gromacs: fixes

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

flake.lock

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

flake.nix

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

m/common/base/env.nix

@@ -1,12 +1,12 @@
-{ pkgs, ... }:
+{ pkgs, config, ... }:
 
 {
   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 perf ldns pv
+    ncdu config.boot.kernelPackages.perf ldns pv
-    # From jungle overlay
+    # From bsckgs overlay
-    osumb nixgen
+    osumb
   ];
 
   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.settings.Manager.RuntimeWatchdogSec = 30;
+  systemd.watchdog.runtimeTime = "30s";
 }

m/fox/configuration.nix

@@ -93,4 +93,20 @@
     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

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

m/module/slurm-client.nix

@@ -1,4 +1,4 @@
-{ lib, pkgs, ... }:
+{ lib, ... }:
 
 {
   imports = [
@@ -21,20 +21,4 @@
   };
 
   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

@@ -1,6 +1,31 @@
 { 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";
@@ -34,6 +59,16 @@
       # 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

@@ -34,15 +34,13 @@ let
       amd-uprof-driver = _prev.callPackage ./pkgs/amd-uprof/driver.nix { };
     });
     lmbench = callPackage ./pkgs/lmbench/default.nix { };
-    # Broken and unmantained
+    mcxx = callPackage ./pkgs/mcxx/default.nix { };
-    # 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 { };
@@ -70,6 +68,8 @@ let
     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 {
@@ -118,16 +118,14 @@ let
   pkgsTopLevel = filterAttrs (_: isDerivation) bscPkgs;
 
   # Native build in that platform doesn't imply cross build works
-  canCrossCompile = platform: default: pkg:
+  canCrossCompile = platform: pkg:
     (isDerivation pkg) &&
-    # If meta.cross is undefined, use default
+    # Must be defined explicitly
-    (pkg.meta.cross or default) &&
+    (pkg.meta.cross or false) &&
-    (meta.availableOn final.pkgsCross.${platform}.stdenv.hostPlatform pkg);
+    (meta.availableOn platform pkg);
 
   # For now only RISC-V
-  crossSet = genAttrs [ "riscv64" ] (platform:
+  crossSet = { riscv64 = final.pkgsCross.riscv64.bsc.pkgsTopLevel; };
-    filterAttrs (_: canCrossCompile platform true)
-      final.pkgsCross.${platform}.bsc.pkgsTopLevel);
 
   buildList = name: paths:
     final.runCommandLocal name { } ''
@@ -147,7 +145,7 @@ let
   # For now only RISC-V
   crossList = buildList "ci-cross"
     (filter
-      (canCrossCompile "riscv64" false) # opt-in (pkgs with: meta.cross = true)
+      (canCrossCompile final.pkgsCross.riscv64.stdenv.hostPlatform)
         (builtins.attrValues crossSet.riscv64));
 
 in bscPkgs // {

pkgs/amd-uprof/default.nix

@@ -90,7 +90,7 @@ in
     meta = {
       description = "Performance analysis tool-suite for x86 based applications";
       homepage = "https://www.amd.com/es/developer/uprof.html";
-      platforms = [ "x86_64-linux" ];
+      platforms = lib.platforms.linux;
       license = lib.licenses.unfree;
       maintainers = with lib.maintainers.bsc; [ rarias varcila ];
     };

pkgs/amd-uprof/driver.nix

@@ -19,7 +19,7 @@ in stdenv.mkDerivation {
   '';
   hardeningDisable = [ "pic" "format" ];
   nativeBuildInputs = kernel.moduleBuildDependencies;
-  patches = [ ./makefile.patch ./hrtimer.patch ./remove-wr-rdmsrq.patch ];
+  patches = [ ./makefile.patch ./hrtimer.patch ];
   makeFlags = [
     "KERNEL_VERSION=${kernel.modDirVersion}"
     "KERNEL_DIR=${kernel.dev}/lib/modules/${kernel.modDirVersion}/build"

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

@@ -1,20 +0,0 @@
-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/cudainfo/default.nix

@@ -1,6 +1,5 @@
 {
   stdenv
-, lib
 , cudatoolkit
 , cudaPackages
 , autoAddDriverRunpath
@@ -12,7 +11,7 @@ stdenv.mkDerivation (finalAttrs: {
   src = ./.;
   buildInputs = [
     cudatoolkit # Required for nvcc
-    (lib.getOutput "static" cudaPackages.cuda_cudart) # Required for -lcudart_static
+    cudaPackages.cuda_cudart.static # Required for -lcudart_static
     autoAddDriverRunpath
   ];
   installPhase = ''
@@ -41,9 +40,4 @@ stdenv.mkDerivation (finalAttrs: {
     '';
     installPhase = "touch $out";
   };
-
-  meta = {
-    platforms = [ "x86_64-linux" ];
-    maintainers = with lib.maintainers.bsc; [ rarias ];
-  };
 })

pkgs/gpi-2/default.nix

@@ -9,6 +9,7 @@
 , automake
 , libtool
 , mpi
+, rsync
 , gfortran
 }:
 
