@
 { config, pkgs, ... }:
 
-let
+{
-  suspendProgram = pkgs.writeShellScript "suspend.sh" ''
-    exec 1>>/var/log/power_save.log 2>>/var/log/power_save.log
-    set -x
-    export "PATH=/run/current-system/sw/bin:$PATH"
-    echo "$(date) Suspend invoked $0 $*" >> /var/log/power_save.log
-    hosts=$(scontrol show hostnames $1)
-    for host in $hosts; do
-      echo Shutting down host: $host
-      ipmitool -I lanplus -H ''${host}-ipmi -P "" -U "" chassis power off
-    done
-  '';
-
-  resumeProgram = pkgs.writeShellScript "resume.sh" ''
-    exec 1>>/var/log/power_save.log 2>>/var/log/power_save.log
-    set -x
-    export "PATH=/run/current-system/sw/bin:$PATH"
-    echo "$(date) Suspend invoked $0 $*" >> /var/log/power_save.log
-    hosts=$(scontrol show hostnames $1)
-    for host in $hosts; do
-      echo Starting host: $host
-      ipmitool -I lanplus -H ''${host}-ipmi -P "" -U "" chassis power on
-    done
-  '';
-
-in {
   services.slurm = {
     controlMachine = "apex";
     clusterName = "jungle";
@@ -59,16 +34,6 @@ in {
       # the resources. Use the task/cgroup plugin to enable process containment.
       TaskPlugin=task/affinity,task/cgroup
 
-      # Power off unused nodes until they are requested
-      SuspendProgram=${suspendProgram}
-      SuspendTimeout=60
-      ResumeProgram=${resumeProgram}
-      ResumeTimeout=300
-      SuspendExcNodes=fox
-
-      # Turn the nodes off after 1 hour of inactivity
-      SuspendTime=3600
-
       # Reduce port range so we can allow only this range in the firewall
       SrunPortRange=60000-61000
 

overlay.nix

@@ -19,11 +19,7 @@ let
     cudainfo = prev.callPackage ./pkgs/cudainfo/default.nix { };
     #extrae = callPackage ./pkgs/extrae/default.nix { }; # Broken and outdated
     gpi-2 = callPackage ./pkgs/gpi-2/default.nix { };
-    intel-apt = callPackage ./pkgs/intel-oneapi/packages.nix { };
     intelPackages_2023 = callPackage ./pkgs/intel-oneapi/2023.nix { };
-    intelPackages_2024 = final.intel-apt.hpckit_2024;
-    intelPackages_2025 = final.intel-apt.hpckit_2025;
-    intelPackages = final.intelPackages_2025;
     jemallocNanos6 = callPackage ./pkgs/nanos6/jemalloc.nix { };
     # FIXME: Extend this to all linuxPackages variants. Open problem, see:
     # https://discourse.nixos.org/t/whats-the-right-way-to-make-a-custom-kernel-module-available/4636
@@ -34,24 +30,26 @@ let
       amd-uprof-driver = _prev.callPackage ./pkgs/amd-uprof/driver.nix { };
     });
     lmbench = callPackage ./pkgs/lmbench/default.nix { };
-    mcxx = callPackage ./pkgs/mcxx/default.nix { };
+    # Broken and unmantained
+    # mcxx = callPackage ./pkgs/mcxx/default.nix { };
     meteocat-exporter = prev.callPackage ./pkgs/meteocat-exporter/default.nix { };
     mpi = final.mpich; # Set MPICH as default
     mpich = callPackage ./pkgs/mpich/default.nix { mpich = prev.mpich; };
     nanos6 = callPackage ./pkgs/nanos6/default.nix { };
     nanos6Debug = final.nanos6.override { enableDebug = true; };
     nixtools = callPackage ./pkgs/nixtools/default.nix { };
+    nixgen = callPackage ./pkgs/nixgen/default.nix { };
     # Broken because of pkgsStatic.libcap
     # See: https://github.com/NixOS/nixpkgs/pull/268791
     #nix-wrap = callPackage ./pkgs/nix-wrap/default.nix { };
     nodes = callPackage ./pkgs/nodes/default.nix { };
     nosv = callPackage ./pkgs/nosv/default.nix { };
-    oneMath = callPackage ./pkgs/onemath/default.nix { };
     openmp = callPackage ./pkgs/llvm-ompss2/openmp.nix { monorepoSrc = final.clangOmpss2Unwrapped.src; version = final.clangOmpss2Unwrapped.version; };
     openmpv = final.openmp.override { enableNosv = true; enableOvni = true; };
     osumb = callPackage ./pkgs/osu/default.nix { };
     ovni = callPackage ./pkgs/ovni/default.nix { };
     ovniGit = final.ovni.override { useGit = true; };
+    papi = callPackage ./pkgs/papi/default.nix { papi = prev.papi; };
     paraverKernel = callPackage ./pkgs/paraver/kernel.nix { };
     prometheus-slurm-exporter = prev.callPackage ./pkgs/slurm-exporter/default.nix { };
     #pscom = callPackage ./pkgs/parastation/pscom.nix { }; # Unmaintaned
@@ -64,12 +62,8 @@ let
     stdenvClangOmpss2NodesOmpv = final.stdenv.override { cc = final.clangOmpss2NodesOmpv; allowedRequisites = null; };
     tagaspi = callPackage ./pkgs/tagaspi/default.nix { };
     tampi = callPackage ./pkgs/tampi/default.nix { };
-    tasycl = callPackage ./pkgs/tasycl/default.nix { };
-    tasycl-acpp = callPackage ./pkgs/tasycl/default.nix { useIntel = false; };
     upc-qaire-exporter = prev.callPackage ./pkgs/upc-qaire-exporter/default.nix { };
     wxparaver = callPackage ./pkgs/paraver/default.nix { };
-
-    gromacs = callPackage ./pkgs/gromacs/default.nix { enableSYCL = true; };
   };
 
   tests = rec {
@@ -77,8 +71,6 @@ let
     #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 { };
-    hello-syclompss = callPackage ./test/compilers/icpx-ompss2.nix { };
     lto = callPackage ./test/compilers/lto.nix { };
     asan = callPackage ./test/compilers/asan.nix { };
     intel2023-icx-c   = hello-c.override   { stdenv = final.intelPackages_2023.stdenv; };
@@ -88,13 +80,6 @@ let
     intel2023-ifort   = callPackage ./test/compilers/hello-f.nix {
       stdenv = final.intelPackages_2023.stdenv-ifort;
     };
-    intel2024-icx-c   = hello-c.override   { stdenv = final.intelPackages_2024.stdenv; };
-    intel2025-icx-c   = hello-c.override   { stdenv = final.intelPackages_2025.stdenv; };
-    intel2024-icx-cpp = hello-cpp.override { stdenv = final.intelPackages_2024.stdenv; };
-    intel2025-icx-cpp = hello-cpp.override { stdenv = final.intelPackages_2025.stdenv; };
-    # intel2023-sycl    = hello-sycl.override { intelPackages = final.intelPackages_2023; }; # broken
-    intel2024-sycl    = hello-sycl.override { intelPackages = final.intelPackages_2024; };
-    intel2025-sycl    = hello-sycl.override { intelPackages = final.intelPackages_2025; };
     clangOmpss2-lto   = lto.override       { stdenv = final.stdenvClangOmpss2Nanos6; };
     clangOmpss2-asan  = asan.override      { stdenv = final.stdenvClangOmpss2Nanos6; };
     clangOmpss2-task  = callPackage ./test/compilers/ompss2.nix {
@@ -118,14 +103,16 @@ let
   pkgsTopLevel = filterAttrs (_: isDerivation) bscPkgs;
 
   # Native build in that platform doesn't imply cross build works
-  canCrossCompile = platform: pkg:
+  canCrossCompile = platform: default: pkg:
     (isDerivation pkg) &&
-    # Must be defined explicitly
+    # If meta.cross is undefined, use default
-    (pkg.meta.cross or false) &&
+    (pkg.meta.cross or default) &&
-    (meta.availableOn platform pkg);
+    (meta.availableOn final.pkgsCross.${platform}.stdenv.hostPlatform pkg);
 
   # For now only RISC-V
-  crossSet = { riscv64 = final.pkgsCross.riscv64.bsc.pkgsTopLevel; };
+  crossSet = genAttrs [ "riscv64" ] (platform:
+    filterAttrs (_: canCrossCompile platform true)
+      final.pkgsCross.${platform}.bsc.pkgsTopLevel);
 
   buildList = name: paths:
     final.runCommandLocal name { } ''
@@ -145,7 +132,7 @@ let
   # For now only RISC-V
   crossList = buildList "ci-cross"
     (filter
-      (canCrossCompile final.pkgsCross.riscv64.stdenv.hostPlatform)
+      (canCrossCompile "riscv64" false) # opt-in (pkgs with: meta.cross = true)
         (builtins.attrValues crossSet.riscv64));
 
 in bscPkgs // {

pkgs/amd-uprof/default.nix

@@ -47,6 +47,7 @@ in
     inherit version;
     src = uprofSrc;
     dontStrip = true;
+    strictDeps = true;
     phases = [ "installPhase" "fixupPhase" ];
     nativeBuildInputs = [ autoPatchelfHook radare2 ];
     buildInputs = [
@@ -90,7 +91,7 @@ in
     meta = {
       description = "Performance analysis tool-suite for x86 based applications";
       homepage = "https://www.amd.com/es/developer/uprof.html";
-      platforms = lib.platforms.linux;
+      platforms = [ "x86_64-linux" ];
       license = lib.licenses.unfree;
       maintainers = with lib.maintainers.bsc; [ rarias varcila ];
     };

pkgs/amd-uprof/driver.nix

@@ -18,8 +18,9 @@ in stdenv.mkDerivation {
     set +x
   '';
   hardeningDisable = [ "pic" "format" ];
+  strictDeps = true;
   nativeBuildInputs = kernel.moduleBuildDependencies;
-  patches = [ ./makefile.patch ./hrtimer.patch ];
+  patches = [ ./makefile.patch ./hrtimer.patch ./remove-wr-rdmsrq.patch ];
   makeFlags = [
     "KERNEL_VERSION=${kernel.modDirVersion}"
     "KERNEL_DIR=${kernel.dev}/lib/modules/${kernel.modDirVersion}/build"

pkgs/amd-uprof/remove-wr-rdmsrq.patch

@@ -0,0 +1,20 @@
+diff --git a/inc/PwrProfAsm.h b/inc/PwrProfAsm.h
+index d77770a..c93a0e9 100644
+--- a/inc/PwrProfAsm.h
++++ b/inc/PwrProfAsm.h
+@@ -347,6 +347,7 @@
+ 
+ #endif
+ 
++/*
+ #define rdmsrq(msr,val1,val2,val3,val4) ({ \
+         __asm__ __volatile__( \
+                               "rdmsr\n" \
+@@ -362,6 +363,7 @@
+                               :"c"(msr), "a"(val1), "d"(val2), "S"(val3), "D"(val4) \
+                             ); \
+     })
++*/
+ 
+ #define rdmsrpw(msr,val1,val2,val3,val4) ({ \
+         __asm__ __volatile__( \

pkgs/bench6/default.nix

@@ -59,6 +59,7 @@ stdenv.mkDerivation rec {
   ];
   hardeningDisable = [ "all" ];
   dontStrip = true;
+  strictDeps = true;
 
   meta = {
     homepage = "https://gitlab.pm.bsc.es/rarias/bench6";

pkgs/bigotes/default.nix

@@ -16,6 +16,8 @@ stdenv.mkDerivation {
   };
   nativeBuildInputs = [ cmake ];
 
+  strictDeps = true;
+
   meta = {
     homepage = "https://github.com/rodarima/bigotes";
     description = "Versatile benchmark tool";

pkgs/cudainfo/default.nix

@@ -1,5 +1,6 @@
 {
   stdenv
+, lib
 , cudatoolkit
 , cudaPackages
 , autoAddDriverRunpath
@@ -9,11 +10,14 @@
 stdenv.mkDerivation (finalAttrs: {
   name = "cudainfo";
   src = ./.;
-  buildInputs = [
+  strictDeps = true;
+  nativeBuildInputs = [
     cudatoolkit # Required for nvcc
-    cudaPackages.cuda_cudart.static # Required for -lcudart_static
     autoAddDriverRunpath
   ];
+  buildInputs = [
+    (lib.getOutput "static" cudaPackages.cuda_cudart) # Required for -lcudart_static
+  ];
   installPhase = ''
     mkdir -p $out/bin
     cp -a cudainfo $out/bin
@@ -22,6 +26,7 @@ stdenv.mkDerivation (finalAttrs: {
     name = "cudainfo-test";
     requiredSystemFeatures = [ "cuda" ];
     dontBuild = true;
+    strictDeps = true;
     nativeCheckInputs = [
       finalAttrs.finalPackage # The cudainfo package from above
       strace # When it fails, it will show the trace
@@ -40,4 +45,9 @@ stdenv.mkDerivation (finalAttrs: {
     '';
     installPhase = "touch $out";
   };
+
+  meta = {
+    platforms = [ "x86_64-linux" ];
+    maintainers = with lib.maintainers.bsc; [ rarias ];
+  };
 })

pkgs/extrae/default.nix

@@ -20,7 +20,7 @@
 #, python3Packages
 , installShellFiles
 , symlinkJoin
-, enablePapi ? stdenv.hostPlatform == stdenv.buildPlatform # Disabled when cross-compiling
+, enablePapi ? true
 }:
 
 let

pkgs/gpi-2/default.nix

@@ -9,7 +9,6 @@
 , automake
 , libtool
 , mpi
-, rsync
 , gfortran
 }:
 
@@ -34,6 +33,7 @@ stdenv.mkDerivation rec {
   };
 
   enableParallelBuilding = true;
+  strictDeps = true;
 
   patches = [ ./rdma-core.patch ./max-mem.patch ];
 
@@ -44,13 +44,24 @@ stdenv.mkDerivation rec {
 
   configureFlags = [
     "--with-infiniband=${rdma-core-all}"
-    "--with-mpi=${mpiAll}"
+    "--with-mpi=yes" # fixes mpi detection when cross-compiling
     "--with-slurm"
     "CFLAGS=-fPIC"
     "CXXFLAGS=-fPIC"
   ];
 
-  buildInputs = [ slurm mpiAll rdma-core-all autoconf automake libtool rsync gfortran ];
+  nativeBuildInputs = [
+    autoconf
+    automake
+    gfortran
+    libtool
+  ];
+
+  buildInputs = [
+    slurm
+    mpiAll
+    rdma-core-all
+  ];
 
   hardeningDisable = [ "all" ];
 
@@ -60,5 +71,6 @@ stdenv.mkDerivation rec {
     maintainers = with lib.maintainers.bsc; [ rarias ];
     platforms = lib.platforms.linux;
     license = lib.licenses.gpl3Plus;
+    cross = false; # infiniband detection does not work
   };
 }

pkgs/gromacs/default.nix

@@ -1,191 +0,0 @@
-{
-  lib,
-  stdenv,
-  fetchurl,
-  cmake,
-  hwloc,
-  fftw,
-  perl,
-  blas,
-  lapack,
-  llvmPackages,
-  intelPackages ? null,
-  mpi,
-  cudaPackages,
-  plumed,
-  singlePrec ? true,
-  config,
-  enableSYCL ? false,
-  enableCuda ? config.cudaSupport,
-  enableMpi ? false,
-  enablePlumed ? false,
-  cpuAcceleration ? null,
-}:
-
-# CUDA is only implemented for single precission
-assert enableCuda -> singlePrec;
-
-assert !(enableSYCL && enableCuda);
-
-assert enableSYCL -> intelPackages != null;
-
-let
-  inherit (cudaPackages.flags) cmakeCudaArchitecturesString;
-
-  # Select reasonable defaults for all major platforms
-  # The possible values are defined in CMakeLists.txt:
-  # AUTO None SSE2 SSE4.1 AVX_128_FMA AVX_256 AVX2_256
-  # AVX2_128 AVX_512 AVX_512_KNL MIC ARM_NEON ARM_NEON_ASIMD
-  SIMD =
-    x:
-    if (cpuAcceleration != null) then
-      x
-    else if stdenv.hostPlatform.system == "i686-linux" then
-      "SSE2"
-    else if stdenv.hostPlatform.system == "x86_64-linux" then
-      "SSE4.1"
-    else if stdenv.hostPlatform.system == "x86_64-darwin" then
-      "SSE4.1"
-    else if stdenv.hostPlatform.system == "aarch64-linux" then
-      "ARM_NEON_ASIMD"
-    else
-      "None";
-
-  source =
-    if enablePlumed then
-      {
-        version = "2024.2";
-        hash = "sha256-gCp+M18uiVdw9XsVnk7DaOuw/yzm2sz3BsboAlw2hSs=";
-      }
-    else
-      {
-        version = "2025.3";
-        hash = "sha256-i9/KAmjz8Qp8o8BuWbYvc+oCQgxnIRwP85EvMteDPGU=";
-      };
-
-  stdenv' =
-    if enableSYCL then intelPackages.stdenv else stdenv;
-
-in
-stdenv'.mkDerivation rec {
-  pname = "gromacs";
-  version = source.version;
-
-  src = fetchurl {
-    url = "ftp://ftp.gromacs.org/pub/gromacs/gromacs-${version}.tar.gz";
-    inherit (source) hash;
-  };
-
-  patches = [ (if enablePlumed then ./pkgconfig-2024.patch else ./pkgconfig-2025.patch) ];
-
-  postPatch = lib.optionalString enablePlumed ''
-    plumed patch -p -e gromacs-${source.version}
-  '';
-
-  outputs = [
-    "out"
-    "dev"
-    "man"
-  ];
-
-  nativeBuildInputs = [
-    cmake
-  ]
-  ++ lib.optional enablePlumed plumed
-  ++ lib.optionals enableCuda [ cudaPackages.cuda_nvcc ];
-
-  env.MKLROOT = intelPackages.mkl;
-
-  buildInputs = [
-    fftw
-    perl
-    hwloc
-    blas
-    lapack
-  ]
-  ++ lib.optional enableMpi mpi
-  ++ lib.optionals enableCuda [
-    cudaPackages.cuda_cccl
-    cudaPackages.cuda_cudart
-    cudaPackages.libcufft
-    cudaPackages.cuda_profiler_api
-  ]
-  ++ lib.optional stdenv.hostPlatform.isDarwin llvmPackages.openmp;
-
-  propagatedBuildInputs = lib.optional enableMpi mpi;
-  propagatedUserEnvPkgs = lib.optional enableMpi mpi;
-
-  cmakeFlags = [
-    (lib.cmakeBool "GMX_HWLOC" true)
-    "-DGMX_SIMD:STRING=${SIMD cpuAcceleration}"
-    "-DGMX_OPENMP:BOOL=TRUE"
-    "-DBUILD_SHARED_LIBS=ON"
-  ]
-  ++ (
-    if singlePrec then
-      [
-        "-DGMX_DOUBLE=OFF"
-      ]
-    else
-      [
-        "-DGMX_DOUBLE=ON"
-        "-DGMX_DEFAULT_SUFFIX=OFF"
-      ]
-  )
-  ++ (
-    if enableMpi then
-      [
-        "-DGMX_MPI:BOOL=TRUE"
-        "-DGMX_THREAD_MPI:BOOL=FALSE"
-      ]
-    else
-      [
-        "-DGMX_MPI:BOOL=FALSE"
-      ]
-  )
-  ++ (lib.optionals enableSYCL [
-    "-DGMX_GPU=SYCL"
-    "-DGMX_OPENMP=OFF" # TODO: enable OpenMP with SYCL?
-  ])
-  ++ lib.optionals enableCuda [
-    "-DGMX_GPU=CUDA"
-    (lib.cmakeFeature "CMAKE_CUDA_ARCHITECTURES" cmakeCudaArchitecturesString)
-
-    # Gromacs seems to ignore and override the normal variables, so we add this ad hoc:
-    (lib.cmakeFeature "GMX_CUDA_TARGET_COMPUTE" cmakeCudaArchitecturesString)
-  ];
-
-  postInstall = ''
-    moveToOutput share/cmake $dev
-  '';
-
-  meta = with lib; {
-    homepage = "https://www.gromacs.org";
-    license = licenses.lgpl21Plus;
-    description = "Molecular dynamics software package";
-    longDescription = ''
-      GROMACS is a versatile package to perform molecular dynamics,
-      i.e. simulate the Newtonian equations of motion for systems
-      with hundreds to millions of particles.
-
-      It is primarily designed for biochemical molecules like
-      proteins, lipids and nucleic acids that have a lot of
-      complicated bonded interactions, but since GROMACS is
-      extremely fast at calculating the nonbonded interactions (that
-      usually dominate simulations) many groups are also using it
-      for research on non-biological systems, e.g. polymers.
-
-      GROMACS supports all the usual algorithms you expect from a
-      modern molecular dynamics implementation, (check the online
-      reference or manual for details), but there are also quite a
-      few features that make it stand out from the competition.
-
-      See: https://www.gromacs.org/about.html for details.
-    '';
-    platforms = platforms.unix;
-    maintainers = with maintainers; [
-      sheepforce
-      markuskowa
-    ];
-  };
-}