@@ -43,24 +44,13 @@ stdenv.mkDerivation rec {
 
   configureFlags = [
     "--with-infiniband=${rdma-core-all}"
-    "--with-mpi=yes" # fixes mpi detection when cross-compiling
+    "--with-mpi=${mpiAll}"
     "--with-slurm"
     "CFLAGS=-fPIC"
     "CXXFLAGS=-fPIC"
   ];
 
-  nativeBuildInputs = [
+  buildInputs = [ slurm mpiAll rdma-core-all autoconf automake libtool rsync gfortran ];
-    autoconf
-    automake
-    gfortran
-    libtool
-  ];
-
-  buildInputs = [
-    slurm
-    mpiAll
-    rdma-core-all
-  ];
 
   hardeningDisable = [ "all" ];
 
@@ -70,6 +60,5 @@ 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

@@ -0,0 +1,191 @@
+{
+  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

@@ -0,0 +1,24 @@
+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

@@ -0,0 +1,36 @@
+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
-, gcc
+, gcc13
 , wrapCCWith
 }:
 
@@ -33,6 +33,8 @@ let
     maintainers = with lib.maintainers.bsc; [ abonerib ];
   };
 
+  gcc = gcc13;
+
   v = {
     hpckit   = "2023.1.0";
     compiler = "2023.1.0";

pkgs/intel-oneapi/packages.nix

@@ -1,46 +1,19 @@
-{
+{ lib
-  lib,
+, stdenv
-  stdenv,
+, callPackage
-  callPackage,
+, dpkg
-  dpkg,
+, fetchurl
-  fetchurl,
+, recurseIntoAttrs
 
-  sqlite,
+, sqlite
-  elfutils,
+, elfutils
 }:
 
 let
   inherit (builtins)
-    attrNames
+    elem attrNames attrValues concatMap filter fromJSON getAttr groupBy head isNull listToAttrs map mapAttrs readFile replaceStrings splitVersion ;
-    attrValues
-    concatMap
-    elem
-    filter
-    fromJSON
-    getAttr
-    groupBy
-    head
-    isNull
-    listToAttrs
-    map
-    mapAttrs
-    readFile
-    replaceStrings
-    splitVersion
-    ;
   inherit (lib)
-    converge
+    converge findFirst groupBy' hasPrefix optional pipe take toInt toList versionAtLeast versionOlder ;
-    findFirst
-    groupBy'
-    hasPrefix
-    optional
-    pipe
-    take
-    toInt
-    toList
-    versionAtLeast
-    versionOlder
-    ;
 
   aptData = fromJSON (readFile ./packages.json);
 
@@ -59,69 +32,44 @@ let
   #
   # To mitigate this, >= is set to take the latest version with matching major
   # and minor (only revision and patch are allowed to change)
-  compareVersions =
+  compareVersions = got: kind: want:
-    got: kind: want:
     let
       g0 = take 2 (splitVersion got);
       w0 = take 2 (splitVersion want);
-    in
+    in if isNull want then true
-    if isNull want then
+    else if kind == "=" then got == want
-      true
+    else if kind == "<<" then versionOlder got want
-    else if kind == "=" then
+    else if kind == "<=" then versionAtLeast want got
-      got == want
+    else if kind == ">>" then versionOlder want got
-    else if kind == "<<" then
+    else if kind == ">=" then (g0 == w0) && versionAtLeast got want # always match major version
-      versionOlder got want
+    else throw "unknown operation: ${kind}";
-    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 =
+  findMatching = { pname, kind, version }:
-    {
-      pname,
-      kind,
-      version,
-    }:
     findFirst (x: pname == x.pname && compareVersions x.version kind version) null aptData;
 
   isIntel = pkg: (hasPrefix "intel-" pkg.pname);
 
-  expandDeps =
+  expandDeps = pkg: (map findMatching (filter isIntel pkg.dependencies)) ++ (optional (pkg.size != 0) pkg);
-    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 =
+  getNewerInMajor = a: b: let
-    a: b:
+    va = a.version;
-    let
+    vb = b.version;
-      va = a.version;
+    va0 = head (splitVersion va);
-      vb = b.version;
+    vb0 = head (splitVersion vb);
-      va0 = head (splitVersion va);
+  in
-      vb0 = head (splitVersion vb);
+  if isNull a then b
-    in
+  else if va0 != vb0 then
-    if isNull a then
+    if va0 > vb0 then b else a
-      b
+  else if versionOlder vb va then a else 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 =
+  resolveDeps = pkg: let deps = _resolveDeps (toList pkg);
-    pkg:
-    let
-      deps = _resolveDeps (toList pkg);
       namedDeps = (map (x: "${x.pname}-${x.version}") deps);
-    in
+    in builtins.traceVerbose (builtins.deepSeq namedDeps namedDeps) deps;
-    builtins.traceVerbose (builtins.deepSeq namedDeps namedDeps) deps;
 
   blacklist = [
     "intel-basekit-env"
@@ -147,53 +95,34 @@ let
   isInBlacklist = pkg: elem pkg.provides blacklist;
   removeBlacklist = filter (e: !(isInBlacklist e));
 