pkgs/gromacs/pkgconfig-2024.patch

@@ -1,24 +0,0 @@
-diff --git a/src/external/muparser/muparser.pc.in b/src/external/muparser/muparser.pc.in
-index 646787cb53..9b97ad57f7 100644
---- a/src/external/muparser/muparser.pc.in
-+++ b/src/external/muparser/muparser.pc.in
-@@ -1,7 +1,5 @@
--prefix=@CMAKE_INSTALL_PREFIX@
--exec_prefix=${prefix}
--libdir=${prefix}/@CMAKE_INSTALL_LIBDIR@
--includedir=${prefix}/@CMAKE_INSTALL_INCLUDEDIR@
-+libdir=@CMAKE_INSTALL_FULL_LIBDIR@
-+includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
- 
- Name: @PACKAGE_NAME@
- Description: Mathematical expressions parser library
-diff --git a/src/gromacs/libgromacs.pc.cmakein b/src/gromacs/libgromacs.pc.cmakein
-index ec1ed6684e..ca1105474a 100644
---- a/src/gromacs/libgromacs.pc.cmakein
-+++ b/src/gromacs/libgromacs.pc.cmakein
-@@ -1,4 +1,4 @@
--libdir=@CMAKE_INSTALL_PREFIX@/@CMAKE_INSTALL_LIBDIR@
-+libdir=@CMAKE_INSTALL_FULL_LIBDIR@
- 
- Name: libgromacs@GMX_LIBS_SUFFIX@
- Description: Gromacs library

pkgs/gromacs/pkgconfig-2025.patch

@@ -1,36 +0,0 @@
-diff --git a/src/external/muparser/muparser.pc.in b/src/external/muparser/muparser.pc.in
-index 646787cb53..d26e84de8f 100644
---- a/src/external/muparser/muparser.pc.in
-+++ b/src/external/muparser/muparser.pc.in
-@@ -1,11 +1,9 @@
--prefix=@CMAKE_INSTALL_PREFIX@
--exec_prefix=${prefix}
--libdir=${prefix}/@CMAKE_INSTALL_LIBDIR@
--includedir=${prefix}/@CMAKE_INSTALL_INCLUDEDIR@
--
--Name: @PACKAGE_NAME@
--Description: Mathematical expressions parser library
--Version: @MUPARSER_VERSION@
--Requires:
--Libs: -L${libdir} -lmuparser
--Cflags: -I${includedir} @PKG_CONFIG_FLAGS@
-+libdir=@CMAKE_INSTALL_FULL_LIBDIR@
-+includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
-+
-+Name: @PACKAGE_NAME@
-+Description: Mathematical expressions parser library
-+Version: @MUPARSER_VERSION@
-+Requires:
-+Libs: -L${libdir} -lmuparser
-+Cflags: -I${includedir} @PKG_CONFIG_FLAGS@
-diff --git a/src/gromacs/libgromacs.pc.cmakein b/src/gromacs/libgromacs.pc.cmakein
-index af9b5a6dc0..5f58d549bf 100644
---- a/src/gromacs/libgromacs.pc.cmakein
-+++ b/src/gromacs/libgromacs.pc.cmakein
-@@ -1,5 +1,4 @@
--prefix=@CMAKE_INSTALL_PREFIX@
--libdir=${prefix}/@CMAKE_INSTALL_LIBDIR@
-+libdir=@CMAKE_INSTALL_FULL_LIBDIR@
-
- Name: libgromacs@GMX_LIBS_SUFFIX@
- Description: Gromacs library

pkgs/intel-oneapi/2023.nix

@@ -10,7 +10,7 @@
 , zlib
 , autoPatchelfHook
 , libfabric
-, gcc13
+, gcc
 , wrapCCWith
 }:
 
@@ -33,8 +33,6 @@ let
     maintainers = with lib.maintainers.bsc; [ abonerib ];
   };
 
-  gcc = gcc13;
-
   v = {
     hpckit   = "2023.1.0";
     compiler = "2023.1.0";
@@ -42,19 +40,45 @@ let
     mpi      = "2021.9.0";
   };
 
-  findMatch = name:
+  aptPackageIndex = stdenv.mkDerivation {
-  let
+    name = "intel-oneapi-packages";
-    aptPackages = builtins.fromJSON (builtins.readFile ./packages.json);
+    srcs = [
-    matches = lib.filter (x: name == x.pname) aptPackages;
+      # Run update.sh to update the package lists
-    n = lib.length matches;
+      ./amd64-packages ./all-packages
-    match = builtins.traceVerbose (name + " -- ${builtins.toString n}") (builtins.head matches);
+    ];
+    phases = [ "installPhase" ];
+    installPhase = ''
+      awk -F': ' '\
+        BEGIN   { print "[ {" } \
+        NR>1 && /^Package: / { print "} {"; } \
+        /: /    { printf "%s = \"%s\";\n", $1, $2 } \
+        END     { print "} ]" }' $srcs > $out
+    '';
+  };
 
-    apthost = "https://apt.repos.intel.com/oneapi/";
+  aptPackages = import aptPackageIndex;
+
+  apthost = "https://apt.repos.intel.com/oneapi/";
+
+  getSum = pkgList: name:
+  let
+    matches = lib.filter (x: name == x.Package) pkgList;
+    #n = lib.length matches;
+    #match = builtins.trace (name + " -- ${builtins.toString n}") (lib.elemAt matches 0);
+    match = lib.elemAt matches 0;
   in
-    {
+    match.SHA256;
-      url = apthost + match.filename;
+
-      sha256 = match.sha256;
+  getUrl = pkgList: name:
-    };
+  let
+    matches = lib.filter (x: name == x.Package) pkgList;
+    #match = assert lib.length matches == 1; lib.elemAt matches 0;
+    n = lib.length matches;
+    match =
+      #builtins.trace (name + " -- n=${builtins.toString n}")
+      (lib.elemAt matches 0);
+  in
+    apthost + match.Filename;
 
   uncompressDebs = debs: name: stdenv.mkDerivation {
     name = name;
@@ -74,7 +98,10 @@ let
 
   joinDebs = name: names:
   let
-    debs = builtins.map (x: builtins.fetchurl (findMatch x)) names;
+    urls = builtins.map (x: getUrl aptPackages x) names;
+    sums = builtins.map (x: getSum aptPackages x) names;
+    getsrc = url: sha256: builtins.fetchurl { inherit url sha256; };
+    debs = lib.zipListsWith getsrc urls sums;
   in
     uncompressDebs debs "${name}-source";
 
@@ -101,6 +128,7 @@ let
 
     phases = [ "installPhase" "fixupPhase" ];
     dontStrip = true;
+    strictDeps = true;
     installPhase = ''
       mkdir -p $out/{bin,etc,lib,include}
       mkdir -p $out/share/man
@@ -152,6 +180,7 @@ let
     ];
     phases = [ "installPhase" "fixupPhase" ];
     dontStrip = true;
+    strictDeps = true;
 
     autoPatchelfIgnoreMissingDeps = [ "libhwloc.so.5" ];
 
@@ -195,6 +224,7 @@ let
     ];
     phases = [ "installPhase" "fixupPhase" ];
     dontStrip = true;
+    strictDeps = true;
 
     autoPatchelfIgnoreMissingDeps = [ "libsycl.so.6" ];
 
@@ -262,6 +292,7 @@ let
     phases = [ "installPhase" "fixupPhase" ];
 
     dontStrip = true;
+    strictDeps = true;
 
     installPhase = ''
       mkdir -p $out/{bin,lib,include}
@@ -350,6 +381,7 @@ let
     phases = [ "installPhase" "fixupPhase" ];
 
     dontStrip = true;
+    strictDeps = true;
 
     installPhase = ''
       mkdir -p $out/{bin,lib}
@@ -443,7 +475,7 @@ let
     '';
   };
 
-  ifort-wrapper = wrapIntel {
+  ifort-wrapper = wrapIntel rec {
     cc = intel-compiler-fortran;
     mygcc = gcc;
     extraBuild = ''