-  dpkgExtractAll =
+  dpkgExtractAll = pname: version: {srcs, deps}: stdenv.mkDerivation {
-    pname: version:
+    inherit pname version srcs;
-    { srcs, deps }:
-    stdenv.mkDerivation {
-      inherit pname version srcs;
 
-      nativeBuildInputs = [ dpkg ];
+    nativeBuildInputs = [ dpkg ];
-      phases = [ "installPhase" ];
+    phases = [ "installPhase" ];
 
-      passthru = { inherit deps; };
+    passthru = { inherit deps; };
 
-      installPhase = ''
+    installPhase = ''
-        mkdir -p $out
+      mkdir -p $out
-        for src in $srcs; do
+      for src in $srcs; do
-          echo "Unpacking $src"
+        echo "Unpacking $src"
-          dpkg -x $src $out
+        dpkg -x $src $out
-        done
+      done
-      '';
+    '';
-    };
+  };
 
   apthost = "https://apt.repos.intel.com/oneapi/";
-  fetchDeb =
+  fetchDeb = p: fetchurl { url = apthost + p.filename; inherit (p) sha256; };
-    p:
-    fetchurl {
-      url = apthost + p.filename;
-      inherit (p) sha256;
-    };
 
-  buildIntel =
+  buildIntel = pkg: pipe pkg [
-    pkg:
+    resolveDeps
-    pipe pkg [
+    removeBlacklist
-      resolveDeps
+    (l: {srcs = map fetchDeb l; deps = l; })
-      removeBlacklist
+    (dpkgExtractAll "${pkg.provides}-extracted" pkg.version)
-      (l: {
+  ];
-        srcs = map fetchDeb l;
-        deps = l;
-      })
-      (dpkgExtractAll "${pkg.provides}-extracted" pkg.version)
-    ];
 
-  findHpcKit =
+  findHpcKit = year: findMatching { pname = "intel-hpckit"; kind = "<<"; version = toString (year+1); };
-    year:
-    findMatching {
-      pname = "intel-hpckit";
-      kind = "<<";
-      version = toString (year + 1);
-    };
   years = map toInt (attrNames components);
 
   patchIntel = callPackage ./patch_intel.nix { };
@@ -259,39 +188,18 @@ let
     };
   };
 
-  replaceDots = replaceStrings [ "." ] [ "_" ];
+  replaceDots = replaceStrings ["."] ["_"];
 
-in
+in recurseIntoAttrs (listToAttrs (map (year: let
-lib.recurseIntoAttrs (
+      year_str = toString year;
-  listToAttrs (
+    in {
-    map (
+      name = "hpckit_${year_str}";
-      year:
+      value = patchIntel {unpatched = buildIntel (findHpcKit year); components = components.${year_str}; };
-      let
+  }) years)) // {
-        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 (
+    (mapAttrs (_: l: listToAttrs (map (pkg: { name = replaceDots ("v" + pkg.version); value = pkg; }) l)))
-      _: l:
+  ] ;
-      listToAttrs (
-        map (pkg: {
-          name = replaceDots ("v" + pkg.version);
-          value = pkg;
-        }) l
-      )
-    ))
-  ];
 
   inherit resolveDeps patchIntel buildIntel;
 }

pkgs/intel-oneapi/patch_intel.nix

@@ -1,189 +1,179 @@
-{
+{ stdenvNoCC
-  stdenv,
+, lib
-  stdenvNoCC,
+, symlinkJoin
-  lib,
+, autoPatchelfHook
-  symlinkJoin,
+, wrapCCWith
-  autoPatchelfHook,
+, overrideCC
-  wrapCCWith,
+, gcc13
-  overrideCC,
+, gcc13Stdenv
-  gcc,
+, hwloc
-  hwloc,
+, libelf
-  libelf,
+, libffi_3_3
-  libffi_3_3,
+, libpsm2
-  libpsm2,
+, libuuid
-  libuuid,
+, libxml2
-  libxml2,
+, numactl
-  numactl,
+, ocl-icd
-  ocl-icd,
+, openssl
-  openssl,
+, python3
-  python3,
+, rdma-core
-  rdma-core,
+, ucx
-  ucx,
+, zlib
-  zlib,
+, makeOverridable
+, recurseIntoAttrs
 }:
 