pkgs/intel-oneapi/packages.nix

@@ -1,205 +0,0 @@
-{ lib
-, stdenv
-, callPackage
-, dpkg
-, fetchurl
-, recurseIntoAttrs
-
-, sqlite
-, elfutils
-}:
-
-let
-  inherit (builtins)
-    elem attrNames attrValues concatMap filter fromJSON getAttr groupBy head isNull listToAttrs map mapAttrs readFile replaceStrings splitVersion ;
-  inherit (lib)
-    converge findFirst groupBy' hasPrefix optional pipe take toInt toList versionAtLeast versionOlder ;
-
-  aptData = fromJSON (readFile ./packages.json);
-
-  # Compare versions in debian control file syntax
-  # See: https://www.debian.org/doc/debian-policy/ch-relationships.html#syntax-of-relationship-fields
-  #
-  # NOTE: this is not a proper version comparison
-  #
-  # A proper version solver, should aggregate dependencies with the same name
-  # and compute the constraint (e.g. a (>= 2) a (<< 5) -> 2 <= a << 5)
-  #
-  # But in the intel repo, there are no such "duplicated" dependencies to specify
-  # upper limits, which leads to issues when intel-hpckit-2021 depends on things
-  # like intel-basekit >= 2021.1.0-2403 and we end up installing the newest
-  # basekit instead of the one from 2021.
-  #
-  # To mitigate this, >= is set to take the latest version with matching major
-  # and minor (only revision and patch are allowed to change)
-  compareVersions = got: kind: want:
-    let
-      g0 = take 2 (splitVersion got);
-      w0 = take 2 (splitVersion want);
-    in if isNull want then true
-    else if kind == "=" then got == want
-    else if kind == "<<" then versionOlder got want
-    else if kind == "<=" then versionAtLeast want got
-    else if kind == ">>" then versionOlder want got
-    else if kind == ">=" then (g0 == w0) && versionAtLeast got want # always match major version
-    else throw "unknown operation: ${kind}";
-
-  findMatching = { pname, kind, version }:
-    findFirst (x: pname == x.pname && compareVersions x.version kind version) null aptData;
-
-  isIntel = pkg: (hasPrefix "intel-" pkg.pname);
-
-  expandDeps = pkg: (map findMatching (filter isIntel pkg.dependencies)) ++ (optional (pkg.size != 0) pkg);
-
-  # get the oldest by major version. If they have the same major version, take
-  # the newest. This prevents most issues with resolutions
-  # versionOlder b a -> true if b is older than a (b `older` a)
-  getNewerInMajor = a: b: let
-    va = a.version;
-    vb = b.version;
-    va0 = head (splitVersion va);
-    vb0 = head (splitVersion vb);
-  in
-  if isNull a then b
-  else if va0 != vb0 then
-    if va0 > vb0 then b else a
-  else if versionOlder vb va then a else b;
-  removeDups = l: attrValues (groupBy' getNewerInMajor null (getAttr "provides") l);
-
-  _resolveDeps = converge (l: removeDups (concatMap expandDeps l));
-  resolveDeps = pkg: let deps = _resolveDeps (toList pkg);
-      namedDeps = (map (x: "${x.pname}-${x.version}") deps);
-    in builtins.traceVerbose (builtins.deepSeq namedDeps namedDeps) deps;
-
-  blacklist = [
-    "intel-basekit-env"
-    "intel-basekit-getting-started"
-    "intel-hpckit-env"
-    "intel-hpckit-getting-started"
-    "intel-oneapi-advisor"
-    "intel-oneapi-common-licensing"
-    "intel-oneapi-common-oneapi-vars"
-    "intel-oneapi-common-vars"
-    "intel-oneapi-compiler-cpp-eclipse-cfg"
-    "intel-oneapi-compiler-dpcpp-eclipse-cfg"
-    "intel-oneapi-condaindex"
-    "intel-oneapi-dev-utilities-eclipse-cfg"
-    "intel-oneapi-dpcpp-ct-eclipse-cfg"
-    "intel-oneapi-eclipse-ide"
-    "intel-oneapi-hpc-toolkit-getting-started"
-    "intel-oneapi-icc-eclipse-plugin-cpp"
-    "intel-oneapi-vtune"
-    "intel-oneapi-vtune-eclipse-plugin-vtune"
-  ];
-
-  isInBlacklist = pkg: elem pkg.provides blacklist;
-  removeBlacklist = filter (e: !(isInBlacklist e));
-
-  dpkgExtractAll = pname: version: {srcs, deps}: stdenv.mkDerivation {
-    inherit pname version srcs;
-
-    nativeBuildInputs = [ dpkg ];
-    phases = [ "installPhase" ];
-
-    passthru = { inherit deps; };
-
-    installPhase = ''
-      mkdir -p $out
-      for src in $srcs; do
-        echo "Unpacking $src"
-        dpkg -x $src $out
-      done
-    '';
-  };
-
-  apthost = "https://apt.repos.intel.com/oneapi/";
-  fetchDeb = p: fetchurl { url = apthost + p.filename; inherit (p) sha256; };
-
-  buildIntel = pkg: pipe pkg [
-    resolveDeps
-    removeBlacklist
-    (l: {srcs = map fetchDeb l; deps = l; })
-    (dpkgExtractAll "${pkg.provides}-extracted" pkg.version)
-  ];
-
-  findHpcKit = year: findMatching { pname = "intel-hpckit"; kind = "<<"; version = toString (year+1); };
-  years = map toInt (attrNames components);
-
-  patchIntel = callPackage ./patch_intel.nix { };
-
-  # Version information for each hpckit. This is used to normalize the paths
-  # so that files are in $out/{bin,lib,include...} instead of all over the place
-  # in $out/opt/intel/oneapi/*/*/{...}.
-  #
-  # The most important is the compiler component, which is used to build the
-  # stdenv for the hpckit.
-  #
-  # NOTE: this have to be manually specified, so we can avoid IFD. To add a
-  # new version, add a new field with an empty attrset, (e.g. "2026" = {}; ),
-  # build hpckit_2026.unpatched and use the values from
-  # result/opt/intel/oneapi/* to populate the attrset.
-  #
-  # WARN: if there are more than one version in the folders of the unpatched
-  # components, our dependency resolution hacks have probably failed and the
-  # package set may be broken.
-  components = {
-    "2025" = {
-      ishmem = "1.4";
-      pti = "0.13";
-      tcm = "1.4";
-      umf = "0.11";
-
-      ccl = "2021.16";
-      compiler = "2025.2";
-      dal = "2025.8";
-      debugger = "2025.2";
-      dev-utilities = "2025.2";
-      dnnl = "2025.2";
-      dpcpp-ct = "2025.2";
-      dpl = "2022.9";
-      ipp = "2022.2";
-      ippcp = "2025.2";
-      mkl = "2025.2";
-      mpi = "2021.16";
-      tbb = "2022.2";
-    };
-    "2024" = {
-      tcm = "1.1";
-
-      ccl = "2021.13";
-      compiler = "2024.2";
-      dal = "2024.6";
-      debugger = "2024.2";
-      dev-utilities = "2024.2";
-      diagnostics = "2024.2";
-      dnnl = "2024.2";
-      dpcpp-ct = "2024.2";
-      dpl = "2022.6";
-      ipp = "2021.12";
-      ippcp = "2021.12";
-      mkl = "2024.2";
-      mpi = "2021.13";
-      tbb = "2021.13";
-
-      extraPackages = [
-        sqlite
-        elfutils
-      ];
-    };
-  };
-
-  replaceDots = replaceStrings ["."] ["_"];
-
-in recurseIntoAttrs (listToAttrs (map (year: let
-      year_str = toString year;
-    in {
-      name = "hpckit_${year_str}";
-      value = patchIntel {unpatched = buildIntel (findHpcKit year); components = components.${year_str}; };
-  }) years)) // {
-  apt = pipe aptData [
-    (groupBy (p: replaceDots p.provides))
-    (mapAttrs (_: l: listToAttrs (map (pkg: { name = replaceDots ("v" + pkg.version); value = pkg; }) l)))
-  ] ;
-
-  inherit resolveDeps patchIntel buildIntel;
-}

pkgs/intel-oneapi/patch_intel.nix

@@ -1,179 +0,0 @@
-{ stdenvNoCC
-, lib
-, symlinkJoin
-, autoPatchelfHook
-, wrapCCWith
-, overrideCC
-, gcc13
-, gcc13Stdenv
-, hwloc
-, libelf
-, libffi_3_3
-, libpsm2
-, libuuid
-, libxml2
-, numactl
-, ocl-icd
-, openssl
-, python3
-, rdma-core
-, ucx
-, zlib
-, makeOverridable
-, recurseIntoAttrs
-}:
-
-makeOverridable (
-{
-  unpatched,
-  components ? { },
-  extraPackages ? components.extraPackages or []
-}:
-
-let
-  inherit (builtins) attrValues filter mapAttrs removeAttrs;
-
-  gcc = gcc13;
-  stdenv = gcc13Stdenv;
-
-  __components = removeAttrs components ["extraPackages"];
-  _components = __components;
-  # _components = lib.traceSeqN 2 {
-  #   inherit unpatched __components;
-  #   deps = builtins.map (x: "${x.pname}-${x.version}") unpatched.deps;
-  # } __components;
-
-  wrapIntel = { cc, extraBuildCommands ? "", extraInstall ? "", ... }@args:
-    let
-      targetConfig = stdenv.targetPlatform.config;
-    in (wrapCCWith {
-      inherit cc;
-      extraBuildCommands = ''
-        echo "-L${gcc.cc}/lib/gcc/${targetConfig}/${gcc.version}" >> $out/nix-support/cc-ldflags
-        echo "-L${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
-        for stddef in ${cc}/lib/clang/*/include/stddef.h ; do
-          dir=$(dirname $(realpath "$stddef"))
-          echo "-isystem $dir" >> $out/nix-support/cc-cflags
-        done
-
-        echo "-isystem ${cc}/include" >> $out/nix-support/cc-cflags
-        echo "-isystem ${cc}/include/intel64" >> $out/nix-support/cc-cflags
-
-        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
-        for dir in ${gcc.cc}/include/c++/*/${targetConfig}; do
-          echo "-isystem $dir" >> $out/nix-support/libcxx-cxxflags
-        done
-
-        # FIXME: We should find a better way to modify the PATH instead of using
-        # this ugly hack. See https://jungle.bsc.es/git/rarias/bscpkgs/issues/9
-        echo 'path_backup="${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: {
-      installPhase = old.installPhase + extraInstall;
-    });
-
-in
-stdenvNoCC.mkDerivation (finalAttrs: {
-  pname = lib.removeSuffix "-extracted" unpatched.pname;
-  inherit (unpatched) version;
-  src = unpatched;
-
-  phases = [ "installPhase" "fixupPhase" ];
-  buildInputs = [
-    libffi_3_3
-    libelf
-    libxml2
-    hwloc
-    numactl
-    libuuid
-    libpsm2
-    zlib
-    ocl-icd
-    rdma-core
-    ucx
-    openssl
-    python3
-    stdenv.cc.cc.lib
-  ] ++ extraPackages;
-
-  autoPatchelfIgnoreMissingDeps = [ "libhwloc.so.5" "libcuda.so.1" "libze_loader.so.1" ];
-
-  # There are broken symlinks that go outside packages, ignore them
-  dontCheckForBrokenSymlinks = true;
-
-  nativeBuildInputs = [ autoPatchelfHook ];
-  installPhase = ''
-    cp -r $src/opt/intel/oneapi/ $out
-  '';
-
-  passthru = let
-    pkgs = mapAttrs
-      (folder: version: symlinkJoin {
-        pname = "intel-${folder}";
-        inherit version;
-        paths = ["${finalAttrs.finalPackage}/${folder}/${version}"];
-      })
-      _components;
-  in pkgs // {
-    inherit unpatched;
-    pkgs = recurseIntoAttrs pkgs;
-    components = _components;
-
-    # This contains all packages properly symlinked into toplevel directories
-    # in $out.
-    #
-    # NOTE: there are clashes with packages that have symlinks outside their
-    # scope (libtcm and env/vars.sh)
-    all = symlinkJoin {
-      pname = finalAttrs.finalPackage + "-symlinked";
-      inherit (finalAttrs.finalPackage) version;
-      paths = filter lib.isDerivation (attrValues finalAttrs.finalPackage.pkgs);
-    };
-
-    stdenv = overrideCC stdenv finalAttrs.finalPackage.cc;
-
-    cc = wrapIntel {
-      cc = finalAttrs.finalPackage.pkgs.compiler;
-      extraBuildCommands = ''
-        wrap icx  $wrapper $ccPath/icx
-        wrap icpx $wrapper $ccPath/icpx
-        wrap ifx  $wrapper $ccPath/ifx
-
-        ln -s $out/bin/icpx $out/bin/c++
-        ln -s $out/bin/icx  $out/bin/cc
-
-        # Use this to detect when a compiler subprocess is called
-        # from icpx (--fsycl-host-compiler)
-        echo 'export "NIX_CC_WRAPPER_INTEL=1"' >> $out/nix-support/cc-wrapper-hook
-
-        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
-      '';
-      extraInstall = ''
-        export named_cc="icx"
-        export named_cxx="icpx"
-        export named_fc="ifx"
-      '';
-    };
-  };
-
-}))