-lib.makeOverridable (
+makeOverridable (
-  {
+{
-    unpatched,
+  unpatched,
-    components ? { },
+  components ? { },
-    extraPackages ? components.extraPackages or [ ],
+  extraPackages ? components.extraPackages or []
-  }:
+}:
 
-  let
+let
-    inherit (builtins)
+  inherit (builtins) attrValues filter mapAttrs removeAttrs;
-      attrValues
-      filter
-      mapAttrs
-      removeAttrs
-      ;
 
-    __components = removeAttrs components [ "extraPackages" ];
+  gcc = gcc13;
-    _components = __components;
+  stdenv = gcc13Stdenv;
-    # _components = lib.traceSeqN 2 {
-    #   inherit unpatched __components;
-    #   deps = builtins.map (x: "${x.pname}-${x.version}") unpatched.deps;
-    # } __components;
 
-    wrapIntel =
+  __components = removeAttrs components ["extraPackages"];
-      cc:
+  _components = __components;
-      let
+  # _components = lib.traceSeqN 2 {
-        targetConfig = stdenv.targetPlatform.config;
+  #   inherit unpatched __components;
-      in
+  #   deps = builtins.map (x: "${x.pname}-${x.version}") unpatched.deps;
-      (wrapCCWith {
+  # } __components;
-        inherit cc;
 
-        nixSupport = {
+  wrapIntel = { cc, extraBuildCommands ? "", extraInstall ? "", ... }@args:
-          cc-ldflags = [
+    let
-            "-L${gcc.cc}/lib/gcc/${targetConfig}/${gcc.version}"
+      targetConfig = stdenv.targetPlatform.config;
-            "-L${gcc.cc.lib}/lib"
+    in (wrapCCWith {
-            "-L${cc}/lib"
+      inherit cc;
-          ];
+      extraBuildCommands = ''
-          cc-cflags = [
+        echo "-L${gcc.cc}/lib/gcc/${targetConfig}/${gcc.version}" >> $out/nix-support/cc-ldflags
-            "--gcc-toolchain=${gcc.cc}"
+        echo "-L${gcc.cc.lib}/lib" >> $out/nix-support/cc-ldflags
-            "-isystem \"${cc.original}/lib/clang/*/include\""
+        echo "-L${cc}/lib" >> $out/nix-support/cc-ldflags
-            "-isystem ${cc}/include"
-            "-isystem ${cc}/include/intel64"
-            "-isystem ${gcc.cc}/lib/gcc/${targetConfig}/${gcc.version}/include"
-          ];
-          libcxx-cxxflags = [
-            # "--gcc-toolchain=${gcc.cc}"
-            "-isystem ${gcc.cc}/include/c++/${gcc.version}"
-            "-isystem ${gcc.cc}/include/c++/${gcc.version}/${targetConfig}"
-          ];
-        };
 
-        extraBuildCommands = ''
+        # echo "--gcc-toolchain=${gcc.cc}" >> $out/nix-support/libcxx-cxxflags
-          # FIXME: We should find a better way to modify the PATH instead of using
+        echo "--gcc-toolchain=${gcc.cc}" >> $out/nix-support/cc-cflags
-          # this ugly hack. See https://jungle.bsc.es/git/rarias/bscpkgs/issues/9
-          echo 'path_backup="${gcc.cc}/bin:$path_backup"' >>$out/nix-support/cc-wrapper-hook
 
-          # Disable hardening by default
+        # For some reason, If we don't resolve the realpath things go wrong
-          echo "" > $out/nix-support/add-hardening.sh
+        for stddef in ${cc}/lib/clang/*/include/stddef.h ; do
+          dir=$(dirname $(realpath "$stddef"))
+          echo "-isystem $dir" >> $out/nix-support/cc-cflags
+        done
 
-          wrap icx  $wrapper $ccPath/icx
+        echo "-isystem ${cc}/include" >> $out/nix-support/cc-cflags
-          wrap icpx $wrapper $ccPath/icpx
+        echo "-isystem ${cc}/include/intel64" >> $out/nix-support/cc-cflags
-          wrap ifx  $wrapper $ccPath/ifx
 
-          ln -s $out/bin/icpx $out/bin/c++
+        for dir in ${gcc.cc}/lib/gcc/${targetConfig}/*/include; do
-          ln -s $out/bin/icx  $out/bin/cc
+          echo "-isystem $dir" >> $out/nix-support/cc-cflags
+        done
 
-          sed -i 's/.*isCxx=0/isCxx=1/' $out/bin/icpx
+        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
 
-          # Use this to detect when a compiler subprocess is called
+        # FIXME: We should find a better way to modify the PATH instead of using
-          # from icpx (--fsycl-host-compiler)
+        # this ugly hack. See https://jungle.bsc.es/git/rarias/bscpkgs/issues/9
-          echo 'export NIX_CC_WRAPPER_INTEL=1' >>$out/nix-support/cc-wrapper-hook
+        echo 'path_backup="${gcc.cc}/bin:$path_backup"' >> $out/nix-support/cc-wrapper-hook
 
-          # oneMath looks for sycl libraries in bin/../lib
+        # Disable hardening by default
-          ln -s ${cc}/lib $out/lib
+        echo "" > $out/nix-support/add-hardening.sh
-          ln -s ${cc}/include $out/include
+      '' + extraBuildCommands;
-        '';
+    } // (removeAttrs args ["cc" "extraBuildCommands" "extraInstall"])
-      }).overrideAttrs
+    ).overrideAttrs (old: {
-        (old: {
+      installPhase = old.installPhase + extraInstall;
-          installPhase = old.installPhase + ''
+    });
-            export named_cc="icx"
-            export named_cxx="icpx"
-            export named_fc="ifx"
-          '';
-        });
 
-  in
+in
-  stdenvNoCC.mkDerivation (finalAttrs: {
+stdenvNoCC.mkDerivation (finalAttrs: {
-    pname = lib.removeSuffix "-extracted" unpatched.pname;
+  pname = lib.removeSuffix "-extracted" unpatched.pname;
-    inherit (unpatched) version;
+  inherit (unpatched) version;
-    src = unpatched;
+  src = unpatched;
 
-    phases = [
+  phases = [ "installPhase" "fixupPhase" ];
-      "installPhase"
+  buildInputs = [
-      "fixupPhase"
+    libffi_3_3
-    ];
+    libelf
-    buildInputs = [
+    libxml2
-      libffi_3_3
+    hwloc
-      libelf
+    numactl
-      libxml2
+    libuuid
-      hwloc
+    libpsm2
-      numactl
+    zlib
-      libuuid
+    ocl-icd
-      libpsm2
+    rdma-core
-      zlib
+    ucx
-      ocl-icd
+    openssl
-      rdma-core
+    python3
-      ucx
+    stdenv.cc.cc.lib
-      openssl
+  ] ++ extraPackages;
-      python3
-      stdenv.cc.cc.lib
-    ]
-    ++ extraPackages;
 
-    autoPatchelfIgnoreMissingDeps = [
+  autoPatchelfIgnoreMissingDeps = [ "libhwloc.so.5" "libcuda.so.1" "libze_loader.so.1" ];
-      "libhwloc.so.5"
-      "libcuda.so.1"
-      "libze_loader.so.1"
-    ];
 
-    # There are broken symlinks that go outside packages, ignore them
+  # There are broken symlinks that go outside packages, ignore them
-    dontCheckForBrokenSymlinks = true;
+  dontCheckForBrokenSymlinks = true;
 
-    nativeBuildInputs = [ autoPatchelfHook ];
+  nativeBuildInputs = [ autoPatchelfHook ];
-    installPhase = ''
+  installPhase = ''
-      cp -r $src/opt/intel/oneapi/ $out
+    cp -r $src/opt/intel/oneapi/ $out
-    '';
+  '';
 
-    passthru =
+  passthru = let
-      let
+    pkgs = mapAttrs
-        pkgs = mapAttrs (
+      (folder: version: symlinkJoin {
-          folder: version:
+        pname = "intel-${folder}";
-          let
+        inherit version;
-            original = "${finalAttrs.finalPackage}/${folder}/${version}";
+        paths = ["${finalAttrs.finalPackage}/${folder}/${version}"];
-          in
+      })
-          (symlinkJoin {
+      _components;
-            pname = "intel-${folder}";
+  in pkgs // {
-            inherit version;
+    inherit unpatched;
-            paths = [ original ];
+    pkgs = recurseIntoAttrs pkgs;
-          }).overrideAttrs
+    components = _components;
-            { passthru = { inherit original; }; }
-        ) _components;
-      in
-      pkgs
-      // {
-        inherit unpatched;
-        pkgs = lib.recurseIntoAttrs pkgs;
-        components = _components;
 
-        # This contains all packages properly symlinked into toplevel directories
+    # This contains all packages properly symlinked into toplevel directories
-        # in $out.
+    # in $out.
-        #
+    #
-        # NOTE: there are clashes with packages that have symlinks outside their
+    # NOTE: there are clashes with packages that have symlinks outside their
-        # scope (libtcm and env/vars.sh)
+    # scope (libtcm and env/vars.sh)
-        all = symlinkJoin {
+    all = symlinkJoin {
-          pname = finalAttrs.finalPackage + "-symlinked";
+      pname = finalAttrs.finalPackage + "-symlinked";
-          inherit (finalAttrs.finalPackage) version;
+      inherit (finalAttrs.finalPackage) version;
-          paths = filter lib.isDerivation (attrValues finalAttrs.finalPackage.pkgs);
+      paths = filter lib.isDerivation (attrValues finalAttrs.finalPackage.pkgs);
-        };
+    };
 