pkgs/intel-oneapi/process.jq

@@ -1,29 +0,0 @@
-#!/usr/bin/env -S jq -f
-
-def extract_fields: {
-        pname : .Package,
-        version : .Version,
-        provides : .Package | sub("[0-9.-]*$"; ""),
-        filename : .Filename,
-        size : ."Installed-Size" | tonumber,
-        sha256 : .SHA256,
-        dependencies : .Depends,
-    } ;
-
-# parses dependencies into a list of [{.pname, .kind, .version}]
-# some dependencies do not have a version specified, in which case, kind = version = null
-#
-# example dependencies:
-# intel-oneapi-common-vars (>= 2023.0.0-25325), intel-oneapi-common-licensing-2023.0.0
-
-def split_dependencies : map(try(.dependencies |= split(",\\s?"; "")) // .dependencies |= []) ;
-
-def match_version : capture("(?<pname>[a-zA-Z0-9_\\-.]*) *(\\((?<kind>[<>=]*) *(?<version>.*)\\))?"; "") ;
-
-def parse_dependencies : map_values(.dependencies.[] |= match_version) ;
-
-def sort_version_decreasing : sort_by(.version | split("[-.]"; "") | map(tonumber)) | reverse ;
-
-map(extract_fields) | split_dependencies | parse_dependencies | sort_version_decreasing
-
-# [.[] | select(.pname == "intel-hpckit") | .version]

pkgs/intel-oneapi/toJson.awk

@@ -1,29 +0,0 @@
-#!/usr/bin/env -S awk -f
-
-BEGIN   {
-    FS=": "
-
-    prev_empty=1
-    t="  "
-
-    print "[ {"
-}
-
-!NF { # empty line, update separator so next non empty line closes the dict
-    prev_empty=1
-    t="},\n{ "
-    next # skip line (we won't match anything else)
-}
-
-{
-    printf t "\"%s\" : \"%s\"\n", $1, $2
-
-    if (prev_empty) {
-        # we were the first after a group of empty lines, following ones have to
-        # have a comma
-        prev_empty=0
-        t=", "
-    }
-}
-
-END     { print "} ]" }

pkgs/intel-oneapi/update.sh

@@ -1,11 +1,4 @@
 #!/bin/sh
 
-out_64=$(mktemp intel-api.64.XXXXXX)
+curl https://apt.repos.intel.com/oneapi/dists/all/main/binary-amd64/Packages -o amd64-packages
-out_all=$(mktemp intel-api.all.XXXXXX)
+curl https://apt.repos.intel.com/oneapi/dists/all/main/binary-all/Packages -o all-packages
-trap 'rm -f "$out_64" "$out_all"' EXIT INT HUP
-
-curl https://apt.repos.intel.com/oneapi/dists/all/main/binary-amd64/Packages -o "$out_64"
-curl https://apt.repos.intel.com/oneapi/dists/all/main/binary-all/Packages -o "$out_all"
-
-# NOTE: we use `jq -r tostring` to minify the json (3.2Mb -> 2.3Mb)
-cat "$out_64" "$out_all" | ./toJson.awk | ./process.jq | jq -r tostring >packages.json

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 ? "880e2341c56bad1dc14e8c369fb3356bec19018e"
+, gitCommit ? "872ba63f86edaefc9787984ef3fae9f2f94e0124" # github-release-2025.11
 }:
 
 let
   stdenv = llvmPackages_latest.stdenv;
 
   release = rec {
-    version = "2025.06";
+    version = "2025.11";
     src = fetchFromGitHub {
       owner = "bsc-pm";
       repo = "llvm";
       rev = "refs/tags/github-release-${version}";
-      hash = "sha256-ww9PpRmtz/M9IyLiZ8rAehx2UW4VpQt+svf4XfKBzKo=";
+      hash = "sha256-UgwMTUkM9Z87dDH205swZFBeFhrcbLAxginViG40pBM=";
     };
   };
 
@@ -48,6 +48,7 @@ in stdenv.mkDerivation {
   inherit (source) src version;
 
   enableParallelBuilding = true;
+  strictDeps = true;
 
   passthru = {
     CC = "clang";

pkgs/llvm-ompss2/default.nix

@@ -2,9 +2,7 @@
   stdenv
 , lib
 , gcc
-, gcc13
 , clangOmpss2Unwrapped
-, writeShellScript
 , openmp ? null
 , wrapCCWith
 , llvmPackages_latest
@@ -29,17 +27,20 @@ let
   # We need to replace the lld linker from bintools with our linker just built,
   # otherwise we run into incompatibility issues when mixing compiler and linker
   # versions.
-  bintools-unwrapped = llvmPackages_latest.tools.bintools-unwrapped.override {
+  bintools-unwrapped = llvmPackages_latest.bintools-unwrapped.override {
     lld = clangOmpss2Unwrapped;
   };
-  bintools = llvmPackages_latest.tools.bintools.override {
+  bintools = llvmPackages_latest.bintools.override {
     bintools = bintools-unwrapped;
   };
   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 = optional (openmp != null) openmp;
   extraBuildCommands = ''
     echo "-target ${targetConfig}" >> $out/nix-support/cc-cflags
     echo "-B${gcc.cc}/lib/gcc/${targetConfig}/${gccVersion}" >> $out/nix-support/cc-cflags
@@ -56,52 +57,14 @@ let
     echo "--gcc-toolchain=${gcc}" >> $out/nix-support/cc-cflags
 
     wrap clang++  $wrapper $ccPath/clang++
+
+  '' + optionalString (openmp != null) ''
+    echo "export OPENMP_RUNTIME=${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 bintools extraPackages;
-    cc = cc.override { gcc = gcc13; }; # Intel uses gcc13, so we have to match it
-    gccForLibs = gcc13;
-    # extraPackages adds packages to depsTargetTargetPropagated
-    extraBuildCommands = intelExtraBuildCommands + envExports;
-  };
-
-in wrappedCC.overrideAttrs (oldAttrs: {
-    passthru = oldAttrs.passthru // {
-      forIcpx = wrappedCCIntel;
-    };
-  })

pkgs/llvm-ompss2/openmp.nix

@@ -39,7 +39,9 @@ stdenv.mkDerivation rec {
     perl
     pkg-config
     python3
-  ] ++ lib.optionals enableNosv [
+  ];
+
+  buildInputs = lib.optionals enableNosv [
     nosv
   ] ++ lib.optionals enableOvni [
     ovni
@@ -54,6 +56,7 @@ stdenv.mkDerivation rec {
   dontStrip = enableDebug;
 
   separateDebugInfo = true;
+  strictDeps = true;
 
   cmakeFlags = [
     "-DLIBOMP_OMPD_SUPPORT=OFF"
@@ -71,6 +74,28 @@ stdenv.mkDerivation rec {
     rm -f $out/libllvmrt/libomp.*
   '';
 
+  doInstallCheck = true;
+  # There are not cmake flags to force nOS-V, it enables it when found through
+  # pkg-config. If enableNosv is set, but we fail to find it at build time,
+  # the build will succeed but won't use nOS-V (libompv won't be created).
+  # This is a sanity check to ensure that after install we have the proper
+  # files.
+  installCheckPhase =
+    if enableNosv then
+      ''
+        test -f $out/lib/libompv.so
+        test -f $out/libllvmrt/libompv.so
+        test ! -f $out/lib/libomp.so
+        test ! -f $out/libllvmrt/libomp.so
+      ''
+    else
+      ''
+        test -f $out/lib/libomp.so
+        test -f $out/libllvmrt/libomp.so
+        test ! -f $out/lib/libompv.so
+        test ! -f $out/libllvmrt/libompv.so
+      '';
+
   passthru = {
     inherit nosv;
   };

pkgs/lmbench/default.nix

@@ -27,6 +27,7 @@ stdenv.mkDerivation rec {
   hardeningDisable = [ "all" ];
 
   enableParallelBuilding = false;
+  strictDeps = true;
 
   preBuild = ''
     makeFlagsArray+=(

pkgs/mcxx/default.nix

@@ -65,6 +65,7 @@ stdenv.mkDerivation rec {
   ];
 
   meta = {
+    broken = true;
     homepage = "https://github.com/bsc-pm/mcxx";
     description = "C/C++/Fortran source-to-source compilation infrastructure aimed at fast prototyping";
     maintainers = with lib.maintainers.bsc; [ rpenacob ];

pkgs/meteocat-exporter/default.nix

@@ -1,12 +1,15 @@
 { python3Packages, lib }:
 
-python3Packages.buildPythonApplication rec {
+python3Packages.buildPythonApplication {
   pname = "meteocat-exporter";
   version = "1.0";
 