-        stdenv = overrideCC stdenv finalAttrs.finalPackage.cc;
+    stdenv = overrideCC stdenv finalAttrs.finalPackage.cc;
 
-        cc = wrapIntel finalAttrs.finalPackage.pkgs.compiler;
+    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/llvm-ompss2/clang.nix

@@ -16,19 +16,19 @@
 , useGit ? false
 , gitUrl ? "ssh://git@bscpm04.bsc.es/llvm-ompss/llvm-mono.git"
 , gitBranch ? "master"
-, gitCommit ? "872ba63f86edaefc9787984ef3fae9f2f94e0124" # github-release-2025.11
+, gitCommit ? "880e2341c56bad1dc14e8c369fb3356bec19018e"
 }:
 
 let
   stdenv = llvmPackages_latest.stdenv;
 
   release = rec {
-    version = "2025.11";
+    version = "2025.06";
     src = fetchFromGitHub {
       owner = "bsc-pm";
       repo = "llvm";
       rev = "refs/tags/github-release-${version}";
-      hash = "sha256-UgwMTUkM9Z87dDH205swZFBeFhrcbLAxginViG40pBM=";
+      hash = "sha256-ww9PpRmtz/M9IyLiZ8rAehx2UW4VpQt+svf4XfKBzKo=";
     };
   };
 

pkgs/llvm-ompss2/default.nix

@@ -2,6 +2,7 @@
   stdenv
 , lib
 , gcc
+, gcc13
 , clangOmpss2Unwrapped
 , writeShellScript
 , openmp ? null
@@ -28,10 +29,10 @@ 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.bintools-unwrapped.override {
+  bintools-unwrapped = llvmPackages_latest.tools.bintools-unwrapped.override {
     lld = clangOmpss2Unwrapped;
   };
-  bintools = llvmPackages_latest.bintools.override {
+  bintools = llvmPackages_latest.tools.bintools.override {
     bintools = bintools-unwrapped;
   };
   targetConfig = stdenv.targetPlatform.config;
@@ -92,7 +93,9 @@ let
   '';
 
   wrappedCCIntel = wrapCCWith {
-    inherit cc bintools extraPackages;
+    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;
   };

pkgs/mcxx/default.nix

@@ -65,7 +65,6 @@ 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

@@ -1,11 +1,9 @@
 { python3Packages, lib }:
 
-python3Packages.buildPythonApplication {
+python3Packages.buildPythonApplication rec {
   pname = "meteocat-exporter";
   version = "1.0";
 
-  pyproject = true;
-
   src = ./.;
 
   doCheck = false;

pkgs/mpich/default.nix

@@ -6,13 +6,6 @@
 , 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
@@ -22,13 +15,10 @@ let
     paths = [ pmix.dev pmix.out ];
   };
 in mpich.overrideAttrs (old: {
-  buildInputs = old.buildInputs ++ [
+  buildInput = old.buildInputs ++ [
     libfabric
     pmixAll
   ];
-  nativeBuildInputs = old.nativeBuildInputs ++ [
-    perl
-  ];
   configureFlags = [
     "--enable-shared"
     "--enable-sharedlib"
@@ -41,21 +31,10 @@ 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" ];
 
   meta = old.meta // {
     maintainers = old.meta.maintainers ++ (with lib.maintainers.bsc; [ rarias ]);
-    cross = true;
   };
 })

pkgs/nixgen/default.nix

@@ -1,22 +0,0 @@
-{
-  stdenv
-, lib
-}:
-
-stdenv.mkDerivation {
-  pname = "nixgen";
-  version = "0.0.1";
-  src = ./nixgen;
-  dontUnpack = 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

@@ -1,97 +0,0 @@
-#!/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/nodes/default.nix

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

pkgs/nosv/default.nix

@@ -13,19 +13,19 @@
 , useGit ? false
 , gitUrl ? "git@gitlab-internal.bsc.es:nos-v/nos-v.git"
 , gitBranch ? "master"
-, gitCommit ? "1108e4786b58e0feb9a16fa093010b763eb2f8e8" # version 4.0.0
+, gitCommit ? "9f47063873c3aa9d6a47482a82c5000a8c813dd8"
 }:
 
 with lib;
 
 let
   release = rec {
-    version = "4.0.0";
+    version = "3.2.0";
     src = fetchFromGitHub {
       owner = "bsc-pm";
       repo = "nos-v";
       rev = "${version}";
-      hash = "sha256-llaq73bd/YxLVKNlMebnUHKa4z3sdcsuDUoVwUxNuw8=";
+      hash = "sha256-yaz92426EM8trdkBJlISmAoG9KJCDTvoAW/HKrasvOw=";
     };
   };
 

pkgs/onemath/default.nix

@@ -1,33 +1,30 @@
-{
+{ lib
-  lib,
+, fetchFromGitHub
-  fetchFromGitHub,
+, cmake
-  cmake,
+, withCFlags
-  withCFlags,
+, intelPackages
-  intelPackages,
 
-  mklSupport ? true,
+, mklSupport ? true
 
-  config,
+, config
 
-  cudaSupport ? config.cudaSupport,
+, cudaSupport ? config.cudaSupport
-  cudaPackages ? { },
+, cudaPackages ? { }
 
-  rocmSupport ? config.rocmSupport,
+, rocmSupport ? config.rocmSupport
-  hipTargets ? null, # only one target at a time supported
+, hipTargets ? null # only one target at a time supported
-  rocmPackages ? { },
+, rocmPackages ? { }
 }:
 
 let
   # rocmSupport is not enough, we need a specific target
   enableHip = rocmSupport && hipTargets != null;
 
-  stdenv = withCFlags (lib.optionals cudaSupport [
+  stdenv = withCFlags (lib.optionals cudaSupport [ "--cuda-path=${cudaPackages.cudatoolkit}" ]) intelPackages.stdenv;
-    "--cuda-path=${cudaPackages.cudatoolkit}"
-  ]) intelPackages.stdenv;
 in
 
-# at least one backend has to be enabled
+  # at least one backend has to be enabled
-assert mklSupport || cudaSupport || enableHip;
+  assert mklSupport || cudaSupport || enableHip;
 
 stdenv.mkDerivation rec {
   pname = "oneMath";
@@ -41,51 +38,47 @@ stdenv.mkDerivation rec {
   };
 
   cmakeFlags = [
-    (lib.cmakeBool "ENABLE_MKLCPU_BACKEND" mklSupport)
+    (lib.cmakeBool "ENABLE_MKLCPU_BACKEND"    mklSupport)
-    (lib.cmakeBool "ENABLE_MKLGPU_BACKEND" mklSupport)
+    (lib.cmakeBool "ENABLE_MKLGPU_BACKEND"    mklSupport)
 
-    (lib.cmakeBool "ENABLE_CUBLAS_BACKEND" cudaSupport)
+    (lib.cmakeBool "ENABLE_CUBLAS_BACKEND"    cudaSupport)
-    (lib.cmakeBool "ENABLE_CUFFT_BACKEND" cudaSupport)
+    (lib.cmakeBool "ENABLE_CUFFT_BACKEND"     cudaSupport)
-    (lib.cmakeBool "ENABLE_CURAND_BACKEND" cudaSupport)
+    (lib.cmakeBool "ENABLE_CURAND_BACKEND"    cudaSupport)
-    (lib.cmakeBool "ENABLE_CUSOLVER_BACKEND" cudaSupport)
+    (lib.cmakeBool "ENABLE_CUSOLVER_BACKEND"  cudaSupport)
-    (lib.cmakeBool "ENABLE_CUSPARSE_BACKEND" cudaSupport)
+    (lib.cmakeBool "ENABLE_CUSPARSE_BACKEND"  cudaSupport)
 
-    (lib.cmakeBool "ENABLE_ROCBLAS_BACKEND" enableHip)
+    (lib.cmakeBool "ENABLE_ROCBLAS_BACKEND"   enableHip)
-    (lib.cmakeBool "ENABLE_ROCFFT_BACKEND" enableHip)
+    (lib.cmakeBool "ENABLE_ROCFFT_BACKEND"    enableHip)
     (lib.cmakeBool "ENABLE_ROCSOLVER_BACKEND" enableHip)
-    (lib.cmakeBool "ENABLE_ROCRAND_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.optionals enableHip [
     (lib.cmakeFeature "HIP_TARGETS" hipTargets)
   ];
 
   nativeBuildInputs = [ cmake ];
-  buildInputs =
+  buildInputs = lib.optionals (mklSupport) [
-    lib.optionals (mklSupport) [
+    intelPackages.mkl
-      intelPackages.mkl
+    intelPackages.tbb
-      intelPackages.tbb
+  ] ++ lib.optionals (enableHip) [
-    ]
+    rocmPackages.rocmPath
-    ++ lib.optionals (enableHip) [
+    rocmPackages.rocblas
-      rocmPackages.rocmPath
+    rocmPackages.rocfft
-      rocmPackages.rocblas
+    rocmPackages.rocsolver
-      rocmPackages.rocfft
+    rocmPackages.rocrand
-      rocmPackages.rocsolver
+    rocmPackages.rocsparse
-      rocmPackages.rocrand
+  ] ++ lib.optionals (cudaSupport) [
-      rocmPackages.rocsparse
+    (lib.getDev cudaPackages.cuda_cudart)
-    ]
+    cudaPackages.cudatoolkit
-    ++ lib.optionals (cudaSupport) [
-      (lib.getDev cudaPackages.cuda_cudart)
-      cudaPackages.cudatoolkit
 