+  pyproject = true;
+
   src = ./.;
 
   doCheck = false;
+  strictDeps = true;
 
   build-system = with python3Packages; [
     setuptools

pkgs/mpich/default.nix

@@ -6,6 +6,13 @@
 , pmix
 , gfortran
 , symlinkJoin
+# Disabled when cross-compiling
+# To fix cross compilation, we should fill the values in:
+# https://github.com/pmodels/mpich/blob/main/maint/fcrosscompile/cross_values.txt.in
+# For each arch
+, enableFortran ? stdenv.hostPlatform == stdenv.buildPlatform
+, perl
+, targetPackages
 }:
 
 let
@@ -15,10 +22,13 @@ let
     paths = [ pmix.dev pmix.out ];
   };
 in mpich.overrideAttrs (old: {
-  buildInput = old.buildInputs ++ [
+  buildInputs = old.buildInputs ++ [
     libfabric
     pmixAll
   ];
+  nativeBuildInputs = old.nativeBuildInputs ++ [
+    perl
+  ];
   configureFlags = [
     "--enable-shared"
     "--enable-sharedlib"
@@ -31,10 +41,22 @@ in mpich.overrideAttrs (old: {
   ] ++ lib.optionals (lib.versionAtLeast gfortran.version "10") [
     "FFLAGS=-fallow-argument-mismatch" # https://github.com/pmodels/mpich/issues/4300
     "FCFLAGS=-fallow-argument-mismatch"
+  ] ++ lib.optionals (!enableFortran) [
+    "--disable-fortran"
   ];
+
+  preFixup = ''
+    sed -i 's:^CC=.*:CC=${targetPackages.stdenv.cc}/bin/${targetPackages.stdenv.cc.targetPrefix}cc:' $out/bin/mpicc
+    sed -i 's:^CXX=.*:CXX=${targetPackages.stdenv.cc}/bin/${targetPackages.stdenv.cc.targetPrefix}c++:' $out/bin/mpicxx
+  '' + lib.optionalString enableFortran ''
+    sed -i 's:^FC=.*:FC=${targetPackages.gfortran or gfortran}/bin/${targetPackages.gfortran.targetPrefix or gfortran.targetPrefix}gfortran:' $out/bin/mpifort
+  '';
+
   hardeningDisable = [ "all" ];
+  strictDeps = true;
 
   meta = old.meta // {
     maintainers = old.meta.maintainers ++ (with lib.maintainers.bsc; [ rarias ]);
+    cross = true;
   };
 })

pkgs/nanos6/check-papi-version-with-pkgconfig.patch

@@ -0,0 +1,67 @@
+diff --git a/m4/papi.m4 b/m4/papi.m4
+--- a/m4/papi.m4
++++ b/m4/papi.m4
+@@ -24,12 +24,13 @@ AC_DEFUN([AC_CHECK_PAPI],
+ 		else
+ 			PKG_CHECK_MODULES(
+ 				[papi],
+-				[papi],
++				[papi >= 5.6.0],
+ 				[
+ 					AC_MSG_CHECKING([the PAPI installation prefix])
+ 					AC_MSG_RESULT([retrieved from pkg-config])
+ 					papi_CPPFLAGS="${papi_CFLAGS}"
+ 					ac_use_papi=yes
++					ac_papi_version_correct=yes
+ 				], [
+ 					AC_MSG_CHECKING([the PAPI installation prefix])
+ 					AC_MSG_RESULT([not available])
+@@ -67,27 +68,29 @@ AC_DEFUN([AC_CHECK_PAPI],
+ 		fi
+ 
+ 		if test x"${ac_use_papi}" = x"yes" ; then
+-			if test x"${ac_cv_use_papi_prefix}" != x"" ; then
+-				papiBinary=${ac_cv_use_papi_prefix}/bin/papi_version
+-			else
+-				papiBinary=papi_version
+-			fi
+-			papiVersion=`$papiBinary | sed 's/[[^0-9.]]*\([[0-9.]]*\).*/\1/'`
++			if test x"${ac_papi_version_correct}" != x"yes" ; then
++				if test x"${ac_cv_use_papi_prefix}" != x"" ; then
++					papiBinary=${ac_cv_use_papi_prefix}/bin/papi_version
++				else
++					papiBinary=papi_version
++				fi
++				papiVersion=`$papiBinary | sed 's/[[^0-9.]]*\([[0-9.]]*\).*/\1/'`
+ 
+-			AX_COMPARE_VERSION(
+-				[[${papiVersion}]],
+-				[[ge]],
+-				[[5.6.0]],
+-				[[ac_papi_version_correct=yes]],
+-				[[ac_papi_version_correct=no]]
+-			)
++				AX_COMPARE_VERSION(
++					[[${papiVersion}]],
++					[[ge]],
++					[[5.6.0]],
++					[[ac_papi_version_correct=yes]],
++					[[ac_papi_version_correct=no]]
++				)
+ 
+-			if test x"${ac_papi_version_correct}" != x"yes" ; then
+-				AC_MSG_ERROR([PAPI version must be >= 5.6.0.])
+-				ac_use_papi=no
+-			else
+-				AC_MSG_CHECKING([if the PAPI version >= 5.6.0.])
+-				AC_MSG_RESULT([${ac_papi_version_correct}])
++				if test x"${ac_papi_version_correct}" != x"yes" ; then
++					AC_MSG_ERROR([PAPI version must be >= 5.6.0.])
++					ac_use_papi=no
++				else
++					AC_MSG_CHECKING([if the PAPI version >= 5.6.0.])
++					AC_MSG_RESULT([${ac_papi_version_correct}])
++				fi
+ 			fi
+ 		fi
+ 

pkgs/nanos6/default.nix

@@ -16,7 +16,7 @@
 , jemallocNanos6 ? null
 , cachelineBytes ? 64
 , enableGlibcxxDebug ? false
-, enablePapi ? stdenv.hostPlatform == stdenv.buildPlatform # Disabled when cross-compiling
+, enablePapi ? true
 , useGit ? false
 , gitUrl ? "ssh://git@bscpm04.bsc.es/nanos6/nanos6"
 , gitBranch ? "master"
@@ -95,16 +95,15 @@ in
     dontStrip = enableDebug;
     separateDebugInfo = true;
 
+    strictDeps = true;
+    patches = [ ./check-papi-version-with-pkgconfig.patch ];
+
     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
-    ] ++ lib.optionals enablePapi [ papi ];
 
     buildInputs = [
       boost

pkgs/nixgen/default.nix

@@ -0,0 +1,23 @@
+{
+  stdenv
+, lib
+}:
+
+stdenv.mkDerivation {
+  pname = "nixgen";
+  version = "0.0.1";
+  src = ./nixgen;
+  dontUnpack = true;
+  strictDeps = true;
+  phases = [ "installPhase" ];
+  installPhase = ''
+    mkdir -p $out/bin
+    cp -a $src $out/bin/nixgen
+  '';
+  meta = {
+    description = "Quickly generate flake.nix from command line";
+    maintainers = with lib.maintainers.bsc; [ rarias ];
+    platforms = lib.platforms.linux;
+    license = lib.licenses.gpl3Plus;
+  };
+}

pkgs/nixgen/nixgen

@@ -0,0 +1,97 @@
+#!/bin/sh
+#
+# Copyright (c) 2025, Barcelona Supercomputing Center (BSC)
+# SPDX-License-Identifier: GPL-3.0+
+# Author: Rodrigo Arias Mallo <rodrigo.arias@bsc.es>
+
+function usage() {
+  echo "USAGE: nixgen [-f] [package [...]] [-b package [...]]" >&2
+  echo "  Generates a flake.nix file with the given packages." >&2
+  echo "  After flake.nix is created, use 'nix develop' to enter the shell." >&2
+  echo "OPTIONS" >&2
+  echo "  -f               Overwrite existing flake.nix (default: no)." >&2
+  echo "  packages...      Add these packages to the shell." >&2
+  echo "  -b packages...   Add the dependencies needed to build these packages." >&2
+  echo "EXAMPLE" >&2
+  echo "  $ nixgen ovni bigotes -b nosv tampi" >&2
+  echo "  Adds the packages ovni and bigotes as well as all required dependencies" >&2
+  echo "  to build nosv and tampi." >&2
+  echo "AUTHOR" >&2
+  echo "  Rodrigo Arias Mallo <rodrigo.arias@bsc.es>" >&2
+  exit 1
+}
+
+mode=package
+packages=
+inputsFrom=
+force=
+
+if [[ $# -eq 0 ]]; then
+  usage
+fi
+
+while [[ $# -gt 0 ]]; do
+    case $1 in -b)
+      mode=build
+      shift
+      ;;
+    -f)
+      force=1
+      shift
+      ;;
+    -h)
+      usage
+      ;;
+    -*|--*)
+      echo "error: unknown option $1" >&2
+      exit 1
+      ;;
+    *)
+      if [ "$mode" == "package" ]; then
+        packages+="${packages:+ }$1"
+      else
+        inputsFrom+="${inputsFrom:+ }$1"
+      fi
+      shift
+      ;;
+  esac
+done
+
+if [ ! "$force" -a -e flake.nix ]; then
+  echo "error: flake.nix exists, force overwrite with -f" >&2
+  exit 1
+fi
+
+cat > flake.nix <<EOF
+{
+  inputs.jungle.url = "git+https://jungle.bsc.es/git/rarias/jungle";
+  outputs = { self, jungle }:
+  let
+    nixpkgs = jungle.inputs.nixpkgs;
+    customOverlay = (final: prev: {
+      # Example overlay, for now empty
+    });
+    pkgs = import nixpkgs {
+      system = "x86_64-linux";
+      overlays = [
+        # Apply jungle overlay to get our BSC custom packages
+        jungle.outputs.bscOverlay
+        # And on top apply our local changes to customize for cluster
+        customOverlay
+      ];
+    };
+  in {
+    devShells.x86_64-linux.default = pkgs.mkShell {
+      pname = "devshell";
+      # Include these packages in the shell
+      packages = with pkgs; [
+        $packages
+      ];
+      # The dependencies needed to build these packages will be also included
+      inputsFrom = with pkgs; [
+        $inputsFrom
+      ];
+    };
+  };
+}
+EOF

pkgs/nixtools/default.nix

@@ -16,6 +16,7 @@ stdenv.mkDerivation rec {
   makeFlags = [ "DESTDIR=$(out)" ];
   preBuild = "env";
   dontPatchShebangs = true;
+  strictDeps = true;
 
   meta = {
     homepage = "https://gitlab.pm.bsc.es/rarias/nixtools";

pkgs/nodes/default.nix

@@ -14,19 +14,19 @@
 , useGit ? false
 , gitUrl ? "ssh://git@gitlab-internal.bsc.es/nos-v/nodes.git"
 , gitBranch ? "master"
-, gitCommit ? "6002ec9ae6eb876d962cc34366952a3b26599ba6"
+, gitCommit ? "511489e71504a44381e0930562e7ac80ac69a848" # version-1.4
 }:
 
 with lib;
 
 let
   release = rec {
-    version = "1.3";
+    version = "1.4";
     src = fetchFromGitHub {
       owner = "bsc-pm";
       repo = "nodes";
       rev = "version-${version}";
-      hash = "sha256-cFb9pxcjtkMmH0CsGgUO9LTdXDNh7MCqicgGWawLrsU=";
+      hash = "sha256-+lR/R0l3fGZO3XG7whMorFW2y2YZ0ZFnLeOHyQYrAsQ=";
     };
   };
 