-      cudaPackages.libcublas
+    cudaPackages.libcublas
-      cudaPackages.libcurand
+    cudaPackages.libcurand
-      cudaPackages.libcufft
+    cudaPackages.libcufft
-      cudaPackages.libcusparse
+    cudaPackages.libcusparse
-      cudaPackages.libcusolver
+    cudaPackages.libcusolver
-    ];
+  ];
 
 }

pkgs/osu/default.nix

@@ -32,11 +32,6 @@ 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
@@ -49,6 +44,5 @@ 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 ? "06432668f346c8bdc1006fabc23e94ccb81b0d8b" # version 1.13.0
+, gitCommit ? "e4f62382076f0cf0b1d08175cf57cc0bc51abc61"
 , 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 = "1.13.0";
+    version = "1.12.0";
     src = fetchFromGitHub {
       owner = "bsc-pm";
       repo = "ovni";
       rev = "${version}";
-      hash = "sha256-0l2ryIyWNiZqeYdVlnj/WnQGS3xFCY4ICG8JedX424w=";
+      hash = "sha256-H04JvsVKrdqr3ON7JhU0g17jjlg/jzQ7eTfx9vUNd3E=";
-    } // { shortRev = "0643266"; };
+    } // { shortRev = "a73afcf"; };
   };
 
   git = rec {

pkgs/paraver/default.nix

@@ -12,7 +12,7 @@
 , paraverKernel
 , openssl
 , glibcLocales
-, wrapGAppsHook3
+, wrapGAppsHook
 }:
 
 let
@@ -64,7 +64,7 @@ stdenv.mkDerivation rec {
     autoconf
     automake
     autoreconfHook
-    wrapGAppsHook3
+    wrapGAppsHook
   ];
 
   buildInputs = [

pkgs/sonar/default.nix

@@ -35,6 +35,5 @@ stdenv.mkDerivation rec {
     maintainers = with lib.maintainers.bsc; [ rarias ];
     platforms = lib.platforms.linux;
     license = lib.licenses.mit;
-    cross = true;
   };
 }

pkgs/tagaspi/default.nix

@@ -5,14 +5,23 @@
 , 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;
@@ -26,18 +35,16 @@ stdenv.mkDerivation rec {
     hash = "sha256-RGG/Re2uM293HduZfGzKUWioDtwnSYYdfeG9pVrX9EM=";
   };
 
-  nativeBuildInputs = [
+  buildInputs = [
     autoreconfHook
     automake
     autoconf
     libtool
-    gfortran
-  ];
-
-  buildInputs = [
     boost
     numactl
     rdma-core
+    gfortran
+    mpiAll
   ];
 
   dontDisableStatic = true;
@@ -56,6 +63,5 @@ 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

@@ -68,6 +68,5 @@ in stdenv.mkDerivation {
     maintainers = with lib.maintainers.bsc; [ rarias ];
     platforms = lib.platforms.linux;
     license = lib.licenses.gpl3Plus;
-    cross = true;
   };
 }

pkgs/upc-qaire-exporter/default.nix

@@ -1,11 +1,9 @@
 { python3Packages, lib }:
 
-python3Packages.buildPythonApplication {
+python3Packages.buildPythonApplication rec {
   pname = "upc-qaire-exporter";
   version = "1.0";
 
-  pyproject = true;
-
   src = ./.;
 
   doCheck = false;

test/compilers/hello-sycl.nix

@@ -1,8 +1,4 @@
-{
+{ intelPackages,  writeText, strace }:
-  intelPackages,
-  writeText,
-  strace,
-}:
 
 let
   stdenv = intelPackages.stdenv;
@@ -38,10 +34,7 @@ in
 stdenv.mkDerivation {
   version = "0.0.1";
   name = "hello-sycl";
-  buildInputs = [
+  buildInputs = [ stdenv strace ];
-    stdenv
-    strace
-  ];
   src = hello_sycl;
   dontUnpack = true;
   dontConfigure = true;

test/compilers/icpx-ompss2.nix

@@ -1,11 +1,4 @@
-{
+{ writeText, intelPackages, nodes, nosv, clangOmpss2Nodes, strace }:
-  writeText,
-  intelPackages,
-  nodes,
-  nosv,
-  clangOmpss2Nodes,
-  strace,
-}:
 
 let
   hello_cpp = writeText "hello.cpp" ''