@@ -48,6 +48,7 @@ in
     enableParallelBuilding = true;
     dontStrip = true;
     separateDebugInfo = true;
+    strictDeps = true;
 
     configureFlags = [
       "--with-nosv=${nosv}"

pkgs/nosv/check-papi-version-with-pkgconfig.patch

@@ -0,0 +1,68 @@
+diff --git a/m4/papi.m4 b/m4/papi.m4
+index de905848..fa3db9a1 100644
+--- a/m4/papi.m4
++++ b/m4/papi.m4
+@@ -24,12 +24,13 @@ AC_DEFUN([AC_CHECK_PAPI],
+ 		else
+ 			PKG_CHECK_MODULES(
+ 				[papi],
+-				[papi],
++				[papi >= 5.6.0],
+ 				[
+ 					AC_MSG_CHECKING([the PAPI installation prefix])
+ 					AC_MSG_RESULT([retrieved from pkg-config])
+ 					papi_CFLAGS="${papi_CFLAGS}"
+ 					ac_use_papi=yes
++					ac_papi_version_correct=yes
+ 				], [
+ 					AC_MSG_CHECKING([the PAPI installation prefix])
+ 					AC_MSG_RESULT([not available])
+@@ -67,27 +68,29 @@ AC_DEFUN([AC_CHECK_PAPI],
+ 		fi
+ 
+ 		if test x"${ac_use_papi}" = x"yes" ; then
+-			if test x"${ac_cv_use_papi_prefix}" != x"" ; then
+-				papiBinary=${ac_cv_use_papi_prefix}/bin/papi_version
+-			else
+-				papiBinary=papi_version
+-			fi
+-			papiVersion=`$papiBinary | sed 's/[[^0-9.]]*\([[0-9.]]*\).*/\1/'`
++			if test x"${ac_papi_version_correct}" != x"yes" ; then
++				if test x"${ac_cv_use_papi_prefix}" != x"" ; then
++					papiBinary=${ac_cv_use_papi_prefix}/bin/papi_version
++				else
++					papiBinary=papi_version
++				fi
++				papiVersion=`$papiBinary | sed 's/[[^0-9.]]*\([[0-9.]]*\).*/\1/'`
+ 
+-			AX_COMPARE_VERSION(
+-				[[${papiVersion}]],
+-				[[ge]],
+-				[[5.6.0]],
+-				[[ac_papi_version_correct=yes]],
+-				[[ac_papi_version_correct=no]]
+-			)
++				AX_COMPARE_VERSION(
++					[[${papiVersion}]],
++					[[ge]],
++					[[5.6.0]],
++					[[ac_papi_version_correct=yes]],
++					[[ac_papi_version_correct=no]]
++				)
+ 
+-			if test x"${ac_papi_version_correct}" != x"yes" ; then
+-				AC_MSG_ERROR([PAPI version must be >= 5.6.0.])
+-				ac_use_papi=no
+-			else
+-				AC_MSG_CHECKING([if the PAPI version >= 5.6.0.])
+-				AC_MSG_RESULT([${ac_papi_version_correct}])
++				if test x"${ac_papi_version_correct}" != x"yes" ; then
++					AC_MSG_ERROR([PAPI version must be >= 5.6.0.])
++					ac_use_papi=no
++				else
++					AC_MSG_CHECKING([if the PAPI version >= 5.6.0.])
++					AC_MSG_RESULT([${ac_papi_version_correct}])
++				fi
+ 			fi
+ 		fi
+ 

pkgs/nosv/default.nix

@@ -7,25 +7,25 @@
 , numactl
 , hwloc
 , papi
-, enablePapi ? stdenv.hostPlatform == stdenv.buildPlatform # Disabled when cross-compiling
+, enablePapi ? true
 , cacheline ? 64 # bits
 , ovni ? null
 , useGit ? false
 , gitUrl ? "git@gitlab-internal.bsc.es:nos-v/nos-v.git"
 , gitBranch ? "master"
-, gitCommit ? "9f47063873c3aa9d6a47482a82c5000a8c813dd8"
+, gitCommit ? "1108e4786b58e0feb9a16fa093010b763eb2f8e8" # version 4.0.0
 }:
 
 with lib;
 
 let
   release = rec {
-    version = "3.2.0";
+    version = "4.0.0";
     src = fetchFromGitHub {
       owner = "bsc-pm";
       repo = "nos-v";
       rev = "${version}";
-      hash = "sha256-yaz92426EM8trdkBJlISmAoG9KJCDTvoAW/HKrasvOw=";
+      hash = "sha256-llaq73bd/YxLVKNlMebnUHKa4z3sdcsuDUoVwUxNuw8=";
     };
   };
 
@@ -40,12 +40,14 @@ let
 
   source = if (useGit) then git else release;
 in
-  stdenv.mkDerivation rec {
+  stdenv.mkDerivation {
     pname = "nosv";
     inherit (source) src version;
     hardeningDisable = [ "all" ];
     dontStrip = true;
     separateDebugInfo = true;
+    strictDeps = true;
+    patches = [ ./check-papi-version-with-pkgconfig.patch ];
     configureFlags = [
       "--with-ovni=${ovni}"
       "CACHELINE_WIDTH=${toString cacheline}"

pkgs/onemath/default.nix

@@ -1,84 +0,0 @@
-{ lib
-, fetchFromGitHub
-, cmake
-, withCFlags
-, intelPackages
-
-, mklSupport ? true
-
-, config
-
-, cudaSupport ? config.cudaSupport
-, cudaPackages ? { }
-
-, rocmSupport ? config.rocmSupport
-, hipTargets ? null # only one target at a time supported
-, rocmPackages ? { }
-}:
-
-let
-  # rocmSupport is not enough, we need a specific target
-  enableHip = rocmSupport && hipTargets != null;
-
-  stdenv = withCFlags (lib.optionals cudaSupport [ "--cuda-path=${cudaPackages.cudatoolkit}" ]) intelPackages.stdenv;
-in
-
-  # at least one backend has to be enabled
-  assert mklSupport || cudaSupport || enableHip;
-
-stdenv.mkDerivation rec {
-  pname = "oneMath";
-  version = "0.8";
-
-  src = fetchFromGitHub {
-    owner = "uxlfoundation";
-    repo = "oneMath";
-    rev = "v${version}";
-    sha256 = "sha256-xK8lKI3oqKlx3xtvdScpMq+HXAuoYCP0BZdkEqnJP5o=";
-  };
-
-  cmakeFlags = [
-    (lib.cmakeBool "ENABLE_MKLCPU_BACKEND"    mklSupport)
-    (lib.cmakeBool "ENABLE_MKLGPU_BACKEND"    mklSupport)
-
-    (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)
-    (lib.cmakeBool "ENABLE_ROCSOLVER_BACKEND" enableHip)
-    (lib.cmakeBool "ENABLE_ROCRAND_BACKEND"   enableHip)
-    (lib.cmakeBool "ENABLE_ROCSPARSE_BACKEND" enableHip)
-
-    (lib.cmakeBool "BUILD_FUNCTIONAL_TESTS" false)
-    (lib.cmakeBool "BUILD_EXAMPLES" false)
-  ] ++ lib.optionals enableHip [
-    (lib.cmakeFeature "HIP_TARGETS" hipTargets)
-  ];
-
-  nativeBuildInputs = [ cmake ];
-  buildInputs = lib.optionals (mklSupport) [
-    intelPackages.mkl
-    intelPackages.tbb
-  ] ++ lib.optionals (enableHip) [
-    rocmPackages.rocmPath
-    rocmPackages.rocblas
-    rocmPackages.rocfft
-    rocmPackages.rocsolver
-    rocmPackages.rocrand
-    rocmPackages.rocsparse
-  ] ++ lib.optionals (cudaSupport) [
-    (lib.getDev cudaPackages.cuda_cudart)
-    cudaPackages.cudatoolkit
-
-    cudaPackages.libcublas
-    cudaPackages.libcurand
-    cudaPackages.libcufft
-    cudaPackages.libcusparse
-    cudaPackages.libcusolver
-  ];
-
-}

pkgs/osu/default.nix

@@ -24,6 +24,7 @@ stdenv.mkDerivation rec {
 
   doCheck = true;
   enableParallelBuilding = true;
+  strictDeps = true;
   nativeBuildInputs = [ mpiAll ];
   buildInputs = [ mpiAll ];
   hardeningDisable = [ "all" ];
@@ -32,6 +33,11 @@ stdenv.mkDerivation rec {
       "CXX=mpicxx"
   ];
 
+  env = {
+    MPICH_CC="${stdenv.cc}/bin/${stdenv.cc.targetPrefix}cc";
+    MPICH_CXX="${stdenv.cc}/bin/${stdenv.cc.targetPrefix}c++";
+  };
+
   postInstall = ''
     mkdir -p $out/bin
     for f in $(find $out -executable -type f); do
@@ -44,5 +50,6 @@ stdenv.mkDerivation rec {
     homepage = "http://mvapich.cse.ohio-state.edu/benchmarks/";
     maintainers = [ ];
     platforms = lib.platforms.all;
+    cross = true;
   };
 }

pkgs/ovni/default.nix

@@ -7,7 +7,7 @@
 , useGit ? false
 , gitBranch ? "master"
 , gitUrl ? "ssh://git@bscpm04.bsc.es/rarias/ovni.git"
-, gitCommit ? "e4f62382076f0cf0b1d08175cf57cc0bc51abc61"
+, gitCommit ? "06432668f346c8bdc1006fabc23e94ccb81b0d8b" # version 1.13.0
 , enableDebug ? false
 # Only enable MPI if the build is native (fails on cross-compilation)
 , useMpi ? (stdenv.buildPlatform.canExecute stdenv.hostPlatform)
@@ -15,13 +15,13 @@
 
 let
   release = rec {
-    version = "1.12.0";
+    version = "1.13.0";
     src = fetchFromGitHub {
       owner = "bsc-pm";
       repo = "ovni";
       rev = "${version}";
-      hash = "sha256-H04JvsVKrdqr3ON7JhU0g17jjlg/jzQ7eTfx9vUNd3E=";
+      hash = "sha256-0l2ryIyWNiZqeYdVlnj/WnQGS3xFCY4ICG8JedX424w=";
-    } // { shortRev = "a73afcf"; };
+    } // { shortRev = "0643266"; };
   };
 
   git = rec {
@@ -40,6 +40,7 @@ in
     inherit (source) src version;
     dontStrip = true;
     separateDebugInfo = true;
+    strictDeps = true;
     postPatch = ''
       patchShebangs --build test/
     '';

pkgs/papi/default.nix

@@ -0,0 +1,22 @@
+{
+  stdenv,
+  papi,
+}:
+
+if stdenv.hostPlatform == stdenv.buildPlatform then
+  papi
+else
+  papi.overrideAttrs (old: {
+    configureFlags = (old.configureFlags or [ ]) ++ [
+      "--enable-perf_event_uncore=no"
+      "--with-sysdetect=no"
+      "--with-ffsll"
+      "--with-tls=__thread"
+      "--with-virtualtimer=clock_thread_cputime_id"
+      "--with-walltimer=clock_realtime"
+      "--with-perf-events"
+      "--with-CPU=${stdenv.hostPlatform.uname.processor}"
+      "--with-arch=${stdenv.hostPlatform.uname.processor}"
+    ];
+    patches = (old.patches or [ ]) ++ [ ./fix-ar-cross.patch ];
+  })

pkgs/papi/fix-ar-cross.patch

@@ -0,0 +1,19 @@
+diff --git a/sde_lib/Makefile b/sde_lib/Makefile
+index 8518f92..90a9953 100644
+--- a/sde_lib/Makefile
++++ b/sde_lib/Makefile
+@@ -1,4 +1,5 @@
+ CC ?= gcc
++AR ?= ar
+ SDE_INC = -I. -I..
+ SDE_LD = -ldl -pthread
+ CFLAGS += -Wextra -Wall -O2
+@@ -18,7 +19,7 @@ dynamic: $(DOBJS)
+ 	rm -f *_d.o
+ 
+ static: $(SOBJS)
+-	ar rs libsde.a $(SOBJS)
++	$(AR) rs libsde.a $(SOBJS)
+ 	rm -f *_s.o
+ 
+ clean:

pkgs/paraver/default.nix

@@ -12,7 +12,7 @@
 , paraverKernel
 , openssl
 , glibcLocales
-, wrapGAppsHook
+, wrapGAppsHook3
 }:
 
 let
@@ -47,6 +47,7 @@ stdenv.mkDerivation rec {
 
   dontStrip = true;
   enableParallelBuilding = true;
+  strictDeps = true;
 
   preConfigure = ''
     export CFLAGS="-O3"
@@ -64,7 +65,7 @@ stdenv.mkDerivation rec {
     autoconf
     automake
     autoreconfHook
-    wrapGAppsHook
+    wrapGAppsHook3
   ];
 
   buildInputs = [

pkgs/paraver/kernel.nix

@@ -34,6 +34,7 @@ stdenv.mkDerivation rec {
   enableParallelBuilding = true;
 
   dontStrip = true;
+  strictDeps = true;
 
   preConfigure = ''
     export CFLAGS="-O3 -DPARALLEL_ENABLED"

pkgs/slurm-exporter/default.nix

@@ -13,6 +13,7 @@ buildGoModule rec {
 
   vendorHash = "sha256-A1dd9T9SIEHDCiVT2UwV6T02BSLh9ej6LC/2l54hgwI=";
   doCheck = false;
+  strictDeps = true;
 
   meta = with lib; {
     description = "Prometheus SLURM Exporter";

pkgs/sonar/default.nix

@@ -18,6 +18,7 @@ stdenv.mkDerivation rec {
   };
   hardeningDisable = [ "all" ];
   dontStrip = true;
+  strictDeps = true;
   configureFlags = [ "--with-ovni=${ovni}" ];
 
   nativeBuildInputs = [
@@ -35,5 +36,6 @@ stdenv.mkDerivation rec {
     maintainers = with lib.maintainers.bsc; [ rarias ];
     platforms = lib.platforms.linux;
     license = lib.licenses.mit;
+    cross = true;
   };
 }

pkgs/tagaspi/default.nix

@@ -5,27 +5,19 @@
 , automake
 , autoconf
 , libtool
-, mpi
 , autoreconfHook
 , gpi-2
 , boost
 , numactl
 , rdma-core
 , gfortran
-, symlinkJoin
 }:
 
-let
-  mpiAll = symlinkJoin {
-    name = "mpi-all";
-    paths = [ mpi.all ];
-  };
-in
-
 stdenv.mkDerivation rec {
   pname = "tagaspi";
   enableParallelBuilding = true;
   separateDebugInfo = true;
+  strictDeps = true;
 
   version = "2.0";
   src = fetchFromGitHub {
@@ -35,16 +27,18 @@ stdenv.mkDerivation rec {
     hash = "sha256-RGG/Re2uM293HduZfGzKUWioDtwnSYYdfeG9pVrX9EM=";
   };
 
-  buildInputs = [
+  nativeBuildInputs = [
     autoreconfHook
     automake
     autoconf
     libtool
+    gfortran
+  ];
+
+  buildInputs = [
     boost
     numactl
     rdma-core
-    gfortran
-    mpiAll
   ];
 
   dontDisableStatic = true;
@@ -63,5 +57,6 @@ stdenv.mkDerivation rec {
     maintainers = with lib.maintainers.bsc; [ rarias ];
     platforms = lib.platforms.linux;
     license = lib.licenses.gpl3Plus;
+    cross = false; # gpi-2 cannot cross
   };
 }

pkgs/tampi/default.nix

@@ -45,6 +45,7 @@ in stdenv.mkDerivation {
   inherit (source) src version;
   enableParallelBuilding = true;
   separateDebugInfo = true;
+  strictDeps = true;
 
   nativeBuildInputs = [
     autoconf
@@ -68,5 +69,6 @@ in stdenv.mkDerivation {
     maintainers = with lib.maintainers.bsc; [ rarias ];
     platforms = lib.platforms.linux;
     license = lib.licenses.gpl3Plus;
+    cross = true;
   };
 }

pkgs/tasycl/default.nix

@@ -1,87 +0,0 @@
-{
-  lib,
-  stdenv,
-  autoconf,
-  automake,
-  autoreconfHook,
-  boost,
-  fetchFromGitHub,
-  gnumake,
-  libtool,
-  withCFlags,
-
-  useIntel ? true,
-  adaptivecpp ? null,
-  intelPackages ? null,
-
-  useGit ? false,
-  gitUrl ? "git@gitlab-internal.bsc.es:task-awareness/tasycl/tasycl.git",
-  gitBranch ? "main",
-  gitCommit ? "78f98dcf60a66e0eaa3b4ebcf55be076bec64825",
-}:
-
-assert !useIntel -> adaptivecpp != null;
-assert useIntel -> intelPackages != null;
-
-let
-  variant = if useIntel then "intel" else "acpp";
-
-  syclStdenv = withCFlags [ "-O3" ] (if useIntel then intelPackages.stdenv else stdenv);
-
-  release = rec {
-    version = "2.1.0";
-    src = fetchFromGitHub {
-      owner = "bsc-pm";
-      repo = "tasycl";
-      rev = version;
-      hash = "sha256-0kXnb0lHeQNHR27GTLbJ8xbiICLU8k2+FqEnnFSrzzo=";
-    };
-  };
-
-  git = rec {
-    version = src.shortRev;
-    src = builtins.fetchGit {
-      url = gitUrl;
-      ref = gitBranch;
-      rev = gitCommit;
-    };
-  };
-
-  source = if (useGit) then git else release;
-
-in
-
-syclStdenv.mkDerivation {
-  pname = "tasycl-${variant}";
-  inherit (source) src version;
-
-  enableParallelBuilding = true;
-  separateDebugInfo = true;
-
-  nativeBuildInputs = [
-    autoreconfHook
-    automake
-    autoconf
-    libtool
-    gnumake
-  ];
-
-  buildInputs = [
-    boost
-  ];
-
-  configureFlags = lib.optionals (!useIntel) [
-    "CXX=${lib.getExe adaptivecpp}"
-  ];
-
-  # add symlinks so we can explicitly link with tasycl-intel / tasycl-acpp
-  postInstall = ''
-    pushd $out/lib
-    for i in libtasycl* ; do
-      ln -s "$i" "''\${i/tasycl/tasycl-${variant}}"
-    done
-    popd
-  '';
-
-  hardeningDisable = [ "all" ];
-}

pkgs/upc-qaire-exporter/default.nix

@@ -1,12 +1,15 @@
 { python3Packages, lib }:
 
-python3Packages.buildPythonApplication rec {
+python3Packages.buildPythonApplication {
   pname = "upc-qaire-exporter";
   version = "1.0";
 
+  pyproject = true;
+
   src = ./.;
 
   doCheck = false;
+  strictDeps = true;
 
   build-system = with python3Packages; [
     setuptools

test/compilers/clang-openmp-ld.nix

@@ -23,9 +23,6 @@ in stdenv.mkDerivation {
   dontUnpack = true;
   dontConfigure = true;
 
-  # nOS-V requires access to /sys/devices to request NUMA information
-  requiredSystemFeatures = [ "sys-devices" ];
-
   buildInputs = [ openmp ];
 
   buildPhase = ''

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
-  '';
-}

test/compilers/icpx-ompss2.nix

@@ -1,74 +0,0 @@
-{ writeText, intelPackages, nodes, nosv, clangOmpss2Nodes, strace }:
-
-let
-  hello_cpp = writeText "hello.cpp" ''
-    #include <cstdio>
-    #include <sycl/sycl.hpp>
-
-    int main(int argc, char** argv) try {
-        sycl::queue queue;
-
-        std::cout << "Running on: "
-                  << queue.get_device().get_info<sycl::info::device::name>()
-                  << std::endl;
-
-        #pragma oss task
-        queue.submit([&] (sycl::handler& cgh) {
-            auto os = sycl::stream{128, 128, cgh};
-            cgh.single_task<class hello_world>([=]() {
-                os << "Hello World! (on device)\n";
-            });
-        }).wait();
-
-        return 0;
-    } catch (sycl::exception &e) {
-        std::cout << "SYCL exception: " << e.what() << std::endl;
-        return 0; // we expect to fail since no devices should be available;
-    }
-
-  '';
-in
-
-intelPackages.stdenv.mkDerivation {
-  version = "0.0.1";
-  name = "hello-syclompss";
-
-  src = hello_cpp;
-
-  nativeBuildInputs = [
-    strace
-    nodes
-    nosv
-  ];
-
-  dontUnpack = true;
-  dontConfigure = true;
-
-  # NODES requires access to /sys/devices to request NUMA information
-  requiredSystemFeatures = [ "sys-devices" ];
-
-  env.NODES_HOME = nodes;
-
-  NIX_DEBUG = 1;
-  buildPhase = ''
-    cp $src hello.cpp
-    set -x
-    echo CXX=$CXX
-    echo NODES_HOME=$NODES_HOME
-    command -v $CXX
-
-    icpx -Wno-deprecated-declarations -fsycl \
-        -fsycl-host-compiler=${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
-
-    ./hello
-    set +x
-  '';
-
-  installPhase = ''
-    touch $out
-  '';
-}